Posted on Authorea 3 Aug 2020 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.159646761.15797764 — This a preprint and has not been peer reviewed. Data may be preliminary. ininLv Jianjian sex and adaptation, determination salinity evolution, its provides into trituberculatus insights Portunus of genome chromosome-level A un-inLiu Guang-Jian aoaoyfrMrn cec n ehooy o ehiRa,AsawiTw,Jm,Qingdao, Jimo, Town, Aoshanwei Road, Wenhai 1 No. Technology, and Science China Marine for Laboratory c Qingdao,China. China 266071 315211, Sciences, Fishery of Academy Chinese b. Institute, Research Fisheries Sea Yellow a Liu Su Zhencheng *, Lv Jianjian determination valuable was sex a crabs. Dmrt1 and provides swimming and of tion, only breeding of not trituberculatus, molecular P. genome genome for chromosome-level of crab useful A swimming genome also the is the but Decoding in studies, time addition, evolutionary region. In first and this biological the observed. in further also for gene for were determination located resource species sex was genomic the key were chromosome of a members the Y growth as to its the rapid identified basis related and and of genetic closely immunity genomes, the region was strong into crab specific insights shrimps, it trituberculatus, in providing the P. suggested and (BSA) expanded in Analysis stage, crabs family Segregant adaptation larval Bulked of gene salinity flea-like and analyses only transcriptome of the with genomic the during Combined 53 comparative and be genes crabs. development into on to of protein-coding crab, embryonic evolution assembled Based found 19,981 swimming early was sequences with the in respectively, (49.43%). family scaffold expressed of Mb, protein repeats the mainly sequence 15.6 finger sequence in of and genome zinc simple species 79.99% kb the C2H2 of farmed 108.7 with report the proportion were important we Gb, values high an Here, ˜1.2 N50 a also covering scaffold and value. is and scale, economic contig trituberculatus chromosome The high P. the and chromosomes. ecological at industry. rate major assembled fisheries growth of was the rapid is which to its crab, to important swimming the due being as China as known well commonly as Brachyura), importance, Decapoda: (Crustacea: trituberculatus Portunus Abstract 2020 3, August 3 2 1 ooeeBonomtc Institute Institute Bioinformatics Research Novogene Fisheries Sea Yellow University Science Ningbo Fishery of Academy Chinese . ucinLbrtr o aieFseisSineadFo rdcinPoess iga National Qingdao Processes, Production Food and Science Fisheries Marine for Laboratory Function e aoaoyo utial eeomn fMrn ihre,Mnsr fArclue P.R.China, Agriculture, of Ministry Fisheries, Marine of Development Sustainable of Laboratory Key e aoaoyo ple aieBoehooy iityo dcto,Nnb nvriy Ningbo University, Ningbo Education, of Ministry Biotechnology, Marine Applied of Laboratory Key a,c hni Wang Chunlin , 1 a,c, ogu Li Ronghua , ,RnhaLi Ronghua *, 3 hni Wang Chunlin , d, ,BounGao Baoquan *, b inLi Jian , 2 hnhn Su Zhencheng , otnstrituberculatus Portunus , b a,c 2 igLiu Ping , a,c igi Ti Xingbin , 3 aqa Gao Baoquan , 1 n inLi Jian and , 1 rvdsisgt noiseouin aiiyadapta- salinity evolution, its into insights provides a eigYan Deping , 1 1 igi Ti Xingbin , a unja Liu Guangjian , 1 eigYan Deping , d 1 Ping , , Posted on Authorea 3 Aug 2020 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.159646761.15797764 — This a preprint and has not been peer reviewed. Data may be preliminary. v hn,Lu i 06 si&Ln 07.Sm coasas re osuyteslnt adaptation salinity the study potential to of hundreds tried salinity and in also involved 2011), scholars understood. mechanisms Liu, molecular & poorly Some complex Xu remain the H. 2007). However, tolerance Q. Lin, identified. 2013; were al., & genes et Tsai salt-tolerance-related (Lv 2016; analyses transcriptome Li, comparative & using Liu, Zhang, Lv, hsooia rcs fslnt dpain o rnpr-eae ee,icuigNa including genes, important decapod transport-related an the is Ion of transport adaptation ion adaptation. by salinity H salinity Faria, mediated of type Osmoregulation & of mechanism curiosity. (McNamara process the scientific adventurers physiological habitats, habitats aroused arboreal challenging long all and innumerous has virtually desert Crustacea the exploited species, including Given freshwater and travelers, and occupied estuarine terrestrial environment, 2012). have marine and the decapods to amphibious wellbeing The restricted and and species physiology include 2012). and abundance, earth, Zeng, distribution, on the & available influences (Romano that crustaceans factor have abiotic of basis dramatic important genetic a an underlying as is interpreted 2012). their Salinity Faria, been and & has evolved (McNamara and crabs elucidated ‘carcinization’, how transforma- called been However, evolutionary a is not The by 2014). crab characterised pleon. (Scholtz, a are ventrally-folded change to crabs a crustacean morphological lobsters, and lobster-like and carapace, a shrimps short morphotype of from “lobster” depressed, tion bodies or a elongate macruran with et the ancestral with (Haug body an Compared from compact Decapoda evolved within 2016). have al., discussion crabs et all and attention. (Haug terms, attention evolutionary research much In considerable drawn have attracted 2016). morphotypes al., have distinct and years, found aquaculture, forms. recent and are parasitic (Warner, most In or fisheries species the crustaceans planktonic in represent These the crabs and crabs Swimming living of of 1982). free groups group species. (Bowman, to commercially-important important largest many benthic families the includes from 47 group of ranging to this to one habitats, Furthermore, belonging marine belonging are crustaceans in they typical species largely most species, 6,000 worldwide, the of about of numbers comprising one of as 1977), terms known are In which crabs, Decapoda. called generally are Brachyuran swimming of breeding chromosome molecular Introduction for Y genomic useful valuable the also a is of provides but only region studies, not evolutionary genome specific of crabs. and crab the genome biological swimming further the addition, the for Decoding In in resource region. time this observed. in first also gene the determination were Analysis it Segregant for species suggested Bulked in located the and adaptation stage, was of salinity transcriptome larval members of growth with its flea-like basis rapid Combined and genetic the and genomes, crabs. the during into crab of insights in evolution and providing expanded the development (BSA) C2H2 family to embryonic of gene the related early N50 only proportion shrimps, closely the and high in scaffold was be crabs a expressed and to of and contig mainly found analyses genes was The were genomic protein-coding family ˜1.2 comparative 19,981 protein covering on chromosomes. finger with Based scale, 53 respectively, zinc chromosome (49.43%). into Mb, repeats the assembled 15.6 report sequence at we and sequences simple Here, assembled kb scaffold value. was 108.7 the economic which were high of values crab, and 79.99% rate swimming growth industry. with the rapid fisheries Gb, of its the to sequence to due genome China important the in being species as farmed well important an as importance, ecological major trituberculatus Portunus author, Abstract Wang), Corresponding * d hs uhr otiue equally contributed authors These ooeeBonomtc nttt,Biig101,China 100016, Beijing Institute, Bioinformatics Novogene + [email protected] APs,adNa and -ATPase, Cutca eaoa rcyr) omnykona h wmigca,i of is crab, swimming the as known commonly Brachyura), Decapoda: (Crustacea: + Pn i)and Liu) (Ping ,K [email protected] + 2Cl , - ornpreshv encoe n tde Gro ta. 2011; al., et (Garcon studied and cloned been have cotransporters [email protected] .trituberculatus P. 2 Ja Li), (Jian and , GaginLiu) (Guangjian .trituberculatus P. Dmrt1 [email protected] a dnie sakysex key a as identified was .trituberculatus P. + togimmunity strong , ,K + APs,V- -ATPase, (Chunlin salso is Posted on Authorea 3 Aug 2020 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.159646761.15797764 — This a preprint and has not been peer reviewed. 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Therefore, disease than body there artificial diseases. strong more large of After exhibit shrimp months and species. and of important shrimps 7-8 rate ecologically diseased outbreaks in growth on important prevent g rapid feed an effectively 400-500 they its As to can because for stocked. up shrimps and famous with reach propagated mixed is can artificially often crabs mass is swimming body Korea and and the Its China, Japan, size. aquaculture, in China, crabs in of edible waters species coastal common crustacean the most in the distributed of widely one is and pebbles, complex or and sand Torrecilla, chromosomes crab, (Z. of crustaceans swimming numbers most The in large determined the be to cannot due analysis Gonz´alezorteg´on, however, karyotype Mart´ınezlage, Perina, Gonz´aleztiz´on, by 1959); & determination 1938, 2017). sex 1937, genomes, In Niiyama, 1995; 2008). 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Data may be preliminary. h eoe,floe yln emnlrpas(T,1.7)adDAtasoos(10.95%) transposons of DNA 27.29% and (LINE, of 17.07%) elements (LTR, that interspersed repeats than long S3) terminal were lower long Fig TEs much by abundant followed was most genome), which the the assembly, sequences, and repetitive the the KEGG, of Among SwissProt, 49.46% proteins), for non-redundant sinensis accounted (RefSeq japonica content NR the repeat of The one least databases at distribu- GO on the based with consistent annotated arthropods were other were which in respectively, features bp, gene 1,231.18 of and tions 10,484.05 were length (CDS) sequence The annotation and prediction the Genome in identified were genes conserved (85.08%) genome completeness. 211 assembled CEGMA, the to in trituberculatus 3.0). 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Data may be preliminary. atlg n oedsrcin hrfr,tecnrcino h w eefmle nca rvdscusto clues similar is provides some crab RA in shows families RA 2014). gene two Liu, ‘carcinization’. the and of self-tolerance. & of hyperplasia, mechanisms contraction immune and Zhuang, molecular the disease, inflammation the of Zhang, Therefore, synovial human study weakness, Bo, failure destruction. common muscle bone Zhang, a a skeletal and as to Q. by cartilage such linked Y. caused carcinization, are to 2019; diseases genes appearances al., autoimmune both proportion interestingly, et systemic body More (Steinz and a number (RA) crab. families gene arthritis to between WDFY crayfish, rheumatoid correlations and to positive actin by shrimp, characterized the from as including respectively, crab, attention, and special metamorphosis. stage deserve and larval development families like S14) in flea gene functions the contracted specific crab at have Two and development may embryonic crayfish, it of early shrimp, that regulation in penaeid suggesting the expressed thus, in in mainly ; genes was proteins 23 family the and gene for 3 the role 0, a identified are supports were There ( research S13) families previous test 2003). gene Com- and exact (Urrutia, contracted family, Fisher’s carbonization. morphogenesis forty-seven protein the in and finger using processes zinc expanded evolutionary and C2H2 species one genomic-level crab crab species, infer of two shrimp to analyses in two inter- time, genomic the been Comparative first has with the which 2019). or- pared for evolutionary ‘carcinization’, (Borradaile, body us, The called change compact allowed is morphological 2014). a shrimp crab dramatic (Scholtz, by a a pleon characterised towards ventrally-folded as are crustacean a preted crabs lobster-like and a lobsters, carapace from or short transformation shrimps depressed, of a with bodies ganization elongate the molting. with ribosome-related and Compared specific neuroendocrine of eyestalk carcinization number of of stages, large regulation basis molting the A different Genetic in to role 2011). related significantly important Mykles, are an endocrine & expressions play major their and (Chang they and eyestalk The molting that eyestalk, the suggesting the in stages. in in role located molting expressed is a are different (Hopkins), genes play in (XOSG) to expressed complex salt known gland mainly low X-organ/sinus is were under the most crustaceans, molting, but development, of of complex processes, analyzed stages above we infection different Furthermore, the in pathogen in pathway genes). upon ribosome (140 the and genes in of stress, genes number of largest expression the and the containing reclamation, enriched, bicarbonate significantly tubule P450 (p pathways most cytochrome proximal enriched by absorption, significantly xenobiotics and of revealed digestion metabolism also and protein analysis ribosome, enrichment adaption, contained KEGG salinity which species. molting, the ( to development, played the genome specific as genes in crab expanded such the contracted some process, in were that suggested physiological that genes stress different families expanded immune in gene the of seven roles species expression and important other the expanded of the enrichment were to Genomes) that compared families genome, gene crab 18 identified We ago years million ˜326.0 that showed of analyses ancestor phylogenetic orthologues, to single-copy related closely Using between families tree. relationship gene phylogenetic OrthoMCL phylogenetic single-copy a using 246 the evolutionary species investigate and twelve the To altogether in into families performed . insights analyses gene cluster important 32,918 family identified provides gene We in species species. related those closely of relationship between families gene Identifying Evolution Genome ute nlsso t xrsini mroi eeomn n avlmtmrhsssoe that showed metamorphosis larval and development embryonic in expression its of analysis Further . hr r 4 ,ad4atngns n 9 ,ad0WF ee npnedsrm,crayfish shrimp, penaeid in genes WDFY 0 and 1, 19, and genes, actin 4 and 8, 84, are There . .trituberculatus P. 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The codn otecutraayi fteepeso atrsdrn h aiiysrs,teepne and expanded the salinity stress, up-regulated the after salinity was genes the of group down-regulation during other showed group patterns the One expression while categories. the two test, into of divided were analysis DEGs cluster unique the in adaptation to salinity and shock According in resistance Heat involved stress were protein, with apoptosis 14-3-3-like associated and are addition, resistance, . and stress In identified, transport, plays ion also 2012). and that were osmoregulation, Zeng, genes in & family involved caspase (Romano was apoptosis two transport A DEGs and subunit the ion 70, from catalytic in protein identified ATPase role were proton genes important V-type unique the an 141 which, and Among genes expanded . 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Pfour AP W , .parahaemolyticus V. − − Finally, .F 12 molecularmarkerssignificantlyassociatedwiththeresistanceof − ( ua,Ci,Hpis Bagrodia, Hopkins, Chiu, ruman, F .parahaemolyticus V. & Abraham, eedniidsnte earsonchi wereidentifiedusingtheP 2017; Silva & Jung, 2013; .u ,Araki, e, Y X.Xu, − & Ahmed, 2012) .After .parahaemolyticus V. neto,theexpressionofthethreegenesinhemocytesandthehepatopancreasweresignificantlychanged infection, Fg7) (Fig Ths thesegenesmayplayanimportantroleintheimmunedefenseof hus, .T .trituberculatus, P. whichcouldberelatedtothedifferentiationofdiseaseresistancetraitsbetweenindividuals. Posted on Authorea 3 Aug 2020 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.159646761.15797764 — This a preprint and has not been peer reviewed. Data may be preliminary. ee,laigt aesxa eeomn Msr ta. 02.I hce n afih hc xii the development exhibit male which induce flatfish, may dosage and gene chicken the In and sex-determining chromosome, 2002). Z XX/XY al., the the on et located In (Masaru is development DMRT1 system, sexual 1999). ZZ/ZW male Lin, to & leading Yuan, genes, conserved Tang, highly Y-linked more Moore, or the one (Meng, by system, characterized domains is which (DM) determination, sex of DNA-binding in involved patterns was gene expression developmental doublesex different The the during and females and sex analyzed, males the successfully in on different were stages, significantly based were genes crabs, (Contig475.8) eight juvenile gene ( Finally, unknown to doublesex including Z1 which, 2018). of of region al., sexes three Y-linked known et chromosome. the with Y (Lv in the stages marker predicted locating developmental in were different accuracy genes during our analyzed 10 the proving in thus, of located 2018); total all al., were A et they contigs(Lv that two found those and on further zero located To to also equal Contig475) 2018). values and CQ al., (Contig153 with contigs et two results in of mechanism(Lv on genotypes determination determination focused heterogametic We sex sex identified chromosome. of also XY mechanism studies the Those the support map. analyze male linkage in high-density (LOD markers a LG24 on using sex-associated located time QTL first significant analysis highly the karyotype a Gonz´alez-Orteg´on,for studies, by Mart´ınez-Lage, previous Perina, & determination our Torrecilla, In sex determined. (Zeltia been genomes, crustaceans in complex most determination and sex in of Gonz´alez-Tiz´on, chromosomes mechanism performed the of Moreover, 2017). be number cannot large the to Due in determination traits Sex insulin growth of to induces differentiation unique LAR the signaling. was which and insulin of growth between of by knock-down one rapid located regulated SNP and that the be one traits, suggested related and that growth data showed proteins with Those 1996), analyses associated cellular BSA . was Goldstein, is of of genes result & diabetes LAR phosphorylation The tandem Zhang, tyrosine 2 two Sale). Li, reversible & type Hodgkinson, of M. and (Mander, (LAR) (P. regulation resistance phosphatase obesity resistance the Protein-tyrosine retardation, cell insulin in 1995). stimulate Growth Phillips, role to also 2000; essential which Flier, 2001). an & metabolism, (Kahn plays lipid Kahn, resistance and & insulin glucose with mechanism (Saltiel of associated rapid regulation differentiation and the and specific for a growth important be is may signalling there Insulin that indicated which genome, in crab’s myogenesis the of & specific in Holland, one its found Bardeesy, and analyses, were (Maccalman, myogenesis genomics in family thereafter comparative role declined matrix important on which an extracellular Based myoblasts, plays the prefusion Blaschuk). 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Cell support from myogenesis. that inseparable substances is and growth energy Rapid chitin essential produce degrade to can the chitin and containing in conditions food found intestinal was that function and fiber gene can stomach dietary AMCase (AMCase) of (GlcNAc) under chitinase source produce mammalian glycosidase a to acidic protease-resistant hydrolyze as substrates that considered that major confirmed been enzymes a studies long are recent as has However, Chitinases chitin digested. 