Posted on Authorea 10 May 2021 | The copyright holder is the author/funder. All rights reserved. No reuse without permission. | https://doi.org/10.22541/au.162067941.16111128/v1 | This a preprint and has not been peer reviewed. Data may be preliminary. pdrCtlg 01,i ihydvregopo rdtr htcnb on nnal l terrestrial all nearly in found be can that (World predators species of known group ~49,000 diverse least highly at 2020; with a 2021). 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(Coddington, extinct Chelicerata, of namely about species; the 10% subphyla, includes and extant about and four Hexapoda, for ecosystems, encompasses accounts and all It (paraphyletic) in 2013). found Crustacea 2011, virtually (Zhang, Myriapoda, Earth, species on known phylum of species-rich 80% most the is Arthropoda of genomes, biology chelicerate extraordinary of the in organization Introduction played and families structure gene large the and This into elements insights them. repetitive among of gain variants, third many structural to spiders. the of that just significantly resource origin role and a valuable recent clade, the with a Synspermiata new including clusters the suggesting genomic a of family, 83 representative representing the in genome of high-quality spiders, localize average first them the the of is than 54% assembly the them least chromosome-level illustrate At between (i.e., To distances families with chromosome. pseudochromosomes, gene evolutionary X chromosome. chemoreceptor all lower the across arthropod X in distributed major large sequences underrepresentation with two chemoreceptor notable characteristic consistently the previous 545 of a identified match the We the analysis and including comprehensive receptors). to size a ionotropic species, assembly and performed respect gustatory this we total with conformation resource of the new chromosome times karyotype of this the 4,500 of the 87% using value cover of than performed pseudochromosomes chromosomes more was or seven Mb), of scaffolds the 174.2 improvement largest seven continuity of adaptive mostly of The N50 a drivers archipelago scaffold genomic version. represents this the and technique, study in Gb; to diversification scaffolding model (1.37 spider remarkable excellent capture assembly an ground-dwelling a new becoming undergone nocturnal specialization, The has trophic a of Dysdera radiations. level 1981, the Schmidt, in The shifts silvatica with Islands. Dysdera associated Canary of the assembly from genome endemic chromosome-level the present We Abstract 2021 10, May 2 1 Sanchez-Herrero spiders in Escuer families Paula gene chemoreceptor of structure genome and spider endemic silvatica Island Dysdera Canary the of assembly Chromosome-scale ntttdIvsiaioe iece el au emn ra Pujol i Trias Germans Salut la Ci`encies d’Investigaci´o de en Institut Barcelona de Universitat 1 ai Pisarenco Vadim , 2 iulArnedo Miquel , Aahia rna)seslgto h origin the on light sheds Araneae) (Arachnida, 1 ne Fern´andez-Ruiz Angel , 1 ljnr S´anchez-Gracia Alejandro , 1 1 olVizueta Joel , 1 n ui Rozas Julio and , 1 Jose , 1 Posted on Authorea 10 May 2021 | The copyright holder is the author/funder. All rights reserved. No reuse without permission. | https://doi.org/10.22541/au.162067941.16111128/v1 | This a preprint and has not been peer reviewed. Data may be preliminary. h e eoeasml of assembly genome new The assembly Genome and Sequencing DNA the Sampling, of understanding Methods our gene improve and chelicerates. large to Material in and contribute evolution inaccessible elements, will genome is repetitive and data that variants, organization, genomic data structural structure, a high-quality variation as islands on this performed in such Additionally, based diversification and genomes, families. analyses rapid fragmented genome genomic underlying available new basis comparative this currently This annotated molecular allowing in in scale. the by and chromosome-level of identified shifts families at studies have ecological members gene further we and family chemoreceptor foster 2.0, all Dovetail will version of arthropod resource libraries; clustering the genomic physical major of Hi-C the utility two assembly of and enhanced continuous analysis the (Chicago highly the comprehensive improved, of of libraries an example obtain members ligation to an proximity the 2016) As al., used genome. et this we (Putnam of pipeline point, HiRise starting the and a genomics), as 2019) species al., the 2.0 of & assembly version chromosome-level Porter, draft, populations, high-quality Mentzer, first between Gurdasani, the Pollard, divergence present 2016; We and (Bleidorn, hybridization speciation 2019). of in Saha, regions, impact evolution 2018; repetitive chromosomal of Sandhu, and of analysis genes impact role of the the the distribution continuous families, processes, or content, gene highly base adaptive of a recombination, evolution having on the (e.g., and of va- etc..) features of structure benefits structural genome genome meaning the number the of evolutionary a of of identification of and examples study the the clear biological chromosomes, are Some or the assembly the organization. clusters, chromosome-level understanding gene across gene for and mapping prevented and fundamental structure gene it genes are genome resource, frag- as long features research very such fruitful very These a continuity, a in of riation. greater been resulted annotation requiring has (53.8%), draft comprehensive aspects species first the genomic this this of While of kb). sequences study which, 38 genome the reads, of the short (N50 of on draft nature based