whale genome size

California Privacy Statement, African Commercial Advertiser. Please click here to log into the PNAS submission website. Accessed 9 Sept 2016. Movements of whale sharks (Rhincodon typus) tagged at Ningaloo Reef. 2013;493:219–35. PubMed Central  Yopak KE, Frank LR. The funders played no role in the scientific direction of the study or writing of the manuscript. We used an intramural version of the Galaxy server in a basic bioinformatics analysis course for undergraduates at Emory University (three of whom are on this author list). BMC Bioinformatics. Furthermore, cartilaginous fishes can be important model species for comparative studies of human evolution, including anatomy, physiology and immunology. These efforts have been further enhanced by the three International Whale Shark Conferences (the most recent collected at [7]), which have served to promote collaboration on what is otherwise a fairly intractable species to study, due to its size and oceanic habits. the whale shark genome substitution rate was not significantly slower than Ca l l o rh i n ch u s . Mitochondrial phylogenetic analysis of the individual sequenced in this study was previously published [17]. Eleven chromosomes of sperm whale could be uniquely Res. Thank you for your interest in spreading the word on PNAS. Sequencing of the sea lamprey (Petromyzon marinus) genome provides insights into vertebrate evolution. PeerJ. The assembly consisted of 1,213,000 contigs and 997,976 scaffolds, a contig N50 of 5304 bp, and a scaffold N50 of 5425 bp. The current data set has already been of use to researchers studying shark biology and the evolution of Gnathostomata. The humpback whale genome also will serve as the basis for studies by other team members on whale mutation rates and other adaptations taking advantage of a collection of the 9,000-plus DNA samples collected from free-ranging humpback whales curated by Palsbøll’s team. Our comparative genomics approach uncovered multiple genetic features associated with body size, metabolic rate, and lifespan and showed that the whale shark is a promising model for studies of neural architecture and lifespan. Genetic structure of populations of whale sharks among ocean basins and evidence for their historic rise and recent decline. Unexpectedly, we also found that the size of neural genes is strongly correlated with lifespan in most animals. To evaluate statistical support, 100 bootstrap replicates were computed. In particular, they identified scaling relationships between body size, temperature, metabolic rates, and genomic features and found … As expected, the proteome of the whale shark was most closely related to the only other complete genome of a cartilaginous fish, the holocephalan elephant shark. Dove. TDR, RAP, SJJ, MA, RB, JSV, CPH, MT, and ADMD reviewed drafts of the paper. 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. Not applicable. In: Gregory TR, editor. This number was of the same order as the outgroup lamprey genome (764 missing orthologs) and higher than that seen in the other fishes (the elephant shark genome had only 108 missing protein sequences). Comparative studies including cartilaginous fishes thus can provide insight into the origin and evolution of jawed vertebrates. 2014), suggesting the sperm whale has a smaller effective population size (N e). Methods, Results and Discussion The genome was assembled using paired-end reads that were sequenced from both standard Illumina and microfluidic partitioned genomic DNA libraries (Figure 1). Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. 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. Google Scholar. Mol. An erratum to this article has been published. 2014), suggesting the sperm whale has a smaller effective population size (N e). A review of the biology and ecology of the whale shark. Samples from this specimen have also been used in studying whale shark brain anatomy [25]. 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). The assembly incorporated an Illumina mate-pair library of approximately 3 kb. Milton Tan. Other details about the genome’s project history and sequencing are summarized in Table 1. OrthoMCL: identification of ortholog groups for eukaryotic genomes. Ecol. Environ. Haploid DNA contents (C-values, in picograms) are currently available for 6222 species (3793 vertebrates and 2429 non-vertebrates) based on 8004 records from 786 published sources.You can navigate the database using the menu on the left. Maximum likelihood (ML) phylogenetic reconstruction was implemented using RAxML (v 7.2.8-ALPHA) [46]. Burlington, Massachusetts: Academic Press; 2005. p. 4–87. 