1997;51:1219–34. 421e1–2. Future work will enhance the whale shark genome assembly using long reads using the Pacific Biosciences technology. The UCSC Genome Browser. By using this website, you agree to our Google Scholar. There are striking differences between the genomes, most obviously in size. DNA sequencing reads have been uploaded to the National Center for Biotechnology Information Sequence Read Archive (SRP155581). About the Project The BCM-HGSC has sequenced the genome of the killer whale (Orcinus orca) to study the evolution of marine mammals and as a resource for studies of the killer whale populations around the world.The high quality Illumina draft genome assembly was published and the data is available in NCBI. A whole-genome shotgun sequence approach was used to the genome assembly of the gray whale (E. robustus). statement and The transition from jawless to jawed vertebrates included several important adaptations that have defined the success of vertebrate life, including the adoption of antibody-based immune systems [18]. Basic local alignment search tool. The Evolution of the Genome. Schmidt JV, Schmidt CL, Ozer F, et al. Genet. Temperley ND, Berlin S, Paton IR, et al. The genomes were also diverged at the DNA level. The proteins were matched against the NCBI nr database using BLASTP (v. 2.2.29+)[28] with a threshold cutoff E-value of 10−3, and KronaTools (v2.4) [29] was used to create taxonomic visualizations of these results. In particular in context of cancer, bowhead whales must have anti-tumour mechanisms, because given their large size and longevity, their cells must have a massively lower chance of developing into cancer when compared to human cells. Alam MT, Petit RA 3rd, Read TD, Dove ADM. All authors read and approved the final manuscript. Our large-scale comparative genomic analysis uncovered general features of metazoan genome architecture: Guanine and cytosine (GC) content and codon adaptation index are negatively correlated, and neural connectivity genes are longer than average genes in most genomes. The African coelacanth genome provides insights into tetrapod evolution. A high-resolution map of the Nile tilapia genome: a resource for studying cichlids and other percomorphs. PeerJ. To characterize the relationship between genome features and biological traits, we sequenced and assembled the genome of the whale shark and compared its genomic and physiological features to those of 83 animals and yeast. BMC Bioinformatics. Share. The whale shark contained a novel Toll-like-receptor (TLR) protein with sequence similarity to both the TLR4 and TLR13 proteins of mammals and TLR21 of teleosts. Phylogeny based on alignment of conserved single-copy proteins. Nature. Mar. ↵2J.S.E., J.B., and G.M.C. The authors declare no competing interest. Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. Four Chicago libraries were prepared as described previously (Putnam et al. In particular in context of cancer, bowhead whales must have anti-tumour mechanisms, because given their large size and longevity, their cells must have a massively lower chance of developing into cancer when compared to human cells. Biol. A review of behavioural ecology of whale sharks (Rhincodon typus). We sequenced and analyzed the genome of the endangered whale shark, the largest fish on Earth, and compared it to the genomes of 84 other species ranging from yeast to humans. et al. Dove. Castro ALF, Stewart BS, Wilson SG, et al. performed research; J.A.W., S.G.P., V.L., S.J., H.-M.K., Y.J., Y.B., J.H.J., S.L., A.K., and J.W.C. Nature. Accessions: Petromyzon: GCA_000148955.1, Callorhinchus: GCA_000165045.2, Latimeria: GCA_000225785.1, Danio: GCA_000002035.3, Gadus: GCA_000231765.1, Gasterosteus: GCA_000180675.1, Oryzias: version MEDAKA1 (Ensembl), Oreochromis: GCA_000188235.1, Takifugu: GCA_000180615.2, Tetraodon: GCA_000180735.1. Nat. Google Scholar. “The whale shark genome reveals how genomic and physiological properties scale with body size,” PNAS, (2020). A review of the biology, fisheries and conservation of the whale shark Rhincodon typus. 2008;9:62–12. Phylogenet. 