Posted on Authorea 9 Apr 2021 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.161792702.20501359/v1 — This a preprint and has not been peer reviewed. Data may be preliminary. e Han Lei targets drug evolution, potential their and into adaptation insights provide roundworms 266 panda of giant sequencing whole-genome and assembly Chromosome-scale hoe He Shaowen igWang Qing Yu ouaingntcaayi n rgpeito rvd nihsfrrvaigteipc fdwrighsoyo population on history deworming of adaptive. impact underlying The mechanisms the revealing the identified. for and were strong insights roundworms prevention. under proteins provide and of under target addition, structure prediction evolution were potential In genetic drug early 47 ced-7) and the and diet. and inferring analysis targets panda-specific bre-4 for genetic drug giant Population reference nrf-6, known the unique (glc-1, 23 a to Finally, genes provides adaptation resistance-related population. genome the captive four metabolism for in that acid essential selection information found amino be positive environmental a essential we to and in report pressures, synthesis inferred involved deworming we chitin genes genome, different epidermal Here, unique giant schroederi to protein- demonstrated B. fossil predicted related we host. the 19,291 Furthermore, living genes the organisms in and of the genome. to Mb important expansion roundworms 262 in roundworms significant are in of a of parasites size Roundworms processing found mechanism genome of We a adaptation study animals. with genes. the schroederi The and coding understanding Baylisascaris humans of for prevention. genome of significance chromosome-scale and health high-quality great transmission the of disease to is mechanisms, threat panda parasitic a studying been for long have diseases Helminth Abstract 2021 9, April 12 Copenhagen of 11 10 9 8 7 6 (CCRCGP) Park National 5 4 3 2 1 Lisby G,BGI-Shenzhen MGI, Sciences University of Zhejiang Academy Panda Chinese Giant of the University Reserve in Nature Animals National Rare Foping of Biology Conservation on SFGA of Laboratory Key BGI-Shenzhen BGI-Shenzhen available Genomics, not Agricultural Affiliation of Laboratory Key State University Forestry Northeast nvriyo Copenhagen University Biology, of University of Department Biomedicine, Molecular and Genomics of Laboratory BGI 2 uogWang Yulong , 11 unLiu Quan , 1 inigLan Tianming , 7 6 hnce Yang Shangchen , aqagZhou Yanqiang , 1 1 ase Kristiansen Karsten , eigSun Heting , 2 ehn Li Desheng , 1 8 ubn Han Ruobing , ii Zhu Yixin , 1 ogin Chai Hongliang , 3 amn Li Haimeng , 3 unLiu Huan , 2 utn Huang Yunting , 1 1 igigLi Lingling , 1 unigYang Huanming , 4 12 ihaDeng Linhua , n hjnHou Zhijun and , 1 ainLu Yaxian , 2 ioagCheng Xiaofang , 5 hwiPeng Zhiwei , 2 u Xu Xun , 1 1 arn Lu Haorong , 9 10 Jieyao , Michael , 3 , 2 , Posted on Authorea 9 Apr 2021 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.161792702.20501359/v1 — This a preprint and has not been peer reviewed. Data may be preliminary. Chai Zhu Yixin Zhou Yanqiang targets insights Han drug provide Lei roundworms potential panda and giant adaptation 266 evolution, of their sequencing into whole-genome and assembly Chromosome-scale oeta agtpoen eeietfid h eoepoie nqerfrnefrifrigteearly drug the and inferring analysis for genetic Population reference unique adaptive. a underlying provides mechanisms genome the The and roundworms identified. of ( were evolution genes proteins resistance-related target four potential that expan- found the significant we in ced-7 a pressures, metabolism found deworming acid We different amino roundworms essential under in genes. in processing involved information protein-coding genes environmental of predicted unique schroederi and genome demonstrated synthesis 19,291 we chromosome-scale chitin and Furthermore, epidermal high-quality Mb to genome. a round- related 262 of genes report of mechanism of adaptation we size sion the parasites Here, genome understanding of for a study significance host. with The great important the of are prevention. is Roundworms to panda and worms animals. giant transmission and fossil disease humans living of mechanisms, the health in parasitic the studying to threat for a organisms been long have diseases Helminth Abstract and * + 15 14 China 150040, Harbin 13 12 11 10 9 8 7 6 5 China 611800, Sichuan (CCRCGP), 4 Denmark Copenhagen, DK-2100 3 2 1 Hou Zhijun orsodn uhr:[email protected], authors: Corresponding China. 518083, Shenzhen China BGI-Shenzhen, 518120, GeneBank, Shenzhen National BGI-Shenzhen, Write, China China and 100049, Read Genome Beijing of Sciences, Laboratory of Key Provincial Academy Guangdong Chinese China of Province, University Technology, Guangdong Future Foshan, University, of Foshan School China Engineering, Park 150040, and National Harbin Sciences Panda Administration, Life Forestry Giant of State School the China Conservation, in Wildlife Animals of Rare Laboratory Key of Biology Conservation on Copenhagen, SFGA of of University Laboratory Biology, Key of Department Biomedicine, Molecular and China 518083, Genomics Shenzhen of BGI-Shenzhen, Laboratory Genomics, China Agricultural 150040, of Harbin University, Laboratory Forestry Key Northeast State Area, Protected and Wildlife of College hs uhr otiue qal oti work. this to equally contributed authors These oigNtoa aueRsre azog730,China 723400, Hanzhong Reserve, China Nature 266555, National Qingdao Foping Sciences, Administration, Life Grassland for and Institute Forestry Advanced National Qingdao-Europe Diseases, Wildlife of Surveillance for 518083,China Station Sciences,Shenzhen of General Academy Chinese of Center,University Education BGI China 518083, China Shenzhen 310058, BGI-Shenzhen, Hangzhou MGI, University, Zhejiang Sciences, Life of College [email protected] 1 unigYang Huanming , eeudrsrn oiieslcini atv ouain ial,2 nw rgtresad47 and targets drug known 23 Finally, population. captive in selection positive strong under were ) 1,5+ 12 eoe nerdt eesnilfrteaatto otegatpnaseicde.I addition, In diet. panda-specific giant the to adaptation the for essential be to inferred genome, 1,5* inigLan Tianming , utn Huang Yunting , 1 ubn Han Ruobing , 2 u Xu Xun , 2,3+ 8,9 1 ehn Li Desheng , ioagCheng Xiaofang , igigLi Lingling , 2,8 ihe Lisby Michael , 1 4+ ainLu Yaxian , amn Li Haimeng , 11 iyoYu Jieyao , 3 unLiu Quan , 2 1 arn Lu Haorong , 2,7 ihaDeng Linhua , 8,9 1,6* uogWang Yulong , ase Kristiansen Karsten , 8,9 [email protected] igWang Qing , 4 hwiPeng Zhiwei , 1 eigSun Heting , glc-1 alssai schroederi Baylisascaris 12 hnce Yang Shangchen , 3,14* , 1 nrf-6 hoe He Shaowen , unLiu Huan , 13 , [email protected] Hongliang , , bre-4 2,3* and 15 10 B. , , , Posted on Authorea 9 Apr 2021 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.161792702.20501359/v1 — This a preprint and has not been peer reviewed. Data may be preliminary. l pcmn fSichuan of specimens All 2.1 insights new provides which identified, were 2 genetic of potential proteins management the of target as disease drug adaptation well potential as potential the the Finally, panda, into giant of resistance. the mechanisms drug of genetic diet of bamboo basis possible specific explored the chromosome-scale especially we environment, a intestinal genome, report we the Here, on al.). Based et of infections(Xie mechanisms of of genetic genome control of reference exploration and prevention in-depth preventing further analyses, and gene adaptations a multiple or that single become and indicating potentially morphological may 2015), variants Deng, These & Although survived. had He, anthelmintics Li, of variety anthelmintics(D. regu- pathogens. a anthelmintic-resistant are with to captivity treatment the resistance in increased in after with occurred of variants pandas days had problem investigations, subtypes Giant 15 the drug-resistant to Moreover, of to development According underestimated. 2014). 10 seriously al., days). feces et be 60 the Li to (every D. likely dewormed 2018; is al., larly et anthelmintics carnivorous Hu to typical populations(H. the resistance have captive challenges pandas and This Giant wild panda, absorption. in giant pandas. and the giant digestibility of low of number data with intestine large diet fatal of small A a even absorption the bamboo, nutrient 2011). in and roundworms, eat found al., blockage, other but mainly characteristics, with et intestinal intestinal is Compared Zhang baylisascariasis, and L. severe 1998). size Malloggi, Yang, 2006; cause in Renzoni, GY Ellis, addition Papini, (NLM) 2006; & in 1989; rupture(Schaul, migrans Boyce, Janssen, can bowel the larva M. Zhang, infections of neural W. Zhang, roundworm (OLM), organs & Wildt, of Kazacos migrans multiple develop R. 1995; larva to hepatitis(K. can Casarosa, ocular migrate and eggs & (VLM), can pneumonia Its migrans Larvae severe larval even or risks. conditions. visceral and safety patent are cause appropriate and as and Lock, and under health 2005), infection birds(Wolf, larvae host public Berlin, 1989), cause infective & potential Boyce, also Ash, into with M. Shafir, species W. directly parasites intermediate Sorvillo, & Baylisascaris Wise, zoonotic an Kazacos 2002; considered humans(Murray, through mammals(K. 2003). and therefore of passing 2007) variety al., Garner, without a & et panda in Carpenter, Silva (LM) giant De migrants the larval 2006; latent infect al., directly et for can host(Bethony implications and far-reaching nematode and transmitted broad with schroederi risks pathogens B. possible detecting and with easily identifying health. deal are for human to relevance eggs and In-depth of actions helminth wildlife soil. information appropriate soil-transmitted or provide feces instigate can period, contaminated wildlife and through incubation in humans long Boyce, helminths to M. even the of and W. and result, studies distribution & livestock, a Kazacos and wide greater(K. As wildlife been its between infections. never transmitted have to helminth wildlife of Due in interface, transmission isolated land-urban worldwide(Hotez, for once 1989). wild wildlife diseases barrier the of effective and and transmission livestock an cities, for towns, humans, longer risks of no of expansion is health the isolation the With geographic to 2009). threat Molyneux, a & Savioli, been Fenwick, long has ascariasis Parasitic structure 1 genetic population on history deworming Keywords: of impact the revealing prevention. and for insights provide prediction | | AEIL N METHODS AND MATERIALS INTRODUCTION | Samples .schroederi B. alssai schroederi Baylisascaris aaii eaoeseicfrtegatpna( panda giant the for specific nematode parasitic a , .schroederi B. .schroederi B. oe het obt idadcpiegatpna,cretsuisaelmtdto limited are studies current pandas, giant captive and wild both to threats poses .schroederi B. .schroederi B. hc sas h rtcrmsm-cl eeec eoeo ascaridoids. of genome reference chromosome-scale first the also is which , o uvvli h ml netn.Bsdo vial epidemiological available on Based intestine. small the in survival for onwrs dpain eei iest,Anthelmintics diversity, Genetic Adaptation, Roundworms, , stelaigcueo et rmpiayadscnayinfection secondary and primary from death of cause leading the is Baylisascaris ouainwr olce rmtegatpna( panda giant the from collected were population 3 n eae roundworms. related and .schroederi B. .schroederi B. iuooamelanoleuca Ailuropoda ouain n that and population, gscnsilb eetdin detected be still can eggs .schroederi B. .schroederi B. .schroederi B. ,i soil- a is ), Ailuropoda ssmaller is othe to Posted on Authorea 9 Apr 2021 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.161792702.20501359/v1 — This a preprint and has not been peer reviewed. Data may be preliminary. eeeautduigst fBSOwt eoemd n ieg aafo eaoeadeukaryote, and nematode from data lineage genome and the mode of genome completeness 2015). with The Zdobnov, BUSCO S2). & Kriventseva, of (Figure Panagiotis, respectively(Sim˜ao, sets Pseudochromosomes Waterhouse, Durand, using into 2018; evaluated oriented al., the soft- were and et visual from ordered review(Dudchenko the Contigs further and into 2016). loaded correction were were for al., 3D-DNA a v1.11.08 et the 3D-DNA, module fragmentsRobinson, from Then, Tools orient generated 2016). Assembly and files al., Juicebox Finally, order Juicer et anchor, 2017). ware Next, Shamim, misassembles, al., aside(Durand, read pairs. correcting et 2) set for DNA(Dudchenko read et removed; are applied of valid pipeline(Servant are locations was million near-duplicates HiC-Pro more pipeline, and 645 ”. or computational duplicates leaving -V three custom both -a to result, 1) aligned 19 mapping assembly: that -k auxiliary the pairs for 16 filtering (v0.7.13- used as -t BWA for was constructed mem using software used “bwa was genome v1.5.7 then which assembled parameters was our library with 2015) against Hi-C 2010) al., mapped single Durbin, first a & chromo- were from to Li conformations. reads scaffolds generated chromosome r1126)(H. Hi-C the were the All ligate data capture described. finally obtained to sequencing To previously then used Hi-C Mb. We was X) data. 1.27 2009) WGS (v1.0.5)(J. of (˜400 the al., NextPolish N50 105Gb using assembly. et with by this technology(Lieberman-Aiden contigs polishing for 639 Hi-C genome correction with somes, for assembly of used further genome round was primary second 2020) a a Liu, out & Sun, carry Fan, to Hu, used then was parameters. algorithm assembly subsequent not evaluate of was beta.1; to setting samples reads the sequenced TGS for the of reference of The distribution a DNA frequency provide the length and that the quality confirm counted sequencing we to the Then database species. NCBI other the by with contaminated data pipeline(Liu raw GCE of the used size compare 110 We genome (about content. the Gb repeat estimate genome 29.32 and to essential heterozygosity, estimate 2013) of to al., analysis level et survey size, genome genome for used including were information, data WGS genome, high-quality obtain To isolated of was RNA individual RNA-seq, male For a platform. and DNBSEQ-T1 female on adult reads an sequenced short and from (WGS) the constructed Biosciences), on separately sequence were cell (Pacific SMRT libraries genome 1 Kit pair-end whole with Repair 100-bp performed a resequencing, was Damage sequencing genome SMRTbell Pacbio For the The SMRTplatform. and PacBio instructions. Tem- s USA) SMRTbell manufacturer’ Biosciences, the the ethanol to (Pacific using and according sodium-dodecyl 1.0 constructed intestinal extraction were a Kit prevent libraries phenol-chloroform using Prep SMRTbell to by them plate 20-Kb followed microscope sequencing, from 2006) PacBio inverted isolated For al., was an precipitation. et DNA under digestion(Gasser genomic individuals K total adult sulphate/proteinase Then, of contamination. intestines microorganism the removed firstly We n 7G a at aao aewr band l rncit eeue oass h opeeeso the of completeness the assess female to of used data were fastq transcripts raw All 2.3 22Gb annotation. obtained. of genome were total assist male A and of assembly data spectrophotometrically Bioanalyzer. genome fastq estimated a raw were using Gb verified yields 27 was RNA and integrity and and instructions 1000), manufacturer’s (NanoDrop the to according USA) University. Forestry Northeast of were Committee handling Use nematodes and 2.2 and Care -80 designs Animal at failed. experimental Institutional Mountains) stored the All (Qinling by then sequencing. approved Reserve and transcriptome (37 Nature for ice saline National solution dry Foping preservation physiological with the sterile transport in in rescues and extensively panda washed wild were after Roundworms died Qinling who of als Samples Panda. Giant melanoleuca | | .schroederi B. eoeasml n ult control quality and assembly Genome sequencing and construction library isolation, acid Nucleic https://github.com/Nextomics/NextDenovo ihntrlyaqie netosfo h hn osrainadRsac etrfor Center Research and Conservation China the from infections acquired naturally with ) eoewsasmlduiga“orc-hnasml”srtg.Frt eteoo(v2.0- NextDenovo First, strategy. “correct-then-assemble” a using assembled was genome × a aBoln ed.Frt eue lsal(222)Cmcoe l,20)to 2009) al., et (v2.2.26)(Camacho Blastall used we First, reads. long PacBio raw ) .schroederi B. .schroederi B. .schroederi B. ouainwr bandfo h netnso individu- of intestines the from obtained were population a sdt orc n sebeadatgnm.Arrow genome. draft a assemble and correct to used was ) o 4 ni s.Svrlseieswr trdi RNA in stored were specimens Several use. until C eescesul lsee no2 rus which groups, 21 into clustered successfully were eoegnm seby egnrtdattlof total a generated We assembly. genome before .schroederi B. sn Rzlraet(Invitrogen, reagent TRlzol using o ) ee eaae,snap-frozen separated, sexes C), Posted on Authorea 9 Apr 2021 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.161792702.20501359/v1 — This a preprint and has not been peer reviewed. Data may be preliminary. eslc igecp eefmle ocntutpyoeei re ae nmxmmlklho using likelihood maximum on based trees al., phylogenetic 2007). et 2004) Jose, construct & (v3.8.31)(Edgar, Li to Gblocks(Gerard MUSCLE (v4.0)(H. by families using TreeFam extracted gene aligned using were single-copy were alignments define CDS family select are conserved each We The nematodes from parameters. sequences six default B. protein with among assembled the Orthogroups Next, our software. performed 2006). to were 2012) protein-level genomes al., and nucleotide-level nematodes et whole-genome 5 at aligning both analysis by ( syntenic mammals The 2019). on Hurd, parasitic roundworms hapla three of files univalens annotation and Genomes 2.7 tion. erto nterslso ertmP20Sre ( Server 2.0 SecretomeP of results v2.0 NNscore transmembrane the with and against Server in proteins peptides secretion The 2008) TMHMM respectively. signal proteins, the and Morton, of predict regions (http://www.cbs.dtu.dk/services/SignalP/) & to used Server batch-BLAST(Rawlings were (http://www.cbs.dtu.dk/services/TMHMM/) MEROPS SignalP-5.0 identified. using re annotated were (E MEROPS PIs and Proteases with blasting by assembled Blast2go databa- was through known genome several obtained mitochondrial was against the information sets Furthermore, GO gene schroederi 2005). above andNR. al., aligned COG et we KEGG, compre- (v.2.5.0)(Conesa TrEMBL, annotation, a SwissProt, functional 2008). form MAKER including gene al., to using ses, et perform merged EVM)(Haas evidence hidden to was (v1.1.1, above order a evidence EvidenceModeler In all build gene using analyzed combining All set to was by gene 2013). training Yandell, non-redundant sequence generated unsupervised and & genome were hensive et Stein, utilizing addition, sets Holt, (v.3.2.3)(Mario 2005) In gene Law, AUGUSTUS Mark, evidence. consistent (v.2.31.8)(Campbell, in & transcript The used (v1.0)(John on model. were based GeneMark Markov structures models program pre- gene gene to the (v2.1.0)(Trapnell, inferred applied train by TopHat was the to using (v.2.1.0) which 2006) PASApipeline assembly strategy. after al., for al.) structure genome et gene the (v2.0.6)(Haas Trinity dict to plus aligned Salzberg) was & Pachter, sequence protein-coding transcriptome the female selected a we annotation, homology-based annota- For ( capsae sequencing-aided species prediction. RNA homologous gene five and of perform search sequences homology-based to prediction, used gene were novo tion de of strategy combined A LTR G.), & schroederi B. For A n RA eepeitd RAcnS v..)Lw dy 97 eeue opeittRNAs. predict respectively. rRNA, to 2.6 and used miRNA were snRNA, 1997) predict Eddy, to & database (v1.3.1)(Lowe miR- tRNAscan-SE snRNA, tRNA, predicted. aligned including We were (ncRNA; RNA rRNA) Non-coding and of types NA, Four 2017). ( al., et online alignment(Michael GeSeq gene on annotated was nome the against queries as used sequences genome the 2.5 with elements, al.). search repeat et to known database(Jurka used for Repbase were sequences 2012) RepeatProteinMask(Tempel, genome and the 2009) Chen, & RepeatMasker(Tarailo-Graovac 2.4 | | | | enovo de eosrcino hlgn n vltoa nlssaoggnmsfo i nematodes six from genomes among analysis evolutional and phylogeny of Reconstruction rtae,poes niios(I n xrtr/ertr rtis(EPs) proteins Excretory/secretory and (PI) inhibitors protease Proteases, annotation function and prediction genes Protein-coding elements repetitive of classification and Detection eedwla rmNB rWrBs aaae(al 1)Mcel,Dbj rc,Drl & Daryl, Price, Dubaj, S10)(Michelle, (Table database WormBase or NCBI from download were ) and ,oefe-iignmtd ( nematode free-living one ), smDAsqec rmNB database(NC NCBI from sequence mtDNA ’s .schroederi B. .canis T. IDRX ho&Ho 07 n eetoee v..)Si,Hbe,&Gen 2015). Green, & Hubley, (v1.0.8)(Smit, RepeatModeler and 2007) Hao, & Zhao FINDER(X. dnicto frpa lmns ecntutdatasoal lmn T)lbayo the of library (TE) element transposable a constructed we elements, repeat of identification < eoet dnie ye frpa lmnsb sn admRpa idr(TRF)(Benson Finder Repeat Tandem using by elements repeat of types identified to genome 1e -10 .Tecnetoa erto rtisadnncnetoa erto rtiswe- proteins secretion non-conventional and proteins secretion conventional The ). rmNB hts/wwnb.l.i.o/.FrRAbsdpeito,aml and male a prediction, RNA-based For (https://www.ncbi.nlm.nih.gov/). NCBI from ) eoeaantRa v20(avr ta. 08 aaaeadivrert rRNA invertebrate and database 2018) al., et (v12.0)(Kalvari Rfam against genome rgamalayi Brugia https://chlorobox.mpimp-golm.mpg.de/geseq.html .elegans C. n n eaoeprstco h oto ln ( plant a of root the on parasitic nematode one and ) http://www.cbs.dtu.dk/services/SecretomeP/ , 5 .elegans C. 1971(i ta. 01.Temtcodilge- mitochondrial The 2011). al., et 015927.1)(Xie schroederi > . eeslce snncnetoa protein non-conventional as selected were 0.9 , rsinhspacificus Pristionchus eoeb sn Ccn(.Wang MCScanX(Y. using by genome .suum A. , sn homologous using ) tienm carpo- Steinernema , .canis T. identifica- ) and M. B. P. Posted on Authorea 9 Apr 2021 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.161792702.20501359/v1 — This a preprint and has not been peer reviewed. Data may be preliminary. hc a ne h eeteetv ouainsz itr.W hsdalSP fec niiulb using by individual each of SNPs 2014) all Durbin, over phased and We & loess history. climate MSMC2(Schiffels Chinese size the in of population implemented changes (MAR) effective we rate reflect recent addition, accumulation the closely In mass infer to comparison. the can for reported added which years we been 250,000 2013), have past al., pandas the et giant Zhao of dust(S. of size atmospheric change population dynamic simulated effective of evaluate the variance the to estimate ( used to times rate default was 100 the sampling both 2011) repeat with for approach, Durbin, we genome results bootstrapping each & analysis, a to applied this Li we reads For 2011), method(H. clean ( the size PSMC SRA053353). map population resequencing the (accession effective to using database Next, by 2009) SRA panda Durbin, giant & from parameters. a Li download on (v0.7.13-r1126)(H. individual analysis BWA an same used the of perform reads simultaneously short We the individual. of 1e one history than from demographic lower E-value the with inferred out We filtered genes were HMMER3 output genes the output family, the second gene 2.11 the the 1e Again, by scanning than family. for lower gene template identified E-value the first PTP with scanning as and were used (PF02460) out is domain filtered file PTCHD roundworms ( were domain (PF00704), P450 The domain four CHIA (PF00782). Cytochrome (PF00045), domain (PF00005), domain of GST domain (PF00067), ABC families main including software, gene (http://hmmer.janelia.org/) detoxification-related Seven meeting 2.10 by identified was ( PSG [?]1. The P-value the probability corrected freedom. and posterior of a hypothesis degree of 1 null requirements with the the distributions Using chi-squared calculate ( PSGs. to dN/dS function potential the detect to whether used estimate schroederi was to 2013) hypothesis Yang, alternative between & PSGs (v4.8)(Bo identify PAML we in TreeFam, the from ( retrieved species families gene on Based n hnfrhrepanterdffrnito ihnterudombranch. roundworm the within differentiation 2.9 their explain further then and , eew efre nlssi w ees )Cmaiggn aiiso onwrst te nematode’ other to the roundworms Comparing of calculated. 2) families also roundworms; were gene in family Comparing genes and ( gene contracted 1) branch roundworms 0.01) and each three levels: expanded of ([?] two details the P-value in the determine overall in and significant to analysis changes calculated each performed the were of estimate we family P-values to gene Here exact number each the gene of with median P-value overall a node The used We size. 2006). family Hahn, gene & Demuth, Cristianini, (v4.2)(Bie, ae ntepyoeei rew osrce sn h 41snl-oygns eepoe significant explored we genes, single-copy ( 2451 nematodes the six using in constructed families , gene we contracted tree and phylogenetic expanded the on Based ebtenec pce yMMte rmtePM v.)B ag 03 akg ihdefault with package 2013) Yang, ti- divergent & the (v4.8)(Bo PAML estimated we the 2.8 2017), from Burnell, MCMCtree & by Pisani, species parameters. Fitzpatrick, each points(Mcgill, between time me reference the between as time divergent the Using bootstrap 500 with model substitution nucleotide replicates. PROTCATGTR with 2014) (v8.2.4)(Alexandros, RAxML .elegans C. | | | | μ dnicto fpstvl eetdgns(PSGs) genes selected positively of Identification xaddadcnrce eefamilies gene contracted and Expanded h hneo ffciepplto ieo h ucino time of function the on size population effective of change The families gene detoxification-related of Identification f9 of ) .suum A. a agrta rnt hnpromn ieiodrtots LT sn “chisq.test()” R using (LRT) test ratio likelihood performing Then not. or 1 than larger was ) and × .schroederi B. 10 .hapla M. -9 , .canis T. n 1.29 and .suum A. Ne .Gn aiyepninadcnrcinaaye eepromduigCAF using performed were analyses contraction and expansion family Gene ). , × , of ) .univalens P. n in ad.W sd01 n 2yasprgnrto g n mutation and (g) generation per years 12 and 0.17 used We panda. giant and .univalens P. 10 -8 .schroederi B. for .elegans C. c n in ad,rsetvl(utr 08.Sneflcutosin fluctuations Since 2008). respectively(Cutter, panda, giant and < , and .5 n otie tlatoepstvl eetdst iha with site selected positively one least at contained and 0.05) .elegans C. .schroederi B. -10 and .canis T. n in ad.FloigL’ rcdr(.L Durbin, & Li procedure(H. Li’s Following panda. giant and hntefitrdgnswr sda eodtmlt for template second as used were genes filtered the then , .suum, A. 6 and oietf anadls fgnsin genes of loss and gain identify to ) ω .suum A. au ftefrgon rnh(akdas (Marked branch foreground the of value ) yueo G aagnrtdb DNBSEQ-T1 by generated data WGS of use by .hapla M. hc a acltdbsdo oslevidence, fossil on based calculated was which , .schroederi B. .Tebac-iemdlo CodeML of model branch-site The ). .schroederi B. , .schroederi B. .canis T. n te five other and , .schroederi B. .univalens P. CYP n other and do- ) -10 . B. E ´ Posted on Authorea 9 Apr 2021 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.161792702.20501359/v1 — This a preprint and has not been peer reviewed. Data may be preliminary. ”snp 0 cffls 1o hc eesprcfflslgtduig15G ˜8 )H- eunigdt Fg 1a; (Fig. data sequencing Hi-C X) (˜386 Gb 105 using ligated be superscaffolds assembled to were the estimated of which was size of size the 21 and genome S1), The scaffolds, 106 Fig. S1). and (Table S2 generated (Tables were analysis distribution reads schroederi depth long K-mer PacBio on X) based Mb (110 266.8 Gb 29 of total A set variant raw the Daly, to & applied was Garimella, filtering Hard Poplin, Banks, population. the 4.0.3.0)(Depristo, within v set Li ”QD SNP (GATK using the (v0.1.19)(H. Toolkit were obtain SAMtools to Analysis wild used parameters. Genome in were genome default 2011) and individuals reference with from 2009) the 2010) samples al., to Durbin, 26 aligned et & were and Li reads captivity (0.7.13-r1126)(H. High-quality BWA-MEM in using platform. individuals DNBSEQ-T1&T5 from the collected using samples -p re-sequenced 240 6 of -t total 20 A -i parameters: following the 2.12 used ( calculated rate mutation it The 2007),then ’10*1+15*2’. Browning, & (v5.0)(Browning beagle gis h agtpoeni IC5Seln ri,21) ial,w eetdcmonsapoe in 3.1 approved compounds selected we compounds compounds. Finally, available chemical commercially 3 suggested 2015). for as Irwin, searched above & we or efficient, ZINC15(Sterling et III protein most in PDBe(Sameer phase screening The protein the the in target structure make 5. the a to 2018); had against order protein Mitreva, In The a the & (6) and Whether 2016). (EP); Parkinson, protein al., targets 4. Seshadri, excretory/secretory drug WS240; an enzyme(Tyagi, WormBase ChEMBL as chokepoint in predicted with identified was predicted Similarity were a phenotypes 1. Lethal was factors: protein phenotypes. sterile each main and evaluate six defect to considering as molt targets adjustments ‘0/1’ ( protein alignment of made the single conserved score and the in highly a all 2018) ‘anthelmintics’ out set Berriman, for screen We & we searching gene. targets, Lomax, by drug O’Boyle, and potential Mutowo, For publications described(Coghlan, database. available 2017) from using al., identified et al.) DrugBank(S were et v26(Anna target ChEMBL drug from Known less proteins values target against P (E[?]1 searched BLASTP with were regions proteins The compound-related All SNPs. interest. all of of population score the XP-EHH in involved2.14 (positive) signals variants maximum significant (v3.1.2; genetic the considered rehh were use uncover package 0.01 R to to than the kb accumulated population. Next, using 50 the wild sweeps of calculate and SNPs. selective ments Captive and detect 0.5% between to SNPs, top comparisons used candidate project.org/web/packages/rehh/vignettes/rehh.html the was searched performed of method We of we sides XP-EHH environments, score The strong different both 2012). iHS of under from Renaud, each adaptation SNPs region adding & in flanking detecting by respectively(Mathieu 5-kb for scores population, the used iHS wild in was and genes methods Captive for iHS of and selection (EHH) positive Homozygosity procedure. Haplotype (CV) of error Extended number cross-validation the the predefined ran we and individuals, 5 of 2.13 of to information convergence 2 the from sequence iqtree K explore using genome To clusters bootstrap an genetic algorithm. 1000 using block-relaxation with and a tree with 2007). 2015), phylogenetic al., ML Quang, et the PLINK(Purcell & EIGENSOFT(Nick univalens in construct using Arndt, conducted to out was Schmidt, SNPs carried analysis (v1.6.12)(Lam-Tung, was whole-genome clustering SNPs the population the of used and We analysis software, PCA 2006) al., 2011). et al., et (v0.1.12a)(Danecek vcftools | RESULTS | le” Nswith SNPs filter”. | | | eoeasml,antto n evaluation and annotation assembly, Genome ouainsrcueof structure Population nw n oeta rgtargets drug potential and Known analysis selection nature Recent sa ugop ouainsrcueo l a nlzduigteAMXUE(130 program (v1.3.0) ADMIXTURE the using analyzed was all of structure Population outgroup. an as eoerahd22M,acutn o 84%o h siae eoe hsgnm contained genome This genome. estimated the of 98.48% for accounting Mb, 262 reached genome < 2.0 × || 10 FS -10 > .W cendotaltpso igepoen nteCEB aaaefrblasting. for database ChEMBL the in proteins single of types all out screened We ). > 60.0 .%msigdt or data missing 0.5% > || 0) .Lc fhmnhmlge;3 eae olta,L ret flaccid, arrest, L3 lethal, to Related 3. homologues; human of Lack 2. 80%); MQ μ .schroederi B. < of ) 40.0 .schroederi B. || MQRankSum < .1mnrall rqec MF eefitrdotusing out filtered were (MAF) frequency allele minor 0.01 .W hnslttegnm nonnoelpigseg- non-overlapping into genome the split then We ). nQnigadSichuan and Qinling in 7 o SC eeue h aevle sfrPSMC. for as values same the used were MSMC2 for < -12.5 || ReadPosRankSum < 80 –filter-name -8.0” https://cran.r- B. P. Posted on Authorea 9 Apr 2021 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.161792702.20501359/v1 — This a preprint and has not been peer reviewed. Data may be preliminary. ubro igecp n ut-oygns(i.S1) olnaiyrslssoe htatog several although that the showed in results consistency Collinearity high show S11c). roundworms (Fig. four genes addition, multi-copy In and 1c). single-copy (Fig. of families number gene homologous 3,906 share univalens P. the clustered We ies ucin eeietfid nldn ,4 ovninlyscee rtisad39nonconventionally3.3 349 2). and Data proteins secreted (Supplementary conventionally proteins 1,046 secreted including identified, were functions diverse of (EPs) proteins excretory/secretory of adaptation the for basis genetic the understand To olce rmwrBs,6 ee eeietfid nldn ebr ftepeiul ecie nematode set described gene previously channel the ion from of ligand-gated members transition the including ( with the identified, classes comparing during were receptor By acetylcholine genes expressed 65 2012). are nematodes. wormBase, al., from signaling, et among collected larvae(Park ascaroside conserved infective mediate to especially completely larvae to families, almost dauer known chemoreceptor were are Some which cycle, (GPCRs), Baysch06944), of life receptors homologues 2). coupled the the G-protein Data example, during For 62 (Supplementary identify expressed inhibitors to differentially us protease those enabled and search genome-wide proteases A 437 S11b). in Fig. classes and protein S10 major several of abundance 2015). al., roundworms(”Ascaris et related Zhu other 2007; of al., those 3.2 to et The similar Ghedin long non-LTRs. were 2011; predominant 17 families the genome,” are identified retrotransposon draft L2 the We suum and SINE). RTE-RTE of 16 CR1, size and and genome. LTRs, and LINE predominant number the (25 the families are dominated retrotransposon Gypsy non-LTRs MULE-MuDR and 41 Pao and and retrotransposon DNA (LTRs) repeats CMC-EnSpm, terminal which of families in transposons suum for nematode DNA account published of 2011) (TEs) expansion among significant genome,” elements found 2018; Transposable draft is Consortium, suum & content 2013). suum(”Ascaris Genomes, repeat Schierenberg, Helminth, the of International, & of 2009; Koutsovoulos, proportion S6-S8 9.51% al., (Table Kraus, the et genome (Berriman Kroiher, in the 48%) Schiffer, variation of to Huge 11.76% 1% for (from mRNA, accounted genomes S10). of transposons) evaluate distributions RNA To Fig. and length S7). and transposons the Fig. (DNA compared and repeats we S5 Total Table genes, in methods; introns protein-coding (see and (Table was proteins, predicted tRNAs roundworms exons encoding (CDS) related the encoding CDS, genes sequences other genes of 12 of coding 22 containing that completeness of and identified, to the was length rRNAs, similar genome average ontology is encoding which mitochondrial The genes gene gene, bp 2 TrEMBL, per S6). 14,767 exons (COG), a 6.87 Fig. Furthermore, proteins of and S4). of average of S5 an encyclopedia groups with Kyoto (Fig. bp orthologous 1,052 InterPro formation,”). of and size clusters Swissprot body (KEGG), highest were (GO), regulates genomes genes the and and protein-coding reflecting signaling genes 19,291 TGFbeta S4), modulates 1). KIN-29 (Fig. (Table kinase respectively genomes 93.4%, roundworm via other and published predicted of 91.9% among that were completeness to databases genome similar eukaryote is that the and which showed than ( further 37%, nematode 2015) better S3b) around al., significantly et and centered Zhu is whole S3a narrowly 2011; and which the content genome,” (Fig. draft of 1), GC distribution suum (Table 98.67% a roundworms(”Ascaris GC-depth for three Mb have The accounting 12.69 regions 2020). Mb, was genomic al., ˜263 N50 most reached et scaffold Hu superscaffolds final genome(Y. 21 The published these of S3). length (Table total genome The S2). Fig. | | ooaacanis Toxocara vltoayadpyoeei eainhp mn i nematodes six among relationships phylogenetic and Evolutionary eeomn-eae ee o e nye,incanl,rcposadsecretome and receptors channels, ion enzymes, key for genes Development-related ”sai umdatgnm, 01 SplmnayDt ) hr r tlat6 N transposon DNA 64 least at are There 1). Data (Supplementary 2011) genome,” draft suum (”Ascaris , binitio, ab .schroederi B. .canis T. .schroederi B. al ) ecmrigUieslSnl-oyOtoos(UC)soe against scores (BUSCO) Orthologs Single-Copy Universal Benchmarking 1). Table ; oooybsdadRAsqecn-ie ehd seMethods)(”serine-threonine (see methods sequencing-aided RNA and homology-based , .elegans, C. .schroederi B. eoe(al 8,wieTscnttt .%ad1.%i h eoe of genomes the in 13.5% and 4.4% constitute TEs while S8), (Table genome deg-3 eemdl ihtegnsfo v te eaoegnms( genomes nematode other five from genes the with models gene anradtseeasdaf-37 elegans Caenorhabditis and , acr-16 .schroederi B. ihtoei te v eaoe Fg 8adFg S9). Fig. and S8 (Fig. nematodes five other in those with eodgn hapla Meloidogyne , and .schroederi B. unc-29 .schroederi B. .cnsZue l,2015) al., et canis(Zhu T. n tlat135Es(.6 fttlpoen with protein) total of (5.26% EPs 1,395 least at and , 8 and .schroederi B. unc-38 oprdto compared al 1) efudta h i nematodes six the that found We S11). Table ; , .suum A. GnI:Byc188 and Baysch11898) (GeneID: (nentoa ta. 08.W predicted We 2018). al., et )(International oteprstclf,w sesdthe assessed we life, parasitic the to , sai suum Ascaris .univalens P. .canis T. epciey eietfida identified We respectively. , Zue l,21)and 2015) al., et (Zhu and , , aacrsunivalens Parascaris daf-38 .canis T. .suum A. (GeneID: (Table A. A. , Posted on Authorea 9 Apr 2021 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.161792702.20501359/v1 — This a preprint and has not been peer reviewed. Data may be preliminary. nomto rcsighdudroesgicn hne Fg 1aadS2) neetnl,asimilar a Interestingly, S12b). to KEGG and compared families, environmental S12a branch gene roundworm and contracted the (Fig. metabolism in and changes development, appeared expanded significant tissue also the undergone expansion to significant both had related show For processing pathways also information nematodes. roundworms that However, showed in life analysis S12). (Table enrichment parasitic family to each ( related ( in families those contracted genes gene significantly are 29 1.61 families in of gene expansion 563 loss that average found an we Specifically, with 2a). (Fig. roundworms of with Compared h irto frudom stemi as fVM(i.4) ci oyeiaini otoldby controlled is polymerization Actin 4a). (Fig. VLM of cause main the is roundworms of migration The (ko00280, isoleucine, in that and found leucine we valine, Finally, 3.6 of degradation 3b). the (Fig. especially behavior acids < eating amino essential of of regulation pathways positive in pathways, involved metabolic schroederi family in actin gene involved the ko00980; the genes P450, of of of cytochrome expansion number ko05100; by significant the xenobiotics (ko05130, highly that of munity showed the (metabolism enrichment to metabolism KEGG due drug including largely 3d). term was 3a, GO which enriched (Fig. significantly contraction, family most muscle The straight (GO:0006941), process (GO:0030036). the contraction metabolic organization was chitin cytoskeleton muscle (GO:0030536), actin striated behavior and in feeding (GO:0006030) involved larval functions (GO:0002119), development with larval families nematode gene panda, expanded giant identified the We of environment intestinal and in genes habitat contracted , specific and the expanded the to analyzed adaptation we the understand better exhibiting To families gene behav- all nematode among to difference related 3.5 significant genes 2c). most among the (Fig. the expanded that roundworms for significantly showed in was accounted analysis expansions family adhesion enrichment actin GO biological according the and 2b). addition, families, ior In gene (Fig. 2018). expanded roundworms be al., of four may et statistics all which proteases(International number family, host copy gene from the inhibitor roundworms chymotrypsin/elastase to of the protection Rap1 a of to and expansion related (ko04145) an pathway observed phagosome we ( study, (ko04530), observed previous junctions was tight (ko04015) the pathway of signaling expansion significant a addition, the that found we ment, roundworms, four the divergence Among the and 1d). (Mya), (Fig. 3.4 ago Mya years 160-26 approximately million is 400-269 canis roundworms approximately T. four to the time between divergence time previous the a from with evidence estimated consistent fossil are we and tree tree database phylogenetic phylogenetic 2011) the a TimeTree(Hedges, in reconstruct the nematodes to 2018). six genomes al., the nematode et among study(International six relationships the The within 1d). shared (Fig. genes of single-copy proportions 2,451 used The We 1b). considerable. is roundworms (Fig. among low differentiation are genomes canis the T. among collinearities between related, collinearity closely are roundworms .univalens P. .1 i.3c). Fig. 0.01; .schroederi B. | | | h infiatepnino ci aiyi saissadpstv eeto ee (PSGs) genes selection positive and Ascariasis in family actin of expansion significant The xaddo otatdgn aiisrltdt h dpainof adaptation the to related families gene contracted or Expanded inAscariasis genes contracted and Expanded a dnie steeris rnht h te he onwrs(prxmtl 3 Mya). 134 (approximately roundworms three other the to branch earliest the as identified was ,4.6 (vs 43.86% ), a 5 nqeanttdpoen,wihwr anyerce ntesnhssadrecycling and synthesis the in enriched mainly were which proteins, annotated unique 654 has and .elegans C. .canis) T. .schroederi B. .suum A. CPG-2 and P . < P .hapla M. eefml ssgicnl xaddi h onwr rnh( branch roundworm the in expanded significantly is family gene .1,ehbtdsgicn hne Fg a.W bevda expansion an observed We 3a). (Fig. changes significant exhibited 0.01), ,ad5.2 (vs 55.12% and ), < .schroederi B. .5.W oue ntecagsi eenme eae ofe ieand life free to related number gene in changes the on focused We 0.05). n h te he onwrsi h eoeseisae3.7 (vs 35.37% are species genome the in roundworms three other the and ag ubro ee aebe oto otatdi h branch the in contracted or lost been have genes of number large a , P < scoeyrltdto related closely is .1 i a.I eaint efdfne ossetwt a with consistent self-defense, to relation In 2a). Fig 0.01; .schroederi B. .univalens P. 9 .suum A. .hapla M. oprdwt he onwrs( roundworms three with compared ,rsetvl,wihidct htgenetic that indicate which respectively, ), .suum A. and Fg 1cd.Frtsu develop- tissue For S12c-d). (Fig. and .elegans C. .univalens P. .schroederi B. P Mgl ta. 2017), al., et (Mcgill < .1 n autoim- and 0.01) codn to According . P < P .1.In 0.01). .suum A. < 0.05), B. P Posted on Authorea 9 Apr 2021 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.161792702.20501359/v1 — This a preprint and has not been peer reviewed. Data may be preliminary. o-eergos oa f58ad30gnswr oae ntepstvl eetdrgosi captive in the regions in selected SNPs positively out distribution the the filtering the in calculated SNPs, within further located 1% We identified were top 3c). were genes the and wild 3b 370 around in Data distance and (Supplementary SNPs kb 518 respectively 18,953 25 populations, of and and wild the captive total captive and the extending a in in By SNPs regions, selection natural 29,553 scores. non-gene recent iHS of under 1% total genes top A detect to populations. (iHS) score wild haplotype integrated used We (PCA) average analysis The components A Principal 6a). S13). methods). and (see between (Fig. S1 filtering separation (Table subspecies after clear respectively obtained panda the were 41-fold, Qinling supported SNPs and million wild 97.91% 6.32 Sichuan reached the of the depth of total of sequencing pandas individuals and captive from coverage from 240 samples sequencing including 26 samples, and 266 of subspecies resequencing whole-genome out carried We i.S4,orrslscnitnl upre w itntgop orsodn oteScunadQinling and Sichuan the and to S13 corresponding (Fig. 3.9 groups diversity and distinct genetic tree two similar phylogenetic supported extremely showed the consistently In compo- populations. populations from results ancestral two 6c). our results shared the S14), the Although no (Fig. supporting Fig. almost in- 6d). cluster were populations, Qinling single (Fig. Sichuan there all PCA another that and the with indicated forming Qinling also population, individuals the analyses Sichuan between whole the structure nents all the of separating and in results PC2 cluster the clusters and addition, single distinct populations a two Sichuan showed forming and which dividuals Qinling method, ( the (ML) clusters separating likelihood two PC1 into with population Sichuan 6b), (Fig. subspecies affected be may population roundworm of the decline and 3.8 to the years, related caused thousand be have few may may past also activities the this. which human in years, by that population 10,000 indicated panda last have giant the Studies the in dynamics. decline population sharp of host Sequentially of a events showed the Multiple size demographic roundworms applied recent of population we the size effective addition, infer population the to In 2014) where schroederi 2004). Durbin, most Kya), Wei, B. The & and (50-30 & method(Schiffels level. Kya pinnacle(Jinchu (MSMC) Period low but Coalescent (300-130 their historical Lake Markovian 5a), a reached periods Greatest reached species glacial also size the (Fig. two roundworm Pleistocene population Kya in the the two effective of 10 occurred The last size to change the population lag. ago) obvious effective slight during the years a significantly and showed (thousand declined Kya), roundworms Kya 50-10 panda the 300 giant of size from the population trend of ( effective same sizes of the change population the exactly effective the almost that have showed panda analysis effective the PSMC of changes the 2011). both estimate to of model size (PSMC) coalescent population Markovian sequentially pairwise the used of we history demographic the reconstruct To ob ne togpstv eeto nthe in the 3.7 selection in positive strong genes alpha-type under subunit 475 be receptor acetylcholine PAML, to the in roundworms, three (P=6.5x10 implemented with deg-3 Compared model 3a). branch-site Data effect (Supplementary the possible Using a suggest finding schroederi interaction. These myosin-actin 1999). M., on & reorganization(Maekawa cytoskeleton actin rho-induced ( selection c.W bevdavr infiatepnino h ci aiyi the in family actin the ( actin of of expansion ( regulators family significant upstream Rho very three the the a Surprisingly, of observed GTPases We small by mediated 4c). are that signals intracellular | | | eetpstv eetosi the in selections positive Recent of structure Population eorpi itr of history Demographic P eoewr on ob ne togpstv eeto oprdwt te he roundworms three other with compared selection positive strong under be to found were genome < n efre eeiin ec eeiinue niiul e ouain.Teeffective The population). per individuals 4 uses repetition (each repetitions 5 performed and 0.01). -3 ,wihi nipratdu agtJns ai,Hdkn atle 07,wsshown was 2007), Sattelle, & Hodgkin, Davis, target(Jones, drug important an is which ), ROCK .schroederi B. hshrltsteLMkns hc hnpopoyae olnt promote to cofilin phosphorylates then which LIM-kinase the phosphorylates .schroederi B. .schroederi B. n h in ad ihntels n ilo erH i&Durbin, & Li year(H. million one last the within panda giant the and P .schroederi B. < .schroederi B. .schroederi B. .5.W osrce hlgntcte sn h maximum the using tree phylogenetic a constructed We 0.05). .schroederi B. populations Rac1 10 rmtecpieScunadtewl iln panda Qinling wild the and Sichuan captive the from populations n xlr h eainhpwt h in panda, giant the with relationship the explore and , eoe(upeetr aa3a). Data (Supplementary genome , ROCK Ne and of ) MLCK .schroederi B. .schroederi B. RhoA ,wr ne togpositive strong under were ), , Rac1 n h otgiant host the and eoe(i.3d). (Fig. genome and , Cdc42 Fig. ; B. Posted on Authorea 9 Apr 2021 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.161792702.20501359/v1 — This a preprint and has not been peer reviewed. Data may be preliminary. 9 b ,2 bad35k,rsetvl Tbe1.I hssuy epeettefis chromosome-scale first the present we study, this In 1). (Table respectively kb, the 375 of published assembly and of of genome kb studies N50s 1,825 in-depth scaffold kb, The The 290 1998). genome. high-quality al., a et of (Zou pandas giant of schroederi references B. provide will compounds and 4 targets anthelmintics. proteins, drug new the of for potential all development potential These Among the greater ( for anthelmintics. 4b). have genes as Data drugs target designed (Supplementary above the three approvals target originally and of each that not potential against III found were encoding compounds the Phase target we compounds available drug evaluate existing commercially the these to all the for although of searched factors Since position protein we main the anthelmintics, 8). located six new we Finally, into considering (Fig. development 8). ‘0/1’ superscaffolds against Fig. of on blasting methods; score (see genes By target a drug set 2018). a as we al., protein Then et complexes(International proteins. protein were may single than we that targets drugs, against (similarities ChEMBL known drugs protein proteins to single target develop addition on In to focused by We 2015). easier compromised targets. al., are be drug et anthelmintics potential Li existing new identifying populations(D. Many to roundworm 2015). committed ‘WHO in effective al., resistance be P02 et of DrugBank to Wang increase proven code searching ivermectin(C. the been and by ATC have drugs collated al.) (WHO) these et further of pyrantel(Xie Organization were Some Health 2017)) 4a). World al., Data corresponding against (Supplementary et with The literature DrugBank(S the humans identified. from and were treat databases targets drugs drug to al.) 10 specific et and used encode ChEMBL(Anna against anthelmintics’ which drugs the searched genes, against (13 were known blasting (E[?]1 90 proteins drugs By targets of BLASTP related identified. total potential using were compound a new the activities databases, All al.) of biological of et identification recorded discovery. identification v26(Anna with enables drug enables molecules ChEMBL also of it from it areas hand, proteins hand, other one target other from the the compounds On on for anthelmintics, compounds. existing anthelmintic of active targets of biologically data genome identify high-quality The to 2017). of Benndorf, (Fig & number (PTP) (60)(Schumacher average 97 family phosphatase of the tyrosine total protein and and A (PTCHD) scale, family genome patched S11d). whole (CHIA), the 18 at family families ( hydrolase gene dependent detoxification-related several ATP scan to including 7c). software HMMER3 (Fig. the population use captive We the in selection deworming positive Similarly, strong different 3.10 under by be 3d). selected to Data positively observed (Supplementary also been were protein populations have resistance wild may multidrug that and the resistance, genes captive encoding for the genes screen comparing the method(Pardis the population. to by Interestingly, wild (XP-EHH) 2007) the homozygosity pressures in 7b). haplotype al., selection not extended but et (Fig. cross-population population, regions Sabeti the captive genome used the C in also flanking selection we the positive addition, in under In found than only lower were significantly genes four were ( genes ced-7 regions 2003)) transporter in al., ABC diversity 2002)), genetic Grant, and the & 1998) Fares ( that 2006; 6 found protein Thomas, fluoxetine and & to ( resistant S13), nose alpha (Fig 2006)), channel al., superscaffolds chloride 21 glutamate-gated the the around on diversity nucleotide of | DISCUSSION | dniyn nhlitcrssac-eae eefml n rgtargets drug and family gene resistance-related anthelmintic Identifying .schroederi B. glc-1 β- ,--ctlaatsmnlrnfrs r- ( bre-4 1,4-N-acetylgalactosaminyltransferase xiissrn niomna dpaiiyadwd itiuin n satra otehealth the to threat a is and distribution, wide and adaptability environmental strong exhibits , nrf-6 uha ledzl(ue l,21) eedzl(ore rcnl,&Bcn 2010), Bacon, & Cracknell, mebendazole(Bourne, 2011), al., et albendazole(Fu as such , ABC yohoep5 ( p450 cytochrome , .schroederi B. > rnpres utps ebaepoen,wr dnie in identified were proteins, membrane multipass transporters, ABC ABC 0)i h igepoendtbs hML eietfid9 ee encoding genes 95 identified we ChEMBL, database protein single the in 80%) ,ctcrm 40(Y) lttin -rnfrs GT,glycoside (GST), s-transferase glutathione (CYP), P450 cytochrome ), rnpre ee nrudom a rae hnta in that than greater was roundworms in genes transporter cmd-1 ihtesaodN0o 26 b ersnigagnm assembly genome a representing Mb, 12.69 of N50 scaffold the with , CYP Ap2s1 nrf-6 aiymmesadohrdu eitnerltdgenes, related resistance drug other and members family ) , HRAS 11 pgp-3 glc-1 uxtn Poa)rssac eeCo,Kemner, gene(Choy, resistance (Prozac) fluoxetine a , bre-4 .suum A. eetrfratemni vretnCo et ivermectin(Cook anthelmintic for receptor a , X ta. 98 hc srltdt ivermectin to related is which 1998) al., et (Xu aeaalbecmonswt hs III/IV Phase with compounds available have ) .schroederi B. eitnet oefrigtxnGitset toxin(Griffitts pore-forming to resistance , ced-7 , .univalens P. .schroederi B. × hgct ope(u&Horvitz, & corpse)(Wu phagocyte , 10 aebe aprdb h lack the by hampered been have -10 ,adattlo ,5 small 4,554 of total a and ), and rvdsa opportunity an provides .canis T. .schroederi B. eoe are genomes .elegans C. , Posted on Authorea 9 Apr 2021 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.161792702.20501359/v1 — This a preprint and has not been peer reviewed. Data may be preliminary. spsil httegn rqec fteegnsi tl nraig n tmycueteeegneand emergence the cause may into evolve it it even and may quantified, infection increasing, of be still sources cannot new is recent areas some drug genes in that resistance shown these drugs of have current of of Studies frequency the use frequency individuals. increased in frequent resistant gene of selection natural an the the increase natural to evaluating indicated that related of for results possible be degree option The is may the This an Although genes. offer populations. decades. resistance-related captive Sichuan), thus, in few and and facing genes a are (Qinling deworming, resistance-related populations of regions two for The trends different pressures frequency. two selection gene selection in from changes different metabolism obtained recent of completely considers were and mainly selection biosynthesis populations analysis positive selection and/or captive natural significant xenobiotics and recent ( other wild the genes a and Although identified resistance-related observed drugs We other We and of members 2015). metabolism compounds. al., the endogenous et in of Wang drug involved drugs(C. widespread be anthelmintic to may leading existing population, of drive the administration may ABC in drugs the resistance of from after drug use shifted pandas Frequent has to the decades related 2008). recent in al., genes in resistance et of pandas Zhang frequency giant ability deaths(J.-S. of increasing locomotion VLM-related death the stronger to of of cause poaching the basis and investigation, starvation genetic previous the a explain to extent, According some to Chisholm, least & of at damage(Suhong migration may, epidermis of the family of nematode to gene muscle migration of significance have actin repair promotes and great may the the movement Actin of family in the is involved actin 1998). which is in the movement(Hall, 2012), actin roundworm role of that the cell important selection shown of and very have positive tissue contraction Studies a and muscle muscle expansion plays The for extreme and expulsion. the avoid force contraction can and driving they motility the that in provided ensure role time key same a the plays at and size, (KO00280; body isoleucine and than to leucine ability of every valine, bamboo discharged ability of of and the produced degradation amounts enhance is the large feces ingest especially of to of acids, amount Yang, families have large gene intestines(Guibo pandas a unique small giant and several the 2007), thick bamboo, al., to and of Accordingly, et panda day. response digestibility short needs(Sims giant low in nutrient with the However, their the evolved carnivores, meet 1997). to gradually of Wei, Due & structure has Yuan, intestinal panda Hu, 1995). evolution(Zhou, the giant of maintained years The of the has millions al.). similar, traits. during et are diet Williamson evolutionary roundworms bamboo 2011; in molecular al., Ascarididae collagen et unique of digest viscera(Hanns in characteristics shows can larvae morphological epidermis of tissue that migration the nematode in shown the the Although involved in have involved in potentially studies be astacins thus genes of Previous and Some products tissues, to homologous host respectively. secretory genes return the again. kinase, including finally in roundworms, eggs serine/threonine-protein develop, wall, in metallopeptidase(s) lay and and intestinal expanded and molt significantly the metallopeptidase been 1989), adults penetrate to have Boyce, harsh into evasion intestine, M. a immune develop the W. and in to enter invasion even & intestine larvae roundworms Kazacos small stage, of significant organs(K. survival the parasitic a and the observed tissues the prolonging have among in We thereby migrate addition, shell, 1970). which In egg years(FAIRBAIRN, shell, roundworm ten chitin environment. the to polysaccharide of up elastic protein formation for and chitin-binding the soil tough the adap- a the the have of in roundworms reflecting expansion persist of useful nematodes to Eggs and free-living eggs valuable life. from enables expulsion. parasitic different a for the provide are development to drug that will tation as characteristics genome well special this as have that roundworms, Roundworms envisage on We research future Ascarididae. for in resource contiguity genetic best the with .schroederi B. , CYP .suum A. , GST hnohrroundworms. other than .schroederi B. .schroederi B. , , .univalens P. .schroederi B. CHIA , PTCHD .schroederi B. ed oasr uret smc spsil.I the In possible. as much as nutrients absorb to needs ouain utemr,teehv enrprso ieeet ngiant in effects side of reports been have there Furthermore, population. and oasr uret.I addition, In nutrients. absorb to .canis T. and CPG-2 eefudt eivle ntemtbls fesnilamino essential of metabolism the in involved be to found were PTP glc-1 osriei h ml netn eas fismc smaller much its of because intestine small the in survive to aiyi onwr rnhs hc a erltdto related be may which branches, roundworm in family eefmle nthe in families gene , 12 nrf-6 .schroederi B. , pgp-3 and ntegatpna h xaso of expansion The panda. giant the in bre-4 .schroederi B. .schroederi B. ncpie(C populations. (SC) captive in ) P .schroederi B. < .1,wihi ieyto likely is which 0.01), ABC eoe hs genes These genome. .schroederi B. ed togrmotor stronger needs .schroederi B. and CYP ntehost. the in genome, family still Posted on Authorea 9 Apr 2021 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.161792702.20501359/v1 — This a preprint and has not been peer reviewed. Data may be preliminary. h aata upr h nig fti td aebe eoie noCG euneArchive Sequence CNGB into deposited been have CNP0001242. ID study project this CNSA with of (CNGBdb)114 DataBase findings GeneBank the National China support of (CNSA)113 that data The interests. AVAILABILITYDATA financial conflict no declare and authors manuscript. H.M.Y. The final Q.L., H.L., H.L., the project. D.S.L., INTERESTS approved D.S.L., the M.L., OF and M.L., K.K., supervised CONFLICT read Z.J.H., Q.L. K.K., from and authors Z.J.H., input K.K. All with H.L., manuscript. manuscript Z.J.H., manuscript. the the X.X. S.C.Y. wrote the wrote and T.M.L. supervised and Y.X.Z., and X.X. T.M.L. Q.W., L.H. DNA and the R.B.H., L.H., and performed H.M.Y. H.M.L., H.L.C., H.R.L. analysis. T.M.L., Q.L., and H.T.S., L.H., data J.Y.Y. Y.L.W., the Y.Q.Z., sequencing. S.W.H., Y.X.L., performed and D.S.L., L.L.L., Z.W.P., construction L.H., library X.F.C., project. extraction, the samples. the initiated collected and L.H.D. designed H.L. and Z.J.H., of Laboratory CONTRIBUTION Key 2017B030301011). AUTHOR Provincial No. Guangdong the (grant the in Forestry Write and Animals State and KLSFGAGP2020.002), Rare of Read of (No. Laboratory Genome Biology Park Key Conservation National on Park of Panda Foundation Administration) for National Giant Park the Funds (State Panda China, Research Administration of Giant River Fundamental of Grassland 2572020AA30) Pearl The and (2019CX01N111), Project the (No. in Province Universities 20180302), Open Animals Central Guangdong (No. 2017YFD0501702), the in Rare project Program of research (No. technology Recruitment Biology Program Talent and Conservation R&D science Forestry on Key No.2020004), SFGA National (CCRCGP, of the by Laboratory supported Key was work population This on history deworming of impact potentially ACKNOWLEDGMENT the have revealing identified chitin prevention. for have and epidermal insights of genomics we structure population provide The example, process genes addition, genetic prediction for the In the biology. drug adaption, in metabolism. of environment molecular and acid loss intestinal amino analysis some and or essential and that morphology and selection selection information case in environmental gene gene synthesis, the of evidence for accompany- also avenues details the of new is the in allowed study It process seen to the clearly differentiation. possibility in be roundworm the specificity can provides This genome host roundworm and evolution. differentiation host significant ing undergone diseases. has parasitic Roundworms other works and such baylisascariasis that of novel envision treatment We as and prevention 5 testing. repurposing of the further for activity for needs anthelmintic considered modalities compounds the be new target Nevertheless, provide could potential will expense. compounds other and and These effort compounds approval. considerable these Supplementary vaccines. 3/4 save and chlorpromazine; phase would drug drugs and which known a follow-up anthelmintics, 90 have trifluoperazine of of development that haloperidol, total the . 4b) a (lonafarnib, for identified 2015) Data basis We compounds al., a level. four providing et genome searched targets, Wang whole We drug the use(C. potential from of 95 screened and new frequency be targets can for increased targets need to drug pressing effects due and side drugs, a of populations serious efficacy, is genome parasite low there chromosome-scale from in Specifically, suffer The resistance drugs Hudson, 2012). existing drug roundworms(James, since Zhou, rising of panda, & giant or expulsion the King, intestinal protect for Utzinger, to drugs drugs Melville, anthelmintic anthelmintic Jia, works. new future 2009; for Davey, in need & essential urgent still an are is individuals drug-resistance There drug-resistant of of identification detection the the Therefore, and 2019). genes Hui, & pathogens(Zumla antibiotic-resistant potential | CONCLUSIONS .schroederi B. rvdsarfrnefrtedvlpeto species-specific of development the for reference a provides 13 Posted on Authorea 9 Apr 2021 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.161792702.20501359/v1 — This a preprint and has not been peer reviewed. Data may be preliminary. eSla .R,Bokr . oe,P . oteo,A,Egl,D,&Svoi .