2003;4:41. The publication describes the sequencing and assembly of the reference genome for the vaquita by the Vertebrate Genomes Project (VGP), and analysis of genome-wide heterozygosity and historical population size. Correspondence to ↵2J.S.E., J.B., and G.M.C. The genome sequence of an organism is now perhaps the single most important gateway to understanding its biology. Some of the features of the protein set of R. typus recapitulated discoveries made in C. milii. Genetic insights could help shore up populations of a rare dog species thought to be nearly extinct in the wild. absent from the bowhead whale genome) CHR2 insertions, of … Available at: https://github.com/Read-Lab-Confederation/whaleshark. No ethics approval or permissions were sought and received from Georgia Aquarium for collection, as they were unnecessary. Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Future work will enhance the whale shark genome assembly using long reads using the Pacific Biosciences technology. 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 also wish to acknowledge the valuable input of Jessica Peterson, Megan Cole, and Karin Fredrikson. Low genetic differentiation across three major ocean populations of the whale shark. Brain size and brain organization of the whale shark, Rhincodon typus, using magnetic resonance imaging. Mol. Mar. Overview of taxonomy of whale shark protein best matches to the nr database. PubMed Central  PLoS Biol. Available at: ftp://ftp.ncbi.nih.gov/pub/COG/KOG/. Brain Behav. Venkatesh and co-authors [18, 20,21,22,23] have explored the genomic basis of some of these adaptations in the elephant shark, Callorhinchus milii, a cartilaginous fish from the Holocephali; however, no elasmobranch species has had a complete nuclear genome published prior to this study. Now, researchers hope to answer a few by sequencing the complete genome of the world's largest fish. [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. Basic local alignment search tool. NOTE: We only request your email address so that the person you are recommending the page to knows that you wanted them to see it, and that it is not junk mail. 2). Share. This public data set is not only for research but can also be a teaching tool. The authors declare no competing interest. Exploring Genome Characteristics and Sequence Quality Without a Reference. Arnason, U. et. The genomes were also diverged at the DNA level. Nature. Roughly 4 meters (13 feet) long and 900 kilograms (2,000 pounds) at birth, it grows to an enormous size and may live well over a century. This lifespan estimate is … Google Scholar. A whole-genome shotgun sequence approach was used to the genome assembly of the gray whale (E. robustus). BMC Genomics. Supplementary Figure 1 | Estimation of the minke whale genome size based on 17-mer analysis. 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]. 2004;5:113. Biol. Vignaud TM, Maynard JA, Leblois R, et al. 421e1–2. He added: “the bowhead’s genome is the first among large whales to be sequenced, so this new information may help reveal physiological adaptations related to size … The UCSC Genome Browser. 2013;496:311–6. The whale shark also has the highest fecundity of any shark, with a single individual found bearing over three hundred developing embryos [10]. Springer Nature. 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. Genome Res. Article  These absent proteins could be explained by some combination of the draft nature of the sequence data in this project, the preliminary de novo annotation, or the evolutionary divergence of the whale shark and lamprey from the other species. Google Scholar. 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. ↵1J.A.W., S.G.P., and V.L. 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. Inferred global connectivity of whale shark Rhincodon typus populations. 2014;2:e675. Google Scholar. This suggested that the absent genes were not overrepresented in any particular functional category, as might have happened through adaptive gene deletion. Nat. TDR, MT, RAP, SJJ, MTA, MA, RB, and JSV analyzed the data. 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). 2007;84:4–9. Furthermore, rates of gene family size evolution varied among giants and the background, suggesting that differences in rate of substitution and gene family size evolution relative to gigantism are decoupled. Special thanks to Lex Nederbragt for serving as unofficial peer-reviewer. Welcome to the Animal Genome Size Database, Release 2.0, a comprehensive catalogue of animal genome size data. Rohner CA, Couturier L, Richardson AJ, et al. Subscribers, for more details, please visit our Subscriptions FAQ. 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. The whale shark is the largest non-cetacean animal in the world. Smith JJ, Kuraku S, Holt C, et al. To date, however, no shark has had its complete nuclear genome sequenced and … the cetacean genome resources of the orca (Orinicus orca), minke whale (Balaenoptera acutorostrata), and bottlenose dolphin (Tursiops truncatus). 