2015). system, not digestive Spaink, is mammalian & the Stougaard, In (Koch, chitin. insects and crustaceans, fungi, Fg10) (Fig . .trituberculatus. P. DMY/Dmrt1bY 2 .trituberculatus P. hc sasuc fcro,ntoe,adeeg Ms ta..Aspecific A al.). et (Misa energy and nitrogen, carbon, of source a is which , Ptdmrt i 9) Fig ( ee ftetlot eaa eecaatrzda sex-determining as characterized were medaka, teleost, the of genes otg7.3,mbSN-ie( myb/SANT-like Contig475.13), , neetnl,tetopeiul-nhrdsxmreswere markers sex previously-anchored two the Interestingly, . .trituberculatus P. eoe hs ugsigteca a ffiinl digest efficiently can crab the suggesting thus, genome, 13 Tbe4) (Table Chst5 eue Qaaye oaco h Y the anchor to analyses CQ used we , n hi xrsinpten were patterns expression their and , eeadoeepnigN-cadherin expanding one and gene .trituberculatus P. Ptmyb .trituberculatus P. otg5.8 n an and contig153.28) , > a o previously not has .trituberculatus P. 4 a identified was 14) Chst5 delayed Chst5 could Posted on Authorea 3 Aug 2020 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.159646761.15797764 — This a preprint and has not been peer reviewed. Data may be preliminary. costegnm;4 Ccnetars h eoe ,represents genes 5, strand negative genome. of the distribution across 3, content genome; GC the across 4, genes genome; strand the positive across of distribution the 2, of genome; features Genomic PR- 1 (https://www.ncbi.nlm.nih.gov/bioproject/ Fig NCBI on table and found Figure be can datasets JNA631920/) sequence genomic manuscript. preparation. the All sample reviewed authors performed All Gao Ti manuscript. Baoquan availability Xingbin the and Data and wrote Zhencheng Liu Yan Su and Ping Deping Zhencheng Liu, Su, and analyses. Zhencheng Guangjian Lv data Li, Jianjian Ronghua research. and Lv, the experiments Jianjian designed the sequencing. and performed genome Liu.conceived the Ping performed and Su and Wang Chunlin (2018YFD0900303 Li, Jian Na- China LJNY2015002), of (CARS-48), (No. System Program contributions Project (41776160). Research Author Talent China R&D Leading Agriculture of Taishan Foundation China Key of Science & Natural Project National tional China Innovation the Agriculture of Eco Agriculture by Efficient of supported Ministry was 2018YFD0901304), research regulatory This the crab. provide clarify economic will to this genome important for reference also MAS Acknowledgements This are and which traits determination. breeding studies, of sex important biological adaptation and of and salinity growth mechanisms evolutionary the the rapid for on immunity, underlying light resources strong mechanisms shed crucial their and comparative data as evolution, and The well annotation structure, ecosystems. as Genomic genomic marine the complex crustaceans. of into aquatic biology insights of provided specie analyses the important genomic of an assembly and genome species brachyuran chromosomal-scale a of present specificity We species and complexity the sex- indicating Conclusions unknown studies, the in previous of mechanisms in pattern determination determination expression sex sex Neither the the in males. stages, involved in crab be higher juvenile to was from and and different megalopal changed, was gene the that, gene related in sex-related was However, unknown genes The phase. two Z4 stages. the crab of juvenile to expression Ptdmrt Z1 the in from between development peak throughout difference second The a reached females. the and differentiation. to stage sex the Similar of Z1 ( to periods the (6.20-times) critical compared during be 18.54-times, phase may (upregulated decreased Z3 periods stage then the egg-zoea was in the Expression expression at peak stage). its study) multicellular reaching development, this stage, embryonic in egg-nauplius of used the stages were different domain the individuals DM During male one 40 including the exons S12), and that three acids, (Fig showed female spans amino also frame (40 265 results reading males PCR open of of in the protein pairs) and amplify putative (RACE), base only ends (2,165 a cloned sequence encodes of cDNA amplification and full-length rapid The by In obtained al.). was al.). et et (Yoshimoto Nanda gene 2014; (ovary)-determining al., et Chen (S. and Ptmyb ugsigthat suggesting Ptdmrt fwihepeso nfml a infiatyhge hnta nml uigZ to Z1 during male in that than higher significantly was female in expression which of , ee h xrsinof expression the gene, Ptdmrt P.trituberculatus Ptdmrt saYlne eeadpasa motn oei e determination. sex in role important an plays and gene Y-linked a is .trituberculatus. P. .laevis X. i 13) Fig eewsepesdi l aetsustse,btnti females in not but tested, tissues male all in expressed was gene Ptmyb rmotrt ne ice:1 itiuino costhe across of distribution 1, circles: inner to outer From . n -ikdgn,D-,wsietfida ieysex likely a as identified was DM-W, gene, W-linked one , hs eut niae htteegze n zoea and egg-zoea the that indicated results Those . 14 nmlswsas infiatyhge hnta in that than higher significantly also was males in Ptmyb Ptdmrt .trituberculatus P. rteukonsxrltdgnswr found were genes sex-related unknown the or xrsinwssgicnl peuae at upregulated significantly was expression P.trituberculatus ersnaieca fthe of crab representative a , Ptmyb Fg11) (Fig a anyexpressed mainly was Fg12) (Fig hoooe.I 5, In chromosomes. .trituberculatus P. . Ptdmrt n RT- and , Ptdmrt can , Posted on Authorea 3 Aug 2020 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.159646761.15797764 — This a preprint and has not been peer reviewed. Data may be preliminary. pce.()Heacia lseigo 22fml ee tsvnendffrn eeomna tgsin of stages Clustering developmental different 4 seventeen Fig at genes (J). family stage C2H2 crab of clustering Hierarchical P.trituberculatus of (B) expression species. and respec- branches, tree their berculatus Phylogenetic values above 3 colors bootstrap red represent Fig Gene and nodes genes. green orthologous ancestral in copy at shown single to 246 points are using (-) Red constructed contraction was tively. and which (+) species, sliding 12 expansion 0.5-Mb of family nonoverlapping tree in Phylogenetic drawn 2 are Fig 2–4 chromosomes. different at genes windows paralogous joins line each g-apissae(n,egze tg E) oasae(1Z) eaoa tg M,adjvnl crab juvenile and (M), stage megalopal (G), (Z1–Z4), stage stage gastrulation (B), zoea stage (Ez), blastula stage (J). (Mc), stage egg-zoea stage (En), multicellular including stage crabs egg-nauplius young to eggs fertilized of Expression 13 Fig 12 475) of Fig Contig sequence cDNA in of located Alignment was (B) gene domain. (Ptdmrt individuals. DM female the and in male structure in of crab features juvenile structural of to and Z1 Sequence from female 11 genes and Fig male 8 represents of Y-axis pattern and Expression values region 10 CQ a (PBC- Fig distinctive represrnts female by X-axis and differentiated genome. (PBX-PSX) be splitted male can the from of sequences individuals. alignments region Y-linked The same how results. the demonstrate CQ in to the data of sequence plot coverage PSC) and Reads 9 Fig respectively. groups, two of screening posiotion the the c. represents group. X-axis analysis. Δ BSA or SNP-index through the differentiation represent growth with of infection fast Contigs following of of tissues Identification different 8 in Fig genes related resistance disease of parahaemolyticus analysis Expression 7 Fig respectively. groups, two of screening the c. group. up Δ or represents posiotion the SNP-index ring represents the X-axis Green represent analysis. of BSA stress. through Contigs salinity differentiation resistance of during disease gene. of DEG Identification regulated unique 6 down Fig and represents ring expanded yellow the and of gene of analysis regulated qPCR Cluster indicated.(B) 5 are Fig genes the of orientation in and stages developmental position relative The (Pvi). SPidx au ffitn eut.a h N-ne rp fPXgop .teS-ne rp fPSX of graph SN-index the b. group. PBX of graph SNP-index the a. results. fitting of value (SNP-index) XT of graph SN-index the b. group. X of graph SNP-index the a. results. fitting of value (SNP-index) P.trituberculatus Ptdmrt. Hox Ptdmrt ee lsesadteEpesosa ieetDvlpetlSae in Stages Developmental Different at Expressions the and Clusters Genes ()Pyoeei reo ee fteepne eefml oprdwt h w shrimp two the with compared family gene expanded the of genes of tree Phylogenetic .(A) h lc o niae h osre Mdmi n h rylbldrgo stezn finger zinc the is region labeled gray the and domain DM conserved the indicates box black The Hox Δ Δ .trituberculatus P. trituberculatus P. mlf nml n eaeindividuals female and male in amplify SPidx rp.Tebu ahdln n upedse ierpeettecniinof condition the represent line dashed purple and line dashed blue The graph. (SNP-index) of condition the represent line dashed purple and line dashed blue The graph. (SNP-index) nldn etlzdegsae() oasae(1Z) eaoa tg M,adjuvenile and (M), stage megalopal (Z1–Z4), stage zoea (F), stage egg fertilized including ee in genes itrso te pce r rmtewbieht:/hlpcogaot#bu –use. http://phylopic.org/about/#about website the from are species other of pictures , Ptdmrt .trituberculatus P. .trituberculatus P. Δ Δ tdffrn eeomna tgs lvndffrn eeomna tgsfrom stages developmental different Eleven stages. developmental different at SPidx au feeySPlcs h e ie hwteSPidxor SNP-index the show lines red The locus. SNP every of value (SNP-index) or SNP-index the show lines red The locus. SNP every of value (SNP-index) n -xsrpeet h N-ne or SNP-index the represents Y-axis and or SNP-index the represents Y-axis and Ptdmrt . . Ptdmrt ( Ptr C2H2 ), eecnit ftreeosadtointrons. two and exons three of consists gene ee.