(03.Soil-transmitted (2003). L. Savioli, & (2011). D., T. Engels, S. A., Sherry, Montresor, picture. . global J., P. the . Hotez, updating . S., infections: A., Brooker, helminth M. R., Depristo, N. E., Silva, Banks, De VCFtools. A., and C. format Albers, Estimates call G., Direct variant Abecasis, from The A., (2006). Inferred Auton, Drosophila A. P., and Danecek, Wolstenholme, Caenorhabditis Rate. & in Mutation Times Neutral L., Divergence the Holden-Dye, orthologues of (2008). functional R., D. are A. Sihota, Cutter, and E., behaviour Siney, receptors. locomotor contortus regulate V., Haemonchus receptors of Portillo, ivermectin N., elegans Caenorhabditis Aptel, A., universal of a Blast2GO: Cook, set (2005). research. screening M. genomics Robles, a functional & in Creating M., analysis Talon, 3676. and J., visualization Terol, (2018). annotation, M., M. for J. tool Garcia-Gomez, Berriman, S., & Gotz, A., J., Conesa, Caenorhabditis Lomax, ChEMBL. in N., using Genes compounds O’Boyle, Fluoxetine-Resistance anthelmintic Transport. P., potential (2006). Drug Mutowo, the in H. A., Act for J. May Coghlan, Kit Thomas, and Tool & Intestine A M., the MAKER-P: J. in Function Kemner, elegans (2013). M., M. K. Annotations. Yandell, R. Genome & Choy, Plant C., of J. Control Stein, Quality (2009). 513. C., L. (2), and Holt, T. Management, Madden, M., Creation, & Law, Rapid K., S., Bealer, M. missing-data J., Campbell, Papadopoulos, and N., applications. phasing Ma, and clustering. haplotype V., architecture Avagyan, haplotype accurate BLAST+: G., localized and Coulouris, of C., Rapid Camacho, use 81 by (2007). Genetics, studies Human L. of association B. Journal whole-genome Browning, (Ursidae). for & bears inference to R., related S. issues Veterinary Browning, (2010). H. PAML. Bacon, 44 yearbook, & for zoo Interface J., the Cracknell, User for D., Graphical tool Bourne, computational A a pamlX: CAFE: (2013). (2006). 12. Z. W. Yang, (12), M. & a. X., Hahn, Bo, Soil- & evolution. P., (2006). family J. J. gene P. Demuth, of Hotez, N., study & Cristianini, D., the D., of Diemert, T. genome A., hookworm. Bie, Loukas, The and trichuriasis, M., (2009). ascariasis, S. al. Geiger, infections: et M., helminth & Albonico, transmitted P., S., G. Brooker, Dillon, J., A., Bethony, R. a Wilson, ChEMBL: mansoni. T., P. Schistosoma L. Loverde, fluke A. J., blood B. Bissan, Haas, sequences. M., . DNA Berriman, analyze to . program a . finder: 573-580. H., repeats Tandem Anne, G. & D., Benson, Mark, (2011). C., genome. draft Jon, suum A., Ascaris discovery. B. drug phylo- Patricia, for large J., database of bioactivity L. post-analysis large-scale and Bellis, analysis G., phylogenetic Anna, for tool a 8: version genies. RAxML (2014). S. Alexandros, REFERENCES Bioinformatics 1,16-32. (1), 9,9. (9), oeua ilg Evolution & Biology Molecular iifrais 22 Bioinformatics, 5,1084-1097. (5), aue 460 Nature, oeua n iceia aaiooy 147 parasitology, biochemical and Molecular aue 479 Nature, iifrais 27 Bioinformatics, m iifrais 10 Bioinformatics, Bmc 75) 352-358. (7253), 77) 529-533. (7374), rnsi aaiooy 19 parasitology, in Trends 1) 1269-1271. (10), 14 1) 2156-2158. (15), 4,4. (4), 1,421. (1), eeis 172 Genetics, h act 367 lancet, The uli cd eerh 27 Research, Acids Nucleic oeua ilg Evolution & Biology Molecular 1) 547-551. (12), iifrais 21 Bioinformatics, 1,118-125. (1), 2,885-892. (2), ln hsooy 164 Physiology, Plant 92) 1521-1532. (9521), h American The International 1) 3674- (18), (2), Posted on Authorea 9 Apr 2021 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.161792702.20501359/v1 — This a preprint and has not been peer reviewed. Data may be preliminary. an,Sbi,Aulasn lhzy ons aeok,...Rnr.(01.Lf yl stage-resolved cycle Life pro- stage-specific (2011). of (2008). ratti–identification Renard. R. Strongyloides . J. from Wortman, excretome/secretome . teases. the . . of Makedonka, analysis Younis, . proteomic Elshazly, Cytoskeleton. Abuelhassan, Actin . Soblik, Assemble the J., Hanns, and to Orvis, GTPases Program Rho E., the (1998). J. A. and Allen, Hall, EVidenceModeler M., De Pertea, using M. W., annotation Lieber, Alignments. Zhu, structure Spliced . L., gene S. . eukaryotic generation Salzberg, Automated . reference J., J., for B. Bowden, platform Haas, Trinity D., P. the using Blood, RNA-seq M., Aroian, analysis. from Grabherr, and . reconstruction M., Yassour, sequence . A., transcript . novo Papanicolaou, R., Pathway Glycosylation J., Muller, Conserved D., B. a Draft L. of Haas, Removal Marroquin, by (2007). D., Mediated D. Is Interactions. B. Toxin Miranda-Saavedra, Toxin-Host Barrows, Bacterial for a L., . to Required J. Resistance . Whitacre, (2003). L., V. . D. R. J., Huffman, Crabtree, S., malayi. J. Z., Brugia Griffitts, Qi, parasite (2006). E., nematode X. filarial Caler, Zhu, the D., of Spiro, . genome S., Wang, . E., aligned ambiguously Ghedin, and . divergent alignments. removing D., after sequence phylogenies Otranto, protein of Improvement J., from (2007). blocks A. C. Jose, Jex, & T., E., Comparative variation. Gerard, B. genetic (2011). of Campbell, S.-X. analysis B., Wang, the 3121-3128. Baylisascaris N. for (6), of (SSCP) . Chilton, polymorphism larvae M., . conformation encapsulated Hu, Single-strand and B., . migrating R. Q., of Wang, Gasser, J.-B., reduction Deng, for mice. levamisole Y., in Xie, and transfuga ivermectin L.-L., Niu, of elegans. Caenorhabditis H.-M., efficacy in Nie, Endocytosis Y., Deciphering Fu, (2002). B. Grant, & throughput. H., Fares, high parasites. helminth and in capacity accuracy genetic of 45 high loss Reviews, and with adaptation Biochemical alignment (1970). sequence D. FAIRBAIRN, multiple MUSCLE: (2016). Research L. Acids E. (2004). Aiden, Nucleic experiments. C. & Hi-C S., R. E. loop-resolution Edgar, Lander, H., analyzing M. for Huntley, L. S., system E. S. one-click Aiden, Rao, 95-98. I., & a Machol, S., provides S., E. M. Juicer zoom. Lander, Shamim, unlimited P., C., with N. J. maps Durand, Mesirov, contact Stamenova, I., Hi-C Machol, for . S., system M. visualization . 3 a Shamim, Aiden, provides . with T., Juicebox genomes R., J. mammalian (2016). . Mostofa, Robinson, of C., T., assembly N. . N. novo Durand, de Musial, facilitates C., . module under N. scaf- C., Tools for Durand, chromosome-length Assembly N. scaffolds S., Juicebox chromosome-length yields Durand, The Batra, Hi-C M., S., using (2018). M. E. genome Hoeger, Shamim, aegypti K., O., Aedes S. Dudchenko, the Nyquist, of D., assembly variation novo for A. framework De Omer, folds. A (2017). S., (2011). P. J. S. A. M. Batra, Daly, & data. O., V., sequencing Dudchenko, K. DNA next-generation Garimella, using R., genotyping Poplin, and E., discovery Banks, A., M. Depristo, 1,99-101. (1), cec,356 Science, oeua ellrPoemc Mcp Proteomics Cellular & Molecular 1,29-72. (1), auePooos 8 Protocols, Nature 63) 92-95. (6333), h oenjunlo aaiooy 49 parasitology, of journal Korean The eoebooy 9 biology, Genome 5,5. (5), 8,1494-1512. (8), ora fBooia hmsr,278 Chemistry, Biological of Journal $ 1000. 1,R7. (1), ytmtcBooy 56 Biology, Systematic . Biorxiv 15 254797. , 2,145. (2), cec,279 Science, 4,564-577. (4), aueGntc,43 Genetics, Nature 55) p.509-514. (5350), 4) 45594-45602. (46), rffi,3 Traffic, elSses 3 Systems, Cell auePooos 1 Protocols, Nature 5,491-498. (5), elSystems, Cell (1). Biological (1), Posted on Authorea 9 Apr 2021 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.161792702.20501359/v1 — This a preprint and has not been peer reviewed. Data may be preliminary. i . e . u . ag . i . a,J,...Yn,G 21) rvlneo emnh ncaptive in helminths of Prevalence (2014). G. Yang, . . . J., Lan, C., Li, C., Wang, H., pandas. Wu, giant Y., He, D., Baylisas- Li, on Pamoate Pyrantel and Effective Ivermectin and of Panda. Experiments Fast Giant nese). Deworming Captive A (2015). of IQ-TREE: L. schroedari Deng, caris & (2015). Y., He, B. D., M. Li, Quang, & H., Phylogenies. V. Maximum-Likelihood 268-274. Estimating Arndt, for A., Algorithm H. Stochastic migrans. larva Schmidt, Baylisascaris N., (1989). Lam-Tung, migrans. M. W. larva Boyce, Baylisascaris & R., K. Kazacos, (1989). M. W. 195 Boyce, A. Association, Medical Petrov, & & K., A., Bateman, Kazacos, database. D., Rfam R. the Finn, using N., analysis Quinones-Olvera, e51. RNA J., Non-coding Update, Argasinska, Repbase (2018). P., J. I. E. Walichiewicz, Nawrocki, & I., O., Kohany, Kalvari, elements. gene P., repetitive Klonowski, receptor eukaryotic A., acetylcholine of Pavlicek, nicotinic database V., a The V. Kapitonov, nomenclature. (2007). J., on B. Jurka, update and D. an eukaryotes Sattelle, : prokaryotes, elegans & in 129-131. Caenorhabditis J., (2), finding nematode Hodgkin, gene the P., of for Davis, family software K., web A. GeneMark: Jones, Their (2005). of B. Ranges Mountain Mark, viruses. Five & the in B., Pandas John, Giant of Ecology rein- Comparative China. helminth in (2004). Soil-transmitted Distribution F. Wei, (2012). & meta-analysis. H., X.-N. and Jinchu, Zhou, review & systematic H., a C. treatment: King, (5). drug J., survival after Utzinger, it is S., fection helminths: Melville, in mechanisms T.-W., resistance Jia, Drug (2009). W. parasitic M. fittest? Davey, major & the L., the of A. of Hudson, E., coevolution genomics C. of Comparative James, signatures Genomic (2018). (2020). F. long Consortium. Wei, for & worms. . tool Genomes, . polishing Helminth, . genome Y., International, roundworms. efficient Nie, parasitic Q., and Wu, and fast G., mammals Huang, a non-model H., between Fan, NextPolish: L., Yu, (2020). Y., S. Hu, Morphology Liu, the & on Z., Investigation assembly. Sun, (2018). read J., X. Fan, Wu, Pandas. J., & Giant Hu, Y., Wild Liu, the through H., in billion Zhang, Parasites 106-111+124. bottom Intestinal L., (2), the of Su, Rescuing Situation J., Infection Pei, (2009). and X., H. Zhang, D. H., Molyneux, Hu, & diseases. L., tropical Savioli, neglected A., of Fenwick, control J., iPhone. P. the P. on Hotez, times divergence species TimeTree2: 2024. (2011). B. S. Hedges, aueGenetics Nature uli cd Research Acids Nucleic ora fEooi nml 18 Animal, Economic of Journal Bioinformatics rnsi aaiooy 25 parasitology, in Trends . 7,894-903. (7), . (suppl act 373 Lancet, ) suppl 2), nmlHsady&Vtrnr eiie 47 Medicine, Veterinary & Husbandry Animal 7,328-335. (7), yoeei eoeRsac,110 Research, Genome & Cytogenetic 4,214-220. (4), 2. 97) 1570-1575. (9674), 16 oeua ilg n Evolution and Biology Molecular urn rtcl nbonomtc,62 bioinformatics, in protocols Current mVtMdAsc 195 Assoc, Med Vet Am J ora fteAeia Veterinary American the of Journal LSngetdtoia iess 6 diseases, tropical neglected PLoS oeua ilg Evolution & Biology Molecular ora fEooi nml 22 Animal, Economic of Journal iifrais 27 Bioinformatics, netbaeNuocec,7 Neuroscience, Invertebrate 14,462-467. (1-4), 0) 79 i Chi- (in 87-90 (06), . 1) p.2023- (14), 7,894-903. (7), (1), (1), Posted on Authorea 9 Apr 2021 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.161792702.20501359/v1 — This a preprint and has not been peer reviewed. Data may be preliminary. ucl,S,Nae . odBon . hms . eria .A . edr . ay .J (2007). J. M. Daly, . analyses. . linkage population-based . D., and Bender, 81 association R., Genetics, whole-genome A. Human for M. of Ferreira, set L., tool Thomas, a K., Todd-Brown, PLINK: (2012). B., L. Neale, D. S., sig- Riddle, Purcell, small-molecule & mediates U., elegans. Kumar, receptors C., Caenorhabditis G-protein–coupled F. in promiscuous Schroeder, naling and A., Bethke, structure-specific experimentally K., of mice R. Interaction Somvanshi, in I., migrans O’Doherty, larva D., Visceral Park, Nematoda). (1995). (Ascarididae: eigenanalysis. L. transfuga Casarosa, and Baylisascaris & structure with M., Population infected Malloggi, G., (2006). Renzoni, R., Papini, Reich. & David, Price, L., Genetics Alkes, Patterson, procyonis. Nick, Baylisascaris roundworm, raccoon the by 24 – caused Newsletter, GeSeq infections Microbiology Human (2017). (2002). J. G. Database. W. Murray, Organism Stephan, Model A & WormBase: B., (2019). Ralph, Quarterly Hurd. Services F., & Daryl, Axel, Price, E., Dubaj, genomes. Michelle, organelle U.-J. of S., and annotation P., insect accurate Tommaso, with and L., versatile calibrated Pascal, clocks divergence T., molecular phylogenetic Michael, of relaxed genome-wide Estimation using in (2017). nematodes M. selection A. other fossils. of Burnell, and crustacean footprints & Panagrolaimidae D., detect Pisani, in to A., initio times package D. ab Fitzpatrick, R M., AUGUSTUS: an L. Mcgill, (2006). rehh: structure. M. haplotype (2012). Burkhard, from V. data & Renaud, SNP W., & Stephan, G., H., Mathieu, Alec, genomic G., transcripts. alternative of Irfan, of and Estimation K., prediction ROCK Oliver, Kinases Protein (2013). S., Through Mario, W. Cytoskeleton Actin Fan, the to genes Rho RNA . from transfer Signaling LIM-kinase. of detection . (1999). improved M. for & program Maekawa, . a N., tRNAscan-SE: (1997). Li, sequence. R. genomic . H., S. in Eddy, projects. Zhang, & genome . M., novo X., T. de Lowe, Hu, in . frequency J., A., k-mer Yuan, analyzing Telling, Y., by T., characteristics Shi, Ragoczy, the B., of M., principles Liu, folding Imakaev, reveals interactions L., long-range of Sequence Williams, mapping The genome. L., Comprehensive human (2009). (2009). R. N. O. Durbin, M. Berkum, . Dorschner, Van . E., . N., Lieberman-Aiden, Homer, J., Ruan, SAMtools. T., and Fennell, format A., Alignment/Map Wysoker, B., sequences. Handsaker, whole-genome individual H., from Li, transform. history Burrows-Wheeler population human with of alignment Inference transform. read 475 (2011). Burrows-Wheeler short Nature, R. accurate with Durbin, and & alignment Fast H., Li, read (2010). short R. curated Durbin, accurate a & and TreeFam: H., Fast (2006). Li, B. Lars, (2009). . R. . Durbin, Bioinformatics . & O., families. H., Lara, gene H., Li, animal Jean-Karim, L., of C. trees James, phylogenetic R., of Jue, database C., Avril, H., Li, . 75) p.493-496. (7357), cec,285 Science, . cec,326 Science, eaooy 19 Nematology, . uli cd eerh 25 Research, Acids Nucleic 3,559-575. (3), 52) 895-898. (5429), 1,1-7. (1), 55) 289-293. (5950), rceig fteNtoa cdm fSine,109 Sciences, of Academy National the of Proceedings (8). uli cd Research Acids Nucleic Bioinformatics iifrais 25 Bioinformatics, 5,955-964. (5), 17 8,1176-1177. (8), ul cd eerh 34 Research, Acids Nuclc uli cd Research Acids Nucleic 1) 2078-2079. (16), (suppl aastlga 36 Parassitologia, ) suppl 2), ri rpitarXiv:1308.2012 preprint arXiv 2. W) W1. (W1), Dtbs su) D572. issue), (Database 3,321-329. (3), 2) 9917-9922. (25), mrcnJournal American eia Reference Medical Clinical Plos . Posted on Authorea 9 Apr 2021 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.161792702.20501359/v1 — This a preprint and has not been peer reviewed. Data may be preliminary. epl .(02.UigadudrtnigRpaMse.In RepeatMasker. understanding and Using Springer. (2012). S. Genomic Tempel, in Elements Repetitive Identify to RepeatMasker 4 Using (2009). N. Sequences. Chen, & G M., A Tarailo-Graovac, elegans. (2012). C. D. Everyone. in A. for closure Discovery Chisholm, wound Ligand & – X., 15 Suhong, ZINC (2015). Modeling J. 1 & J. May, mation Irwin, Accessed Last & org, 2008–2015. T., repeatmasker. Determination Sterling, Open-1.0. httpwww. (2007). RepeatModeler from: J. (2015). B. Available P. Rude, Green, Biology. & & Systems R., R., J. pandas. Hubley, Ouellette, giant A., S., by Smit, R. output Sikes, fecal A., BUSCO: and H. digestibility Bissell, (2015). bamboo-diet L., (2015). M. of J. Parsons, E. E. A., Zdobnov, Barillot, J. orthologs. & Sims, single-copy . V., with E. completeness . Kriventseva, annotation I., . 19. and Panagiotis, J.-P., assembly M., Vert, genome R. processing. C.