Posted on Authorea 8 Oct 2020 | The copyright holder is the author/funder. All rights reserved. No reuse without permission. | https://doi.org/10.22541/au.160218269.98008776/v1 | This a preprint and has not been peer reviewed. 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All rights reserved. No reuse without permission. | https://doi.org/10.22541/au.160218269.98008776/v1 | This a preprint and has not been peer reviewed. 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No reuse without permission. | https://doi.org/10.22541/au.160218269.98008776/v1 | This a preprint and has not been peer reviewed. Data may be preliminary. 02 o cuaeyslcdainet.Tasrpoi aa(x5 p oae-00pafr)generated platform) NovaSeq-6000 bp, al., (2x150 et data (Doerks homologous Transcriptomic (v2.4.0) The GeneWise alignments. 1e-5). using by spliced [?] proteins accurately (E-value matching tBLASTn for the with using against 2002) by aligned 1997) genome then burbot were Karlin, the sequences to genome & aligned and (Burge database NCBI GenScan the and of sequences 2006) protein al., prediction, et assembly. homology-based genome the (Stanke polyacanthus For burbot (v2.7) the settings. 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All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.160218269.98008776/v1 — This a preprint and has not been peer reviewed. Data may be preliminary. otgN0o .5M Tbe2.Telnt fti sebywscnitn ihtegnm ieestimated size genome a the with with consistent assembly was assembly genome this Mb using of 575.83 assembled length a The were covering analysis. produced data 2). library, k-mer (Table which These by long-read Mb polishing, 2.15 the S4). pilon of Table from N50 and Supplementary contig data racon 1, high-quality by (Table Gb followed assembly 95.24 NextDenovo genome generated the platform of 36.60% genome 173.16-fold II of assembled Sequel content the PacBio repeat of The and completeness f 0.57% and of of assembly number heterozygosity Genome with total 3.2 representing Mb The library, ˜550 insert-size be S2). 150 to S3). 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Data may be preliminary. 1) ovrey h ubtcerysoe otatdgn aiisi oohlccl deinvaplasma corrected via and adhesion rected (GO:0098742, S10 cell molecules Tables homophilic corrected (Supplementary adhesion in system membrane families (GO:0007156, immune gene molecules contracted and adhesion showed binding, clearly membrane ion burbot repair, the Conversely, damage S11). cell with associated were 34 and terms rected GO corrected 73 (GO:0046914, in binding enriched Atlantic 639 significantly displayed corrected and divergence were genome (GO:0015074, P burbot corrected burbot The burbot integration of (GO:0006259, of The DNA ancestor process families 4). metabolism common including gene (2018). (Figure the mainly expanded pathways, with Mya al. 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All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.160218269.98008776/v1 — This a preprint and has not been peer reviewed. Data may be preliminary. hswr a upre yteNtoa e eerhadDvlpetPormo China of Program Development and Research Key National (LH2019C070). the China of Province by Heilongjiang of Foundation supported Science Natural was and (2017YFA0604904) work burbot. This of history evolutionary the detecting elucidating useful flow, Acknowledgements and also gene populations in are assessing involved the data units, of genes These conservation adaptation in identifying candidate change. to beneficial local environment including of were analysis under applications, series results conservation Gadiformes genome A The diverse order whole in for analyses. species. process for genomics evolution cod comparative data the these other elucidating genomic in with identified second important burbot were the adaptation of and supplied widest freshwater annotation evolution the Gadiformes and represents the assembly order and investigate genome family the further The cod of long the world. 