()Ncetd n eue mn cdsequence acid amino deduced and Nucleotide (A) genes. .sinensis E. 15 aiya ieetdvlpetlsae in stages developmental different at family ( Esi Ptdmrt > ), .vannamei L. 0i 0 xeiet.I addition In experiments. 100 in 90 n N euneo otg475 Contig of sequence DNA and Δ Δ SPidx.Teclrdots color The (SNP-index). dots color The (SNP-index). ( Lva .trituberculatus. P. Hox ,and ), ee tdifferent at genes .virginalis P. .tritu- P. (A) V. Posted on Authorea 3 Aug 2020 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.159646761.15797764 — This a preprint and has not been peer reviewed. Data may be preliminary. v.oe.otg61 yohoecoiaeasml atr6hmlgO=oospesG=O6P= SV=1 SV=2 PE=1 PE=2 GN=COA6 GN=Fbxl6 sapiens musculus OS=Homo OS=Mus SV=1 homolog 6 PE=2 6 protein GN=MFSD6 factor F-box/LRR-repeat scrofa assembly OS=Sus oxidase 6 c protein Cytochrome SV=3 domain-containing SV=2 PE=2 superfamily PE=1 GN=CHST5 facilitator GN=Kirrel sapiens norvegicus Major OS=Homo OS=Rattus 5 1 sulfotransferase protein Carbohydrate IRRE-like of Kin SV=1 - PE=1 GN=TRIM59 sapiens OS=Homo 59 - protein SV=1 motif-containing Tripartite PE=1 SV=2 GN=ine PE=1 melanogaster GN=KIAA1524 OS=Drosophila - sapiens ine OS=Homo transporter CIP2A GABA evm.model.Contig37.39 Protein chloride-dependent and Sodium- SV=1 evm.model.Contig66.12 PE=2 GN=FP1 coruscus OS=Mytilus SV=1 evm.model.Contig82.11 - protein PE=2 matrix GN=GABRB4 plaque gallus evm.model.Contig28.13 Adhesive OS=Gallus beta-4 SV=1 subunit SV=2 PE=2 receptor evm.model.Contig35.4 PE=1 GN=Prune acid GN=Chia musculus Gamma-aminobutyric musculus OS=Mus OS=Mus homolog evm.model.Contig51.19 chitinase prune mammalian Protein Acidic SV=1 evm.model.Contig1679.4 PE=1 GN=COMMD4 sapiens OS=Homo evm.model.Contig139.4 - 4 protein SV=2 domain-containing PE=1 evm.model.Contig693.3 COMM GN=CadN melanogaster SV=1 OS=Drosophila PE=2 evm.model.Contig58.27 Neural-cadherin sanguineus OS=Hemigrapsus BCRH2 SV=1 opsin evm.model.Contig3.89 PE=1 eye GN=Nc Compound SV=1 melanogaster PE=2 SV=2 OS=Drosophila evm.model.Contig639.9 sanguineus PE=1 Nc OS=Hemigrapsus GN=ZNF418 Caspase BCRH2 sapiens opsin OS=Homo evm.model.Contig3.172 eye 418 Compound protein finger evm.model.Contig397.12 Zinc evm.model.Contig1675.1 - evm.model.Contig6.77 evm.model.Contig39.49 evm.model.Contig166.1 evm.model.Contig15.40 evm.model.Contig128.21 evm.model.Contig1407.2 evm.model.Contig128.16 evm.model.Contig238.5 evm.model.Contig153.38 in Gene specific or expanded also genes, growth-related 42 3 Table scaffolding after Contig ** of statistics Assembly 2 Table the for used data Sequencing 1 Table oa 1.7–264.81 100.66 71.64 92.51 – 150 – 317.77 150 85.97 120.79 – 111.01 (X) – coverage – Sequence (bp) length 350 Read Total Genomics (G) 10X data Total reads Pacbio size Insert reads Illumina libraries Pair-end DSisrtannotation SwissProt ID 9 0321069807384 51 8,037 34 5,734 26 4,132 130,609 20 2,431,430 2,951 - 8,722,939 2,055 12,181,407 30,342 15,593,479 44,666 62,400 - 2,165 82,211 number 33,040,454 108,682 12,101 number N90 864,453,619 6,277,820 N80 N70 846,564,517 Length N60 N50 Number Length Max Total ID Sample > 20 2072,165 12,077 - - =2000 P.trituberculatus .trituberculatus P. otg*b)Saodb)Cni* Scaffold Contig** Scaffold(bp) Contig**(bp) 16 eoeassembly genome .trituberculatus P. Posted on Authorea 3 Aug 2020 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.159646761.15797764 — This a preprint and has not been peer reviewed. Data may be preliminary. i 5Tesaitc fKG aha niheto xaddfamilies expanded of enrichment pathway KEGG of statistics species The different S5 in the Fig in genes sequence of consensus distribution the The and S4 genome the Fig the in in TEs elements of TE type identified each the novo between of calculated rate was divergence rate of Distribution S3 Fig . among features size=total gene , ’Genome of formula genome Comparison The the S2 represented by 41. Fig volume was Gb high K-mer 1.2 of and peak frequency as volume low estimated main at was The peak size errors. left-hand sequencing The random essentially occur. containing they K-mer which at frequency in the frequency against 17-mer of Distribution S1 Fig SV=1 PE=2 GN=timm10b laevis OS=Xenopus B Tim10 subunit translocase SV=2 membrane PE=1 inner GN=Lar import melanogaster Mitochondrial OS=Drosophila Lar phosphatase Tyrosine-protein SV=1 SV=1 PE=2 PE=1 GN=dok7 - GN=Arhgef11 rubripes norvegicus OS=Takifugu OS=Rattus region Dok-7 11 Y-linked Protein factor the exchange in - nucleotide predicted guanine genes Rho ten of information The - 4 Table SV=1 PE=2 GN=stk10 rerio - OS=Danio SV=2 10 PE=1 kinase GN=Lrrc16a Serine/threonine-protein musculus OS=Mus SV=1 16A PE=2 protein evm.model.Contig708.7 GN=BCAT1 repeat-containing aries Leucine-rich SV=2 OS=Ovis PE=1 cytosolic evm.model.Contig180.1 GN=SLC17A5 aminotransferase, Branched-chain-amino-acid sapiens SV=2 OS=Homo PE=1 evm.model.Contig317.10 Sialin GN=CadN melanogaster OS=Drosophila evm.model.Contig1137.1 Neural-cadherin SV=1 evm.model.Contig597.4 PE=1 GN=GBF1 griseus OS=Cricetulus evm.model.Contig89.6 - 1 factor - exchange nucleotide evm.model.Contig96.7 guanine SV=1 A-resistance PE=1 brefeldin GN=IDS evm.model.Contig188.4 Golgi-specific sapiens OS=Homo 2-sulfatase evm.model.Contig246.3 Iduronate evm.model.Contig954.14 evm.model.Contig348.16 evm.model.Contig15.39 evm.model.Contig499.7 evm.model.Contig0.31 evm.model.Contig23.18 evm.model.Contig3.60 evm.model.Contig23.12 evm.model.Contig526.3 Gene ahi pulex Daphnia irr eused. we library DSisrtannotation SwissProt ID , xdsscapularis Ixodes otg7 687868 evm.model.Contig475.13 evm.model.Contig475.11 evm.model.Contig475.10 evm.model.Contig475.9 + - evm.model.Contig475.8 866685 evm.model.Contig475.7 - 539131 865887 - 538208 Contig475 538896 + evm.model.Contig153.40 537678 evm.model.Contig153.39 Contig475 537720 - 497352 evm.model.Contig153.29 Contig475 537316 477231 Contig475 + 490225 evm.model.Contig153.28 Gene Contig475 - 2213665 369282 Strand Contig475 2210559 2212469 - Contig153 2210235 + 1515057 End Contig153 1310130 1514797 Contig153 1307889 Start Contig153 CHROM v.oe.otg.2RsrltdpoenRb3O=rspiamlngse NRb E1SV=1 PE=1 GN=Rab3 melanogaster OS=Drosophila Rab-3 protein Ras-related evm.model.Contig0.32 , aataoatepidariorum Parasteatoda otnstrituberculatus Portunus trituberculatus P 17 , erncu urticae Tetranychus , kmer eau vannamei Penaeus P.trituberculatus eoe h oueo -e splotted is K-mer of volume The genome. ID num/kmer , depth’ eoe h divergence The genome. rspiamelanogaster Drosophila , rblu castaneum Tribolium de Posted on Authorea 3 Aug 2020 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.159646761.15797764 — This a preprint and has not been peer reviewed. Data may be preliminary. env uuts4,9 ,6.7845 .9266 1,847.03 246.65 3.59 884.59 5,661.67 44,493 Homology Augustus novo De prediction gene of Statistics S5 Table the of assessment F:Fragmented CEGMA BUSCOs S4 searched Table Duplicated groups BUSCO D:Complete n:Total BUSCOs BUSCOs M:Missing Single-Copy BUSCOs S:Complete BUSCOs C:Complete the of assessment BUSCO S3 Table in SNP of statistics General S2 study.xlsx Table this in used Primers S1 Table of RT-PCR genes stress S12 growth-related salt Fig of during analysis DEGs enrichment specific KEGG and stress S11 expanded salt Fig up-regulated during of DEGs enrichment specific KEGG and S10 expanded Fig down-regulated of low enrichment stage, KEGG stress molting S9 salinity development, Fig during of DEGs stages of different Trend in S8 pathway Fig ribosome infection in pathogen genes and families stress of specific salt expression identified the of enrichment S7 pathway Fig KEGG of statistics The S6 Fig %opeees h rprincr ee nterfrnecr eelibrary. gene core reference the in genes core proportion the gene; gene %completeness: core core of 4. partial Number and #Prots: complete 3. partial: completeness + a Complete with gene 2. core Complete: 1. pce opeecmlt opee+prilcmlt partial + complete partial + complete complete complete P.trituberculatus species eed2,5 0298 4.150 4.34,869.99 3,329.43 3,862.21 3,133.17 148.93 275.99 175.53 202.98 5.01 4.97 3.91 2.50 1,372.20 746.01 686.97 507.15 length(bp) intron Average 14,596.29 length(bp) 20,269.88 exon Average 11,939.92 39,969 Dme gene 28,958 per exons Average 77,306 Cgi length(bp) Cel CDS Average Genscan length(bp) transcript 5,202.15 Average Geneid Number SNAP 142,367 GlimmerHMM set Gene pce UC oainassmn results assessment notation BUSCO P.trituberculatus Species Ptdmrt oooySP4,7 0.0067 0.3604 2,586,394 47,872 0.3537 2,538,522 SNP Homology SNP Heterozygosis SNP All nml n eaetsusof tissues female and male in 8 54 1 85.08 211 %completeness 75.40 Prots # %completeness 187 Prots # 0854200 9.832 7.31,503.38 1,277.38 1,265.61 275.13 397.52 315.45 3.24 1.98 2.55 891.58 787.48 803.49 4,260.04 2,040.56 2,761.53 10,815 29,696 8,768 P.trituberculatus P.trituberculatus P.trituberculatus C:84.7%[S:82.5%,D:2.2%],F:2.9%,M:12.4%,n:1066 > 70% ubrPercentage(%) Number 18 genome genome genome .trituberculatus P. Posted on Authorea 3 Aug 2020 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.159646761.15797764 — This a preprint and has not been peer reviewed. Data may be preliminary. V V 3938590 ,4.144 5.32,132.77 2,194.55 genome in % (bp) 2,346.33 Length 2,197.63 TRF) without (all TEs Combined 255.33 TRF) without (all 236.02 TEs Combined protiens 221.40 TE 256.30 protiens TE (Repbase+Denovo) 4.49 Repeatmasker 5.22 (Repbase+Denovo) Repeatmasker 6.28 Type sequences. 4.76 repetitive of Categorization S7 Table 1,147.41 1,231.18 1,389.51 1,219.26 8,599.08 10,484.05 23,993 databases. different 19,981 in annotation Gene S6 13,768.62 Table 9,475.94 注 44,920 set* Final EVM 23,395 set* Pasa-update* Final Pasa-update* PASA EVM RNAseq *otisteutasae region. untranslated the :*contains uik 6511,0.43096 .3475 2,700.67 467.53 6.63 3,099.64 18,303.84 56,571 length(bp) intron Average Cufflinks length(bp) exon Average Tur gene per exons Average Tca length(bp) Spu CDS Average Pva length(bp) transcript Average Ptep Number Isc Hsa Dpu set Gene nePoal1,7 98.50 98.90 Total 84.90 74.10 19,677 19,763 16,959 Annotated Total 14,806 Annotated 76.90 all KEGG NR InterPro 15,357 Swiss-Prot KEGG Swiss-Prot NR 8862745 1.022 1.41,536.27 1,340.60 1,334.03 1,349.24 1,419.70 1,252.86 1,416.63 1,493.25 416.34 390.59 428.30 302.06 368.69 360.28 303.93 279.70 2.20 2.51 2.39 3.10 2.27 1.58 2.86 2.04 914.90 981.52 1,023.85 935.76 836.84 567.46 869.14 571.79 2,754.58 3,009.75 18,806 2,878.81 22,091 3,766.29 15,073 2,639.54 26,412 1,287.92 23,660 3,503.53 47,137 2,131.13 13,798 31,971 O1,5 91.40 72.50 18,257 14,492 GO Pfam 19 ubrPret(%) Percent Number 991- 19,981 Posted on Authorea 3 Aug 2020 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.159646761.15797764 — This a preprint and has not been peer reviewed. Data may be preliminary. 38 Others 17.07 147,540,995 1.79 15,507,775 16.48 142,449,802 LTR 0.02 134,806 0 0 0.02 134,806 SINE 27.29 235,904,361 10.44 90,240,215 23.80 205,758,594 LINE 10.95 94,695,859 0.89 7,698,813 10.20 88,177,866 DNA genome in % (bp) Length genome in % (bp) Length 20 Posted on Authorea 3 Aug 2020 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.159646761.15797764 — This a preprint and has not been peer reviewed. Data may be preliminary. al 9Tedsrbto fgnsi ieetspecies different in genes of distribution The S9 Table species each in clustering family gene for used Genes S8 Table 47.08 406,978,948 13.11 113,294,828 45.45 392,875,521 Total 3.42 7,689,177 0 0 0.89 7,689,177 Unknown 0.000004 38 0 0 0.000004 s 5 491316248 15655 163 5888 1489 762 657 orthologs Other 869 Unique orthologs Cse Multiple-copy Cgi orthologs Single-copy Species Nve Cel Pvi Mye Gene Cgi Lva Esi Dpu Oni Cse Dre Ptr Name Species eaotlavectensi Nematostella elegans Caenorhabditis virginalis Procambarus yessoensis Mizuhopecten gigas Crassostrea vannamei Litopenaeus sinensis Eriocheir pulex Daphnia niloticus Oreochromis semilaevis Cynoglossus rerio Danio trituberculatus Portunus 21 24773 20060 20761 23930 27265 24825 7502 30280 21209 20211 31951 23694 Posted on Authorea 3 Aug 2020 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.159646761.15797764 — This a preprint and has not been peer reviewed. Data may be preliminary. al 1 h S nlssrsl fgot trait.xlsx growth of result analysis BSA The markers.xlsx S18 12 Table of analysis frequency Genotype DEGs.xlsx S17 unique Table and expanded of crab.xlsx Information and S16 crayfish Table stress.xlsx shrimp, salinity penaeid crab.xlsx during in and DEG families crayfish S15 WDFY shrimp, Table and penaeid actin in of family Genes protein S14 finger Table Ptr).xlsx zinc and C2H2 (Esi of crab Genes of S13 family Table gene contracted and identified.xlsx Expanded families S12 gene Table unique of information The S11 Table in families gene contracted and P.trituberculatus expanded of information The S10 Table otat141Hydrolysis 1 184 Contract differentiation and Growth 14 54 Expand e 0 6 255794 10517 7245 23564 11779 2091 4551 3452 11577 2242 319 10968 10057 5159 15747 10633 17458 7382 2925 602 564 740 2367 958 239 755 768 404 667 908 1689 854 484 Cel 811 Ptr 1004 Dre 886 Lva 889 Esi 944 Nve orthologs 925 Other Dpu 621 Unique Pvi orthologs Mye Multiple-copy Oni orthologs Single-copy Species 1 muiyrelated Immunity differentiation and growth Metabolism expression, gene of Regulation transportation Material Opsin 1 transportation Material Sulfate 10 related Immunity 11 related Growth 11 regulator response transduction Signal 211 8 differentiation related metabolism and Disease 9 Energy growth cell expression, 7258 gene 13 of Regulation 6224 4 Metabolism 6221 12 Antibiosis expression 4982 gene 16 of Regulation 4936 10 Glycometabolism 9 3920 Metabolism 18 2218 9 1691 2 1257 16 1118 3 967 8 598 410 378 303 287 147 eefml DGn ubrClasses number Gene ID family Gene 22 Posted on Authorea 3 Aug 2020 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.159646761.15797764 — This a preprint and has not been peer reviewed. Data may be preliminary. hn .(04.UigRpaMse oIetf eeiieEeet nGnmcSequences. Genomic in Elements perspectives. Repetitive our Identify and to review RepeatMasker A 5 Bioinformatics, Using molting: in Protocols crustacean (2004). of N. Regulation Chen, (2011). L. 172 Endocrinology, D. Comparative the Mykles, and in & General Opacity S., Corneal E. and Fragility Chang, Skin Assembly: Fibril Lumican. Collagen of Regulates Absence Lumican S. & assem- Chakravarti, enhancing synteny. and conserved repairing and for set maps tool genetic a of doi:10.1101/2020.02.04.934711 Chromonomer: integration by through (2020). DNA11Edited S. genomes genomic Bassham, bled & human A., in Amores, structures J., gene Catchen, complete of Prediction Cohen. (1997). E. S. F. Karlin, Crustacea. & recent C., the Burge, of Classification carcinization. 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No reuse without permission. — https://doi.org/10.22541/au.159646761.15797764 — This a preprint and has not been peer reviewed. Data may be preliminary. v . hn,D,Lu . i .(06.Eet fslnt clmto n ysakalto nN , for + correlate Na molecular on :a ablation trituberculatus eyestalk Portunus and of acclimation gill salinity the of in Effects expression gene (2016). for cotransporter J. Identification - Li, Marker 2Cl & and , P., Mapping + Liu, K QTL D., Zhang, (2018). tritubercula- J., (Portunus J. Crab Lv, Li, Swimming & the P., in Liu, System L., Determination tus). Sex Song, XY P., Indicating trituber- Huan, Osmoregulation. Portunus Sex-Determining: D., of of Basis Sun, Analysis Molecular for J., Transcriptome the Lv, loci (2013). into J. trait Insights Li, quantitative Provides & Stress of P., 8 Salinity Chen, Identification ONE, to B., Response Gao, (2015). in Y., Y. Wang, culatus P., Du, Liu, & J., Lv, B., trituberculatus. 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G. determination. the Niiyama, Goodwin, sex includes avian . 9 on . chromosome (re)view human . comparative and F., a proteases- Tzner, chromosome uuml, a sex Gr, is Z Z., chitinase chicken Shan, mammalian E., Acidic Zend-Ajusch, I., Onuki. is Nanda, system. terra, . digestive gene, . mouse doublesex-related . in Drosophila Miyazaki, glycosidase A Haruko, resistant Kimura, (1999). Masahiro, transport S. Ohno, Lin, ion Misa, & gill vertebrates. B., Yuan, in and somitogenesis H., patterns Tang, in involved B., osmoregulatory Moore, of A., Evolution Meng, M. (2012). DePristo, 182 Physiology, C. review. DNA Environmental . a S. and next-generation Crustacea: Faria, decapod analyzing . the & for in mechanisms . framework C., A., MapReduce J. Kernytsky, a McNamara, K., Toolkit: Cibulskis, Analysis A., Genome Sivachenko, data. The sequencing E., a Banks, is (2010). M., DMY A. genes. Hanna, (2002). box S. homeo A., Nobuyoshi, mouse McKenna, two . of . fish. expression medaka . Region-specific the K., W. in Tohru, development McGinnis, M., male Chika, for flowers. S., required the Tadashi, gene and S., DM-domain - Ai, Y-specific bees N., Yoshitaka, the M., and Masaru, birds The (2002). J. D. Martins, Methods. Sequencing DNA 9 Next-Generation identi- Genetics, pathway (2008). and R. annotation E. vocabulary. genome Mardis, controlled Automated a (2005). as induces (KO) L. Wei, phosphatase Orthology & doi:10.1093/bioinformatics/bti430 tyrosine KEGG G., protein the J. using LAR Olyarchuk, fication of T., ab Knock-down Cai, X., source J. Mao, G. open two Sale, GlimmerHMM: & and P., resistance. TigrScan C. insulin Hodgkinson, (2004). A., L. Mander, S. Salzberg, & gene-finders. M., eukaryotic Pertea, initio H., W. differentiation. terminal Majoros, myoblast during regulation levels developmental mRNA Noncoordinate fibronectin 195 W. O. and Dyn, Blaschuk, integrin, & N-CAM, C., P. N-cadherin, Holland, of N., Bardeesy, D., C. 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Salzberg, in & 25 system Bioinformatics, L., chromosome Pachter, sex C., X1X1X2X2/X1X2Y Trapnell, a reveals species chromosome Palaemon sex elegans. Y marine Palaemon 2 of X 1 analysis 2/X cytogenetic X 2 Gonz´alezorteg´on, X A., Gonz´aleztiz´on, Mart´ınezlage, Comparative Perina, 1 & Z., (2017). A., X Torrecilla, E., M. 1 A. X a elegans. reveals Palaemon species in Palaemon system marine resources. of and analysis cytogenetic knowledgebase rative Ontology Gonz´alez-Orteg´on, A., Gonz´alez-Tiz´on, Compa- Gene Mart´ınez-Lage, Perina, & (2017). Z., A., the E., M. Torrecilla, Assembly A. Genome of High-Quality Expansion 45 (2020). research, Y. (2016). acids Li, Consortium. Nucleic . Ontology Evolution. . . Genome Gene (2019). X., Unique T. The Li, Its J. S., Reveals Jiang, Lanner, sinensis H., . japonica Zhang, Eriocheir . Q., of . Liu, arthritis. Z., E., Wang, rheumatoid Ahlstrand, B., in Tang, J., weakness A. muscle Cheng, skeletal that K., promote eukaryotes doi:10.1172/jci.insight.126347 Olsson, 16. actin in B., on prediction Aresh, hotspots M., gene Oxidative Persson, for M., server M. web Steinz, a AUGUSTUS: (2005). constraints. B. user-defined Morgenstern, allows & M., thousands Stanke, with models. analyses mixed phylogenetic provides and analysis likelihood-based taxa maximum transcriptomic sinensis. of RAxML-VI-HPC: Comparative Eriocheir (2006). in (2015). lifestyle A. X. benthic Stamatakis, Li, to & adaptation Y., and brachyurization Li, 558 of Y., basis Gene, Liu, molecular BUSCO: M., the (2015). Hui, into insights Z., M. Cui, E. C., Zdobnov, Song, & V., orthologs. E. single-copy Kriventseva, with doi:10.1093/bioinformatics/btv351 completeness P., 3210-3212. annotation convergence. Ioannidis, and of assembly M., genome example assessing R. Waterhouse, prime (2013). A., a U. Sim˜ao, F. of J. Jung, deconstruction & and M., L. history Silva, metabolism. - lipid crabs and 83 Zoology, glucose of to of Evolution Contributions regulation (2014). the and G. signalling Scholtz, Insulin (2001). R. C. 414 Kahn, Nature, & correction. R., error A. read Saltiel, long efficient and accurate LoRDEC: (2014). 30 E. Rivals, & L., Salmela, pro- aquaculture pathogen- exposure. to ammonia their implications elevated and crustaceans: with interactions caspases decapod 334 and in three improvement Osmoregulation potential of (2012). for S. Characterization methods ductivity, C. (2017). Zeng, J. & geno- N., Li, large Romano, & in trituberculatus. P., Portunus families Liu, in repeat pattern B., of expression Gao, identification induced novo X., De Yu, (2005). X., A. Ren, P. Pevzner, Tolerance. & Glucose C., and N. mes. Mass Jones, Muscle L., Adult A. to Price, Growth Fetal of Relation 12 (1995). Medicine, W. I. D. Phillips, 2) 5631.doi:10.1093/bioinformatics/btu538 3506-3514. (24), iifrais 21 Bioinformatics, 22.doi:10.1016/j.aquaculture.2011.12.035 12-23. , 1,8-8 doi:10.1016/j.gene.2014.12.048 88-98. (1), 66) 9-0.doi:10.1038/414799a 799-806. (6865), 8,686-690. (8), rnir nZooy 14 Zoology, in Frontiers 9,10-11 doi:10.1093/bioinformatics/btp120 1105-1111. (9), (suppl iifrais 22 Bioinformatics, D) 31D3.doi:10.1093/nar/gkw1108 D331-D338. (D1), rnir nZooy 14 Zoology, in Frontiers 2,87-105. (2), uli cd eerh 33 research, acids Nucleic ) 31i5.doi:10.1093/bioinformatics/bti1018 i351-i358. 1), uohg n Immunity and Autophagy 1,47. (1), 2) 6829.doi:10.1093/bioinformatics/btl446 2688-2690. (21), 27 1,47. (1), ih&Sels muooy 66 Immunology, Shellfish & Fish (suppl . ) 45W6.doi:10.1093/nar/gki458 W465-W467. 2), rnir nGntc,10 Genetics, in Frontiers iifrais 31 Bioinformatics, c nih,4 Insight, Jci 189-197. , Bioinformatics, Aquaculture, 1340. , Diabetic (19), (9), Posted on Authorea 3 Aug 2020 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.159646761.15797764 — This a preprint and has not been peer reviewed. Data may be preliminary. hn,X,Ya,J,Sn . i . a,Y,Y,Y,...Xag .(09.Pnedsrm geno- shrimp Penaeid (2019). J. Xiang, . . . Y., Yu, Y., Gao, molting. AnimalTFDB frequent S., (2015). and A.-Y. Li, adaptation Guo, benthic Y., doi:10.1038/s41467-018-08197-4 . into Sun, insights . provides J., . me Yuan, W., factors. transcription X., Liu, animal X., Zhang, of study Zhang, functional S., and prediction Song, 43 expression, research, C.-J., for Liu, resource a 105 T., America, 2.0: Liu, of laevis. W-linked States H.-M., A Xenopus United Zhang, M. in the Ito, development of . ovary Sciences . primary . of C., Academy in Nishida-Umehara, National participates Y., Uno, DM-W, K., gene, Tamura, H., DM-domain Umemoto, E., Okada, S., the Yoshimoto, Clarifies Likelihood. Sequence Maximum Genome by Clam Analysis (2019). Phylogenetic 24 4: D. PAML Li, (2007). . Z. . Yang, Diversity. . Color L., Shell Yan, Extraordinary Z., and Li, Adaptation doi: Benthic J., Its Ding, of Z., Basis Huo, Molecular H., Nie, X., Yan, immunity. and metabolism LTR linking (2007). mTOR, posons. H. Wang, (2012). & R. Z., Xu, Ahmed, & K., Araki, 24 L., Immunology, exposed Ye, trituberculatus Portunus X., crab swimming Xu, the of profiles Their expression stress. Gene and (2011). salinity Genes Y. to Liu, Hox & (2015). H., Q. X. Xu, Jianhai, & L., Fuhua, vannamei. Litopenaeus Z., of 045 Xiaojun, Development Early Y., in Jianbo, Pattern mitten Expression W., Chinese Jiankai, the S., crabs. of Xiaoqing, of response biology antibacterial (1977). the F. G. to Warner, linked from variants genes genetic Apoptosis nm23: of crab. and annotation Caspase functional (2014). ANNOVAR: Q. K. Wang, (2010). S. H. Young, Hakonarson, . data. & sequencing . M., high-throughput . Li, improvement. S., assembly K., Sakthikumar, genome Wang, A., and detection Abouelliel, variant M., microbial 9 comprehensive Priest, ONE, for PLoS T., proteins. tool Shea, integrated T., an repressor Pilon: Abeel, J., zinc-finger B. Walker, KRAB-containing (2003). crabs doi:10.1186/gb-2003-4-10-231 euryhaline R. 13 of gills Urrutia, the in Na+,K+-ATPase and H+-ATPase acclimation. V-type salinity (2007). during (2010). H.-C. L. Lin, Pachter, & switching . J.-R., isoform . Tsai, and . J., transcripts M. unannotated Baren, reveals differentiation. van cell RNA-Seq G., Kwan, by during A., quantification Mortazavi, and G., assembly Pertea, Transcript A., B. gene Williams, Differential Cufflinks. C., (2012). Trapnell, and L. TopHat Pachter, . with . experiments . doi:10.1038/nprot.2012.016 RNA-seq R., 562-578. D. of Kelley, (3), analysis D., Kim, expression G., transcript Pertea, and L., Goff, A., Roberts, C., Trapnell, 8,18-51 doi:10.1093/molbev/msm088 1586-1591. (8), https://doi.org/10.1016/j.isci.2019.08.049 08,52-62. (008), iegnee us 2 Bugs, Bioengineered uli cd eerh 35 research, acids Nucleic Dtbs su) 7-8.doi:10.1093/nar/gku887 D76-D81. issue), (Database (11). 6,429-435. (6), aieBooy 158 Biology, Marine aueBoehooy 28 Biotechnology, Nature ora fEprmna ilg,210 Biology, Experimental of Journal 3,174-177. (3), IDR necetto o h rdcino ullnt T retrotrans- LTR full-length of prediction the for tool efficient an FINDER: uli cd eerh 38 research, acids Nucleic WbSre su) 25W6.doi:10.1093/nar/gkm286 W265-W268. issue), Server (Web 1) 1127.doi:10.1007/s00227-011-1721-8 2161-2172. (10), air eBooi aie 19 Marine, Biologie de Cahiers 28 5,5155 doi:10.1038/nbt.1621 511-515. (5), 1) 14e6.doi:10.1093/nar/gkq603 e164-e164. (16), 4,6067 doi:10.1242/jeb.02684 620-627. (4), eidclo ca nvriyo China, of University Ocean of Periodical 7,2469-2474. (7), aueCmuiain,10 Communications, Nature 1,115-115. (1), oeua ilg n Evolution, and Biology Molecular eoeBooy 4 Biology, Genome Sine 19 iScience, auePooos 7 Protocols, Nature rceig fthe of Proceedings uli acids Nucleic eiasin Seminars 1225-1237. , 1,356. (1), 1) 8. (10), Posted on Authorea 3 Aug 2020 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.159646761.15797764 — This a preprint and has not been peer reviewed. Data may be preliminary. adaptation-and-sex-determination level-genome-of-portunus-trituberculatus-provides-insights-into-its-evolution-salinity- 2.pdf Fig file Hosted Arthri- Rheumatoid ETS1) with ( Patients Specific-1 Transformation- Chinese E26 in (2014). Polymorphisms P. R. WDFY4) Liu, ( & 4 C., Member Zhuang, tis. H., Family Zhang, WDFY L., and Bo, Q., Y. Zhang, fws npruutiuecltsfo i-utr od fpan n crabs. and prawns of effect ponds lethal mud mix-culture of from study from Quantitative gene trituberculatus (2008). Sinica G. 70 portunu Songye, on protein & H., wssv shock Weixian, of X., heat Wenjun, W., cytosolic Zhizheng, W., a Zhongfa, of analysis expression serrata. and Scylla cloning crab Molecular M. Zhong, nentoa ora fMlclrSine,15 Sciences, Molecular of Journal International 2,90-95. (2), vial at available ih&Sels muooy 34 Immunology, Shellfish & Fish https://authorea.com/users/348321/articles/473714-a-chromosome- 2,21-71 doi:10.3390/ijms15022712 2712-2721. (2), 29 5,1306-1314. (5), caooi tLimnologia et Oceanologia Posted on Authorea 3 Aug 2020 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.159646761.15797764 — This a preprint and has not been peer reviewed. Data may be preliminary. 30 Posted on Authorea 3 Aug 2020 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.159646761.15797764 — This a preprint and has not been peer reviewed. Data may be preliminary. 31 Posted on Authorea 3 Aug 2020 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.159646761.15797764 — This a preprint and has not been peer reviewed. Data may be preliminary. 32 Posted on Authorea 3 Aug 2020 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.159646761.15797764 — This a preprint and has not been peer reviewed. Data may be preliminary. 33 Posted on Authorea 3 Aug 2020 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.159646761.15797764 — This a preprint and has not been peer reviewed. Data may be preliminary. 34 Posted on Authorea 3 Aug 2020 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.159646761.15797764 — This a preprint and has not been peer reviewed. Data may be preliminary. 35 Posted on Authorea 3 Aug 2020 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.159646761.15797764 — This a preprint and has not been peer reviewed. Data may be preliminary. 36 Posted on Authorea 3 Aug 2020 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.159646761.15797764 — This a preprint and has not been peer reviewed. Data may be preliminary. *contig Contig Contig contig153.39 475 153 475 . . . 11 28 9 37 *Contig475.8 *Contig contig153.40 Contig 475 475 . 10 . 13 Posted on Authorea 3 Aug 2020 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.159646761.15797764 — This a preprint and has not been peer reviewed. Data may be preliminary. A B