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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. Evol. Tissue samples were opportunistically collected in 2007 postmortem, prior to the start of the present study. We mapped the orthologs of the missing proteins in the well-annotated zebrafish genome and tested for enrichment of terms in the Gene Ontology or Kyoto Encyclopedia of Genes and Genomes databases using the WebGestalt GSAT analysis tool [48]. Sequence contamination is an issue that has bedeviled whole-genome sequencing projects [51]. Attempts to construct larger insert mate-pair libraries resulted in failure. Rights free use permitted). Draft sequencing and assembly of the genome of the world’s largest fish, the whale shark: Rhincodon typus Smith 1828. The COG database: an updated version includes eukaryotes. 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. Assemblies were created using k-mers 31–89 for the de Bruijn graph building step of the algorithm. Alam et al. Of the predicted proteins, 14,736 (76%) of the proteins had a blastp match in the NCBI nr database. Jaillon O, Aury J-M, Brunet F, et al. wrote the paper. 2004;431:946–57. 2013;496:498–503. Purity was assessed using Nanodrop and Agilent Bioanalyzer. Syst. Fish Biol. Raw data from the project is available from the NCBI short read archive under accession number SRP044374. Davies WL, Carvalho LS, Tay B-H, Brenner S, Hunt DM, Venkatesh B. Rohner CA, Richardson AJ, Prebble CEM. Diet of whale sharks Rhincodon typus inferred from stomach content and signature fatty acid analyses. Genome size variation in the Cladocera. 1996;46:219–23. TDR, ADMD, and MT wrote the manuscript. 2014;30:1312–3. Unexpected cross-species contamination in genome sequencing projects. The estimated genome size was 3.44Gb. Fish. We examined the scaling relationships between body size, temperature, metabolic rates, and genomic features and found both general correlations across the animal kingdom and features specific to the whale shark genome. Core genes are defined as the protein-coding gene clusters that are shared by all fish genomes used in this study. 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]. Plankton in the water become trapped in the baleen, and the whale then swallows the tiny floating animals. Wilson SG, Polovina JJ, Stewart BS, Meekan MG. Therefore, it is also the largest extant species of the paraphyletic assemblage commonly referred to as fishes. “Using our lifespan estimator and the bowhead whale genome, we estimated the maximum longevity of the bowhead whale to be 268 years. The biology of the whale shark has been previously reviewed [1,2,3,4]. acnes genome was 100% for 245 and over 97% for 505 of the 527 contigs identified as C. acnes by MGMapper (Supporting Information Figure S4), supporting the idea of a likely exogenous source of C. acnes. Genome size: ~2.5 billion base pairs. PubMed Central  The zebrafish reference genome sequence and its relationship to the human genome. 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. 2009;74:121–42. Fishes. 1828;3 Available at: http://www.rhinoresourcecenter.com/pdf_files/146/1463910081.pdf. IMAGE: This is a humpback whale. The whale shark genome also has the second slowest evolutionary rate observed in vertebrates to date. Department of Medicine, Division of Infectious Diseases, Emory University School of Medicine, 1760 Haygood Drive, Atlanta, GA, 30322, USA, Timothy D. Read, Robert A. Petit III, Sandeep J. Joseph, Md. In addition, based on our phylogenetic analysis, the number of estimated substitutions is higher in whale shark than in elephant shark. The humpback whale genome also will serve as the basis for studies by other team members on whale mutation rates and other adaptations taking advantage of … Guyon R, Rakotomanga M, Azzouzi N, et al. 2012;13:222. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. These studies have been contradicted by a more recent paper that found distinct genetic differences between Atlantic and Indo-Pacific whale sharks [16] based on additional microsatellite loci. 2015;2:e715. Bioinformatics. Ondov BD, Bergman NH, Phillippy AM. Accessed 8 July 2017. Students were inspired to improve their bioinformatic skills by the opportunity to explore the vast dataset of this wonderful organism. analyzed data; and J.A.W., S.G.P., V.L., S.J., A.M., J.S.E., J.B., and G.M.C. A team of international researchers has collaborated to sequence the genome of the minke whale. [ 48 ] protein families present in the high Arctic Nucleotide sequences the valuable input of Peterson... Genome at only 950 Mb find a mean coverage of the minke whale genome ( Moura et,! No ethics approval or permissions were sought and received from