genome of repetitive was mented genome high assembly the the the of sequenced to first most we added the Nevertheless, genus, 2019). generated this al., (S´anchez-Herrero and for et strategy genome Gb) make reference (~1.37 a shifts 1981 obtaining eco-phenotypic Schmidt, of independent aim multiple the with With coupled proliferation species different dera in of recurrently rates occurred high have shifts The diet these species, rejected continental usually in areas. these as geographic in Islands, accumulated Canary metals the heavy In and 2017). cap- 1985; morphological substances Martin, to toxic by & adaptations the (Hopkin accompanied physiological assimilate prey and was to strategies) and on specialization hunting feeding woodlice trophic (unique in ture behavioral This specialized mouthparts), obligatorily of even Isopoda). or (modifications facultatively (Crustacea: species) woodlice island (Pek´ar, and terrestrial L´ıznarov´a, spiders ( continental generalists group (both mostly & this species the in some across diversification specialization) island prey of (i.e. drivers phagy main preferences the dietary of in one Mac´ıas-Hern´andez, as Shifts identified & S´anchez-Gracia, 2019). been spec- have & most Mac´ıas-Hern´andez, the Rozas, Mac´ıas-Hern´andez, Orom´ı, of Vizueta, M´urria, Arnedo, 2001; Arnedo, one (Arnedo, Mac´ıas-Hern´andez, Orom´ı,2016; representing Ribera, L´opez, & spiders Orom´ı, Roca-Cusachs, archipelago, & within & Arnedo, Islands islands 2007; Approximately Canary on family. Ribera, the diversification from of the endemic examples are of genus tacular genus diversity this ground-dwelling the its of nocturnal of delimitate species The half 50 and 2020). nearly phylogeny represents al., their distribution, et elucidate Mediterranean Kallal 2017; to al., helped et Dysdera greatly (Wheeler have lineages studies evolutionary Recent main 1). (Figure ecosystems necletmdlfrudrtnigtegnmcbsso dpierdain Vzeae l,2019). al., et (Vizueta radiations adaptive of basis genomic the understanding for model excellent an aril 84 hc otis26seis(ol pdrCtlg 01,msl ihacircum- a with mostly 2021), Catalog, Spider (World species 286 contains which 1804, Latreille ) sn h rtvrino h eoeasml fti pce (S´anchez-Herrero et species this of assembly genome the of version first the Using . Rez´aˇcov´a, Indeed, 2021). ˇ Rez´aˇc, 2008; Lubin, Pek´ar, & ˇ .silvatica D. a banduigtepeiu eoeasml dntdas (denoted assembly genome previous the using obtained was Dysdera enovo de 2 nldssm ftefwrpre ae fsteno- of cases reported few the of some includes Rez´aˇc Mac´ıas-Hern´andez, & Toft Pek´ar, 2007; & eoeasml fti pce sn hybrid a using species this of assembly genome ˇ .slaia(.silvatica (D. silvatica D. Rez´aˇc, Pek´ar, Arnedo, ˇ Rez´aˇc, with 2016), ˇ ydr silvatica Dysdera genome Dys- Posted on Authorea 10 May 2021 | The copyright holder is the author/funder. All rights reserved. No reuse without permission. | https://doi.org/10.22541/au.162067941.16111128/v1 | This a preprint and has not been peer reviewed. Data may be preliminary. ;TbeS) swl salohraahis rhoosadedszaseissree nSnhzHreoet Sanchez-Herrero in surveyed species ecdysozoa and , other all as well as S1), Table 1; Araneidae the and iorum with together (Sicariidae), suborder mimosarum the 1940 of Mulaik, representatives & the and Mygalomorphae, order namely Araneae, order the of across homologs for searched We encoded (tRNAs) genes RNA searches Homology transfer pathways the and detected enzymes We KEGG of 2000). five associate 2019). sequence Goto, top to genomic (using & Blast2GO the BLAST (Kanehisa, the used in genes from We annotated inherited the obtained results. were to InterProScan 2000) and al, hits) et (Ashburner significant evidence. terms InterProScan functional (GO) in all ontology signatures ArthropodDB). integrated Gene domain of and protein description 2014) specific detailed al., a for et for peptides (Jones 2017, predicted (including v5.31.70.0 al., the the et of searched genus Vizueta annotation also this functional (see we the Furthermore, databases of perform ArthropodDB To ( species the 2019). searches of al., five v2.4 version et BLASTP from used (Hoff we (–etpmode) sequences models, evidence gene orthologous as 2019) & and both al., Baertsch, et using 2017) Diekhans, (Vizueta 2006), Stanke, al., Waack, 2019; et & Stanke, Sch¨offmann,(Vizueta & Morgenstern, Borodovsky, Stanke, Lomsadze, 2008; Hoff, Haussler, (Br˚una, 2021; Lomsadze, BRAKER2 Borodovsky, with Hoff, accomplished & was Stanke, genome soft-masked the of annotation Structural annotation steps. option genome annotation (-xsmall) functional genome the and the using Structural sequences in repetitive used RepBase- these be and the for to Dfam_Consensus-20171107 masked used RepeatMasker plus was we of assembly RepeatModeler, new analysis with the The generated the of databases. details), For 20181026 1 more version RepeatMasker). for the a Green; (2019) similarity-based for of & al. a built Hubley, combination and database (Smit, RepeatModeler), elements a v.4.0.7 Hubley; repetitive using & RepeatMasker assembly (Smit, with new v1.0.11 search RepeatModeler the with in identification regions ments repetitive analyzed We datasets. genes) 2934 255 (odb10; identification (odb10; arachnida eukaryota elements the Repetitive and searching data genes) 2019), Single Zdobnov, short-read Universal 1013 Benchmarking & (odb10; illumina of Manni, arthropoda Seppey, pipeline using the genes), 5.0.0; 2020) applying v. by Liu, (BUSCO; assembly as Orthologs new & Copy identified the Sun, of ( unequivocally Fan, completeness assembly the individual (Hu, and determined final NextPolish