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A first generation BAC-based physical map of the half-smooth tongue sole (Cynoglossus semilaevis) genome

文献类型： 外文期刊

作者： Zhang, Junjie 1 ; Shao, Changwei 1 ; Zhang, Liyan 1 ; Liu, Kun 1 ; Gao, Fengtao 1 ; Dong, Zhongdian 1 ; Xu, Peng 4 ; Chen 1 ;

作者机构： 1.Chinese Acad Fishery Sci, Yellow Sea Fisheries Res Inst, Qingdao 266071, Peoples R China

2.Shanghai Ocean Univ, Coll Fisheries & Life Sci, Shanghai 201306, Peoples R China

3.Xinjiang Agr Univ, Coll Anim Sci, Urumqi 830052, Peoples R China

4.Chinese Acad Fishery Sci, Ctr Appl Aquat Genom, Beijing 100141, Peoples R China

关键词： Half-smooth tongue sole;Cynoglossus semilaevis;BAC library;Physical map;Genome

期刊名称：BMC GENOMICS （ 影响因子：3.969； 五年影响因子：4.478 ）

ISSN： 1471-2164

年卷期： 2014 年 15 卷

页码：

收录情况： SCI

摘要： Background: Half-smooth tongue sole (Cynoglossus semilaevis Gunther) has been exploited as a commercially important cultured marine flatfish, and female grows 2-3 times faster than male. Genetic studies, especially on the chromosomal sex-determining system of this species, have been carried out in the last decade. Although the genome of half-smooth tongue sole was relatively small (626.9 Mb), there are still some difficulties in the high-quality assembly of the next generation genome sequencing reads without the assistance of a physical map, especially for the W chromosome of this fish due to abundance of repetitive sequences. The objective of this study is to construct a bacterial artificial chromosome (BAC)-based physical map for half-smooth tongue sole with the method of high information content fingerprinting (HICF). Results: A physical map of half-smooth tongue sole was constructed with 30, 294 valid fingerprints (7.5 x genome coverage) with a tolerance of 4 and an initial cutoff of 1e-60. A total of 29,709 clones were assembled into 1,485 contigs with an average length of 539 kb and a N50 length of 664 kb. There were 394 contigs longer than the N50 length, and these contigs will be a useful resource for future integration with linkage map and whole genome sequence assembly. The estimated physical length of the assembled contigs was 797 Mb, representing approximately 1.27 coverage of the half-smooth tongue sole genome. The largest contig contained 410 BAC clones with a physical length of 3.48 Mb. Almost all of the 676 BAC clones (99.9%) in the 21 randomly selected contigs were positively validated by PCR assays, thereby confirming the reliability of the assembly. Conclusions: A first generation BAC-based physical map of half-smooth tongue sole was constructed with high reliability. The map will promote genetic improvement programs of this fish, especially integration of physical and genetic maps, fine-mappings of important gene and/or QTL, comparative and evolutionary genomics studies, as well as whole genome sequence assembly.

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[1]Construction of Two BAC Libraries from Half-Smooth Tongue Sole Cynoglossus semilaevis and Identification of Clones Containing Candidate Sex-Determination Genes. Shao, Chang-Wei,Chen, Song-Lin,Xu, Jian-Yong,Sha, Zhen-Xia,Dong, Xiao-Li,Shao, Chang-Wei,Scheuring, Chantel F.,Zhang, Hong-Bin,Shao, Chang-Wei,Scheuring, Chantel F.,Zhang, Hong-Bin.

[2]Induction of Mitogynogenetic Diploids and Identification of WW Super-female Using Sex-Specific SSR Markers in Half-Smooth Tongue Sole (Cynoglossus semilaevis). Chen, Song-Lin,Ji, Xiang-Shan,Shao, Chang-Wei,Li, Wen-Long,Yang, Jing-Feng,Liang, Zuo,Liao, Xiao-Lin,Xu, Gen-Bo,Xu, Ying,Song, Wen-Tao,Ji, Xiang-Shan. 2012

[3]Growth differences and differential expression analysis of pituitary adenylate cyclase activating polypeptide (PACAP) and growth hormone-releasing hormone (GHRH) between the sexes in half-smooth tongue sole Cynoglossus semilaevis. Ji, Xiang-Shan,Chen, Song-Lin,Xu, Tian-Jun,Yang, Jing-Feng,Tian, Yong-Sheng,Ji, Xiang-Shan,Jiang, Yun-Liang. 2011

[4]Molecular cloning, characterization and expression analysis of Sox9a and Foxl2 genes in half-smooth tongue sole (Cynoglossussemilaevis). Dong Xiaoli,Chen Songlin,Shao Changwei,Dong Xiaoli,Ji Xiangshan. 2011

[5]Application of AFLP markers for population genetic study on half-smooth tongue sole Cynoglossus semilaevis. Liu Yunguo,Liu Yunguo,Li Junfeng,Ye Naihao. 2011

[6]Establishment and characterization of a testicular cell line from the half-smooth tongue sole, Cynoglossus semilaevis. Zhang, Bo,Wang, Xianli,Sha, Zhenxia,Yang, Changgeng,Liu, Shanshan,Wang, Na,Chen, Song-Lin,Zhang, Bo,Liu, Shanshan.