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UV presence environment. freshwater of to The three ocean PSGs exposure in the The of convergent levels in damage. functionally high that had DNA the genes with with cause these consistent compared may was that environment selection radiation freshwater positive in UV under radiation repair the to DNA al., of fish in et component involved freshwater (Yao genes a of repair is break exposure ino80e double-strand The Protein DNA the 2007). to al., contributes et and 2008). (Das complex arrest INO80 cycle remodeling chromatin cell damage-induced DNA promotes Genes repair. (burbot, damage lineages point DNA freshwater to three related were with ) detected were PSGs affinis 38 Additionally, corrected (GO:0090304, S16). compound process Table metabolic cyclic acid organic nucleic and the =4.13E-03), genome in burbot corrected enriched the (GO:0034641, in functionally PSGs cess corrected were as (GO:1901360, PSGs identified were process burbot genes metabolic The 377 ratio of S15). likelihood total Table different A two (Supplementary adaptation, performed. freshwater were for model) selection (branch-site fatty positive tests omega-3 under capabilities. evolving acids, osmoregulatory genes fatty provide the omega-6 identify and To the fluidity with of membrane Compared cell components species. improve different freshwater help than the G (Ta¸sbozanacids acids & with gene fish fatty in consistent freshwater environment contracted omega-3 and ionic are of the stable marine levels findings for a between These found of acids was requirements fatty permeability. pathway functional omega-3 membrane reduced KEGG cell the concentra- enriched reflect for ion no may freshwater the However, families adjusting gene cell. for Such the critical families. outside are and functions associ- These inside families tions gene S14). contracted Table two (Supplementary and =0.00E+00) corrected families value gene (GO:0007155: adhesion expanded cell no with ated shared species freshwater three Notably, S13). corrected and (ko04621, S12 Tables signaling plementary receptor NOD-like and value=1.52E-04), znf385a . sfrgon rnh(upeetr al 1) orPG ( PSGs Four S17). Table (Supplementary branch foreground as ) slc19a1 slctdusra ntep3atvtn pathway. activating p53 the in upstream located is slc19a1 a nipratrl nflt rnmmrn rnpr.Lwomtcpesr has pressure osmotic Low transport. transmembrane folate in role important an has a mrv oi cdasrto o rswtrseis hs aawl serve will data These species. freshwater for absorption acid folic improve may P au 41E0) N eaoi rcs G:067,corrected (GO:0016070, process metabolic RNA =4.11E-03), value P t3 n nabp1 and stk33 au 18E0) ellrntoe opudmtblcpro- metabolic compound nitrogen cellular =1.83E-02), value P au=.0+0 n ebae(O0100 corrected (GO:0016020, membrane and value=0.00E+00) 6 atcpt ntemttcDAdmg check- damage DNA mitotic the in participate znf385a P kc ,21) aiefihhv higher have fish Marine ¨ ok¸ce, 2017). P stk33 au 61E0 (Supplementary ) =6.16E-03 value au=.1-2 ahas(Sup- pathways value=2.41E-02) neat ihp3T5 and p53/TP53 with interacts , ino80e slc19a1 , nabp1a .albus M. corrected , and P znf385a and value G. P P Posted on Authorea 8 Oct 2020 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.160218269.98008776/v1 — This a preprint and has not been peer reviewed. Data may be preliminary. ihBiol Fish Muˇska burbot M, Matˇena of J, Koˇcvara J˚uza Assessment L, ( T, (2018) J, burbot Duras of P, movements Blabolil Winter USA. Wyoming, (1993) Lake, RJ Bull Baldes in sequences. drawdown MF, DNA Cook analyze EP, to Bergersen program figshare a in the finder: available repeats with openly 573. Tandem (1999) database also G is Assembly Benson