Comparative analysis of the transcriptome of the Amazonian fish species Colossoma macropomum (tambaqui) and hybrid tambacu by next generation sequencing

PloS One
Fátima GomesIracilda Sampaio

Abstract

The C. macropomum is a characiform fish from the Amazon basin that has been hybridized with other pacu species to produce commercial hybrids, such as the tambacu. However, little is known of the functional genomics of the parental species or these hybrid forms. The transcriptome of C. macropomum and tambacu were sequenced using 454 Roche platform (pyrosequencing) techniques to characterize the domains of Gene Ontology (GO) and to evaluate the levels of gene expression in the two organisms. The 8,188,945 reads were assembled into 400,845 contigs. A total of 58,322 contigs were annotated with a predominance of biological processes for both organisms, as determined by Gene Ontology (GO). Similar numbers of metabolic pathways were identified in both the C. macropomum and the tambacu, with the metabolism category presenting the largest number of transcripts. The BUSCO analysis indicated that our assembly was more than 40% complete. We identified 21,986 genes for the two fishes. The P and Log2FC values indicated significant differences in the levels of gene expression, with a total of 600 up-regulated genes. In spite of the lack of a reference genome, the functional annotation was successful, and confirmed a considerable difference i...Continue Reading

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Datasets Mentioned

BETA
DQ480074
AF283959
SRX2375119

Methods Mentioned

BETA
454 sequencing
genotyping
PCRs
electrophoresis
PCR
chip

Software Mentioned

HIT
MIRA
BUSCO ( Benchmarking Universal Single - Copy Orthologs )
Star
mixOmics
Ggplot
IDEG6
HTSeq
Newbler
EST

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