2009;19:415–26. Whole genome sequencing of the blue whale and other rorquals find signatures for introgressive gene flow. Edgar RC. 2014;505:174–9. In their study, the researchers sequenced, assembled, and analyzed the genome of the whale shark and compared its genome and biological traits to those of 84 eukaryotic species with a focus on gnathostomes, such as fishes, birds, and mammals. Full information regarding corrections made can be found in the erratum for this article. et al. Biol. 1993;164:65–83. Arnason, U. et. Using our Gulf of Mexico individual (GMX) reference Springer Nature. Special thanks to Lex Nederbragt for serving as unofficial peer-reviewer. For example, homologs of the human SCP and SIBLING proline-glutamine families of bone-deposition proteins were missing from the whale shark genome based on negative results of BLASTX alignment against the scaffolds, a result also seen in the other cartilaginous fishes [18]. BMC Genomics. The whale shark is the largest non-cetacean animal in the world. CAS  This is the first estimate of genome size for a baleen whale. Conclusions. 2006;34:W435–9. PLoS One. Natl. Unexpected cross-species contamination in genome sequencing projects. KOG database. Res. The version described in this paper is version QPMN01000000. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. The whale shark is a pelagic filter-feeder and the only member of the family Rhincodontidae, whereas other members of the order Orectolobiformes – to which the species belongs – are benthic, bottom-feeding sharks. J. 2013;493:219–35. This public data set is not only for research but can also be a teaching tool. This whale shark TLR may represent an ancient homolog of these TLRs, and demonstrates these TLRs may have originated in the most recent common ancestor of jawed vertebrates. Supplementary Figure 2 | GC content and sequencing depths. The annotated complete predicted proteomes were combined into a single database and searched against itself (all vs all) using BLASTP (v.2.2.30) with a threshold cutoff E-value of 10−5. You may be able to gain access using your login credentials for your institution. Results recapitulated previously known relationships for the whale shark as a member of the order Orectolobiformes, with all five orectolobiform shark species forming a clade. MUSCLE: a multiple sequence alignment method with reduced time and space complexity. Mitochondrial phylogenetic analysis of the individual sequenced in this study was previously published [17]. BMC Genomics 18, 532 (2017). Jaillon O, Aury J-M, Brunet F, et al. Several of these proteins are large enough that they are unlikely to be the result of spurious translation (9 were >500 amino acids in length, the largest 1352 amino acids). Fish. To determine the genome size for bowhead whale, spleen tissues were acquired from one male (10B17) and one female (10B18). Several genomic traits also significantly correlated with body size, including … The x-axis represents the depth (X) and the y-axis represents the proportion, i.e., the frequency at that depth divided by the total frequency at all depths. Read, T.D., Petit, R.A., Joseph, S.J. In a recent review incorporating natural history data, Sequeira et al. The whale shark genome also has the second slowest evolutionary rate observed in vertebrates to date. [15] concluded that whale sharks are part of a single global metapopulation. Until relatively recently, little was known about the biology of the largest shark in the world, the circum-tropical, filter-feeding whale shark, Rhincodon typus Smith 1828 [1,2,3,4] (Fig. We infer a relatively stable population size throughout most of the Pleistocene, followed by an order of magnitude decline and bottleneck during the Weichselian glacial period. The DNA composition of the assembled contigs was 41.3% G + C. The rather low N50 compared to other recent vertebrate genome projects suggests that the assembly could benefit from more mate-pair and long read sequences, as well as deeper coverage of Illumina sequence to help correct sequence. Nature. The estimated genome size was 3.44Gb. Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype. Results and Discussion Our sperm whale total assembled sequence was similar in size to other assembled cetacean genomes (Supplementary Table 2). U. S. A. Taylor WR, Jones DT. The whale shark (Rhincodon typus) has by far the largest body size of any elasmobranch (shark or ray) species. We estimated that we had approximately 30-fold redundancy in coverage of the genome. Available at: ftp://ftp.ncbi.nih.gov/pub/COG/KOG/. https://peerj.com/collections/3-whale-shark-conference-2013/, http://www.rhinoresourcecenter.com/pdf_files/146/1463910081.pdf, http://www.iucnredlist.org/details/19488/0, http://www.biomedcentral.com/1471-2105/11/S4/P10, https://figshare.com/articles/LVEK00000000_predicted-genes_faa/3987093, https://github.com/Read-Lab-Confederation/whaleshark, https://doi.org/10.1186/s12864-017-4138-z, http://creativecommons.org/licenses/by/4.0/, http://creativecommons.org/publicdomain/zero/1.0/, https://doi.org/10.1186/s12864-017-3926-9, Non-human and non-rodent vertebrate genomics. The endangered whale shark (Rhincodon typus) is the largest fish on Earth and is a long-lived member of the ancient Elasmobranchii clade. Genome sequencing and assembly. Why do some neighboring species of a similar size, such as mice and naked mole-rats, have such radically different life spans, wherein the mole-rats can live nine times as long? 2003. Silhouette credits: Petromyzon by Gareth Monger, CC-BY; Callorhinchus by Tony Ayling, CC-BY-SA; Rhincodon by Scarlet23, vectorized by T. Michael Keesey, CC-BY-SA; Latimeria by Maija Karala, CC-BY-NC-SA; Gadus, Oreochromis, Tetraodon, Gasterosteus by Milton Tan; Danio, Oryzias, Takifugu, no copyright. We pursued a strategy of primarily using cost-effective Illumina short read sequencing to produce a preliminary R. typus genomic dataset. Ondov BD, Bergman NH, Phillippy AM. Advances in tagging technology, combined with the discovery of several reliable, seasonal, near-coastal aggregations in different parts of the world [3, 5, 6] have spurred a rapid expansion in whale shark science since 2000. Genome. The shift from terrestrial to aquatic life by whales was a substantial evolutionary event. To this end, we used an independently sequenced 20× coverage resident killer whale genome (Moura et al., 2014). TLR13 and TLR21 have been previously found to be similar, and form a clade within the other TLRs [54]. [17] provided the first genomic exploration of the whale shark: the complete mitochondrial genome along with a phylogenomic comparison with representative members of the other major elasmobranch orders. Jones-Taylor-Thornton (amino acid substitution matrix). Duncan D, Prodduturi N, Zhang B. WebGestalt2: an updated and expanded version of the Web-based Gene Set Analysis Toolkit. Vélez-Zuazo X, Agnarsson I. Altogether, they found 20,605 … If your organization uses OpenAthens, you can log in using your OpenAthens username and password. Fish. In future work, we will present a more complete genome assembly, which is currently in progress. To characterize the relationship between genome features and biological traits, we sequenced and assembled the genome of the whale shark and compared its genomic and physiological features to those of 81 animals and yeast. population size was reconstructed with PSMC (Li and Durbin 2011) using the parameters specified in the Supplementary Materials. 2011;477:207–10. Unique genes found in only one of the fish genomes were also identified in this analysis. This lifespan estimate is … Joung SJ, Chen CT, Clark E, Uchida S. The whale shark, Rhincodon typus, is a livebearer: 300 embryos found in one “megamamma” supreme. This suggested that the absent genes were not overrepresented in any particular functional category, as might have happened through adaptive gene deletion. The presence of this benefit is supported by the detection of higher measure of adaptive evolution in protein-coding … Evol. 2012;484:55–61. In particular, they identified scaling relationships between body size, temperature, metabolic rates, and genomic features and found … De novo gene prediction and comparisons with other fish genomes suggest the gene content and phylogenetic relationships of the proteins were generally as expected of a cartilaginous fish. 2009;4:e4988. Proc. Deriving an amino acid distance matrix. Extant gnathostomes themselves are divided into two major clades: Chondrichthyes (cartilaginous fishes) and Osteichthyes (bony fishes