[7]Molecular and phenotypic characterization of Vibrio aestuarianus, a pathogen of the cultured tongue sole, Cynoglossus semilaevis Gunther. Zhang, X-J,Qin, G-M,Yan, B-L,Liang, L-G,Bing, X-W. 2011

[8]Comparison of chromosome preparation methods for the different developmental stages of the half-smooth tongue sole, Cynoglossus semilaevis. Shao, Chang-Wei,Wu, Peng-Fei,Wang, Xian-Li,Tian, Yong-Sheng,Chen, Song-Lin. 2010

[9]Construction of a microsatellite-based genetic linkage map for half-smooth tongue sole Cynoglossus semilaevis. Song, Wentao,Miao, Guidong,Zhao, Yongwei,Niu, Yuze,Pang, Renyi,Liao, Xiaolin,Shao, Changwei,Chen, Songlin,Song, Wentao. 2013

[10]Isolation of Female-Specific AFLP Markers and Molecular Identification of Genetic Sex in Half-Smooth Tongue Sole (Cynoglossus semilaevis). Chen, Song-Lin,Li, Jing,Deng, Si-Ping,Tian, Yong-Sheng,Wang, Qing-Yin,Zhuang, Zhi-Meng,Sha, Zhen-Xia,Xu, Jian-Yong.

[11]Establishment and characterization of a new fish cell line from head kidney of half-smooth tongue sole (Cynoglossus semilaevis). Zheng, Yuan,Wang, Na,Xie, Ming-Shu,Sha, Zhen-Xia,Chen, Song-Lin,Zheng, Yuan,Xie, Ming-Shu.

[12]Molecular cloning, genomic structure and expression analysis of major histocompatibility complex class I alpha gene of half-smooth tongue sole (Cynoglossus semilaevis). Chen, Song-lin,Xu, Tian-jun. 2011

[13]Genomic structure, polymorphism and expression analysis of growth hormone-releasing hormone and pituitary adenylate cyclase activating polypeptide genes in the half-smooth tongue sole (Cynoglossus semilaevis). Ma, Q.,Liu, S. F.,Zhuang, Z. M.,Lin, L.,Sun, Z. Z.,Liu, C. L.,Tang, Q. S.,Ma, Q.,Lin, L.,Su, Y. Q.. 2011

[14]Characterization of the cyp19a1a gene from a BAC sequence in half-smooth tongue sole (Cynoglossus semilaevis) and analysis of its conservation among teleosts. Shao Changwei,Shao Changwei,Liu Shanshan,Liu Changlin,Chen Songlin,Liu Geng. 2013

[15]Unexpected variations Of beta(2)-microglobulin gene in the half-smooth tongue sole. Xu, Tian-jun,Sha, Zhen-xia,Chen, Song-lin,Xu, Tian-jun. 2010

[16]Molecular characterization and expression analysis of Patched 1 gene in the half-smooth tongue sole (Cynoglossus semilaevis). Dong Zhongdian,Qi Qian,Zhang Ning,Wen Haishen,Dong Zhongdian,Qi Qian,Zhang Ning,Shao Changwei,Zhang Liyan,Chen Songlin,Dong Zhongdian,Qi Qian,Zhang Ning,Shao Changwei,Zhang Liyan,Chen Songlin. 2016

[17]Genomic structure, polymorphism and expression analysis of the growth hormone (GH) gene in female and male Half-smooth tongue sole (Cynoglossus semilaevis). Ma, Qian,Liu, ShuFang,Zhuang, ZhiMeng,Lin, Lin,Sun, ZhongZhi,Liu, ChangLin,Ma, Hui,Tang, QiSheng,Ma, Qian,Lin, Lin,Su, YongQuan,Ma, Hui.

[18]Molecular characterization and expression profiles of LPXRFa at the brain pituitary-gonad axis of half-smooth tongue sole (Cynoglossus semilaevis) during ovarian maturation. Wang, Bin,Liu, Quan,Liu, Xuezhou,Xu, Yongjiang,Shi, Bao,Wang, Bin,Liu, Xuezhou,Xu, Yongjiang,Shi, Bao,Liu, Quan. 2018

[19]Effects of different dietary DHA: EPA ratios on gonadal steroidogenesis in the marine teleost, tongue sole (Cynoglossus semilaevis). Xu, Houguo,Cao, Lin,Wei, Yuliang,Zhang, Yuanqin,Liang, Mengqing,Liang, Mengqing. 2017

[20]Evaluation of reference genes for quantitative real-time PCR analysis of gene expression during early development processes of the tongue sole (Cynoglossus semilaevis). Ma Qian,Zhuang Zhimeng,Feng Wenrong,Liu Shufang,Tang Qisheng. 2015

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