Hypophthalmichthys molitrix
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA294224 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR2209405.fastq.gz | Fastqsanger.gz |
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Project description:We applied high throughput sequencing technology to identify microRNA genes in bighead carp and silver carp. We identified 167 conserved miRNAs in bighead carp and 166 in silver carp. By two computational stragegies, we obtained 39 novel miRNAs in bighead carp and 54 in silver carp, for which, no homologs were found in other species. Several miRNA* sequences were found in our dataset as well, some particular ones might have gene regulation function. Gain and loss of family members were observed in several miRNA families, which partially reflected the fate of miRNA gene duplicates. Total RNA of juvenile bighead carp and silver carp were sequenced on one Solexa lane, respectively.
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Project description:Bighead carp (Hypophthalmichthys nobilis) and silver carp (Hypophthalmichthys molitrix), collectively called bigheaded carps, are invasive species in the Mississippi River Basin (MRB). Interspecific hybridization between bigheaded carps has been considered rare within their native rivers in China; however, it is prevalent in the MRB. We conducted de novo transcriptome analysis of pure and hybrid bigheaded carps and obtained 40,759 to 51,706 transcripts for pure, F1 hybrid, and backcross bigheaded carps. The search against protein databases resulted in 20,336-28,133 annotated transcripts (over 50% of the transcriptome) with over 13,000 transcripts mapped to 23 Gene Ontology biological processes and 127 KEGG metabolic pathways. More transcripts were detected in silver carp than in bighead carp; however, comparable numbers of transcripts were annotated. Transcriptomic variation detected between two F1 hybrids may indicate a potential loss of fitness in hybrids. The neighbor-joining distance tree constructed using over 2,500 one-to-one orthologous sequences suggests transcriptomes could be used to infer the history of introgression and hybridization. Moreover, we detected 24,792 candidate SNPs that can be used to identify different species. The transcriptomes, orthologous sequences, and candidate SNPs obtained in this study should provide further knowledge of interspecific hybridization and introgression.
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