Sequencing and analysis of full-length cDNAs, 5'-ESTs and 3'-ESTs from a cartilaginous fish, the elephant shark (Callorhinchus milii).

Handle URI:
http://hdl.handle.net/10754/303148
Title:
Sequencing and analysis of full-length cDNAs, 5'-ESTs and 3'-ESTs from a cartilaginous fish, the elephant shark (Callorhinchus milii).
Authors:
Brenner, Sydney; Kodzius, Rimantas ( 0000-0001-9417-8894 ) ; Tan, Yue Ying; Tay, Alice; Tay, Boon-Hui; Venkatesh, Byrappa
Abstract:
Cartilaginous fishes are the most ancient group of living jawed vertebrates (gnathostomes) and are, therefore, an important reference group for understanding the evolution of vertebrates. The elephant shark (Callorhinchus milii), a holocephalan cartilaginous fish, has been identified as a model cartilaginous fish genome because of its compact genome (∼910 Mb) and a genome project has been initiated to obtain its whole genome sequence. In this study, we have generated and sequenced full-length enriched cDNA libraries of the elephant shark using the 'oligo-capping' method and Sanger sequencing. A total of 6,778 full-length protein-coding cDNA and 10,701 full-length noncoding cDNA were sequenced from six tissues (gills, intestine, kidney, liver, spleen, and testis) of the elephant shark. Analysis of their polyadenylation signals showed that polyadenylation usage in elephant shark is similar to that in mammals. Furthermore, both coding and noncoding transcripts of the elephant shark use the same proportion of canonical polyadenylation sites. Besides BLASTX searches, protein-coding transcripts were annotated by Gene Ontology, InterPro domain, and KEGG pathway analyses. By comparing elephant shark genes to bony vertebrate genes, we identified several ancient genes present in elephant shark but differentially lost in tetrapods or teleosts. Only ∼6% of elephant shark noncoding cDNA showed similarity to known noncoding RNAs (ncRNAs). The rest are either highly divergent ncRNAs or novel ncRNAs. In addition to full-length transcripts, 30,375 5'-ESTs and 41,317 3'-ESTs were sequenced and annotated. The clones and transcripts generated in this study are valuable resources for annotating transcription start sites, exon-intron boundaries, and UTRs of genes in the elephant shark genome, and for the functional characterization of protein sequences. These resources will also be useful for annotating genes in other cartilaginous fishes whose genomes have been targeted for whole genome sequencing.
KAUST Department:
Computational Bioscience Research Center (CBRC)
Citation:
Tan YY, Kodzius R, Tay B-H, Tay A, Brenner S, et al. (2012) Sequencing and Analysis of Full-Length cDNAs, 5--ESTs and 3--ESTs from a Cartilaginous Fish, the Elephant Shark (Callorhinchus milii). PLoS ONE 7: e47174. doi:10.1371/journal.pone.0047174.
Publisher:
Public Library of Science (PLoS)
Journal:
PLoS ONE
Issue Date:
8-Oct-2012
DOI:
10.1371/journal.pone.0047174
PubMed ID:
23056606
PubMed Central ID:
PMC3466250
Type:
Article
ISSN:
1932-6203
Sponsors:
Biomedical Research Council of A*STAR, Singapore
Appears in Collections:
Articles; Computational Bioscience Research Center (CBRC)

Full metadata record

DC FieldValue Language
dc.contributor.authorBrenner, Sydneyen
dc.contributor.authorKodzius, Rimantasen
dc.contributor.authorTan, Yue Yingen
dc.contributor.authorTay, Aliceen
dc.contributor.authorTay, Boon-Huien
dc.contributor.authorVenkatesh, Byrappaen
dc.date.accessioned2013-10-10T07:49:09Z-
dc.date.available2013-10-10T07:49:09Z-
dc.date.issued2012-10-08en
dc.identifier.citationTan YY, Kodzius R, Tay B-H, Tay A, Brenner S, et al. (2012) Sequencing and Analysis of Full-Length cDNAs, 5--ESTs and 3--ESTs from a Cartilaginous Fish, the Elephant Shark (Callorhinchus milii). PLoS ONE 7: e47174. doi:10.1371/journal.pone.0047174.en
dc.identifier.issn1932-6203en
dc.identifier.pmid23056606en
dc.identifier.doi10.1371/journal.pone.0047174en
dc.identifier.urihttp://hdl.handle.net/10754/303148en
dc.description.abstractCartilaginous fishes are the most ancient group of living jawed vertebrates (gnathostomes) and are, therefore, an important reference group for understanding the evolution of vertebrates. The elephant shark (Callorhinchus milii), a holocephalan cartilaginous fish, has been identified as a model cartilaginous fish genome because of its compact genome (∼910 Mb) and a genome project has been initiated to obtain its whole genome sequence. In this study, we have generated and sequenced full-length enriched cDNA libraries of the elephant shark using the 'oligo-capping' method and Sanger sequencing. A total of 6,778 full-length protein-coding cDNA and 10,701 full-length noncoding cDNA were sequenced from six tissues (gills, intestine, kidney, liver, spleen, and testis) of the elephant shark. Analysis of their polyadenylation signals showed that polyadenylation usage in elephant shark is similar to that in mammals. Furthermore, both coding and noncoding transcripts of the elephant shark use the same proportion of canonical polyadenylation sites. Besides BLASTX searches, protein-coding transcripts were annotated by Gene Ontology, InterPro domain, and KEGG pathway analyses. By comparing elephant shark genes to bony vertebrate genes, we identified several ancient genes present in elephant shark but differentially lost in tetrapods or teleosts. Only ∼6% of elephant shark noncoding cDNA showed similarity to known noncoding RNAs (ncRNAs). The rest are either highly divergent ncRNAs or novel ncRNAs. In addition to full-length transcripts, 30,375 5'-ESTs and 41,317 3'-ESTs were sequenced and annotated. The clones and transcripts generated in this study are valuable resources for annotating transcription start sites, exon-intron boundaries, and UTRs of genes in the elephant shark genome, and for the functional characterization of protein sequences. These resources will also be useful for annotating genes in other cartilaginous fishes whose genomes have been targeted for whole genome sequencing.en
dc.description.sponsorshipBiomedical Research Council of A*STAR, Singaporeen
dc.language.isoenen
dc.publisherPublic Library of Science (PLoS)en
dc.rightsArchived with thanks to PloS oneen
dc.subjectComplementary DNAen
dc.subjectcDNA libraryen
dc.subjectTranscriptomeen
dc.subjectEvolutionen
dc.subjectExpressed Sequence Tagsen
dc.subject.meshAnimalsen
dc.subject.meshDNA, Complementaryen
dc.subject.meshExpressed Sequence Tagsen
dc.subject.meshFishesen
dc.subject.meshAnimalsen
dc.subject.meshDNA, Complementaryen
dc.subject.meshExpressed Sequence Tagsen
dc.subject.meshFishesen
dc.titleSequencing and analysis of full-length cDNAs, 5'-ESTs and 3'-ESTs from a cartilaginous fish, the elephant shark (Callorhinchus milii).en
dc.typeArticleen
dc.contributor.departmentComputational Bioscience Research Center (CBRC)en
dc.identifier.journalPLoS ONEen
dc.identifier.pmcidPMC3466250en
dc.eprint.versionPublisher's Version/PDFen
dc.contributor.institutionComparative Genomics Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore, Singapore.en
dc.contributor.affiliationKing Abdullah University of Science and Technology (KAUST)en
kaust.authorKodzius, Rimantasen

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