data NCBI genome at the deposited References addition, SRR12577979). been In deposited and have been SRR12550374 has annotations at PRJNA663985. SRR12549430, genome and accession (SRR12549297, burbot for (SRA) genome GenBank data) Archive assembled RNA-seq Read and The Sequence Hi-C the Illumina, at (PacBio, data sequencing Raw Statement Accessibility Data manuscript. final the approved No and reviewed data. authors the interests analyzed All samples. of Z.Q.H. sequencing manuscript. Conflicts sequencing. the the genome collected wrote the H.Z. G. performed and T.X. and M.H.L. and DNA/RNA project. Z.Q.H. the the extracted managed X.S.J. and and conceived Q.L. Z.Q.H. and G. T.X. contributions Author ocmn ,BiohA pelrR lte ,Etece ,GsegrE atnM ihu K, Michoud its M, and knowledgebase Martin protein E, SWISS-PROT Gasteiger The A, (2003) Estreicher M Schneider M, 2003. S, Blatter in Pilbout TrEMBL R, I, supplement Apweiler Phan A, C, O’Donovan Bairoch B, Boeckmann orsT olyR,ShlzJ otn P okP(02 ytmtcietfiaino oe protein novel of identification Systematic (2002) P Bork CP, gene functions. Ponting of nuclear study J, with the Schultz associated for families RR, tool domain computational Copley A T, survival CAFE: cell Doerks (2006) Determines MW Hzf Hahn (2007) JP, Demuth SW evolution. N, Lee family Cristianini SA, T, Aaronson Bie A, transactivation. De Bernstein p53 Y, modulating by Kimura stress B, genotoxic Zhao upon L, Raj S, Das J, Huddleston long-read A, from assemblies Copeland genome A, microbial Clum (2008) finished C, Nonhybrid, Heiner M (2013) J, Yandell data. J Drake sequencing AS, Korlach SMRT AA, Alvarado SW, Klammer Turner P, C, EE, Marks Holt Eichler DH, B, Alexander genomes. CS, Moore organism Chin E, model emerging Ross for G, designed Parra pipeline , annotation SMC, easy-to-use Robb an L, MAKER: scaffolding Korf interactions. Chromosome-scale chromatin BL, (2013) on J Cantarel Shendure based JO, assemblies Kitzman genome R, novo Qiu de RP, of Patwardhan DNA. A, genomic Adey human JN, in Burton structures gene complete of Prediction 78. (1997) , S Karlin C, Burge noain iulzto n nlssi ucinlgnmc research. genomics functional in analysis and visualization annotation, G A, Conesa 18 https://doi.org/10.6084/m9.figshare.12927203 188-196. , , 92 t ,Gr´aGoe M eo ,Tlo ,Rbe 20)BatG:auieslto for tool universal a Blast2GO: (2005) M Robles Tal´on M, J, Garc´ıa-G´omez Terol S, JM, ¨ otz 1545-1559. , Bioinformatics a Methods Nat oalota Lota uli cd Res Acids Nucleic , 22 1269-1271. , , L 78 ouainssanblt ncnrlErpa reservoirs. European central in sustainability population 1758) (L. 10 clFeh Fish Freshw Ecol 563. , Lu 2020). (Liu, , 31 eoeres Genome 7 365-370. , Cell , 2 , 141-145. , a Biotechnol Nat , ´ h ,Vjrı ,HlbvaM eek J Peterka Vejˇr´ık Holubov´aR´ıha M, M, L, 130 ˇ 12 47-56. , 624-637. , Bioinformatics oalota Lota , 31 uli cd Res Acids Nucleic 1119-1125. , uiga extreme an during ) , 21 o Biol Mol J 3674. , eoeRes Genome , , 27 268 J , Posted on Authorea 8 Oct 2020 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.160218269.98008776/v1 — This a preprint and has not been peer reviewed. Data may be preliminary. ,Bloa ,Za M iX,Wn ,Fn ,XeB huZ,HagH hnS,VnaehB h Q Shi B, Venkatesh SL, Chen genomic H, and Huang transcriptomic ZC, on Zhou Becker B, based CH, Xie Li (Actinopterygii) C, R, fishes Fang Betancur-R ray-finned data. M, D, of Wang Arcila phylogeny XF, AW, Comprehensive Li Thompson (2018) XM, CC, Zhao Baldwin N, Y, Bellorae Sun L, Y, Huang Ort´ı G, LC, Hughes RNAs Non-Coding Annotating Rfam: (2005) A Bateman Genomes. A, Complete Khanna M, in Marshall Cufflinks. S, and Moxon Elbe, TopHat S, River Griffiths-Jones Using the Data in RNA-Seq of lota Analysis Lota (2016) Biology burbot, CKK of Chan use S, Ghosh structure bank Fishes. and Cottoid Freshwater Migration and (2002) Germany. Marine HH in Arzbach Morphology