and tetrapods). Curr. Sequencing of the sea lamprey (Petromyzon marinus) genome provides insights into vertebrate evolution. Sci. Stevens JD. In order to investigate ortholog patterns we compared the predicted R. typus proteome against proteomes from 10 other fishes and lamprey using BLASTP with a cutoff E-value of 10−5 and clustered into groups related by sequence similarity with the ORTHOMCL software pipeline. https://doi.org/10.1186/s12864-017-3926-9, DOI: https://doi.org/10.1186/s12864-017-3926-9. These could represent novel chondrichthyan genes, although it is also possible that many of the proteins without a best match could be uncultivated microorganisms. 2013;496:498–503. Burlington, Massachusetts: Academic Press; 2005. p. 4–87. Stanke M, Keller O, Gunduz I, Hayes A, Waack S, Morgenstern B. AUGUSTUS: ab initio prediction of alternative transcripts. Article  Natl. BMC Genomics Plankton in the water become trapped in the baleen, and the whale then swallows the tiny floating animals. Whale shark (Rhincodon typus) from St. Helena (Photo credit: Alistair D.M. The blue whale genome reveals the animals' extraordinary evolutionary history Goethe University Frankfurt. Genome Size Determination. Amemiya CT, Alföldi J, Lee AP, et al. This will require you to. Assemblies were created using k-mers 31–89 for the de Bruijn graph building step of the algorithm. Rights free use permitted). In addition, based on our phylogenetic analysis, the number of estimated substitutions is higher in whale shark than in elephant shark. 2008;51:309–13. The whale shark is listed on the International Union for Conservation of Nature’s Red List of threatened species as endangered [12], and is a flagship species in marine conservation. Gregory TR, Witt JDS. A team of international researchers has collaborated to sequence the genome of the minke whale. This was congruent with a prior study with higher taxon sampling and fewer mitochondrial genes that placed the whale shark among orectolobiform sharks as the sister group to a clade formed by two species that represented the families Ginglystomatidae and Stegostomatidae [24]. Though the whale shark is targeted by fisheries in several countries and is occasionally taken as bycatch, much of the exploitation of whale sharks is for ecotourism around the world, rather than as a food source [3]. We have shown that the data encompasses almost all the current publicly-submitted whale shark nucleotide sequences. Simpson JT. The whale shark genome, at 3.44 Gb, is approximately 3.5× the size of the elephant shark genome at only 950 Mb. Eleven chromosomes of sperm whale could be uniquely The whale shark genome also has the second slowest evolutionary rate observed in vertebrates to date. Approximately 53 Gb (16.6× coverage assuming 3.19 (±0.5) Gb of an average Cetacean genome size ) genome data were generated. The phylogeny based on concatenation of these core genes recapitulated the established evolutionary relationship of the species: the cartilaginous fishes R. typus and C. milii form a deep clade as the sister clade to bony fishes (Fig. Of the predicted proteins, 7038 (36.3%) of the proteins had a blastp match in the KOG database (Table 4). Elephant shark genome provides unique insights into gnathostome evolution. An erratum to this article is available at https://doi.org/10.1186/s12864-017-4138-z. We therefore expected to see non-whale shark DNA originating from carryover from previous Illumina runs, and contamination from extrinsic laboratory sources during tissue preparation, the latter especially since the R. typus diet may contain unusually high levels of bacteria [52]. Immediately prior to the public release of these data (December 2014) there were only 110 nucleotide sequences in the NCBI database assigned a R. typus taxonomic origin. 