-J., Waterhouse, assessing data Chen, A., Hi-C E., F. for Simao, Viara, pipeline flexible R., and B. optimized an formation. Lajoie, brief size HiC-Pro: N., disease—A body Varoquaux, cardiovascular regulates N., in and Servant, signaling proteins TGFbeta transport modulates KIN-29 ABC kinase serine-threonine (2017). of A. genome in The R. toolkit Benndorf, (2013). summary. genetic & E. developmental T., Schierenberg, core Schumacher, & the D., in G. changes multiple Koutsovoulos, fundamental from C., Nematoda. Revealing history Kraus, separation culicivorax: M., and Romanomermis Kroiher, size H., population P. human Schiffer, Inferring (2014). H. R. sequences. Pauline, Durbin, genome . & S., . Schiffels, . EMDB. University, J., and State M. Ohio PDB Conroy, The from M., data (2006). J. J. structure Berrisford, Schaul, (2007). macromolecular M., R. of G. Gaudet, accessibility Battle, Research improved . A., Acids Younes, PDBe: . G., V. (2016). . Glen, C., V., Cotsapas, Sameer, E., populations. human major Hostetter, in a J., selection Mcdonald, positive 5.0: Lohmueller, . of 913-918. DrugBank B., . characterization Fry, and (2017). . P., detection F., S. Varilly, Genome-wide S. Zinat, structure. C., Schaffner, haplotype P. J., . from D. genome Sabeti, Richter, . human P., the Z. . in H. selection J., Levine, positive 832-837. G. recent M., (6909), R, Detecting J. M., Higgins, (2002). Ana, E., J. D. G. E., Reich, and L. C., peptidases J, P. 2018. detect A., Sabeti, for G. to database C, DrugBank tool the Y., A to F. BLAST: update D, batch D., MEROPS W. The S, genome. (2008). a R. in F. homologues Morton, non-peptidase their & D., N. Rawlings, Ui ) nt4.10. Unit 4), (Unit oeue,22 Molecules, urn rtcl nbonomtc dtrlbad nra .Bxvns...[ta.,Chapter al.], [et . . . Baxevanis D. Andreas board, editoral / bioinformatics in protocols Current m eois 14 Genomics, Bmc D) D385-D395. (D1), alssai rnfg ncpieadfe-agn ouain fbas(aiy Ursidae). (Family: bears of populations free-ranging and captive in transfuga Baylisascaris aueGntc,46 Genetics, Nature 2324. , 4,589. (4), urn ilg,21 Biology, Current 1,923. (1), 8,919-925. (8), uli cd Research Acids Nucleic icii,90 Biochimie, α -asgaigptwypooe ci-eitdepidermal actin-mediated promotes pathway signaling q-Ca 2,1960-1967. (2), 18 2,p.243-259. (2), ru,18 Ursus, oieGntcElements Genetic Mobile D) D1. (D1), eoebooy 16 biology, Genome 1,38-45. (1), ora fCeia Infor- Chemical of Journal etl,UA nttt for Institute USA: Seattle, 2018. , Bioinformatics aue 449 Nature, 1,259. (1), p.29-51): (pp. aue 419 Nature, Nucleic (7164), (19), Posted on Authorea 9 Apr 2021 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.161792702.20501359/v1 — This a preprint and has not been peer reviewed. Data may be preliminary. ho . a,W 20) LTR sequencing Whole-genome (2007). (2013). W. W. Hao, transposons. Fan, & . adaptation. X., . local Zhao, and . history X., individual- Guo, demographic pandas: Q., into giant Wu, insights 67-U99. of X., provides parasites Zhan, pandas The S., giant Dong, (2011). of P., F. Zheng, Wei, S., & Zhao, Y., Hu, animals. X., wild threat Gu, in Parasite H., measurement Wu, (2008). based S. X., Yang, Zhang, L., & M., Zhang, A. Kilpatrick, G.-Y., conservation. Yang, panda H.-L., Huang, to P., Daszak, melanoleuca. J.-S., Ailuropoda Zhang, of parasitology and parasites on Panda.206-208. Advances Giant the (1998). of G. Mucosa Yang, Gut the in Cells Pekinesis Endocrine Universitis of mitochondrial Naturalum Morphology in The Complete resistance (1995). Ivermectin G. (2011). Yang, (1998). X. R. homolog. Prichard, P-glycoprotein Gu, & of R., alteration . Beech, by 91 P., caused Ribeiro, . be W., may red Blackhall, nematodes . panda, M., giant Z., Molento, from M., Chen, Xu, transfuga Y., of Baylisascaris genomes Li, and bear. mitochondrial J., polar ailuri Complete and Baylisascaris Lan, X. panda schroederi, C., Gu, Baylisascaris Wang, and of . Z., panda genomes . Zhang, red panda, Y., . protein giant Xie, Z., a from Chen, transfuga encodes Y., Baylisascaris ced-7 Li, bear. and gene J., polar ailuri engulfment Lan, Baylisascaris corpse C., schroederi, cell Wang, Baylisascaris Z., elegans a Zhang, C. in Y., The Infection Xie, procyonis (1998). Baylisascaris R. transporters. central H. ABC (2007). to fatal Horvitz, M. similar & and M. C., Severe Garner, Y. & Wu, (2005). W., G. J. moluccensis). O. Carpenter, (Cacatua Berlin, B., Cockatoo raccoons: Moluccan & Lock, of roundworm R., N., A. common K. L. Loukas, the Wolf, Ash, procyonis, literature. . Baylisascaris C., current by S. of caused . review Shafir, humans a J., in . disease F. S., system Sorvillo, nervous Mendez, E., J., M. Is Plieskatt, Larvae, Wise, Hookworm V., Infective by Deumic, Migration. Secreted Tissue Y., Metalloprotease in Astacin-Like (2006). Oksov, Involved an S. S., MTP-1, Ellis, caninum Lustigman, & Ancylostoma L., L., toolkit A. D. a Williamson, MCScanX: Janssen, H., (2012). Zhang, H. management Guo, A., and Zhang, . medicine Pandas E., Giant . collinearity. D. of and . Shock Wildt, synteny Toxic X., Wang, gene (2015). J., of M. Li, analysis Li, X., evolutionary e49-e49. Tan, . and D., . detection J. DeBarry, . for H., Y., Tang, Zhi, Y., W., Wang, Huang, L., Li, Ivermectin. F., by Shen, Caused J., parasitic Lan, in metabolism C., of Wang, analysis Comparative (2018). M. Mitreva, RNA-Seq. & J., with worms. Parkinson, junctions S., splice Seshadri, R., discovering Tyagi, TopHat: L. S. Salzberg, 25 & matics, L., Pachter, C., Trapnell, 2,327-335. (2), 9,1105-1111. (9), 482 uli cd Research Acids Nucleic 12,0-67. (1-2), chat,5 Ecohealth, ee 482 Gene, hns ora fWildlife of Journal Chinese abig nvriyPress. University Cambridge : irbsadIfcin 7 Infection, and Microbes . 12,0-67. (1-2), 1,6-9. (1), ora fWllf iess 47 Diseases, Wildlife of Journal IDR necetto o h rdcino ullnt T retro- LTR full-length of prediction the for tool efficient an FINDER: (suppl ora fAinMdcn ugr,21 Surgery, & Medicine Avian of Journal ) suppl 2), . 19 2. 2,317-323. (2), oeua n iceia parasitology, biochemical and Molecular 1,164-171. (1), in ads ilg,veterinary biology, Pandas: Giant uli cd eerh 40 Research, Acids Nucleic aueGntc,45 Genetics, Nature hnJVtSi 18 Sci, Vet J Chin 3,220-225. (3), Actacentiarum Bioinfor- (1), (7), , Posted on Authorea 9 Apr 2021 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.161792702.20501359/v1 — This a preprint and has not been peer reviewed. Data may be preliminary. eeiiesqecs()95 . 13.5 39.95 - 39.07 4.4 37.85 317,115,901 3,511 66,363; 253,353,821 5,747 13,874; - 2,991 204,976; 265,545,801 37.26 6,918 16,980 198,864; 375,067; 10,466 (5.82%) 48,674; 18,474,532 20,376 1,825,986; (0.38%) 966,507 6,506 8,420; 46,632 290,558; (0.7%) 1,980,846 281,639,769 7439 ( 104,281; 15,567 2,778; 9.53 (4.70%) 13,257,555 37.34 42,126 888,870; 161,963 7,262,801; 1,154,808 262,743,947 12,688,039; # (0.10%) 266,500 - (%) 639 sequences 106; Repetitive (%) content GC (bp) Genome Contigs Scaffolds; of (bp) N90 Contigs 410,763 Scaffolds; genome) 2,478,717; of of N50 % (bp; (bp) length Contigs Gap Scaffolds; of length Average Contigs Scaffolds; of Number (bp) size Genome Description the of features the of Summary overview. 1. global Table diseases: infectious protective reemerging and and Tables diseases Emerging of factors (2019). Lethal S. 33 D. Clinics, (1998). Disease Hui, Kongju. & A., . pandas. Min, Zumla, Giant . . penned and . . wild Lujin, . of G., Zeng, canis. countermeasures Samson-Himmelstjerna, Aimin, Toxocara Von Wang, pathogen P., Mabian Xinghuai, Nejsum, zoonotic in Zou, D., the behaviour N. of feeding Young, blueprint and H., Genetic Cai, habits (2015). K., food P. J. pandas Korhonen, Giant Q., X. (1997). Zhu, F. Wei, & Reserve. C., Natural Yuan, Dafengding J., Hu, C., Zhou, h au fsaitclSdksmlil oprsn et fepninadcnrcino ee comparing ( of in genes contraction contraction) of and contraction represents Expansion (or and Fig.3 asterisk expansion expansion red of significant The tests with comparisons genes. multiple contraction) family Sidak’s (or with gene statistical expansion roundworms; of the of value in number p in families total enrichedthe gene genes the are expanded to functional that significantly compared pathways KEGG GO roundworms the KEGG of top of top with number proportion the the compared copy The represent represent Ascariasis gene triangle triangle of and enrichment open families solid function the gene the and contracted with and compared circle the Ascariasis circle open in of The families solid gene families.(a) respectively. The expanded the , gene in families enriched roundworm families. gene are that gene of of pathways number roundworm contraction the in and represent decreases expansion nodes the The below Fig.2 numbers respectively. The contracted, intersection. and bifurcations. each maintained, in the expanded, count significantly at family intersection shown gene the total are represent the times rows indicates the barplot between The lines vertical (d) species. edge. and between circles families the Black expanded to of nematode. center a the represents row from Each scaffolds blocks. and synteny coverage and different sequencing characteristics content, GC genomic (b) content, and repeat nematodes number, gene six among of relationships synteny phylogenetic The Fig.1 LEGENDS FIGURE .su .univalens P. suum A. h ulse eoeifrainof information genome published The ytn of Synteny ieclbae aiu ieiodpyoeei reo i eaoe.Teetmtddivergent estimated The nematodes. six of tree phylogenetic likelihood maximum Time-calibrated .elegans C. .schroederi B. .schroederi B. or .hapla M. 4,xiii-xix. (4), (c) and Oeatrs ersn 10 represent asterisk (One .(a) pe ltsoigteitreto fgn aiyepnin nnematodes. in expansions family gene of intersection the showing plot Upset ora fScunTahr College Teachers Sichuan of Journal with .canis T. eoi hrceiainof characterization Genomic .univalens P. .schroederi B. .schroederi B. .schroederi B. .(a) ). .schroederi B. and niheto h EGptwyi oesignificantly some in pathway KEGG the of Enrichment ora fFrsr Research Forestry of Journal 20 eefmle oprdwt he roundworms three with compared families gene .canis T. -1 genome. ntrlae)Y ue l,2020). al., et Hu released)(Y. (not ). ti study) (this .elegans C. .schroederi B. ttegn ee.Dffrn oosrepresent colors Different level. gene the at . or .schroederi B. .hapla M. eoe h gr hw the shows figure The genome. . infiaticessand increases Significant respectively. , .elegans C. # > 00b)3,3;4,0 ,7 287 51,969 22,857; 1,274 40,509 31,538; bp) 1000 or Infectious .hapla M. (b) .umP nvln .canis T. univalens P. A.suum GO (c) Posted on Authorea 9 Apr 2021 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.161792702.20501359/v1 — This a preprint and has not been peer reviewed. Data may be preliminary. i. nlsso aua eeto ncpieppltos (a) (QLI) wild (b) populations. and captive (SC) in captive in selection ( individual’s signals the natural individuals. of sweep different proportion of the tion the quantifies shows axis Analysis axis y x The Fig.7 and 5). population, to 2 ancestral from inferred (K from populations used genome QLI We and SC information. of structure SNPs (QLI) whole-genome Qinling using to comparison constructed populations; in two of (SC) analysis Sichuan PCA of relationships (a) and population. structure Population 6 ( Fig. generation per rate population. mutation ( Sichuan sizes neutral population The effective ( respectively. loess. years, Chinese 12 sequence and original the 0.17 schroederi from were resampled panda randomly giant sequences 100 for estimates It schroederi (PSGs). B. genes (a) selected sexual polymerization. genomes. positively through the actin resequencing are in of worms involved history red adult families Demographic in into gene Fig.5 migration key genes develop organ three and and internal of intestine polymerization, expansion of small actin significant stage shows the in the involved to represent are return L4 pathways larvae and L5 L3 Stage maturation. stage. larva. infective the the into of developing after body the of whereas history of Ascariasis, history of Life roundworms four Fig.4 the families. represents the axis represents x axis The y contracted. terms. or GO expanded of significantly similarity genes). semantic in (background on families pathway based gene is the in bubbles expanded in the significantly genes of for all position items The to GO over-represented genes) significantly (target of pathway clusters the in located genes of families gene expanded hntp;()Apeitdmtblccoeon;()Apeitdeceoysceoypoen(P;()The alignment (6) conserved (EP); protein highly the excretory/secretory a predicted criteria, having A condition. six (5) mismatch targets chokepoint; the indicating drug metabolic represent predicted circle known A targets hollow ChEMBL (4) drug a phenotype; with potential and Similarity the condition (1) following match ( were: indicating circles criteria circle The formulas solid structural six chemical drawn. red The onsuperscaffolds. are a targets. genes drugs with drug target known potential drug indicates 23 black potential of and The and drugs, to known known transformed different line. also of indicate dashed target, position vertical comparison haplotype. The the a a Fig.8 and by sharing subject indicated scaffolds the is between of furca- marker) nucleotide number The same (focal P the the haplotypes root to figure. showing shared The corresponds core the extended SNP lines of of 2002). the concept side al., of the right et thickness in the contained Sabeti on information C. displayed complete EHH(Pardis were the marker represent focal structures tion a around diversity around Nucleotide homozygosity line. haplotype horizontal dashed the above transporter shown were 1%) P top test (3.89, Z to (corresponding requirement regions selected the θ > ,ωιλδ(ΧΛΙ) π, ausadpotdi oaihi scale. logarithmic in plotted and values 0) 2 ako ua ooous 3 eae olta,L ret acd otdfc rsterile or defect molt flaccid, arrest, L3 lethal, to Related (3) homologues; human of Lack (2) 80%); .schroederi B. lto H hwn oiudrpstv eeto fcpie(C ouain Nswith SNPs population. (SC) captive of selection positive under loci showing iHS of Plot .schroederi B. n in ad ee0.9 were panda giant and ced7 / (b) θ n ot epciey h 0 rycre of curves gray 100 The respectively. host, and ,ςαπτιvε(Σ῝) π, b) suiu eefamilies. gene unique ’s and ceai iga faaoia rs-eto of cross-section anatomical of diagram Schematic h egahcdsrbto ftesmln oain o L n Cpopulations. SC and QLI for locations sampling the of distribution geographic The ogtdnlcag fteeetv ouainsz fthe of size population effective the of change Longitudinal bre-4 .schroederi B. 1adL ersn nvtodvlpetlsae,adL aveetrtehost the enter larvae L2 and stages, developmental vitro in represent L2 and L1 . and ) .schroederi B. Ne oiuig1-bsiigwnoswr ipae bv h ee.Tedcyof decay The genes. the above displayed were windows sliding 10-kb using loci Fst eeetmtduigteMM2mto.QI iln ouain SC: population; Qinling QLI: method. MSMC2 the using estimated were ) h e n upeln ersn h siae ffciepplto ieof size population effective estimated the represent line purple and red The (c) f5 bwnoswt 0k tp.Rddt ersn idw fulfilling windows represent dots Red steps. kb 10 with windows kb 50 of aiu ieiod(L hlgntcte ih10bosrptests bootstrap 100 with tree phylogenetic (ML) likelihood maximum A × .schroederi B. 10 n h ffc fatngn nmsl otato.(a) contraction. muscle on gene actin of effect the and h rprinrpeet h ai ftenme fexpanded of number the of ratio the represents proportion The . (d) -8 n . 10 x 1.3 and eta hwn h eefmle of families gene the showing Heatmap eosrce rmterfrneadpopulation and reference the from reconstructed 21 .schroederi B. -8 epciey h lc iesosteMRof MAR the shows line black The respectively. , < .schroederi B. .univale P. .0,where 0.005, .schroederi B. ouain itiuino nratio ln of Distribution population. (c) steoutgroup; the as niheto EGpathways KEGG of Enrichment . Fst n otrpeettePSMC the represent host and .schroederi B. eoi ein ihselec- with regions Genomic eeaintm g of (g) time Generation > .1adl ratio ln and 0.21 ; (c) (c) .schroederi B. PEHfo each from XP-EHH glc-1 utpesignaling Multiple ouain.The populations. ieetcolors Different (d) .schroederi B. (b) , | nrf-6 iHS Population μ REVIGO | htare that [?]iHS > of ) ABC , e 0.34). Life and (b) B. m . Posted on Authorea 9 Apr 2021 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.161792702.20501359/v1 — This a preprint and has not been peer reviewed. Data may be preliminary. rti a tutr ntePB.Ptnildu agtpoen noiggnso ahsuperscaffold each on genes encoding proteins target drug Potential (black). marked PDBe. are the scores in corresponding and structure a has protein B. schroederi P. univalens C. elegans M. hapla c a A. suum