F, and Fredrich Diet in Convergence (2017) D Finnegan ( Ichthyol burbot the Appl of J preferences throughput. Habitat high (2013) and D Eick accuracy high with alignment sequence Res multiple Acids MUSCLE: (2004) RC Edgar oeT,Ed R(97 RAcnS:Apormfripoe eeto ftase N ee in species. declining genes six on RNA action current transfer fishes: of British Biol of detection conservation Fish Practical improved (1990) AA for Lyle PS, program Maitland A tRNAscan-SE: (1997) sequence. SR genomic Eddy (BLAST). Tool TM, Search Lowe Alignment Local evolutio- Basic the (2008) genomic into I insights of https://doi.org/10.6084/m9.figshare.12927203.v1 Lobo provides Estimation Dataset. lota) (2013) figshare. (Lota W freshwater. burbot Fan in of DS, adaptations assembly Mu nary genome YX, projects. Chromosome-level Chen genome (2020) novo N, Q, de Li Liu, in H, Zhang frequency XS, k-mer Hu analyzing JY, by transform. Yuan characteristics Burrows-Wheeler YJ, with Shi alignment BH, read Liu short accurate and and Fast Timetrees, (2009) Timelines, matics L.). R lota for Durbin (Lota H, Resource burbot Li A of biology TimeTree: Winter (2017) (1998) H S Lehtonen Hedges M, Suleski Times. G, genomes. Divergence and Stecher genes S, of a Kumar encyclopedia Update, Kyoto Repbase KEGG: (2005) (2000). J 27-30. S Walichiewicz Goto O, M, Kohany Kanehisa P, elements. Klonowski repetitive A, eukaryotic Pavlicek fishes. of of VV, database osmoregulation Kapitonov and J, excretion Jurka of aspects Some (1988) Z Jara the of history evolutionary the on view mitogenic A ( (2005) burbot F Volckaert gadoid, freshwater A, Perretti Holarctic LD, Cleyn JKJV, Houdt etaM i ,Pre M ekJ,Slbr L(06 rncitlvlepeso nlsso RNAseq of analysis expression Transcript-level (2016) SL Ballgown. Salzberg and JT, StringTie Leek HISAT, GM, with Pertea experiments D, Alignment Kim Local M, Basic Application. Pertea using and reads Theory sequencing (BLASR): molecule Refinement single Successive Mapping with (2012) Tesler Glenn Chaisson, Mark alAa Sci Acad Natl P , , 25 1374 , etcrf f Zeitschrift , 7SplA) 37(Suppl 32 1754-1760. , 1792-97. , 339. , , 29 uli cd Res Acids Nucleic o ilEvol Biol Mol 541-548. , rFischkunde ur ¨ , uli cd Res Acids Nucleic 115 319-334. : 66249-6254. , , 34 , oalota Lota , 1812-1819. , Spl1.) (Suppl 25 , 955-964. , yoee eoeRes Genome Cytogenet 33 D121-D124. , ). oalota Lota o Ecol Mol 159-178. , a Protoc Nat 8 rmteRvrEb:A xeietlapproach. experimental An Elbe: River the from ) , eoScFuaFoaFennica Flora Fauna Soc Memo 14 o Biol Mol J , 2445-2457. , M Bioinformatics BMC 11 , 1650. , 110 reldZoologiczny Przeglad , 462-467. , ri rpitarXiv preprint ArXiv 215 403-410. , uli cd Res Acids Nucleic ehd nMolecular in Methods , 13 , 238. , 32 , 74 . . Bioinfor- 45-52. , Nucleic , 28 J , Posted on Authorea 8 Oct 2020 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.160218269.98008776/v1 — This a preprint and has not been peer reviewed. Data may be preliminary. hoR ipBv ,Vsni ,GlmnI 21)Mcaim fmmrn rnpr ffltsinto folates LTR of (2007) transport sons. W membrane Hao of X, the Mechanisms Zhao in (2011) enzyme ID Co- epithelia. Goldman deubiquitinating RC, across M, Uch37 Conaway and Visentin L, the cells N, Florens of Diop-Bove MP, regulation R, Washburn complex. Zhao of chromatin-remodeling SK, Ino80 Swanson modes the H, Distinct in Takahashi (2008) and Y, JW proteasome Cai Conaway JJ, RE, Jin hen J, L, likelihood. Wortman Song maximum Q, by TT, analysis Yao Zeng and phylogenetic CA, Detection 4: Variant PAML Cuomo Microbial (2007) S, Comprehensive Z Sakthikumar for Yang Tool A, Integrated Abouelliel An Improvement. M, Pilon: Assembly (2014) Priest Genome AM T, Earl DA R, Shea Natale SK, Mazumder T, Young JJ, DM, eukaryotes. Yin Abeel Krylov AI, includes BJ, Wolf version EV, Walker S, updated Vasudevan Koonin AV, An Sverdlov B, database: S, COG Kiryutin Smirnov The