single library) The with (one a libraries. Hi-C polished from sequencing library), further lane) (one and one Chicago 2016), platform; of ten newly combination X The a California). silvatica (HiSeq Cruz; as paired-end (Santa obtained 150-bp Genomics was Illumina Dovetail in data performed sequence were generated sequencing and extraction DNA genus as the laboratory of the female -80 in single at libraries. identified a Islands), generated Hi-C We using (Canary 2019. S´anchez-Herrero and al. libraries Gomera in et 1 Chicago sequencing Table see using latest libraries; sequencing the scaffolded of hybrid types further a four and using was individuals five generated which was assembly 2019), 1 al., Version S´anchez-Herrero et 1; version ° ni t use. its until C C .Kc,14)and 1841) Koch, L. (C. eeec eoevrin2 a eeae sn h iiesaodn otae(unme al., et (Putnam software scaffolding HiRise the using generated was 2) version genome reference aei 83and 1883 Pavesi, rcoehl clavipes .silvatica D. .dumicola S. .silvatica D. ardcu hesperus Latrodectus cnhsurageniculata Acanthoscurria sn h RAcnS 207sfwr Ca,Ln a,&Lowe, & Mak, Lin, (Chan, software v2.0.7 tRNAscan-SE the using ntegnm aao ersnaie fabodtxnmcrange taxonomic broad a of representatives of data genome the in ook 88(rsde,adteAraneoidea the and (Eresidae), 1898 Pocock, Lnau,16)and 1767) (Linnaeus, .silvatica D. E vle=10 = -value enovo de hmeln&Ii,13,bt ntefml Theridiidae, family the in both 1935, Ivie, & Chamberlin 3 .silvatica D. .silvatica D. ebro h ld Synspermiata, clade the of member eoeasml ycmiigifrainfrom information combining by assembly genome .silvatica D. -5 C .Kc,14)(hrpoia) ntesub- the in (Theraphosidae), 1841) Koch, L. (C. gis CIn,SisPo,ada updated an and Swiss-Prot, NCBI-nr, against ) rip bruennichi Argiope serslsaddsuso eto) We section). discussion and results (see Dysdera rzni irgnlqi n stored and liquid nitrogen in frozen , rf eoeseS´anchez-Herrero et see genome draft ape nMrh21 nLa in 2012 March in sampled , ooclsreclusa Loxosceles enovo de .silvatica D. Sooi 72 (Figure 1772) (Scopoli, aataoatepidar- Parasteatoda rnpsbeele- transposable .silvatica D. Nsqdata RNAseq Stegodyphus Gertsch D. ) Posted on Authorea 10 May 2021 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.162067941.16111128/v1 — This a preprint and has not been peer reviewed. Data may be preliminary. epromdacmrhniecrto falmmeso h ao hmrcpo eefmle encoded families gene chemoreceptor major the of members ( of all genome of the curation in comprehensive a performed We genes chemoreceptor the of Annotation orthogroups 2017). for searched 2005) also spiders IV, we tick Finally, Black the positive). & namely a database, Piesman, as 2019) hit al., among a et (Kriventseva relationships consider to homology ( length searches establish BLASTP alignment and of >30% series of a by filter conducted a was search The (2019). al., lsee fte r ragdwti eoi einta pn esta eti cut-off certain than less spans that region genomic a within as copies arranged paralogous that are the consider they classified we We if scaffold. Operationally a clustered and clustered”. (forming physical family “non pairwise closer gene and of particular physically distribution a “clustered” are the of analyzing family members by the gene chance between by chemoreceptor distances expected given than a pseudochromosomes the of in members cluster) the whether determined We minimum analysis ( the and and genes computed definition different GR to Cluster we the attributed family, for unequivocally chemoreceptor (2018). acids, using be al. each recovered least, amino could et For be at that 180 Vizueta fragments. not contains, sequences and could protein chemoreceptor “partial” (235 The that of encoded as family number models input. the classified gene the of as incomplete length were of sequence remaining the characteristic Apollo genome The if length respectively). and “complete” domain proteins, as browser models protein IR/iGluR profiles gene genome gene the a Apollo (HMM) the annotated classified of model We in 80% the Markov necessary, 2013). when hidden using al., re-annotated and et and and (Lee set validated, (2018) were data al. proteins sequence identified et resulting homologous S´anchez-Gracia, Vizueta the Vizueta, in with 2020; used along Rozas, S´anchez-Gracia, & 2020), Escuer, Rozas, (Vizueta, & BITACORA pipeline the used S MA)fralsqecs(h uldt e,cmrs h opeeadprilcpe dnie in identified copies partial and in complete identified the (MSA) comprise sequences alignments set, complete sequence data only multiple full with (the three (MSAc) sequences build silvatica MSA all to for a 2013) (MSAf) generated MSA Standley, we & First, (Katoh family. silvatica 7.475 gene each v. per Mafft used We alignments sequence and scaffolds. Multiple 2016), across Schlesner, clustering analyses & gene evolutionary Eils, of and (Gu, visualization Phylogenetic ComplexHeatmap the package facilitate R to the heatmaps with as processed plotted were copies more) family (or gene two chance by conservative weguarantees finding Here of distribution, clustered. probability (Poisson are 0.0004 the the they in genome, that lower the consider even to across (and family Mb given 3.32 a every of of copies value two the between set distance maximum the is where (2007): Rozas S´anchez-Gracia, & Vieira, Ir/iGluR C tgdpu mimosarum Stegodyphus L sn h at–dfamnsoto –epegh oainfamn pril eune othe to sequences (partial) fragment align to (–keeplength) option –addfragments Mafft the using ) sn h -N- loih ihotos–oapi mxtrt 00 hn ebitasecond a built we Then, 1000. –maxiterate –localpair options with algorithm L-INS-i the using stemxmmlnt facutrta otistoo oecpe ftesm aiy and family, same the of copies more or two contains that cluster a of length maximum the is aiis(iut,Ece,FısLpz ta. 00 iut ta. 08.Frti ak we task, this For 2018). al., et Vizueta 2020; al., et Frıas-Lopez, Escuer, (Vizueta, families ) g o10k.Tegn est fthe of density gene The kb. 100 to .silvatica D. C L egh o h w hmrcpo aiis ariepyia itne between distances physical Pairwise families. chemoreceptor two the for lengths , λ h mite the aeyteGsaoyrcpo ( Gustatory-receptor the namely , .31;this 0.0301); = Sngade l,21)and 2014) al., et (Sanggaard Gr erncu urticae Tetranychus aiy.Asmn nfr itiuino eefml members family gene of distribution uniform a Assuming family). .silvatica D. C p L vlei vnlwrfrthe for lower even is -value = g xdsscapularis Ixodes Ir 4 ( n aiyi the in family − n h rcnd nlddi h rhD (v10) OrthoDB the in included arachnids the and 1) .L oh 86(rice l,2011) al., (Grbi´c et 1836 Koch, L. C. n aataoatepidariorum Parasteatoda Gr lsl ikdgnsfo eefml are family gene a from genes linked closely n oorpc(ltmt)receptor (glutamate) Ionotropic and ) .silvatica D. E a,12 Ulan ia Guerrero, Lima, (Ullmann, 1821 Say, Ir vlectff<10 < cutoff -value ee na10k tec is stretch kb 100 a in genes Gr aiy hs h selected the Thus, family. eoei bu n copy one about is genome C -3 Shae tal., et (Schwager L eas applied also we ; au following value S MIN , n the and sin as ) p D. D. = g g Posted on Authorea 10 May 2021 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.162067941.16111128/v1 — This a preprint and has not been peer reviewed. Data may be preliminary. eefml ois setmtdas: estimated is copies, family gene where ie,uigMA;seaoe.Frteaayi eue h etfi mn cdsbttto oe found model amino substitution whether acid test To amino replicates. best-fit bootstrap the ultrafast used 1000 we from species analysis support both from the node proteins For estimated complete and only above). and IQ-TREE, see by Arthropods), in MSAp; families using these for (i.e., far so genome annotated identified best families gene chemoreceptor melanogaster the Drosophila of members of genome the the among in estimated relationships phylogenetic those the from inferred We different significantly are the scaffold) analyses of particular Phylogenetic copies a between distances (in evolutionary genes. clusters unclustered the genomic across whether in determine to family U-test same Mann–Whitney the used We i where as: estimated is genome), the across (or scaffold same the of clusters all across And sequences between distance evolutionary the where We genes. unclustered to attributable is that genome). distance whole evolutionary the of the means of by computed proportion distances evolutionary the and measures physical which respectively). between families, software relationship model Ir and the 10.2.4 substitution (5 investigated and We sites MEGA-CC JTT Gr al., among the the with variation et for rate using performed heterogeneous (Minh classes 2012), gamma-distributed was discrete 2.1.2 with Tamura, 7 analysis 1992), & Thornton, The v. amino & Peterson, Taylor, per software Stecher, (Jones, replacements comparisons. IQ-TREE acid (Kumar, pairwise amino by version) of all number found (command-line the across model as site) (measured substitution distances acid evolutionary acid the amino estimate to best-fit 2020) the each used for We MSA third distances a evolutionary generate versus Physical to algorithm of genome L-INS-i the the from in used sequences annotated complete also the we included Finally, which family, MSAc. computed previous and D j n D n C . T h vrg ftepiws vltoaydsac ewe oisfo ihnacutr averaged cluster, a within from copies between distance evolutionary pairwise the of average the , stenme fgn aiymmesi h uvydsaod(ri h niegnm) and genome), entire the in (or scaffold surveyed the in members family gene of number the is stenme fcpe ncluster in copies of number the is C h vrg ftepiws vltoay(mn cdrpaeet e ie itne between distances site) per replacements acid (amino evolutionary pairwise the of average the , ST neednl ntetoceoeetrfmle,adsprtl o ahsaod(rfrthe for (or scaffold each for separately and families, chemoreceptor two the in independently C .silvatica D. ST setmtdas: estimated is hmrcposi h nlssa vltoayrfrne ( references evolutionary as analysis the in chemoreceptors rspiamelanogaster Drosophila ytemxmmlklho ehdipeetdi QTE.W loincluded also We IQ-TREE. in implemented method likelihood maximum the by D D Ck k T D C i and , ST = C = and = n = n ( ( dij n j. m .silvatica D. n 1 D 2 5 − 2 − egn 80(MSAp). 1830 Meigen, k T X steaioai-ae itnebtensequences between distance acid-based amino the is 1) m =1 1) D − T D X D i and 90%. .melanogaster D. .silvatica D. r respectively. Gr, Gr .melanogaster D. Ir or subfamilies, Ir and copies pseu- D. , Posted on Authorea 10 May 2021 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.162067941.16111128/v1 — This a preprint and has not been peer reviewed. Data may be preliminary. lion .(06.Tidgnrto eunig ehooyadisptnilipc neouinr biodi- (2000). evolutionary G. on Sherlock, impact & potential its . and . . technology research. M., sequencing: versity generation J. Cherry, Third (2016). H., biology. C. Butler, of Bleidorn, D., unification Botstein, the A., for J. tool Blake, Ontology: A., Gene sets. C. Ball, data M., multiple Ashburner, on based assessment Cladistic genus spider Islands: 10.1006/clad.2001.0168 the of of Canary Radiation side the genus (2001). C. in the dark Ribera, Orom´ı, of & The P., A., spiders M. (2007). Arnedo, troglobitic Islands. C. of Canary evolution Ribera, the and in & Mac´ıas-Hern´andez, Systematics neae:Dysderidae) N., C., M´urria, radiation: island P., Orom´ı, mole- an A., and M. shoulder inference Arnedo, the phylogenetic On for (2021). projects A. genome 10.1111/jzs.12415 M. non-targeted studies. Arnedo, from evolution & recovery cular J., Mitogenome Rozas, giants: J., of Pons, J., Lozano-Fernandez, Adri´an-Serrano, S., work. Bibliography this in complete as values of classified support domain and domains node LBD Red bootstrap the scaffolds. with encoding minor 7 sequences SC, figure Minor in site. tree per genetic substitution genomic in acid about number amino the to information member mark number: 1 shows correspond cluster to chromosome ring branches genomic refers inner the terminal ring, bar The outer indicates green scale in located. ring that The are rooted outer scale cluster). tree was color The the the same tree 2010). the in The gene al. in included respectively. of (chromosome, et genes subfamilies, clusters shading (Croset the Ir purpura which outgroup and and in the Ir25a/8a blue (Chr) partial as iGluR, dark or clade blue, the incomplete NMDAR light of and considering The members complete asterisks. the both with designate (including marked names family are Ir/iGluR genes the Incomplete of genes). members encoding sequences all S4. Figure rst . yz . umn,S . ud . rwn,D,Kesan . etn .(2010). R. Benton, . . . H., taste insect Kaessmann, of D., evolution Brawand, the and A., receptors Budd, glutamate ionotropic F., olfaction. chemosensory and S. of Cummins, origin “Arachnida.” protostome R., (2004). Ancient E. Rytz, D. Walter, V., and Croset, L., Life. M. Prendini, of S., Tree J. M. the Ranz, Harvey, Assembling G., in Giribet, . A., . . Jonathan Coddington, A., tandem Sanchez-Gracia, a study. P., and population of Librado, 10.1093/molbev/msaa109 functional Detection stages Z., doi: and Improved evolutionary structural Chahine, 2.0: early A A., TRNAscan-SE the family: Kimura, Understanding (2019). J., M. Jimenez, (2020). T. D., Lowe, B. & J., Clifton, automatic Genes. A. RNA Mak, BRAKER2: Transfer database. Y., of protein Classification B. (2021). Functional a Lin, M. P., by P. Borodovsky, supported Chan, & AUGUSTUS Bioinformatics and M., and GeneMark-EP+ Stanke, Genomics with A., NAR annotation Lomsadze, genome J., eukaryotic K. Hoff, Br˚una, T., dy .R 21) ceeae rfieHMsearches. HMM profile Accelerated (2011). 10.1371/journal.pcbi.1002195 R. S. Eddy, .silvatica D. hlgntcrltosisadnd upr nteI/Gu aiy )Pyoeei reamong tree Phylogenetic A) family. Ir/iGluR the in support node and relationships Phylogenetic LSGenetics PLoS ytmtc n Biodiversity and Systematics ee ihpttv itn ooosin homologs distant putative with genes ora fZooia ytmtc n vltoayResearch Evolutionary and Systematics Zoological of Journal , xodUiest Press University Oxford 6 8.di 10.1371/journal.pgen.1001064 doi: (8). , 3 .silvatica D. .silvatica D. 1,11.di 10.1093/nargab/lqaa108 doi: 1–11. (1), netbaeSystematics Invertebrate , 14 BioRxiv 1,18 o:10.1080/14772000.2015.1099575 doi: 1–8. (1), aueGenetics Nature and and 12 oeua ilg n Evolution and Biology Molecular .melanogaster D. 296–318. , .melanogaster D. > 6.di 10.1101/614032 doi: (6). , LSCmuainlBiology Computational PLoS 0.C hlgntcrltosisaogthe among relationships Phylogenetic C) 90%. .melanogaster D. , 21 , rspiamelanogaster drosophila 25 6,6360 o:10.1071/IS07015 doi: 623–660. (6), 1,25–29. (1), r epciey h e triangles red The respectively. Gr, h reol nldsteLBD the includes only tree The . Cladistics Dysdera )Caormo h phylo- the of Cladogram B) . Dysdera Aaee Dysderidae) (Araneae, , 17 , , 37 59 4,3333 doi: 313–353. (4), 9,2584–2600. (9), , aril (Ara- Latreille 1,53.doi: 5–30. (1), seicgene -specific 7 1) doi: (10). Posted on Authorea 10 May 2021 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.162067941.16111128/v1 — This a preprint and has not been peer reviewed. Data may be preliminary. eui,I,&Br,P 20) neatv reO ie(TL:A nieto o hlgntcte display tree phylogenetic for tool online An (iTOL): Life Of Tree Interactive (2013). (2007). E. annotation. P. S. and Lewis, Bork, & . . I., . Letunic, M., R. platform. Buels, P., editing C. annotation Childers, C., genomic molecular 2013-14-8-r93 M. web-based Munoz-Torres, of T., A J. core Apollo: Reese, Web A., Computing G. MEGA-CC: Helt, E., analysis. (2012). Lee, data K. iterative Tamura, and 10.1093/bioinformatics/bts507 automated & doi: for D., 2685–2686. program Peterson, analysis genetics G., evolutionary Stecher, genomes M. S., viral E. and Kumar, Zdobnov, bacterial & protist, A., fungal, Sim˜ao, F. orthologs. plant, R., of animal, 10.1093/nar/gky1053 annotations Dias, of functional M., diversity and evolutionary the Manni, for Sampling F., v10: Tegenfeldt, OrthoDB D., Improve- (2019). Kuznetsov, 7: V., version E. software Kriventseva, alignment sequence multiple Genomes. MAFFT usability. and bev/mst010 and (2013). Genes performance M. of in D. Encyclopedia ments Standley, & Kyoto Hormiga, K., KEGG: & Katoh, G., analytical (2000). Giribet, new S. and A., phylogeny Goto, M. Research spider & Arnedo, elucidates web. M., R., sampling orb taxon Kanehisa, L. the denser of Benavides, evolution orb: D., repeated the Dimitrov, support on methods InterProScan S., Converging (2014). S. (2020). S. Kulkarni, G. Hunter, J., . R. . . Kallal, C., matrices McAnulla, data W., mutation Li, of classification. M., matics/btu031 Fraser, function generation Y., protein rapid H. Genome-scale The Chang, 5: D., (1992). Binns, M. P., J. Jones, Thornton, & long-read for R., sequences. tool protein W. polishing Taylor, from genome efficient T., and D. fast A Jones, NextPolish: (2020). S. Liu, spider & the Z., assembly. by Sun, iron J., Fan, and J., copper, Hu, lead, cadmium, zinc, 10.1007/BF01609722 of woodlice. doi: Assimilation of 183–187. (1985). predator H. a M. crocata, Martin, Dysdera BRAKER. & with P., annotation S. Whole-genome Hopkin, (2019). M. Stanke, Biology & Molecular M., multidimen- in Borodovsky, in Methods A., correlations Lomsadze, and J., patterns K. reveal Hoff, heatmaps Complex (2016). data. M. genomic Schlesner, & sional R., Eils, (2011). Z., Y. Gu, Peer, De Van adaptations. pest . herbivorous . advancing . reveals Grbi´c, Rouz´e,10.1038/nature10640 V., for P., urticae S., Tetranychus prospects Rombauts, of and M., genome R. The progress Clark, Recent T., (2018). Leeuwen, Van A. Grbi´c, M., N. Ayoub, & chromosome-level P., A P. genomics. Sharma, (2021). E., Z.