Sequencing and analysis of full-length cDNAs, 5'-ESTs and 3'-ESTs from a cartilaginous fish, the elephant shark (Callorhinchus milii).
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Sequencing and Analysis of Full-Length cDNAs, 5′-ESTs and 3′-ESTs from Elephant Shark pone.0047174.pdf
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Sequencing and Analysis of Full-Length cDNAs, 5′-ESTs and 3′-ESTs from Elephant Shark
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Sequencing and Analysis of Full-Length cDNAs, 5′-ESTs and 3′-ESTs from Elephant Shark supplement
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ArticleKAUST Department
Computational Bioscience Research Center (CBRC)Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division
Date
2012-10-08Permanent link to this record
http://hdl.handle.net/10754/303148
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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.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.Sponsors
Biomedical Research Council of A*STAR, SingaporePublisher
Public Library of Science (PLoS)Journal
PLoS ONEPubMed ID
23056606PubMed Central ID
PMC3466250ae974a485f413a2113503eed53cd6c53
10.1371/journal.pone.0047174
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