T. canis Expanded gene familly intersectin count S19 S18

1000 2000 3000 4000 S20

12 8

4 12 0

0 4

S17 8 8 12

0 4 0 0

12

4 8 8 3906

4 12 ● ● ● ● ● ● S16

0 16 1881

8 20 S21 ● ● ● ● ●

4 24 1663 S15

0 28 ● ● ● ● 32

4 398 Mya 797.9-1435.9 ● ● ● 36

S14 0 396 40

● 4 44

0

299

S13

● ● 48 294 4 52 ● ● ● 0 0

266 S1

S12

● ● ● ● ● 4 4

265 0 ● ●

● ● ● 0

12 S2

255 4 ● 8 ● ● ●

Mya 273.7-402.8 S11

339/13047984 4

242 0

● ●

0 4 178 S3

667/49658783 12 8 ● ● ●

d 8 12

119

● ● ● ● ● S10 4 0

0 4 75 S4

8 ● ● 4 12

0 0 67

8 4

● ● ● ● S9

4 8 0

12 S5 12

0 197/129301243

8 4

4 8

0 64 ● ● ● S8 S6 Mya 103-159.6 55

● ● ● ● S7 0.1 0 1615/75515204

0.4

53 4 ● ● ● ● ●

0.7 36 ● ● ● ● Sequencing coverage Scaffolds GC content Gene numbers Repeat content Expansion/MaintenanceContraction 22 ● ● ● 22 19 ● ● ● ● Mya 51.9-89.5 16 ● ● b 969/11724/1677 13 ● ● ● 13 ● ● ● ● 12 ● ● ● ● 11 Mya 25.5-44.7 ● ● ● ● P. univale (host: horse) ● 5 ● 743/11602/2025 ● ● ● 5 ● ● ● ● 5 535/120661769 425/13092853 ● ● ● 3 (host: giantpanda) ● ● ● 3 B. schroederi C. M. A. P. B. T.

canis suum

univalens elegans schroederi hapla

(host: pig) (host: A. suum A. Posted on Authorea 9 Apr 2021 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.161792702.20501359/v1 — This a preprint and has not been peer reviewed. Data may be preliminary. c a · · absorption · · · · · absorption · · · · Carbohydrate digestionand Rap1 signalingpathway Starch andsucrosemetabolism Regulation ofactincytoskeleton Tight junction Metabolic pathways Phagosome pathway Carbohydrate digestionand Regulation ofactincytoskeleton Tight junction Metabolic pathways Ascariasis Expansion 0.25 Roundworms vsM.hapla Roundworms vsC.elegans 0.20 toC.elegans/M.hapla Contracted genefamiliescompared toC.elegans/M.hapla Expanded genefamiliescompared Expansion +29 +30 · · -worm · · · cytochromeP450 · sugarmetabolism · P450 · · · 0.15 Longevity regulatingpathway Platinum drugresistance Protein digestionandabsorption Metabolism ofxenobioticsby Metabolic pathways Amino sugarandnucleotide Drug metabolism-cytochrome Carbon metabolism Calcium signalingpathway Hedgehog signalingpathway -407 -563 Contraction C. elegans M. hapla Free live Plant 0.10 0.05 Phosphenplpyruvate carboxykinase,GTP-utilising,C-terminal Cysteine-rich secretoryprotein,allergenV5/Tpx-1-related Glutamate/phenylalanine/leucine/valine dehydrogenase 0 0 7TM GPCR,serpentinereceptorclasst(Srt) Cell kill Bi Det Cel Protein ofunknownfunctionDUF1647 Be Glutathione S-transferase,N-terminal Grow olog 0.05 L b Presyna ox oco AMP-dependent synthetase/ligase l hav 23 Negativ M Coenzyme AtransferasefamilyI pr R ification R i Glycosyl transferase,family14 ulti in RNA recognitionmotifdomain Reverse transcriptasedomain Glycoside hydrolasefamily31 cal eproduc IQ motif,EF-handbindingsite th oli moti eproducti i or L Posit Cel g Major facilitatorsuperfamily Ribosomal proteinL22/L17 Develo oca fera Mu -organ adhes Si pti on Zinc finger,CCCH-type l gn 0.10 SEPARIN coredomain e ular compon DNA helicasePif1-like **** lti l c p

t ive regu ization regu io ali c t e i n Unknown function roce i pmental i ve C-type lectin-like ng R sm proces l on on l ular esp l NIDO domain ati process OTU domain R Bio Actin family ss egu on l *** Contraction ons 0.15

ati Cadherin organ * logica i

nv of on l ent o proce a e t olv

biolog i s to sti of on

ismal p A. suum l ed in

rganization biolog

re s of s 0.20 gul mulus B. schroederi Contraction (vsC.elegans) Expansion (vsC.elegans) i biolog cal proces c atio ro hemi i M cal proces ces e n

i P. univalens t c ** ab s cal s al or bi 0.25 oli proce * s c Cel ynaptic og

process s T. canis ene l s ular proce * s sis tr C. elegans ansmi Contraction (vsM.hapla) Expansion (vsM.hapla) ** ** s s s M. hapla s i on Copy number 0 10 20 30 40 50 Posted on Authorea 9 Apr 2021 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.161792702.20501359/v1 — This a preprint and has not been peer reviewed. Data may be preliminary. c a V V V c a aline asopressin−regulated w aline Pro Carboh Metabolism ofx Amino sugarand Fc gammaR−mediatedphagocytosis ximal tub , leucineandisoleucinebiosynthesis

Rho family , leucineandisoleucinedegr P entose andglucuronateinterco ydr Steroid hor Cdc42 Dr ate digestionandabsor RhoA mRNA surveillancepathway Rac1 ule bicarbonatereclamation Ascorbate andalda ug metabolism−cytochromeP450 P Propanoate metabolism Regulation ofactincytos enobiotics Steroid ho AR signalingpathw Pyr n Ar Salmonella inf ucleotide sugarmetabolism mone biosynthesis achidonic acidmetabolism Miner uv ater reabsor Linoleic acidmetabolism Glutathione metabolism Oocyte meiosis ate metabolism L3 &L4 Galactose metabolism RNA tr VLM b al absor Spliceosome L3 Endocytosis r y cytochromeP450 mone biosynthesis Shigellosis Adherens junction r ate metabolism F Adults L5& anspor adation ocal adhesion Tight junction ection Phagosome ption ption ption Apoptosis n a v y t ersions k eleton 0 Proportion (target/background) -Log10(Pvalue) 10 0.12 N-WASP 1 Gene Count PAK L2 0.16 2 20 -Log10(Pvalue) Gene Count 0.20 L1 3 ROCK b Gene Number Phosphoenolp -Log10(P) 30 20 10 5 10 15 20 +p Ser ine−threonine/tyrosine−protein kinase d b T yr r anslation initiationf 24 uv ate carbo Arp2/3 MLCK semantic space x JNK1/MAPK8−associated membr UDP−glucuronosyl/UDP−glucosyltr −5 0 5 Nucleotide−diphospho−sugar tr −10 xykinase anatomical str Domain ofunkno actor regulation oflocomotion , GTP−utilising,conser Glycosyltr Heat shockprotein70f zinc c2h2typef My , betapropellor−lik ucture f Imm osin head,motordomain NAD(P)−binding domain unoglob Histone H2A/H2B/H3 or wn functionDUF148 mation in ansf Ribosomal protein −5 , catalyticdomain Actin Polymerization er +p +p ulin subtype2 ShKT domain NIDO domain ase f amily protein O v olv Actin f ane protein Histone H4 TU domain single−organism cellularprocess ansf ansf semantic spacey ed inmor e domain amily 92 Anne v response tobioticstim f eeding beha +p ed site er er cell comm amily amily ase ase xin phogenesis MLCP A. suum cellular componentbiogenesis MLC Actin unication vior 0

B. schroederi -p response tootherorganism localization ofcell ulus microtub

P. univalens se xual reproduction PSGs (P value) catabolic process cuticle ule−based process biosynthetic process 5 0.05 0.025 0

T. canis muscle epidermal intestine ovary oviduct uterus eggs Versatility Copy number low medium high Expansion Contraction 0 5 10 15 20 25 Posted on Authorea 9 Apr 2021 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.161792702.20501359/v1 — This a preprint and has not been peer reviewed. Data may be preliminary. A c a branch length=9.95

SICHUAN Effective population size (Ne; x10⁴) 10 15 20 0 5 10 4 SC (n=240) (outgroup) P. univale GANSU QLI Chengdu Years beforethepresent Tree scale:0.1 QLI (n=26) 100 100 Xi’an 10 5 SHAANXI SC Giant panda(host) B. schroederi 25 b d K=4 K=3 K=2 PCA2 (14.22%) -0.1 0.0 0.1 10 10

10 15 20 25 30 6 6 1.0 0.0 0.2 0.4 0.6 0.8 0.0 0.2 0.4 0.6 0.8 1.0 0.2 0.4 0.6 0.8 1.0