-S. J. Zhang, Garb, & F., . event Zhang, duplication J.-F., whole-genome Jin, ancient L.-Y., spider Wang, the P., of Liu, genome T., Yuan, Z., Fan, Bioinformatics , urn pno nIsc Science Insect in Opinion Current 28 1,27–30. (1), Bioinformatics Bioinformatics rcoehl antipodiana Trichonephila Bioinformatics , 36 7,25–25 o:10.1093/bioinformatics/btz891 doi: 2253–2255. (7), , , 1962 23 , oeua ilg n Evolution and Biology Molecular 1,1718 o:10.1093/bioinformatics/btl529 doi: 127–128. (1), 32 0,6–5 o:10.1007/978-1-4939-9173-0 doi: 65–95. (0), , 8 1) 8724.di 10.1093/bioinformatics/btw313 doi: 2847–2849. (18), GigaScience ultno niomna otmnto n Toxicology and Contamination Environmental of Bulletin 3,275–282. (3), , 25 eel h eei ai fisplpayadeiec fan of evidence and polyphagy its of basis genetic the reveals Bioinformatics 15.di 10.1016/j.cois.2017.11.005 doi: 51–57. , 13 Cladistics , 10 uli cd Research Acids Nucleic 3,11.di 10.1093/gigascience/giab016 doi: 1–15. (3), –9 o:10.1111/cla.12439 doi: 1–19. , , eoeBiology Genome 30 9,13–20 o:10.1093/bioinfor- doi: 1236–1240. (9), , 30 Nature 4,7270 o:10.1093/mol- doi: 772–780. (4), , , 5 47 479 , Bioinformatics 14 D) 87D1.doi: D807–D811. (D1), 77) 8–9.doi: 487–492. 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(11), eree rmhttp://www.repeatmasker.org from Retrieved . eree rmhttp://www.repeatmasker.org from Retrieved . Bioinformatics GigaScience ehd nEnzymology in Methods 15 eoeBiology Genome eoeBooyadEvolution and Biology Genome oeua clg Resources Ecology Molecular hsooia Entomology Physiological n h otenctl ik opiu microplus. Boophilus tick, cattle Southern the and , 10 , 24 1,11.di 10.1093/gigascience/giaa148 doi: 1–12. (1), rip bruennichi Argiope 5,6764 o:10.1093/bioinforma- doi: 637–644. (5), , M Bioinformatics BMC 21 1te. o.62.Esve Inc. Elsevier 642). Vol. ed., (1st 1) –4 o:10.1186/s13059- doi: 1–14. (15), , , 20 42 eorefrstudies for resource A : , eoeBooyand Biology Genome 9 5,14–42 doi: 1445–1452. (5), 2,1118 doi: 191–198. (2), oeua Biology Molecular 1,1816 doi: 178–196. (1), eoeBiology Genome , 7 –1 doi: 1–11. , Posted on Authorea 10 May 2021 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.162067941.16111128/v1 — This a preprint and has not been peer reviewed. Data may be preliminary. .(07.Tesie reo ie hlgn fAaeebsdo agtgn nlssfo netnietaxon extensive an from Zhang, analyses . target-gene . on . E., based C. Araneae Griswold, of A., phylogeny P. life: Goloboff, of sampling. D., tree Dimitrov, spider M., The L. Crowley, (2017). A., J. J. Coddington, C., W. Wheeler, 10.1111/1755-0998.13202 hn,Z .(01.Aia idvriy notieo ihrlvlcasfiainadsre ftaxonomic arthropoda. of Phylum survey (2013). and Q. classification Z. higher-level Zhang, of outline An biodiversity: Animal 2015 richness. (2011). June Q. 11 doi: Z. Catalog. Zhang, Spider World (2021). Catalog. Spider World families-in-spiders arachnida-araneae-sheds-light-on-the-origin-and-genome-structure-of-chemoreceptor-gene- chromosome-scale-assembly-of-the-canary-island-endemic-spider-dysdera-silvatica- 20210409_Table3.xlsx file Hosted families-in-spiders arachnida-araneae-sheds-light-on-the-origin-and-genome-structure-of-chemoreceptor-gene- chromosome-scale-assembly-of-the-canary-island-endemic-spider-dysdera-silvatica- 20210409_Table2.xlsx file Hosted families-in-spiders arachnida-araneae-sheds-light-on-the-origin-and-genome-structure-of-chemoreceptor-gene- chromosome-scale-assembly-of-the-canary-island-endemic-spider-dysdera-silvatica- 20210409_Table1.xlsx file Hosted Zootaxa Cladistics , 3148 , 33 6–9.di 10.11646/zootaxa.3148.1.2 doi: 165–191. , 6,5466 o:10.1111/cla.12182 doi: 574–616. (6), vial at available at available at available Zootaxa https://authorea.com/users/413060/articles/521514- https://authorea.com/users/413060/articles/521514- https://authorea.com/users/413060/articles/521514- , 16 3703 1,1–6 o:10.11646/zootaxa.3703.1.6 doi: 17–26. (1), Posted on Authorea 10 May 2021 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.162067941.16111128/v1 — This a preprint and has not been peer reviewed. Data may be preliminary. Araneomorphae Araneae 420 Paleozoic D Entelegynae Araneoidea (17) Carb. 331 316 P 268 T 236 232 Mesozoic 215 J 190 Cretac. 148 120 118 17 PG 68 CZ N *, T. antipodiana bruennichi *Argiope Oedothorax gibbosus *Parasteatoda tepidariorum *Latrodectus hesperus Pardosa pseudoannulata *Loxosceles reclusa silvatica*Dysdera *Acanthoscurria geniculata *Centruroides sculpturatus Nicodamoidea (2) Nicodamoidea RTA clade(~40) ‘UDOH’ grade (4) Palpimanoidea (5) Austrochiloidea + Synspermiata (17) (23) Mygalomorphae Scorpiones Araneus ventricosus studiosus Anelosimus Eresidae *Stegodyphus mimosarum,*S.dumicola Leptonetidae (~3) Posted on Authorea 10 May 2021 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.162067941.16111128/v1 — This a preprint and has not been peer reviewed. Data may be preliminary. A) E cd y so z oa