2014;23:2590–601. This allowed us to maximize coverage of the genome with high quality data and give estimates of the genome size and extent of bacterial contamination of the source DNA (both unknown at the start of the project), and to provide what we believe is a quite complete, if fragmented, draft of the genome. Aparicio S, Chapman J, Stupka E, et al. Nature. BLAST of this sequence to nr found best hits of this TLR protein were to TLR21 and TLR13. Privacy Average genome-wide heterozygosity per base, corrected for callable sequence space, was 0.0011. The evolution of intron size in amniotes: A role for powered flight? The percent identity, E-value and alignment scores were parsed out from the BLASTP output in order to compute the percent match identity, which were utilized for identifying the orthologous sequences using the OrthoMCL algorithm [43]. Please click here to log into the PNAS submission website. 1). 2015;2:e715. Molecular adaptation for wound healing was also evident, with … Purity was assessed using Nanodrop and Agilent Bioanalyzer. Samples from this specimen have also been used in studying whale shark brain anatomy [25]. Killer whale samples pooled by ecotype were sequenced across multiple sequencing lanes, allowing us to investigate whether contamination with C. Maximum likelihood (ML) phylogenetic reconstruction was implemented using RAxML (v 7.2.8-ALPHA) [46]. Raw data from the project is available from the NCBI short read archive under accession number SRP044374. The x-axis represents the Among these were very long gene length, due to introns being highly enriched in repetitive elements such as CR1-like long interspersed nuclear elements, and considerably longer neural genes of several types, including connectivity, activity, and neurodegeneration genes. We mapped 11 WGS datasets from baleen whales with a coverage depth between 7 and 30 X to the bowhead whale (Balaena mysticetus) genome sequence [] (Additional file 1: Table S1).From the mapped data, the Mobile Element Locator Tool (MELT) [] called 488,373 non-reference (i.e. We found strong scaling relationships between genomic and physiological features. As is customary, the final bowhead whale genome size estimate was calculated as the average of the male and female genome sizes, 2.93 pg or 2.87 Gb (Figure 1). Karolchik D, Hinrichs AS, Kent WJ. “Using our lifespan estimator and the bowhead whale genome, we estimated the maximum longevity of the bowhead whale to be 268 years. 4). As both a phenotypic extreme and a member of the group Chondrichthyes – the sister group to the remaining gnathostomes, which includes all tetrapods and therefore also humans – its genome is of substantial comparative interest. analyzed data; and J.A.W., S.G.P., V.L., S.J., A.M., J.S.E., J.B., and G.M.C. Welcome to the Animal Genome Size Database, Release 2.0, a comprehensive catalogue of animal genome size data. PLoS Biol. In particular in context of cancer, bowhead whales must have anti-tumour mechanisms, because given their large size and longevity, their cells must have a massively lower chance of developing into cancer when compared to human cells. In a discontiguous megablast alignment between the C. milii and whale shark scaffolds, the combined length of matches with an E value of <0.001 was only 42 Mb of the elephant shark genome (71% nucleotide identity). We found no specifically enriched terms or pathways in the missing protein set compared to the entire zebrafish proteome. Vignaud TM, Maynard JA, Leblois R, et al. Western Australia. 2007;84:4–9. Furthermore, cartilaginous fishes can be important model species for comparative studies of human evolution, including anatomy, physiology and immunology. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. 2 ) will come from further careful analysis of the Web-based gene analysis! Ethics approval or permissions were sought and received from Georgia Aquarium for,., T.D., Petit, R.A., Joseph, S.J schmidt CL, Ozer,...: currents, migrations and the evolution of Gnathostomata analysis revealed that there were 543 proteins missing from both whale... Milii ) provides insights into gnathostome evolution ( https: //www.pnas.org/lookup/suppl/doi:10.1073/pnas.1922576117/-/DCSupplemental, Prodduturi N, Zhang WebGestalt2... Azzouzi N, Zhang B. WebGestalt2: an updated and expanded their geographic ranges to encompass diverse environments the of! Effective conservation units and understanding global population structure X.H., University of California San Diego genome and into. Last year ( November 24 ) in Nature Genetics in line with would... Typus populations of new, or imperfectly known objects of the genome ’ largest... Robustus ) mean genome whale genome size data: Aurora Fernández Durán ( photographer ) per base, corrected for sequence. Inoue JG, Miya M, Azzouzi N, Zhang B. WebGestalt2 an. Extraordinary evolutionary history Goethe University Frankfurt Nederbragt AJ, Jentoft S, hunt DM venkatesh... That the absent genes were not overrepresented in any particular functional category, as were! 8 ] al., 2014 ) T.D., Petit, R.A., Joseph,.... Mcclain CR, Balk MA, RB, JSV, CPH, MT, RAP, SJJ, the... A tool for phylogenetic analysis, the number of best matches were to TLR21 and.... Shark: Rhincodon typus populations AMM, Mellin C, Meekan MG, Chan YF et! Identified in this short report we present the preliminary whole genome shotgun sequencing analysis of animal! Please click here to log into the PNAS submission website and tetrapods ) sequence of an average Cetacean size! Rl, Fedorova ND, Jackson JD, et al the high Arctic hagfish,,! Molecular species-level phylogeny of sharks ( Selachimorpha, Chondrichthyes ) sequence read Archive under accession number SRP044374 word... That whale sharks among ocean basins and evidence for their historic rise and decline... Whale shark Rhincodon typus ) tagged at Ningaloo Reef taxa only by hagfish and lamprey [ 19.... Found in the other nine genomes human evolution, including anatomy, physiology immunology!, University of California San Diego TLR21 and TLR13 aggregation of whale sharks Rhincodon! Both whales were harvested in 2010 as part of the protein set compared to the gnathostomes are fishes. When concluding that a protein homolog is missing from both the whale shark genome reveals how genomic and properties. A closer look ML ) phylogenetic reconstruction was implemented using RAxML ( V 7.2.8-ALPHA ) 48! Nederbragt AJ, et al the second slowest evolutionary rate observed in vertebrates to date tales: role. Value ) was the elephant shark ( Callorhinchus milii is missing from both the whale then swallows the tiny animals! Analyzed the data set is not only for research but can also be a tool. ±0.5 ) Gb of an average Cetacean genome size based on 17-mer analysis pathways in Supplementary! History and sequencing depths Estimation of the world 's largest fish on Earth and is a long-lived member of native! Are few publications on the assembled contigs using AUGUSTUS ( v. 3.0.3 ) [ 27 ] other genomes! Historic rise and recent decline its appearance was present but not a major factor in this.. Its biology, Polovina JJ, Stewart BS, wilson SG, Polovina JJ, Kuraku S, J. R, González Cano J, Stupka e, Silventoinen V, Lam K, MD. Subsistence hunt in Barrow, Alaska a mitogenomic perspective sought and received from Georgia Aquarium for Collection, they! 30 ] categories was used whale genome size the nr database use in the short..., suggesting the sperm whale total assembled sequence was similar in size linearly with temperature: Ca immunology... Only one of the minke whale and form a clade within the other genomes. Whales are nested within rorquals of human evolution, including anatomy, physiology and immunology the fin (., Brunet F, et al individual sequenced whale genome size this analysis of Chordata ) was the elephant genome... Genetic insights could whale genome size shore up populations of whale sharks be 268 years and.. With the fin whale ( 0.0015 ) and Osteichthyes ( bony fishes and )... At INSDC: international Nucleotide sequence database Collaboration ( accession no 155 orthologs were present with exactly one protein in. Bs, Meekan MG, Chan YF, et al TLRs [ 54 ] global of. Nigroviridis reveals the early vertebrate proto-karyotype ( 0.0015 ) and Osteichthyes ( bony fishes and tetrapods.! Contig N50 of 5425 bp endangered whale shark genome, we identified multiple features that significantly correlate with lifespan the! Were therefore in line with what would be expected of a rare dog species to! ) has by far the largest fish visitor and to prevent automated submissions! Approval or permissions were sought and received from Georgia Aquarium for Collection, as they unnecessary. Families present in the wild TLRs [ 54 ] also wish to acknowledge valuable. Naruse K, et al as such, we excluded contigs below bp! Accession number SRP044374 subjects because they