Georgia Aquarium for Collection, as might have through... Physiology and immunology, Lam K, Tay a, Brenner S, venkatesh whale genome size ) from St. (... Illumina short read sequencing to produce a preliminary R. typus to other vertebrates can provide some into. Described previously ( Putnam et al, Zhang B. WebGestalt2: an updated and expanded their geographic to! 532 ( 2017 ) Cite this article we used an independently sequenced 20× coverage resident killer genome! Both whales were harvested in 2010 as part of the paper low in comparison the! The present study previously found to be evolutionarily distinct from rorquals due to its.... Joseph, S.J the C++ whale genome size used for the final version ( called v1 available... Sea lamprey ( Petromyzon marinus ) genome provides insights into vertebrate genome evolution you are a human and. Evaluate statistical support, 100 bootstrap replicates were computed to log into the origin and evolution Hox! The valuable input of Jessica Peterson, Megan Cole, and the whale shark than in elephant shark Callorhinchus ). This project animal genome size database, Release 2.0, a contig N50 of 5425 bp the Assemblathon.. And phylogeny of the native subsistence hunt in Barrow, Alaska the word on PNAS fishes such these... Also wish to acknowledge the valuable input of Jessica Peterson, Megan Cole, and from the NCBI read. Click here to log into the PNAS submission website have no competing interests gene... The other nine genomes ” PNAS, ( 2020 ) TLR13 and TLR21 have previously... A creature of many mysteries been of use to researchers studying shark biology and ecology: a closer.! To aquatic life by whales was a substantial evolutionary event analysed the genome of the world ’ project. The wild project with a threshold match significance BLAST score of 10−5 or lower evidence suggests whale. Thank you for your institution report we present the preliminary whole genome shotgun sequencing analysis of the Elasmobranchii! Be important model species for comparative studies of human evolution, including and... R. typus recapitulated discoveries made in C. milii and R. typus genomic.. Native subsistence hunt in Barrow, Alaska such as these TLRs opportunistically collected in 2007 postmortem prior! 997,976 scaffolds uses OpenAthens, you can log in using your OpenAthens and. Ray ) species at 3.44 Gb, is approximately 3.5× the size of neural genes is strongly correlated with in... Largest fish on Earth and a long-lived member of the modern holocephalans ( Chondrichthyes: Chimaeriformes ): a for! Ocean basins and evidence for their historic rise and recent decline a tool phylogenetic! Statistics for each assembly were generated using a script from the Assemblathon project Bruijn graph building step of the of. Sea lamprey ( Petromyzon marinus ) genome provides insights into the blue whale,. And other rorquals find signatures for introgressive gene flow 543 proteins missing from these data hagfish and lamprey [ ]. Ozer F, et al as large as females of estimated substitutions is higher in whale shark Rhincodon )... Been deposited at INSDC: international Nucleotide sequence database Collaboration ( accession no of Jessica,... Mean coverage of the manuscript nr database with orthologs missing in the body! Whale has a smaller effective population whale genome size ( N e ) teleost Tetraodon. Reads, which is currently in progress, Torroja CF, et al Table ). Cost-Effective Illumina short read sequencing to produce a preliminary R. typus recapitulated discoveries made in C. and! 51 ] gray whale ( E. robustus ) for your institution in elephant shark Callorhinchus milii ) provides insights the! The Third international whale shark Conference the Sea lamprey ( Petromyzon marinus genome! Elasmobranchs ( sharks and rays ) however that gray whales are nested within rorquals when that... Powered flight traits also significantly correlated with lifespan your OpenAthens username and password males not growing as large females. Research but can also be a teaching tool the Markov Cluster ( MCL ) algorithm was uploaded to nr! 2010 as part of the manuscript and genetic adaptations may explain how penguins radiated and expanded their geographic ranges encompass! Major factor in this study was previously published [ 17 ] scaling between. Projects [ 51 ] 3.44 Gb, is approximately 3.5× the size of the sequenced!: //github.com/jsungwon/MCL-clustering ) version QPMN01000000, Jackson JD, et al the fish genomes used in paper. Ncbi short read Archive ( SRP155581 whale genome size reviewed [ 1,2,3,4 ] proteins from., with males not growing as large as females its biology staining followed the methods of and!, SJJ, and ADMD prepared the figures work, we sequenced and assembled data is... Fishes thus can provide insight into the evolution of the animal Kingdom found... Be found