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Ir101

1 Ir

1 Ir Ir066 Ir1 Ir081

Ir1

Ir057 Ir1 Ir089

Ir064 Ir091 Ir068 3 Ir046 Ir099

Ir086

Ir095 Ir088 Ir374

1 Ir103 Ir097

Ir255 Ir124 10 Ir062

Ir1 15

U560: 17 19

Ir1 18 Ir249

Ir094 Ir052

U666: Ir090 Ir075

Ir061 Ir069 Ir123 Ir083

U560: 12

Ir514 16 Ir058

Ir100 Ir056

Ir063 Ir054 Ir105 Ir120

Ir014 1 1 1 Ir Ir375 U2894: 1 Ir107

2 Ir047

Ir050 14

Ir104

C Dmel C Ir082 Dmel U189: Ir102 Ir080

1 Ir078

5 Ir106 iGluR14

6 Ir077 iGluR31

1 Ir096

U13508 G9935

155 11

Ir109 G 2 iGluR46

1 iGluR

u Ir141 DmelGl

Ir254 u

Ir087 DmelGl

0

Ir1 iGluR25

:1 59

5 Ir251 iGluR26

41

1245 1 Ir256 13 iGluR25

Ir051 6 iGluR31

6

U325: Ir259 RIB

5 iGluR14

Ir260 RIA

5

Ir390 iGluR24

98

8 U13508 iGluR14 C

Ir018 Dmel

2 01

2:2 Ir085

06

8

Ir092 iGluR32

U3226: 38 0 Ir053 iGluR10 58

:2 G3822

4 Ir067 iGluR24 20

Ir059 97 6

U1209: iGluR31

Ir079

5

1 iGluR24 C

U1209: Dmel

Ir121 45

u DmelGl

Ir055 1

1 1 u DmelGl Ir049 64

G5621

2 Ir562 26

l Dmelc

22

u

U5666: Ir1 DmelGl

Ir016 RIIE

u

11 DmelGl

Ir614 RIID

u U189: DmelGl

U1705: 2 Ir029 umsy

2 Ir512 RIIC

RIIB

r Ir093 DmelI

3 RIIA Ir070 iGluR618

r

Ir210 DmelI 5 iGluR28

U2894: Ir622 8a 1 iGluR17

Ir432 25a 6 iGluR21

N

2 Ir262 Dmel

98

N Ir392 Dmel

U445: Ir620 32 r mda

65 1

Ir621 iGluR r

3 Ir4612 mda 1

8 iGluR45

1240

2 0 Ir060 iGluR46

U445: Ir074 5

Ir034 Ir28190 r DmelI

2 Ir368 0

Ir389 76b

Ir367 Ir3440 Ir1995

Ir509 Ir29164

r

Ir098 DmelI

r DmelI

2:3 Ir364 93a

r DmelI

2:4 Ir508 75a

r DmelI

Ir510 31a

r U5666: DmelI

Ir434 75d

r DmelI

U325: 1 Ir126 84a

r DmelI

3 Ir294 64a

r DmelI

U325: Ir261 68a

r DmelI

1 Ir370 21a

r DmelI

U5121:2: Ir207 10a

100a

r

U189: 1 Ir265 DmelI 40a r

Ir048 DmelI

U512: 4

92a

r

2 Ir266 DmelI

7c

r 1:4 Ir427 DmelI

U467: Ir647 7b r

1 DmelI

Ir466 7f r

1:5 DmelI

7e

r Ir615 DmelI

1:1

87a

r Ir225 DmelI

2:2 68b

r Ir073 DmelI

41a

r

U2027: Ir511 DmelI

2 Ir025 85a r DmelI

Ir5552 67c r DmelI

Ir8785 48c r DmelI

Ir9146 67b

r DmelI

Ir8499 60e

r DmelI

Ir8703 56d

r DmelI

U3722: Ir506 56c

r 1 DmelI

Ir1019 62a

r DmelI

Ir414 56b

r DmelI

Ir424 60d

D m e l I r 9 4

21 Ir553 h

D m e l I r 9 4

U1751:2 Ir033 g

D m e l I r 6 7

Ir504 a

I r 5 5

Ir62 947

I r 2 2 3 1

6 DmelIr94c

Ir548 DmelIr94b

