Characterization of Common Carp Transcriptome: Sequencing, De Novo Assembly, Annotation and Comparative Genomics

Abstract

BackgroundCommon carp (Cyprinus carpio) is one of the most important aquaculture species of Cyprinidae with an annual global production of 3.4 million tons, accounting for nearly 14% of the freshwater aquaculture production in the world. Due to the economical and ecological importance of common carp, genomic data are eagerly needed for genetic improvement purpose. However, there is still no sufficient transcriptome data available. The objective of the project is to sequence transcriptome deeply and provide well-assembled transcriptome sequences to common carp research community.ResultTranscriptome sequencing of common carp was performed using Roche 454 platform. A total of 1,418,591 clean ESTs were collected and assembled into 36,811 cDNA contigs, with average length of 888 bp and N50 length of 1,002 bp. Annotation was performed and a total of 19,165 unique proteins were identified from assembled contigs. Gene ontology and KEGG analysis were performed and classified all contigs into functional categories for understanding gene functions and regulation pathways. Open Reading Frames (ORFs) were detected from 29,869 (81.1%) contigs with an average ORF length of 763 bp. From these contigs, 9,625 full-length cDNAs were identified with sequence length from 201 bp to 9,956 bp. Comparative analysis revealed that 27,693(75.2%) contigs have significant similarity to zebrafish Refseq proteins, and 24,371(66.2%), 24,501(66.5%) and 25,025(70.0%) to teraodon, medaka and three-spined stickleback refseq proteins. A total of 2,064 microsatellites were initially identified from 1,730 contigs, and 1,639 unique sequences had sufficient flanking sequences on both sides for primer design.ConclusionThe transcriptome of common carp had been deep sequenced, de novo assembled and characterized, providing the valuable resource for better understanding of common carp genome. The transcriptome data will facilitate future functional studies on common carp genome, and gradually apply in breeding programs of common carp, as well as closely related other Cyprinids.

De Novo Assembly and Analysis of the Testes Transcriptome from the Menhaden, Bervoortia tyrannus

“…Based on a phylogenetic tree analysis with the eleven publically available fish genomes on Ensembl, it was determined that zebrafish along with Mexican tetra were the closest related genera to menhaden. The BLASTX alignments for the menhaden against the zebrafish (42.56%) and Mexican tetra (41.34%) yielded analogous results with other non-model fish de novo transcriptome assembly studies signifying that the assemblies are reliable [9,12,13,47,48]. The low number of hits for both zebrafish and Mexican tetra could be due the presence of menhaden-specific contigs, as menhaden belong to separate clades in the phylogenetic tree ( Figure 2).…”

“…In this study, the percentage of matches for the menhaden was 46.23%. This percentage is comparable to other non-model fish de novo assemblies, further establishing the credibility of the assemblies [9,12,13,47,50]. It should be noted that the number of matches is affected by the amount of available sequence data, and there is a limited number of publically available fish genomes to contribute to the overall success of the annotation [49].…”

“…The first is the reduction fishery that turns the menhaden into fish oil omega-3 supplements for example, and into fishmeal for livestock and aquaculture consumption [4,5]. The second is the bait fishery that uses the menhaden as bait for bluefish, crab, and lobster [6][7][8][9][10][11][12][13][14][15]. They have been rarely studied at the genetic level most likely due to the lack of genomic and transcriptome data.…”

Transcriptome analysis of the plateau fish (Triplophysa dalaica): Implications for adaptation to hypoxia in fishes

“…Compared with other fish transcriptomes sequenced within Cypriniformes (Fu and He, 2012;Gao et al, 2012;Ji et al, 2012;Liao et al, 2013;Long et al, 2013;Zou et al, 2014), the de novo assembly and annotations of T. dalaica transcriptome were best (Table 2). In terms of the gene expression level, T. dalaica transcriptome showed the highest similarity to zebrafish, which can be explained by the fact that Triplophysa fishes and zebrafish belonging to the same order Cypriniformes.…”

“…To assess the quality of our assembled unigenes, we made comparisons with other fish transcriptomes sequenced within Cypriniformes, Carassius auratus, Megalobrama amblycephala, Hypophthalmichthys molitrix, Elopichthys bambusa and Cyprinus carpio (Fu and He, 2012;Gao et al, 2012;Ji et al, 2012;Liao et al, 2013;Long et al, 2013;Zou et al, 2014). Furthermore, cDNA template was prepared using highquality RNA with a first-strand DNA synthesis kit (Promega).…”