1003

1093

1183 1294 AAATTCCGCACACAGTCTTCATCTGCTTGCAGGAAACTGGTAACGCGATAAATTGCCTTGCGTTCAAACTATGTAACGCTACATATGATTGAATATGTTTTGACAAGGTTTGTAGAGTAA 1414 TCCTTGCAATGTTTAGATAAAGAAACAACATAATCAGATATATAAATGTTGACTGAAAATGCTCAGTTAGTAAGAATACAATGATAACGTCTACCTACGAATAACCCTCGCTAA 1534 TTTTCCTCATAGAGACAACCACTCTTATAATAAGTAAACAATAGGTCTTTAAAGAGATAAAACTAAAAAAAAAAAAAATATATCAACCGGGATGCTACCTTCAGGAATTTATGCTGATTA 1654 GATGATCGTTCATTCTATGAGCTAAAGCCAAATTGAATTTCTTGATGTCAGATATCCAATTTGAAAATAGAACAGCACCCCTTACCCAGCGAGCAACTGTGTGGGTTAATGTTTGTGTCG 17 1894 2014 2134 ATAACAACAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATGATAATAATAATAATAATAATAATAATAATAATAATGATAATAATAATAATAATAATAATAACA 2254 A 2374 CACGTACGCCTCCTGCCTCTTGTTTGCTCGGTTTACACTTGTTGTGTAGTGTGCTACCGTAAATACACTTTCATAATACCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA

121 CCCCATCGTGCCCTGCCGTCAGTGTCCTGTCACCCTTAATATAAAATAACTTACCTAGTCAGAAATTTATCTCGCATCAGTTGTATGTATAGTGACAATCCACCAGGAATACACCAATCC 241 ACCGTCTACTTATCAGCTGCTACAACCATAACTATTTTGATAATGTGTTTTGGTAGTGATCGATGAGTGTGTCAGACAAGTGACTTCTTTACATGTTAATTGTTGGCATAGTGACTCTGC

361

463

553

643

733

823

913

74 GGGTGTGCAGGATTACAATTATCTATTGCAATGGAGCGAGGCGCCAGTTAAGCGACCACCTGCATTACATAGATTTGATATAAATCTTATTCACAACAATTACTTAAACAATAGTGGCAG Contig Contig Ptdmrt

1 CTACTTCTCCTAAAGCACCGTGTCACTGTTGCCATATGGAGCATGTGGTGATGTCGAACGCTGCTGCTCCACCTATTTCGTAAGACGGGCTGGCTTTCTTGGTGATGACATCTCTGATCA

CCAAGACGCATGTAAGATGCCGTACATTTAGCAGCTGACACCACTTACCGCTGGACTAGGGAAGGCATACAGGCTGTGAAAAGTGGCACTAGGATTATACTCCATTCGCCGATATCCAAT

CCACCATCTCTTCATTTCCGTGTACTCGACAGGTGAGGTAAGGTTGTCAGC ATG GCG TCG GCG CCT AAG AAG AGA GAC TTT TTT AAT GGA TCA CAA AGA CT AGA CAA TCA GGA AAT TTT TTT GAC AGA AAG AAG CCT GCG TCG GCG ATG CCACCATCTCTTCATTTCCGTGTACTCGACAGGTGAGGTAAGGTTGTCAGC

AAC TTA ACG GAG ACA CAG GAA GAG AGT ATG GTT CCT GAG CAA AAT GTC ACC AGT GGA GGA AGA AAT GGC TTC TCT TCC TCC CAG GAT TT GAT CAG TCC TCC TCT TTC GGC AAT AGA GGA GGA AGT ACC GTC AAT CAA GAG CCT GTT ATG AGT GAG GAA CAG ACA GAG ACG TTA AAC

CTT GGG CAC TCT TCA GGC GAC TGT CCT TTC CCA TCT TTC TCC AAT AGA CAA AGT TCT CCT GTG TAC AAT TGT CAA GAC AGC TGC CCA TC CCA TGC AGC GAC CAA TGT AAT TAC GTG CCT TCT AGT CAA AGA AAT TCC TTC TCT CCA TTC CCT TGT GAC GGC TCA TCT CAC GGG CTT

CTC TCT TCA CGA TAT AGT ATC CGA ACG AAA AGG GAC GAA TAC GAA AAC TCC AAA GGC ACT TCA TAC GAG TCT AAT TCA GTT CCA GAA GAA CCA GTT TCA AAT TCT GAG TAC TCA ACT GGC AAA TCC AAC GAA TAC GAA GAC AGG AAA ACG CGA ATC AGT TAT CGA TCA TCT CTC

TTA TCT TCG GCG GGC TCC GCT GAA GTT GCT TCC TTA GCC AAG CAC GAT GGA AAC TAC GAA AGG AAG AAG AAA GTG GAA AAG AGA AA AGA AAG GAA GTG AAA AAG AAG AGG GAA TAC AAC GGA GAT CAC AAG GCC TTA TCC GCT GTT GAA GCT TCC GGC GCG TCG TCT TTA

AGG TGT CGA TTG TGC GCC AAT CAC GGC AAG TAC GAA GAG ATT AAA GGT CAC AAG TGG TAC TGC GAA TAC AGG AAA CCA CAA CAC AAG TG AAG CAC CAA CCA AAA AGG TAC GAA TGC TAC TGG AAG CAC GGT AAA ATT GAG GAA TAC AAG GGC CAC AAT GCC TGC TTG CGA TGT AGG

TCC CTG TGT GAA ATC ACC CAC AAG AAA CGA CTC TTC CTA CCG AAA AAT GAG ATC AGA CGC AAA CAG CAT GAC CAA GAG CAG CAG CTA CA CTA CAG CAG GAG CAA GAC CAT CAG AAA CGC AGA ATC GAG AAT AAA CCG CTA TTC CTC CGA AAA AAG CAC ACC ATC GAA TGT CTG TCC

CAA CAA TTA AAC GTG CAG AAC CGA TCG ACA GAT GAA CCA TGG CTG GAT GGT TAT GGT CGG GTC GGC TTA CCA CCC TCG CCA ACT ACC ACC ACT CCA TCG CCC CCA TTA GGC GTC CGG GGT TAT GGT GAT CTG TGG CCA GAA GAT ACA TCG CGA AAC CAG GTG AAC TTA CAA CAA

CAC ATA GAC TTC CCC CGG CTA CAG GAA CTA GTA GAA GAG ACA GCA TCT ATC TTG GAC GAC GAG GAT TTG TTC CGC CAA ATC AAT GA AAT ATC CAA CGC TTC TTG GAT GAG GAC GAC TTG ATC TCT GCA ACA GAG GAA GTA CTA GAA CAG CTA CGG CCC TTC GAC ATA CAC

ATC CCG TTG AAT GTC CTT CAA CAT TGA TTACCTACTGTCCTCCCTAATCTACCTACCTGGTCCAGCGGAAGAATCGATGCTTGTAAAGGGATGCAGCTATTTC TGA CAT CAA CTT GTC AAT TTG CCG ATC

CCACGTGCGCATCCATACTAACAAAGATGATTATTATATGCCACACCGAGGGTCTTCTCTGAGACTGAAGTATTATTTTTACCAGTGATTAATTCTCATAACTACTAAATCTTAAAGTG

L E Q E M P Q V S G N F S Q D Q S S S F G N R G G S T V N Q E P V M S E E Q T E T L N

L G H S S G D C P F P S F S N R Q S S P V Y N C Q D S C P P C S D Q C N Y V P S S Q R N S F S P F P C D G S S H G L

S R S R K D Y N K T Y S S P E P V S N S E Y S T G K S N E Y E D R K T R I S Y R S S L

S A S E A L K D N E K K V K K K R E Y N G D H K A L S A V E A S G A S S L

C L A H K E I G K Y E R P H K H Q P K R Y E C Y W K H G K I E E Y K G H N A C L R C R

L E T K R F P N I R R I E N K P L F L R K K H T I E C L S

Q N Q R T E W D Y R G P S T T T P S P P L G V R G Y G D L W P E D T S R N Q V N L Q Q

I F R Q L E T S L D D F Q N E N I Q R F L D E D D L I S A T E E V L E Q L R P F D I H

I

TAATAACAATGATGATGATACTACTACTATGTTAGCATGTCCTTTATTTTCCCATACTCCTTTTCTGTCTGACGTCACGTCTTTCCCCTCAGTCCTCGCTCGCTGCCGCCCGAGGTTGA

P

L cDNA 475 475 DNA

V Q * * H Q L V N

38

M

A

A A S

P

K

K Q H D Q E Q Q L L Q Q E Q D H Q K

K

R

F N S R L R Q S G N F F D

K K K R K E

CACGTGC

TCGGAT

A CA A

G CG G

GA

TA

T

A

G

C

C

T

C

A

C

F

A

S

C

Q

C

R

E

Q

Y

Posted on Authorea 3 Aug 2020 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.159646761.15797764 — This a preprint and has not been peer reviewed. Data may be preliminary.

Relative expression of Ptdmrt Female 39 Male Control Ptdmrt Control Ptdmrt Control Ptdmrt Control Ptdmrt