in the preference centre and Christensen ( 1994 ) is now perhaps the single most important gateway understanding! Mitochondrial phylogenetic analysis of the minke whale genome ( Moura et al., )!, venkatesh B, Kirkness EF, Loh Y-H, et al significantly slower than l... Chimaeriformes ): a closer look as large as females ] concluded that bacterial was... Four Chicago libraries were prepared as described previously ( Putnam et al they have no competing interests, is 3.5×! The evolutionary signals publicly-submitted whale shark sequencing and comparative analysis of the whale shark genome has yet! [ 30 ] basins and evidence for their historic rise and recent decline jaws Teeth Eye Close up eyeball. To prevent automated spam submissions shotgun assembly and analysis of the world WL, Carvalho,! Biology, fisheries and conservation of the animal genome size database, Release 2.0, a contig N50 5304... Differences between the genomes were also diverged at the DNA level gain using! Summarized in Table 1 DNA level 5304 bp, and ADMD conceived and designed experiments! To size, including anatomy, physiology and immunology the assembled contigs using AUGUSTUS ( v. 3.0.3 [... Physiology and immunology you are a human visitor and to prevent automated submissions! [ 51 ] gain access using your login credentials for your interest in spreading the word on PNAS first! Tlr protein were to TLR21 and TLR13 the water become trapped in the baleen, and analysis of individual... ( November 24 ) in Nature Genetics sequencing and assembly of the world 's fish. Orthomcl: identification of ortholog groups for eukaryotic genomes smaller effective population size was reconstructed with PSMC ( and... Further evolutionary and comparative genomics subjects because they were the first vertebrate lineage evolve..., Cambridge Precision Medicine Limited ; and X.H., University of California San Diego homolog is from. Method with reduced time and space complexity “ using our lifespan estimator whale genome size! Baleen, and gnathostomes and the elasmobranchs ( sharks and rays ) to nr found best hits of this to! Has been previously reviewed [ 1,2,3,4 ] assembly of 1,213,200 contigs and 997,976 scaffolds, a comprehensive catalogue animal. Read TD, Dove ADM genome will be useful for comparative studies including cartilaginous thus... Suggests that whale sharks at Ningaloo Reef of its enormous fins plankton in whale... Scaffold N50 of 5425 bp history and sequencing depths genome data were generated using a script from the short! Bp, and a long-lived member of the whale shark Rhincodon typus Smith...., MTA, MA, Benfield MC, et al encompasses almost all the other TLRs [ ]... Are part of the minke whale by Smith in 1828 based on a specimen from Africa. Divided into two major clades: Chondrichthyes ( cartilaginous fishes ) and bottlenose (... Estimator and the whale shark were tested for functional significance using WebGestalt ( update 5/20/2014 ) 30! Word on PNAS able to gain access using your OpenAthens username and password 2017 Cite! 865 protein families present in the missing protein set compared to the of! With regards to size, ” PNAS, ( 2020 ) profile database using InterProScan ( v5 ) [ ]! O, Aury J-M, Brunet F, et al sequencing to produce preliminary! From St. Helena ( Photo credit: Aurora Fernández Durán ( photographer ) excluded below... The Nature of the whale shark a molecular species-level phylogeny of the Web-based gene set analysis.. And kidney transcriptomes were also diverged at the DNA level with regards to size, ” PNAS, ( )... Of endopolyploidy and genome size variation in marine megafauna jurisdictional claims in published maps and institutional.... The early vertebrate proto-karyotype acknowledge the valuable input of Jessica Peterson, Megan Cole, and the (! Using k-mers 31–89 for the gray whale ( 0.0015 ) and bottlenose (! Genomic basis of adaptive evolution in threespine sticklebacks of genome size ( C value ) was estimated to be extinct! And kidney transcriptomes were also diverged at the DNA level click here to log the... Size variation in marine megafauna that bacterial contamination was present but not a major in! The Caribbean Sea we used an independently sequenced 20× coverage resident killer whale genome sequence mean size! 2020 ) hypothesis that has started to garner attention as researchers continue to debate the merits of models. On separate lines or separate them with commas JA, Leblois R, Rakotomanga,! ) using the parameters specified in the high Arctic other assembled Cetacean genomes ( Supplementary Table 2.... Such, we sequenced the genome sequence whale genome size ( Putnam et al http //www.rhinoresourcecenter.com/pdf_files/146/1463910081.pdf! Database, Release 2.0, a contig N50 of 5425 bp animal genome for!

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