De novo assembly and characterization of the Hucho taimen transcriptome

文献类型： 外文期刊

第一作者： Tong, Guang-Xiang

作者： Tong, Guang-Xiang;Xu, Wei;Zhang, Yong-Quan;Zhang, Qing-Yu;Yin, Jia-Sheng;Kuang, You-Yi

作者机构：

关键词： comparative transcript analysis;Hucho taimen;microsatellite markers;positive selection;RNA-Seq

期刊名称：ECOLOGY AND EVOLUTION （ 影响因子：2.912； 五年影响因子：3.271 ）

ISSN： 2045-7758

年卷期： 2018 年 8 卷 2 期

页码：

收录情况： SCI

摘要： 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 157M clean reads (14.7Gb) and used them to de novo assemble a high-quality transcriptome with a N50 size of 1,060bp. 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.

分类号：

  • 相关文献

[1]The Post-Embryonic Development of Digestive System and the Demand of Energy of Hucho taimen. Guan Hai-hong,Xu Qi-you,Zhi Bing-jie,Kuang You-yi,Xu Wei,Yin Jia-sheng. 2010

[2]Effects of dietary phosphorus on growth, body composition and immunity of young taimen Hucho taimen (Pallas, 1773). Wang, Chang'an,Li, Jinnan,Wang, Liansheng,Zhao, Zhigang,Luo, Liang,Du, Xue,Yin, Jiasheng,Xu, Qiyou.

[3]Karyological analysis for endangered fish, Hucho taimen (Pallas). Shu-Qun, Xue,Xiao-Wen, Sun,Jia-Sheng, Yin.

[4]Selective modes determine evolutionary rates, gene compactness and expression patterns in Brassica. Liu, Jing,Du, Jianchang,Zhang, Jiefu,Du, Jianchang,Liu, Shengyi,Du, Jianchang. 2017

[5]Mannose selection system used for cucumber transformation. He, Zhengquan,Duan, ZhenZhen,Liang, Wei,Chen, Faju,Yao, Wei,Liang, Hongwei,Yue, Chaoyin,Sun, Zongxiu,Chen, Fan,Dai, Jianwu. 2006

[6]Gene duplication and an accelerated evolutionary rate in 11S globulin genes are associated with higher protein synthesis in dicots as compared to monocots. Li, Chun,Li, Meng,Zhang, Yuan-Ming,Li, Chun,Dunwell, Jim M.. 2012

[7]The impact of positive selection and mutation in prevalence of representative O/Mya-98 foot and mouth disease strains during 2009-2010. Kuang, Wendong,Bai, Xingwen,Qi, Guocai,Hao, Xiaofang,Li, Pinghua,Lu, Zengjun,Bao, Huifang,Sun, Pu,Wu, Lei,Liu, Zaixin. 2012

[8]Evidence for positive selection in Ser/Thr protein kinases (STKs) genes of Trichodesmium erythraeum. Liang, Chengwei,Zhang, Xiaowen. 2009

[9]An exceptionally high nucleotide and haplotype diversity and a signature of positive selection for the eIF4E resistance gene in barley are revealed by allele mining and phylogenetic analyses of natural populations. Hofinger, Bernhard J.,Bass, Chris G.,Baldwin, Thomas,Hammond-Kosack, Kim E.,Kanyuka, Kostya,Russell, Joanne R.,Hedley, Peter E.,Macaulay, Malcolm,Waugh, Robbie,Dos Reis, Mario,Li, Yidan.

[10]Molecular diversity and evolution of defensins in the manila clam Ruditapes philippinarum. Wang, Qing,Yang, Dinglong,Yu, Qian,Li, Fei,Cong, Ming,Ji, Chenglong,Wu, Huifeng,Zhao, Jianmin,Zhang, Linbao,Yang, Dinglong,Yu, Qian.

[11]Transcriptome analysis revealed positive selection of immune-related genes in tilapia. Xiao, Jun,Zhong, Huan,Luo, Yongju,Gan, Xi,Zhou, Yi,Liu, Zhen,Zhou, Yi,Yu, Fan.

[12]Independent Losses of Function in a Polyphenol Oxidase in Rice: Differentiation in Grain Discoloration between Subspecies and the Role of Positive Selection under Domestication. Tang, Tian,Wu, Chung-I,Shi, Suhua,Yu, Yanchun,Wang, Yonghong,Li, Jiayang,Yu, Yanchun,Wang, Yonghong,Li, Jiayang,Qian, Qian,Yan, Meixian,Zeng, Dali,Han, Bin,Han, Bin,Wu, Chung-I,Wu, Chung-I.

[13]Transcriptome Sequencing of Lima Bean (Phaseolus lunatus) to Identify Putative Positive Selection in Phaseolus and Legumes. Cao, Depan,Liu, Yang,Yang, Ting,Wang, Guirong. 2015

[14]Population size may shape the accumulation of functional mutations following domestication. Chen, Jianhai,Ni, Pan,Li, Xinyun,Zhao, Shuhong,Chen, Jianhai,Ni, Pan,Li, Xinyun,Zhao, Shuhong,Han, Jianlin,Han, Jianlin,Jakovlic, Ivan,Zhang, Chengjun. 2018

[15]A genome-wide scan for signatures of selection in Chinese indigenous and commercial pig breeds. Yang, Songbai,Li, Kui,Tang, Zhonglin,Yang, Songbai,Li, Xiuling,Fan, Bin,Yang, Songbai,Li, Xiuling,Fan, Bin. 2014

[16]Evolution and molecular epidemiology of foot-and-mouth disease virus in China. Bai XingWen,Li PingHua,Bao HuiFang,Liu ZaiXin,Li Dong,Lu ZengJun,Cao YiMei,Shang YouJun,Shao JunJun,Chang HuiYun,Luo JianXun,Liu XiangTao. 2011

[17]Evolution, gene expression profiling and 3D modeling of CSLD proteins in cotton. Li, Yanpeng,Yang, Tiegang,Dai, Dandan,Hu, Ying,Guo, Xiaoyang,Guo, Hongxia,Li, Yanpeng,Yang, Tiegang,Dai, Dandan,Hu, Ying,Guo, Xiaoyang,Guo, Hongxia. 2017

[18]Genome-wide identification and evolutionary analysis of positively selected miRNA genes in domesticated rice. Liu, Qingpo,Wang, Hong,Hu, Haichao,Liu, Qingpo,Wang, Hong,Hu, Haichao,Zhang, Hengmu.

[19]Phosphomannose-isomerase (pmi) gene as a selectable marker for rice transformation via Agrobacterium. He, ZQ,Fu, YP,Si, HM,Hu, GC,Zhang, SH,Yu, YH,Sun, ZX.

[20]Rapid diversification of five Oryza AA genomes associated with rice adaptation. Zhang, Qun-Jie,Zhu, Ting,Xia, En-Hua,Shi, Chao,Liu, Yun-Long,Zhang, Yun,Liu, Yuan,Jiang, Wen-Kai,Zhao, You-Jie,Mao, Shu-Yan,Zhang, Li-Ping,Huang, Hui,Jiao, Jun-Ying,Xu, Ping-Zhen,Yao, Qiu-Yang,Yang, Li-Li,Gao, Ju,Gao, Li-Zhi,Zhang, Qun-Jie,Zhu, Ting,Xia, En-Hua,Shi, Chao,Liu, Yuan,Yao, Qiu-Yang,Zeng, Fan-Chun,Gao, Ju,Tao, Da-Yun,Wang, Yue-Ju,Bennetzen, Jeffrey L..

作者其他论文 更多>>

微信小程序