Genome sequence and genetic diversity of the common carp, Cyprinus carpio

Xu, Peng; Zhang, Xiaofeng; Wang, Xumin; Li, Jiong-Tang; Liu, Guiming; Kuang, Youyi; Xu, Jian; Zheng, Xianhu; Ren, Lufeng; Wang, Guoliang; Zhang, Yan; Huo, Linhe; Zhao, Zhen; Cao, Dan; Lu, Cuiyun; Li, Chao; Zhou, Yi; Liu, Zhanjiang; Fan, Zhonghua; Shan, Guangle; Li, Xingang; Wu, Shuangxiu; Song, Liguo; Hou, Guangyuan; Jiang, Yanliang; Jeney, Zsigmond; Yu, Dan; Wang, Li; Shao, Changjun; Song, Lai; Sun, Jing; Ji, Peifeng; Wang, Jian; Li, Qiang; Xu, Liming; Sun, Fenyong; Feng, Jianxin; Wang, Chenghui; Wang, Shaolin; Wang, Baosen; Li, Yan; Zhu, Yaping; Xue, Wei; Zhao, Lan; Wang, Jintu; Gu, Ying; Lv, Wenjing; Wu, Kejing; Xiao, Jingfa; Wu, Jiayan; Zhang, Zhang; Yu, Jun; Sun, Xiaowen

doi:10.1038/ng.3098

Cited by 580 publications

(515 citation statements)

References 73 publications

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“…The Ks value of paralogous genes can be used to reveal WGD events (Wang et al., 2012; Xu et al., 2014). Northern pike is a species of teleost whose genome underwent third round WGD.…”

Section: Discussionmentioning

confidence: 99%

De novo assembly and characterization of the Hucho taimen transcriptome

Tong

Xü

Zhang

et al. 2017

Ecology and Evolution

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Taimen (Hucho taimen) is an important ecological and economic species that is classified as vulnerable by the IUCN Red List of Threatened Species; however, limited genomic information is available on this species. RNA‐Seq is a useful tool for obtaining genetic information and developing genetic markers for nonmodel species in addition to its application in gene expression profiling. In this study, we performed a comprehensive RNA‐Seq analysis of taimen. We obtained 157 M clean reads (14.7 Gb) and used them to de novo assemble a high‐quality transcriptome with a N50 size of 1,060 bp. In the assembly, 82% of the transcripts were annotated using several databases, and 14,666 of the transcripts contained a full open reading frame. The assembly covered 75% of the transcripts of Atlantic salmon and 57.3% of the protein‐coding genes of rainbow trout. To learn about the genome evolution, we performed a systematic comparative analysis across 11 teleosts including eight salmonids and found 313 unique gene families in taimen. Using Atlantic salmon and rainbow trout transcriptomes as the background, we identified 250 positive selection transcripts. The pathway enrichment analysis revealed a unique characteristic of taimen: It possesses more immune‐related genes than Atlantic salmon and rainbow trout; moreover, some genes have undergone strong positive selection. We also developed a pipeline for identifying microsatellite marker genotypes in samples and successfully identified 24 polymorphic microsatellite markers for taimen. These data and tools are useful for studying conservation genetics, phylogenetics, evolution among salmonids, and selective breeding for threatened taimen.

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“…The Ks value of paralogous genes can be used to reveal WGD events (Wang et al., 2012; Xu et al., 2014). Northern pike is a species of teleost whose genome underwent third round WGD.…”

Section: Discussionmentioning

confidence: 99%

De novo assembly and characterization of the Hucho taimen transcriptome

Tong

Xü

Zhang

et al. 2017

Ecology and Evolution

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“…Tandem repeats were identified by searching for two or more contiguous, approximate copies of a pattern of nucleotides using Tandem Repeats Finder (v4.07b) 70 under default parameters. Gene prediction and functional annotation were performed primarily following the procedure described in previous studies 71,72 . Briefly, three de novo gene prediction tools, Augustus (v2.7) 73 , GlimmerHMM (v3.02) 74 and SNAP (2006-07-28) 75 , were used to predict genes in the repeat-masked genome sequences.…”

Section: Nature Ecology and Evolutionmentioning

confidence: 99%

Scallop genome provides insights into evolution of bilaterian karyotype and development

et al. 2017

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Reconstructing the genomes of bilaterian ancestors is central to our understanding of animal evolution, where knowledge from ancient and/or slow-evolving bilaterian lineages is critical. Here we report a high-quality, chromosome-anchored reference genome for the scallop Patinopecten yessoensis, a bivalve mollusc that has a slow-evolving genome with many ancestral features. Chromosome-based macrosynteny analysis reveals a striking correspondence between the 19 scallop chromosomes and the 17 presumed ancestral bilaterian linkage groups at a level of conservation previously unseen, suggesting that the scallop may have a karyotype close to that of the bilaterian ancestor. Scallop Hox gene expression follows a new mode of subcluster temporal co-linearity that is possibly ancestral and may provide great potential in supporting diverse bilaterian body plans. Transcriptome analysis of scallop mantle eyes finds unexpected diversity in phototransduction cascades and a potentially ancient Pax2/5/8-dependent pathway for noncephalic eyes. The outstanding preservation of ancestral karyotype and developmental control makes the scallop genome a valuable resource for understanding early bilaterian evolution and biology.

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“…Further work is needed to generate other antigens such as GPCRs and developing more highly sensitive assay methods. Cyprinidae contributes over 20 million metric tons to fish production in the worldwide and accounts for approximately 40% of total global aquaculture production and 70% of total freshwater aquaculture production [16]. However, goldfish farming have declined in recent years, so it is hoped that the researching of goldfish utilization as an immune hosts contributes to the revitalization of goldfish farming.…”

Section: Discussionmentioning

confidence: 99%

Determining and Estimation of Antibody Production in the Bubble Eye, Goldfish

Nukada¹,

AvÅar-Ban²,

Tamaru³

2016

J Marine Sci Res Dev

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Development of antibody production technologies is necessary for diagnostic treatments and drug discovery. In general, mammals are used as host animals to produce antigen-specific antibody. However, such host animals have never produced several specific antibodies because host animals may not recognize foreign proteins. To overcome this problem, we used teleost to produce antibodies because teleost are evolutionally localized in the origin of vertebrates and have an acquired immune system in addition to the innate immune system. In particular, we attempt to produce antibody using "Bubble Eye" as a kind of goldfish (Carassius auratus), which has sacs filled with lymph liquid, as an immune animal. In this study, a recombinant EGFP-His was expressed in E. coli and then injected into Bubble Eye's sac in every two weeks. The antibodies were collected from sac instead of blood. Furthermore, a sandwich dot blotting was developed for detection of antibodies against EGFP-His. The antigen-specific antibodies were detected after 42 days from first immunization.

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Genome sequence and genetic diversity of the common carp, Cyprinus carpio

Cited by 580 publications

References 73 publications

De novo assembly and characterization of the Hucho taimen transcriptome

De novo assembly and characterization of the Hucho taimen transcriptome

Scallop genome provides insights into evolution of bilaterian karyotype and development

Determining and Estimation of Antibody Production in the Bubble Eye, Goldfish

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