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Dong C.,Chinese Academy of Fishery Sciences | Dong C.,Shanghai Ocean University | Xu J.,Chinese Academy of Fishery Sciences | Wang B.,Chinese Academy of Fishery Sciences | And 4 more authors.
Marine Biotechnology

Common carp (Cyprinus carpio L.) is one of the oldest, most widely farmed commercially important freshwater fish in the world. However, many undetermined phylogenetic relationships and origins of common carp lineages remain, which are obstacles to conservation and genetic breeding of this species. Phylogenetic analyses based on molecular tools are helpful to distinguish the origin of species, understand and clarify their evolutionary history, and provide a genetic basis for selective breeding. In this study, we demonstrated a method to extract complete mitochondrial genome sequences from whole-genome resequencing data using the Illumina platform. The complete mitochondrial genome sequences of 26 individuals representing nine strains were obtained and subjected to a phylogenetic analysis. We reconstructed the phylogenetic topologies of the nine strains and analyzed the haplotypes. Results from both analyses suggested that the genome sequences belonged to two distinct subspecies from Europe and East Asia. We also estimated the time of divergence of the nine strains, which was up to 100 KYA. The phylogenetic results clarified the breeding history of Songpu mirror carp and suggest that this species may be hybrid of paternal European mirror carp and maternal Xingguo red carp. The results also support a previous hypothesis that koi may have originated from or have close ancestry with Oujiang color carp in China. © 2015, Springer Science+Business Media New York. Source

Jiang Y.,Chinese Academy of Fishery Sciences | Zhang S.,Chinese Academy of Fishery Sciences | Xu J.,Chinese Academy of Fishery Sciences | Feng J.,Henan Academy of Fishery science | And 5 more authors.

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. © 2014 Jiang et al. Source

Wang G.,Henan Normal University | Chen S.,Henan Normal University | Zhao C.,Henan Normal University | Li X.,Henan Normal University | And 4 more authors.

Osteopontin (OPN; gene Spp1), as a pro-inflammatory cytokine, has a range of activities relevant to the occurrence and progression of hepatitis, liver fibrosis or liver tumors. However, little is known about the role of OPN in liver regeneration (LR). To reveal the expression profiles of OPN and its receptors and the possible regulatory role of OPN in rat LR, Rat Genome 230 2.0 was used to detect expression profiles of OPN-mediated signaling pathway-associated genes after partial hepatectomy (PH), and the results showed that 81 genes were significantly changed at mRNA level, and among which, 65 genes were up-regulated. Then, k-means clustering was employed to classify above 81 genes into 5 clusters based on gene expression similarity, and EASE analysis further indicated that the above genes were mainly associated with stress response, inflammatory response, cell activation, proliferation, adhesion and migration. Thereafter, IPA software and Western blot were used to analyze potential effects of every branch of OPN signaling pathways during LR, and the results suggested that the genes expression changes of OPN signaling pathways may account for enhanced cell proliferation, survival, adhesion and migration, augmented inflammation response and attenuated apoptosis during LR. © 2015 Elsevier B.V. Source

Jiang L.,Shanghai Ocean University | Chen B.,Shanghai Ocean University | Feng J.,Henan Academy of Fishery science | Mahboob S.,King Saud University | And 2 more authors.
Mitochondrial DNA

The complete mitochondrial genome of the first individual Rhinogobio typus collected from the Yellow River were sequenced and compared with the previously reported complete mitochondrial sequence of Rhinogobio typus from the Yangtze River. The length of their circular mitochondrial genome was determined to be 16 599 and 16 608 bp respectively. The comparison of two mitochondrial genomes revealed 237 base pair substitutions and 17 insertions or deletions (indels), including 182 base pair substitutions and 2 indels in protein-coding region. Phylogenetic tree was constructed based on complete mitogenomes of the two populations and closely related 13 teleost species to assess their phylogenic relationship and evolution. © 2015 Taylor & Francis. Source

Liu X.,Chinese Academy of Fishery Sciences | Liu X.,Shanxi University | Li S.,Chinese Academy of Fishery Sciences | Peng W.,Chinese Academy of Fishery Sciences | And 7 more authors.

The ATP-binding cassette (ABC) gene family is considered to be one of the largest gene families in all forms of prokaryotic and eukaryotic life. Although the ABC transporter genes have been annotated in some species, detailed information about the ABC superfamily and the evolutionary characterization of ABC genes in common carp (Cyprinus carpio) are still unclear. In this research, we identified 61 ABC transporter genes in the common carp genome. Phylogenetic analysis revealed that they could be classified into seven subfamilies, namely 11 ABCAs, six ABCBs, 19 ABCCs, eight ABCDs, two ABCEs, four ABCFs, and 11 ABCGs. Comparative analysis of the ABC genes in seven vertebrate species including common carp, showed that at least 10 common carp genes were retained from the third round of whole genome duplication, while 12 duplicated ABC genes may have come from the fourth round of whole genome duplication. Gene losses were also observed for 14 ABC genes. Expression profiles of the 61 ABC genes in six common carp tissues (brain, heart, spleen, kidney, intestine, and gill) revealed extensive functional divergence among the ABC genes. Different copies of some genes had tissue-specific expression patterns, which may indicate some gene function specialization. This study provides essential genomic resources for future studies in common carp. © 2016 Liu et al.This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Source

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