AR, BS, (2003) Rao Jacobs AN, and Nikolskaya JD, SL, Jackson fish Mekhedov ND, on Fedorova eutrophication RL, of Tatusov Effects sampling. (1999) random a J on reveals Vuorenmaa based G cod Ta¸sbozan survey M, O, Atlantic a Rask of Nilsen lakes: J, S, sequence Finnish Lien Mannio in genome S, K, fisheries A, The Searle Lappalainen Lagesen S, (2011) Johansen J, O, K L, Tammi Jakobsen Andersen Du Skage R, N, B, T, Reinhardt Stenseth Aken Moum K, system. S, B, Malde J, immune Karlsen J, Omholt unique Vogel C, Thorsen I, J, Previti H, Jonassen C, Knight Kuhl Nepal F, T, R, Neufeld M, Gjoen Solbakken Winer P, Espelund J, MJ, Berg K, Paulsen A, M, TB, Tina Evenson Lanzen Rounge R, TF, Edvardsen OF, Gregers J, A, Wetten M, Tooming-Klunderud Malmstrom A, Lappalainen U, Sharma Grimholt JR, S, MH, Jentoft A, Jackson measures. Nederbragt conservation B, CP, and Star burbot Madenjian of empirical An status VL, Worldwide Erie: (2010) Lake Paragamian MD in L.) MA, lota (Lota Stapanian burbot of Recruitment prediction (2010) initio A approach. ab Cook modelling AUGUSTUS: LD, (2006) Witzel B MA, Morgenstern Stapanian S, Waack A, Phy- Hayes transcripts. Large I, alternative of Gunduz of Post-Analysis O, and Keller Analysis M, Phylogenetic Stanke for tool A 8: genome Version logenies. assessing RAxML BUSCO: (2014) (2015) A orthologs. Stamatakis EM single-copy Zdobnov with matu- EV, completeness gonadal Kriventseva annotation P, of and Induction Ioannidis assembly (2016) RM, Waterhouse S lota. FA, Wuertz Lota J, Simao burbot Adriaen in W, temperatures Meeus different P, at (Teleostei). Husmann ration fish B, gadoid Hermelink freshwater FJ, a lota), Schaefer (Lota burbot the Resour from Ecol Microsatellites Mol (2005) absence A the Meyer in M, times divergence Sanetra and principles evolution reveals molecular clock. resolution of molecular kilobase rates a absolute at Inferring of genome r8s: human (2003) the MJ of Sanderson map Omer 3D I, Machol A AL, looping. (2014) Sanborn chromatin EL JT, of Robinson Aiden ID, ES, Bochkov EK, Lander Stamenova AD, NC, Durand MH, Huntley SSP, Rao uli cd Res Acids Nucleic Bioinformatics kc A(07 at cd nFish. in Acids Fatty (2017) ¨ ok¸ce MA , 5 Bioinformatics 390-392. , clFeh Fish Freshw Ecol Cell Nature , , nuRvNutr Rev Annu 30 35 uli cd Res Acids Nucleic , 159 1312-1313. , W265-W268. , IDR necetto o h rdcino ullnt T retrotranspo- LTR full-length of prediction the for tool efficient an FINDER: , 477 1665-1680. , lsOne Plos , 19 207-210. , , 19 301-302. , , 31 , 326-337. , 9 , ,177. 34 e112963. , W435-439. , 9 ihBiol Fish J o cell Mol ihre aa Ecol Manag Fisheries , 89 Bioinformatics ihFish Fish M Bioinformatics BMC , 2268-2281. , o ilEvol Biol Mol 31 909-917. , , 11 , 34-56. , 31 , , 24 6 3210-3212. , 173-186. , 1586-1591. , , 4 41. , Posted on Authorea 8 Oct 2020 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.160218269.98008776/v1 — This a preprint and has not been peer reviewed. Data may be preliminary. iue4Pyoeei nlssaddvrec iete ftebro ihohrtlotspecies. teleost other with burbot (LTR). the repeats of tandem tree long content time and GC divergence TE, distribution, and DNA gene analysis depth, circle: Phylogenetic read inner 4 long to Figure depth, circle read outer short From genome, burbot. the of of characteristics Genome burbot. 3 the Figure of heatmap Hi-C Genome-wide 2 Figure ( burbot The 1 Figure legend Figure oalota Lota 1000 800 600 400 200 0 0 ) 200 400 10 600 800 1000 3 4 5 6 7 8 9 10 Posted on Authorea 8 Oct 2020 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.160218269.98008776/v1 — This a preprint and has not been peer reviewed. Data may be preliminary. in-freshwater genome-assembly-of-burbot-lota-lota-provides-insights-into-the-evolutionary-adaptations- tables.pdf file Hosted vial at available https://authorea.com/users/365476/articles/485566-chromosome-level- 11 F E D C B A