) years 1,000 ³/ (g/cm MAR B Effective population size 10 10 10 10 0.0 4 5 6 7 10 2 Years beforethepresent(B.schroederi) SC PCA1 (19.50%) QLI SC SC 0.1 QLI 10 3 0.2 QLI 10 4 Posted on Authorea 9 Apr 2021 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.161792702.20501359/v1 — This a preprint and has not been peer reviewed. Data may be preliminary. b a 45679830. 45640260.0 43103608. 40474780. 39673316. 39603028. 38426488. 38011384. 37502912. 36639960. 35807804. 35557880. 35428200. 35370588. 35005740. 34201608. 31079718. 30533424. 21153306. 17833320. 16033398. 14005958. 11676326. 29236794. 26756106. 25768420. 21491572. 5701050. 3916670. 2105169. 1659693. 9736713. 7765001. 7322561. 5748580. 5520828. 5510710. 5371814. 4346851. 1835281. 1069073. 3809774. 2887666. 1997382. 514290. 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 0 0 0 0 0 0 0 Density 0.6 0 0 0 -log(P) Fst 10 15 0 5 . . . 0 0 0 0 0 2 4 S 15 10 0 5 1 - S 4 4 1 S 9 ln ratio(θπ,wild(QLI)/θπ,captive(SC)) 1 B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B B a a a a a a a a a a a a a a a a a a a a a a a a a a a a a a a a a a a a a a a a a B B B B y y y y y y y ysch11393 ysch11314 y y ysch11212 y y y y y y y y y ysch10039 ysch10015 y y y y y y y y y ysch09137 y y y y y y y y 0.0 0.1 0.2 0.3 0.4 0.5 H a a a a s s s s s s s s s s s s s s s s s s s s s s s s s s s s s s s s s s s 3 C y y y y ch12076 (Piperazine) ch11869 ch11646 c ch12073 (Pyrvinium) ch11234 ch11201 ch11189 ch11148 ch10719 ch10378 ch10311 ch09750 ch08796 ch08540 ch08984 ch08948 ch08829 ch11574 ch11569 ch11440 ch11082 ch10777 ch10605 ch09626 ch08808 ch08730 ch08494 ch09492 ch09299 ch08810 ch19282 ch19115 ch19424 ch19163 s s s s h11463 ch13011( ch12834( ch12705( ch12920( glc-1 - ( ( ( ( ( ( ( ( ( ( ( ( ( ( ( ( (Iv ( ( ( ( ( ( (Iv ( ( ( ( (Iv ( ( ( ( ( ( ( ( ( ( 2 P P P P P P P P P P P P P P P M N M M N B O O O O O T T T T T T P P L T HO h h h h h h o o o o o o o o o y o o o y o u h i i e o o x x x x x P P H Pyr oxi e e e e e r r r r i i i i i i t t t t t t t t t t t t t pheni cant i i i i i i t t i bendazol i pacr r r r o o acet acet acet acet acet acet e abendazol b b b b b v v e e e e e e e e e e e e e dazol dazol e e Fst m m m xyl t t i i n n n n n n n n n n n n n endazol endazol endazol endazol endazol n n d e e a n n H ectin ectin ectin tia tia tia tia tia tia tia tia tia tia tia tia tia tia tia ectin 3 n n n i i C u u hone, r 1 i a a a a a a tia tia t n e e m m u l l l l l l l l l l l l l l l r r r r r r e e ) ) ) ) ) ) ) ) ) ) ) ) ) ) ) H N N H e s sam sam sam sam sam sam l m l l , ) ) ) ) ) OH o , , , ) ) L ) M M M , r evam L e e e e e e c P oxi oxi oxi S , evam i i i i i i e ) ) ) ) ) i O r d d d d d d nol , azi P x ) ) ) ) ) ) dectin dectin dectin i y bendazol i ) quant s r i v 0 o s i l o n Epn-2 e H N l i , ) ) ) N NH e u B N e , m iHS S Pyr e l N ) pheni , N A O NH e a ) S l bendazol H CH H n 3 3 C 2 t O e N u CH tin-9.2 l CH m ) 10517769. 10489782. ASU_12729 3 8251208. 8229775. 3559876. 2085833. 3 9181572. 5591362. 3935072. 2515062. 1778907. ) 811933. 548499. 75350. O Fst ≥0.21 ln ratio e 2 ) 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7678408. 7626316. 7563093. 6280917. 5224287. 4286296. 1899788. 343651. S S S 1 6 2 0 0 0 0 0 0 0 0 0 5907015. 4577958. 4183263. 4154164. 3911780. 2927089. 2148785. 1399939. ≥ 0.34 4 S B B B B B B B B B B B B B B 1 Ttbk1 a a a a a a a a a a a a a a 0 0 3 8 8 0 0 0 5 y y y y y y y ysch20623 ysch20555 y y y y y s s s s s s s s s s s s ch07130 ch07129 ch07000 ch06999 O S ch21300 ch20930 ch20752 ch20454 ch14812 ch14749 ch15028( ch14906( S 5 B B B B B B B B 4 2 a a a a a a a a dpy-5 HN O 0 CH y y y y ysch01691 y y y 0.06 0.08 0.10 0.12 3 s s s s s s s N ch01636 ch01311 ch01885 ch01880 ch01873 ch01760 ch01430 ( ( ( ( O P P P B B B B B B B B N 0 O 0 ( ( ( ( ( ( ( ( r r r L M x P P P P T T 6 P P a a a a a a a a azi azi azi RNF212B u CH i e h h y ysch02266( ysch02232( ysch02229( y y ysch02045( y N o o o o b o o H Scaffolds 0 0 1.0 1.5 cant 3 3 pacr s s s s i i endazol t t t t t t C quant quant quant CH acet acet . . e e e e e e ch01984( ch02382( ch02206( ch02117( 0 5 3 n n n n n n ced-7 tia tia tia tia tia tia ( ( ( ( ( ( ( ( O hone) H P A i P P P M P T 1 a a n O O h e e e y r r r r l l l l r l l 7 r r 0.5 e e ) ) ) ) O ) ) azi azi azi azi l l l t sam sam r i Cumulative e ) ) ) pacr e ) acet Density v ) H s O i quant quant quant quant n unat Fst P P P A T T T T Cumulative i CH O i i u h h h h o r r d d l i a bendazol 3 n azi azi 2 m i i i i t ) ) r H CH acet acet acet acet e e sam e 8 ) n 3 ) e e e e quant quant ) tia l l l l ) ) ) ) 1.0 a a a a O i 0.04 0.06 0.08 l d r r r r 11722122. 10978884. ) sam sam sam sam 9844499. 8255195. 7148374. 5981292. 5554014. 4544352. ) OH 900416. 3 e e e H 3 l l C 9 , ) ) P H 13355178. 12620896. 10031238. i i i i Fst 3 Cl 7457228. 6400256. 3137637. d d d d C y nrf-6 ) ) ) ) 0 0 5 0 0 0 0 0 0 r 5717916. 3683951. N v H GRE2 1.5 i 3 n C 6598952. 6542660. 6451809. 4 825003. 10 i c S 0 0 0 0 0 0 u m 7 0 3 N NH , T S 0 0 0 0 smc4 h S 3 i 1 B B B B B B B B B abendazol 11 S a a a a a a a a a 6 y y y y y y y y y 1 NH N O s s s s s s s s s -log(P) 10 -log(P) 10 1 B B B B B B ch16880 ch16816 ch16614 ch16507 ch16377 ch16330 ch16241 ch15934 ch16730 O CH a a a a a a 2 4 6 8 0 2 4 6 8 B B O 3 y y y y y y N a a 12 s s s s s s y y B B B B ch14686 ch13592 ch14081 ch13968 ch14350 ch14616 N s s a a a a e H ASU_14704 ch01078 ch00905 3 y y y y C Tcan_14228 ) 26 S s s s s S ten-1 glc-1 CH N ch05821 ch05828 ch05815 ch05256 ( ( ( ( ( ( ( ( ( N 3 13 P P P P P P P M L u o o y o o o o e O r cant t t t t t t bendazol N v e e e e e e ( ( ( ( ( ( P O P O O O i n n n n n n n 5293525. 5021856. 1314574. 1174989. nrf-6 ( ( CH N y r tia tia tia tia tia tia x x x x P H 14 i azi 3 NH hone, r u i i i i o CG9801 e b b b b v ( ( ( ( m l l l l l l xachl t M N P C ) ) ) ) ) ) i endazol endazol endazol endazol quant e Scaffolds n ) r H i y e n 3 i r azi 9 0 0 0 0 C u c t i tia e dazol 15 r P l m i o , Tcan_16034 H f O quant r o l onat s ) N 3 S azi ) C e XP-EHH r x por H ophene) l 2 i e e e e ) bendazol 16 O 3 CH quant e 1 1 C ) ) ) ) 3 ) e i 0.07 0.09 HLCS 0.08 0.10 0.1 e n ) 1 l e ) O O P ) 10932970. 10433511. 17 B B B B 3230013. 2282893. e a a a a pgp-3 l Fst ) y y y y Cl s s s s e 17 bre-4 18 ch02808( ch02511( ch02832( ch02500( ) OH 0 0 0 0 5571489. 4404993. 4397446. 4380768. 4379644. 4372343. 4341802. 4340932. 4333450. 3088513. HLCS Cl 7320703. 7292525. 5956342. 4540754. 3609840. 3496858. 3057457. 2416716. 19 7886509. 6103405. 4296010. 1354231. 1162682. Cl 957391. S 91556. 4 0 0 0 0 0 0 0 0 0 0 20 P P P C 0 0 0 0 0 0 0 0 o o r y 0 0 0 0 0 0 0 S ASU_07490 azi c t t ASU_03085 e e B B B B 1 l 21 o n n quant a a a a S 7 S s tia tia y y y y por 1 8 s s s s l l 2 ch04919 ch04175 ch04966 ch04099 ) ) B B B B B B B B B B i e n a a a a a a a a a a l e B B B B B B B B ) y y y y y y y y y y B B B B B B B ) s s s s s s s s s s a a a a a a a a a a a a a a a ch20230 ch20125 ch20124 ch20120 ch20118 ch20116 ch20109 ch20108 ch20107 ch20004 ysch22461 ysch22458 y y y y y y y y y y y y y s s s s s s s s s s s s s ch22202 ch22099 ch22067 ch22028 ch22330 ch22111 ( ( (Iv ( H O ch02967 ch02893 ch03769 ch03608 ch03323 ch03005 ch02985 P P N 3 H C 3 C o o i e r t t i r e e H dazol m 3 C n n H H ( ( ( ( ( ( ( ( ( ( ectin 3 tia tia C 3 C C N P P P P P P P P P o o o o o o o o o y ( ( ( ( ( ( ( ( CH N NH N O l l 5.510 ( ( ( ( ( ( ( M P P P O P T T e ) ) c t t t t t t t t t P P M M P M P 3 e e e e e e e e e ) l h h CH o o o r O x , e 380 o o o r r n n n n n n n n n azi M e e e i i t t t 3 i azi azi bendazol s acet acet O t t NH O tia tia tia tia tia tia tia tia tia H N b e e e bendazol bendazol bendazol e e oxi por H n n n endazol H 3 quant n n 3 C CH N O C quant quant l l l l l l l l l tia tia tia ) ) ) ) ) ) ) ) ) tia tia 3 O dectin CH Haplotype furcationsaround‘ced-7’ a a Haplotype furcationsaround‘glc-1’ i CH l l l n H O CH r r 3 H Haplotype furcationsaround‘bre-4’ l l ) ) ) 3 CH O C N H 3 sam sam ) ) 3 3 e 330 Haplotype furcationsaround‘nrf-6’ C 4.525 H 3 H HO ) e 3 S CH C N CH O 3 e e OH H O C l e 3 e l l ) 3 e e e H H OH ) ) , ) i i ) P , , , d d HN O O O O O H N O CH N y H ) ) 3 x x x O H H C CH r 3 3 3 H C C CH N H 3 O v i i i 3 C bendazol bendazol bendazol 5.515 O i 3 n Cl Cl i O N CH CH u O N H CH 3 3 m CH 385 3 N O 3 Cl O ) CH N 3 O e e e N NH CH ) ) ) CH 3 3 11567507. 11525025. 11096301. 12274551. 12266184. 11569648. 335 CH 4515156. 4513538. 4506591. 4501224. 4497000. 4493255. 3538850. 2735574. 2568028. 2505025. 1720674. 4.530 O NH 497899. 3 Positon (kb) Positon (Mb) Positon (Mb) Positon (kb) 1711828. 4347057. 4087008. 4053519. 4036236. 3412992. 2736662. 2735888. 2707305. 2700482. 2693657. 2677855. 2664044. 2636813. 2629251. 2621244. 6351343. 5436560. 4105540. 4087868. O 521906. CH 5743779. 4244900. 3164716. 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 5.520 0 0 8 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 390 S S S 9 S 1 5 8 1 B B B B B B B B B B B B B B B B B B 3 a a a a a a a a a a a a a a a a a a B B y y y y y y y y y y y y y y y y y y 340 s s s s s s s s s s s s s s s s s s B B B B B B B B B B B B B B B B B B B a a 4.535 ch08346 ch08345 ch08281 ch08280 ch08270 ch08229 ch07654 ch07653 ch07651 ch07649 ch07648 ch07646 ch07553 ch07492 ch07481 ch07408 ch07326 ch07472 y y a a a a a a a a a a a a a a a a a a a B B B s s HO y y y y y y y y y y y y y y y y y y y O a a a ch18107 ch18298 s s s s s s s s s s s s s s s s s s s y y y ch00344 ch00339 ch00338 ch00334 ch00327 ch00271 ch00232 ch00231 ch00228 ch00223 ch00222 ch00221 ch00218 ch00217 ch00216 ch00215 ch00537 ch00444 ch00047 H s s s 3 OH CH C 3 ch17598 ch17392 ch17270 5.525 O O H O O H 3 C 3 ( ( ( ( ( ( ( ( ( ( ( ( ( ( ( ( ( ( C P P P P P P P P P P P P P P P P P H CH 395 O HO 3 o o o o o o o o o o o o o o o o o e ( ( O O P H O xachl t t t t t t t t t t t t t t t t t ( ( ( ( ( ( ( ( ( ( ( ( ( ( ( ( ( ( (Iv H e e e e e e e e e e e e e e e e e O 3 CH o P P P P P P P P P P P P P P P P O C e C O n n n n n n n n n n n n n n n n n 3 ( ( ( xachl t o o o o o o o o o o o o o o o o H y P H O x e 3 tia tia tia tia tia tia tia tia tia tia tia tia tia tia tia tia tia e C c t t t t t t t t t t t t t t t t CH i r o e n x b e e e e e e e e e e e e e e e e 3 CH m l o xachl t l l l l l l l l l l l l l l l l l i tia o n n n n n n n n n n n n n n n n 3 endazol ) ) ) ) ) ) ) ) ) ) ) ) ) ) ) ) ) b e HO r Cl ectin s 345 tia tia tia tia tia tia tia tia tia tia tia tia tia tia tia tia HO n ophene) endazol o 4.540 l por H tia ) 3 C r O HO Cl l l l l l l l l l l l l l l l l ophene) ) ) ) ) ) ) ) ) ) ) ) ) ) ) ) ) o l i ) , n r M CH ophene) 3 O e e oxi H O HO 3 ) H Cl Cl C ) O 3 5.530 Cl e C ) O Cl H dectin 3 O OH CH C 400 3 O O O CH ) 3 O O H 3 C CH 3 CH 3