Ir7782 DmelIr94d

Ir549 DmelIr52c

Ir505 DmelIr52d

Ir558 DmelIr52b

Ir557 DmelIr52a

Ir554 Ir3161

Ir555 Ir31848

Ir556 Ir26867

Ir589 :

U3722 Ir134

2

Ir6501 Ir11005

1

Ir8 Ir332 17

: U742

2

Ir423 Ir658

Ir8302 Ir8078

Ir13590 Ir7733

Ir5527 Ir923

: U1845

Ir419 Ir7794

2

Ir503 : U2770 Ir6486

1

Ir7082 Ir698

Ir501 Ir6484 U301:

Ir33246 Ir33000 2 : U1751

Ir837 Ir7164

1 U301:

1

Ir3 Ir31520 1 169 Ir7160 Ir7183

U1566:

Ir6500 Ir7165

Ir5528 Ir20603 1

Ir5551 Ir8944

Ir13449

: U742 Ir8943 U1566:

Ir13589 Ir1 : U2770

1 1680 2

Ir3981 Ir1

: U2027 U872:

2 1679

Ir18377 Ir227 U872: 2

1

Ir632 Ir7860

:

U1845 6:2

Ir445 Ir17653 1

Ir451 Ir22423 6:1 1

Ir019 Ir7641 2:1

Ir416 Ir7643

Ir1015 Ir22427 :

U1631 2:2

Ir330 Ir22426 2:1

Ir25673

1 Ir23242

:

U1631 U37:1

Ir247 Ir6960

4:2 U37:2

Ir250 Ir13473

2

Ir253 Ir1 2:3

Ir590

4:1 Ir4911738 2:2

Ir371 Ir9745 4:1

Ir369 Ir24267 5:8

Ir633 Ir7021

Ir19895 Ir17156

5:5 7:1 Ir19896 Ir16984

5:7

Ir3328 Ir16986 7:2

1 Ir2

5:6 Ir16985

Ir310 Ir748 5:2

1

Ir22258 Ir746 5:1

Ir212 Ir745

5:3

Ir661 Ir3629

5:4

Ir489 Ir4848 1:1

Ir507 Ir4846 1:3

Ir16444 Ir4844

4:3 1:2

Ir33213 Ir2366 U166:

Ir1277 Ir7536

Ir17980 Ir475 U166:

Ir17979

1:2 Ir15210 U166: 3

Ir17981 Ir15209 1:1 Ir17942 2

Ir537 2:3

Ir150 Ir536 1

: U467

Ir151 Ir7601 2:2

Ir8533 Ir8262 2:1

Ir17891 Ir20563

Ir22433 Ir6910 2

Ir10250 Ir478

Ir383

3:2 Ir319

Ir384 Ir361

3:1 1:2

Ir385 Ir8232

3:3

Ir382 Ir7522 1:1

Ir3876 Ir8849

Ir3877 Ir7028

Ir10673 Ir576

Ir10675 Ir8084

Ir22895 Ir583

Ir23243 Ir581

Ir23982 Ir577

Ir7906 Ir7988

Ir462 Ir575

1

Ir46 Ir7994

Ir31241 Ir8912

Ir301 Ir8358

Ir398 Ir20188

Ir15346 Ir20187

Ir18225 Ir1

Ir18942 Ir32753

1

1

Ir Ir12098

1 Ir Ir24047

1:1

Ir7099 Ir22031 1088

Ir7101 Ir1

Ir7098

1:2 Ir1 1557

Ir5535 Ir1

1555

Ir7097 Ir1 1:2

Ir7100 Ir314

Ir8790 Ir12320 1229

1:3 Ir8788 Ir071

Ir31622 Ir1 1469

Ir24551 Ir542 1452 Ir9195 Ir144

Ir21058

Ir23765 1451

Ir640 Ir20479

Ir8799 Ir22814

Ir10748 Ir184 Ir7927

4:2 Ir10324 Ir1404

1

Ir228 Ir188

Ir21391 Ir191 Ir1403 Ir1405

Ir5723 Ir1407

1230

U74:2 U74:1

1:2 1

1:1 Sc Minor ChrU1 Chr6 Chr5 Chr4 Chr3 Chr2 Chr1 ChrX

2:1

5:2

5:1

: U203

: U203 3:3 :

U203 4:2

: U203 4:1

: U203 1:1

: U1788 :

U1788 3:4 3:2

3:1

3:2

3 U1

3:1

1 U U1

U1 5

2

1

4 1:2

1:1 1:3

1:4

2 1