Dataset Information

Comparative transcriptome analysis reveals the genetic basis of skin color variation in common carp.

ABSTRACT:

Background

The common carp is an important aquaculture species that is widely distributed across the world. During the long history of carp domestication, numerous carp strains with diverse skin colors have been established. Skin color is used as a visual criterion to determine the market value of carp. However, the genetic basis of common carp skin color has not been extensively studied.

Methodology/principal findings

In this study, we performed Illumina sequencing on two common carp strains: the reddish Xingguo red carp and the brownish-black Yellow River carp. A total of 435,348,868 reads were generated, resulting in 198,781 assembled contigs that were used as reference sequences. Comparisons of skin transcriptome files revealed 2,012 unigenes with significantly different expression in the two common carp strains, including 874 genes that were up-regulated in Xingguo red carp and 1,138 genes that were up-regulated in Yellow River carp. The expression patterns of 20 randomly selected differentially expressed genes were validated using quantitative RT-PCR. Gene pathway analysis of the differentially expressed genes indicated that melanin biosynthesis, along with the Wnt and MAPK signaling pathways, is highly likely to affect the skin pigmentation process. Several key genes involved in the skin pigmentation process, including TYRP1, SILV, ASIP and xCT, showed significant differences in their expression patterns between the two strains.

Conclusions

In this study, we conducted a comparative transcriptome analysis of Xingguo red carp and Yellow River carp skins, and we detected key genes involved in the common carp skin pigmentation process. We propose that common carp skin pigmentation depends upon at least three pathways. Understanding fish skin color genetics will facilitate future molecular selection of the fish skin colors with high market values.

SUBMITTER: Jiang Y

PROVIDER: S-EPMC4177847 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Comparative transcriptome analysis reveals the genetic basis of skin color variation in common carp.

Jiang Yanliang Y Zhang Songhao S Xu Jian J Feng Jianxin J Mahboob Shahid S Al-Ghanim Khalid A KA Sun Xiaowen X Xu Peng P

PloS one 20140925 9

<h4>Background</h4>The common carp is an important aquaculture species that is widely distributed across the world. During the long history of carp domestication, numerous carp strains with diverse skin colors have been established. Skin color is used as a visual criterion to determine the market value of carp. However, the genetic basis of common carp skin color has not been extensively studied.<h4>Methodology/principal findings</h4>In this study, we performed Illumina sequencing on two common ...[more]

PMID: 25255374

Similar Datasets

Project description:BackgroundBody color and coloration patterns are important phenotypic traits to maintain survival and reproduction activities. The Oujiang color varieties of common carp (Cyprinus carpio var. color), with a narrow distribution in Zhejiang Province of China and a history of aquaculture for over 1,200 years, consistently exhibit a variety of body color patterns. The molecular mechanism underlying diverse color patterns in these variants is unknown. To the practical end, it is essential to develop molecular markers that can distinguish different phenotypes and assist selective breeding.Methodology/principal findingsIn this exploratory study, we conducted Roche 454 transcriptome sequencing of two pooled skin tissue samples of Oujiang common carp, which correspond to distinct color patterns, red with big black spots (RB) and whole white (WW), and a total of 737,525 sequence reads were generated. The reads obtained in this study were co-assembled jointly with common carp Roche 454 sequencing reads downloaded from NCBI SRA database, resulting in 43,923 isotigs and 546,676 singletons. Over 31 thousand (31,445; 71.6%) isotigs were found with significant BLAST matches (E<1e-10) to the nr protein database, which corresponds to 12,597 annotated zebrafish genes. A total of 70,947 isotigs and singletons (transcripts) were annotated with Gene Ontology, and 60,221 transcripts were found with corresponding EC numbers. Out of 145 zebrafish pigmentation genes, orthologs for 117 were recovered in Oujiang color carp transcriptome, including 18 found only among singletons. Our transcriptome analysis revealed over 52,902 SNPs in Oujiang common carp, and identified 63 SNP markers that are putatively unique either for RB or WW.ConclusionsThe transcriptome of Oujiang color varieties of common carp obtained through this study, along with the pigmentation genes recovered and the color pattern-specific molecular markers developed, will facilitate future research on the molecular mechanism of color patterns and promote aquaculture of Oujiang color varieties of common carp through molecular marker assisted-selective breeding.

Project description:BACKGROUND: Common 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. RESULT: Transcriptome 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. CONCLUSION: The 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.

Project description:BackgroundHericium erinaceus, also known as lion's mane mushroom, is a widely distributed edible and medicinal fungus in Asian countries. H. erinaceus harbors diverse bioactive metabolites with anticancer, immunomodulating, anti-inflammatory, antimicrobial, antihypertensive, antidiabetic and neuroprotective properties. Although the chemical synthesis processes of these bioactive metabolites are known, the biosynthetic processes remain unknown.ResultsIn this study, we obtained the transcriptomes of six H. erinaceus strains using next-generation RNA sequencing and investigated the characteristics of the transcriptomes and biosynthesis of bioactive compounds, especially polysaccharides. The transcriptomes ranged in size from 46.58 to 58.14 Mb, with the number of unigenes ranging from 20,902 to 37,259 across the six H. erinaceus strains. Approximately 60% of the unigenes were successfully annotated by comparing sequences against different databases, including the nonredundant (NR), Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), clusters of orthologous groups for eukaryotic complete genomes (KOG) and Swiss-Prot databases. Most of the transcripts were putatively involved in signal transduction, carbohydrate metabolism, translation, transport and catabolism, and amino acid metabolism. Genes involved in polysaccharide biosynthesis were identified, and these genes encoded phosphoglucomutase (PGM), glucose phosphate isomerase (PGI), UDP-glucose pyrophosphorylase (UGP), glycoside hydrolase family proteins, glycosyltransferase family proteins and other proteins. Moreover, the putative pathway for the intracellular polysaccharide biosynthesis of H. erinaceus was analyzed. Additionally, the open reading frames (ORFs) and simple sequence repeats (SSRs) were predicted from the transcriptome data of the six strains.ConclusionsOverall, the present study may facilitate the discovery of polysaccharide biosynthesis processes in H. erinaceus and provide useful information for exploring the secondary metabolites in other members of the Basidiomycetes genus.

Dataset Information

Comparative transcriptome analysis reveals the genetic basis of skin color variation in common carp.

Background

Methodology/principal findings

Conclusions

Publications

Comparative transcriptome analysis reveals the genetic basis of skin color variation in common carp.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets