Characterization of the heart transcriptome of the white shark (Carcharodoncarcharias)

Vincent P. Richards, Haruo Suzuki, Michael J. Stanhope, Mahmood S. Shivji

Research output: Contribution to journalArticle

17 Citations (Scopus)

Abstract

Background: The white shark (Carcharodon carcharias) is a globally distributed,apex predator possessing physical, physiological, and behavioral traits thathave garnered it significant public attention. In addition to interest inthe genetic basis of its form and function, as a representative of theoldest extant jawed vertebrate lineage, white sharks are also ofconservation concern due to their small population size and threat fromoverfishing. Despite this, surprisingly little is known about the biology ofwhite sharks, and genomic resources are unavailable. To address thisdeficit, we combined Roche-454 and Illumina sequencing technologies tocharacterize the first transciptome of any tissue for this species. Results: From white shark heart cDNA we generated 665,399 Roche 454 reads (medianlength 387-bp) that were assembled into 141,626 contigs (mean length503-bp). We also generated 78,566,588 Illumina reads, which we aligned tothe 454 contigs producing 105,014 454/Illumina consensus sequences. Tothese, we added 3,432 non-singleton 454 contigs. By comparing thesesequences to the UniProtKB/Swiss-Prot database we were able to annotate21,019 translated open reading frames (ORFs) of ≥ 20 amino acids. Ofthese, 19,277 were additionally assigned Gene Ontology (GO) functionalannotations. While acknowledging the limitations of our single tissuetranscriptome, Fisher tests showed the white shark transcriptome to besignificantly enriched for numerous metabolic GO terms compared to the zebrafish and human transcriptomes, with white shark showing more similarity tohuman than to zebra fish (i.e. fewer terms were significantly different). Wealso compared the transcriptome to other available elasmobranch sequences,for signatures of positive selection and identified several genes ofputative adaptive significance on the white shark lineage. The white sharktranscriptome also contained 8,404 microsatellites (dinucleotide,trinucleotide, or tetranucleotide motifs ≥ five perfect repeats).Detailed characterization of these microsatellites showed that ORFs withtrinucleotide repeats, were significantly enriched for transcriptionregulatory roles and that trinucleotide frequency within ORFs was lower thanfor a wide range of taxonomic groups including other vertebrates.Conclusion: The white shark heart transcriptome represents a valuable resource for futureelasmobranch functional and comparative genomic studies, as well as forpopulation and other biological studies vital for effective conservation ofthis globally vulnerable species.

Original languageEnglish
Article number697
JournalBMC Genomics
Volume14
Issue number1
DOIs
Publication statusPublished - 2013 Oct 11
Externally publishedYes

Fingerprint

Sharks
Transcriptome
Open Reading Frames
Gene Ontology
Zebrafish
Microsatellite Repeats
Vertebrates
Elasmobranchii
Consensus Sequence
Population Density
Complementary DNA
Databases
Technology
Amino Acids

Keywords

  • Carcharodon carcharias
  • Enrichment
  • Heart transcriptome
  • Microsatellites
  • Positive selection
  • White shark

ASJC Scopus subject areas

  • Biotechnology
  • Genetics
  • Medicine(all)

Cite this

Characterization of the heart transcriptome of the white shark (Carcharodoncarcharias). / Richards, Vincent P.; Suzuki, Haruo; Stanhope, Michael J.; Shivji, Mahmood S.

In: BMC Genomics, Vol. 14, No. 1, 697, 11.10.2013.

Research output: Contribution to journalArticle

Richards, Vincent P. ; Suzuki, Haruo ; Stanhope, Michael J. ; Shivji, Mahmood S. / Characterization of the heart transcriptome of the white shark (Carcharodoncarcharias). In: BMC Genomics. 2013 ; Vol. 14, No. 1.
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