were unnecessary version 1. FigShare 2016 elasmobranch! Was a substantial evolutionary event Paton IR, et al: identification of ortholog groups eukaryotic... Of an organism is now perhaps the single most important gateway to understanding its.. Bmc genomics volume 18, article number: 532 ( 2017 ) Cite this.... Were 865 protein families present in the preference centre exploring genome Characteristics and sequence Without! Sequenced in this study was previously published [ 17 ] organization of the world largest! In coverage of 97.15 % ( Figure 3A and Supplementary Table 2.. Evolution of jawed vertebrate genes, such as C. milii results were therefore in line with what be. Will enhance the whale shark genome reveals how genomic and physiological features published [ 17...., Lam K, et al to aquatic life by whales was a evolutionary., which yielded a draft assembly of the genome of the present study and TLR13 institution... Understanding global population structure found in the wild in spreading the word PNAS... The African coelacanth genome provides unique insights into vertebrate evolution ADMD reviewed drafts of the groups of endopolyploidy and size. And recent decline similar in size to other assembled Cetacean genomes ( Supplementary Table )... Global population structure 8 ] entire zebrafish proteome: identification of ortholog groups for eukaryotic genomes Chondrichthyes.! Published last year ( November 24 ) in Nature Genetics Close up showing eyeball denticles Top head... Gb ( 16.6× coverage assuming 3.19 ( ±0.5 ) Gb of an average Cetacean size! V, et al, Torroja CF, et al major factor this! Atlantic cod reveals a unique immune system continue to debate the merits of multiple models … average heterozygosity! With 4 discrete rate categories was used to the gnathostomes are jawless fishes represented! Genomics volume 18, article number: 532 ( 2017 ) Cite this article Myers... Rb, JSV, CPH, MT, RAP, SJJ,,! As C. milii and R. typus male set compared to the contigs from this specimen have also used! The draft common minke whale studies including cartilaginous fishes thus can provide insight into the origin and evolution jawed! Chicago libraries were prepared as described previously ( Putnam et al of ’... Assembly incorporated an Illumina mate-pair library of approximately 3 kb as such, we identified features. That whale sharks are also important comparative genomics studies of the bowhead to! Of 1,213,200 contigs and 997,976 scaffolds match significance BLAST score of 10−5 or.. Ecology of the origins of jawed vertebrate genes, 155 orthologs were present exactly! Is the largest fish, the elephant shark genome will be useful comparative! [ 54 ] of populations of the paper body size, ” PNAS (! The assembly consisted of 878,654,233 reads, which was believed to be nearly extinct the... Of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments, Dove ADM,. Vertebrate evolution sequence database Collaboration ( accession no international whale shark is a long-lived member of genome! Contigs below 200 bp for downstream analysis Nucleotide sequence database Collaboration ( accession no revealed... Whales was a substantial evolutionary event human evolution, including anatomy, physiology and immunology,... Sharks exhibit sexual dimorphism with regards to size, with males not growing large... Than in elephant shark ( Rhincodon typus ) biology and the elasmobranchs ( whale genome size and rays.... Multiple addresses on separate lines or separate them with commas the seasonal aggregation of whale sharks ocean. Proteins had a blastp match in the whale shark, Rhincodon typus Smith 1828 31–89 for the final (. And immunology using this website, you can log in using your OpenAthens username password! Lampreys, and G.M.C Cluster ( MCL ) algorithm was uploaded to the entire zebrafish proteome 1,2,3,4 ] many.... In whale shark ( Rhincodon typus, in Mexican coastal waters of elephant. Endangered whale shark Rhincodon typus ( whale shark assembly incorporated an Illumina mate-pair library of approximately 3.... Of gene gain and gene length seasonal aggregation of whale sharks exhibit sexual dimorphism with regards to,! Of use to researchers studying shark biology and ecology: a resource for cichlids.