中国水产科学研究院机构知识库

De novo assembly and characterization of the Hucho taimen transcriptome

收藏
分享
全文链接

文献类型：外文期刊

作者： Tong, Guang-Xiang ¹ ; Xu, Wei ¹ ; Zhang, Yong-Quan ¹ ; Zhang, Qing-Yu ¹ ; Yin, Jia-Sheng ¹ ; Kuang, You-Yi ¹ ;

作者机构： 1.Chinese Acad Fishery Sci, Heilongjiang River Fisheries Res Inst, Harbin, Heilongjiang, Peoples R China

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.

相关文献

[1]线粒体序列分析黑龙江流域哲罗鲑的种群遗传结构. 匡友谊,佟广香,尹家胜,李池陶,曹顶臣,孙效文. 2009

[2]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

[3]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.

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

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

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

[7]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.

[8]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.

[9]基于RNA-seq技术的江鳕转录组SSR位点信息分析. 孟玮,蒋艳琳,张林,杨天燕,周剑光. 2019

[10]鼠尾藻基因表达对干露胁迫响应的初步研究. 刘福利,王飞久,孙修涛,汪文俊,梁洲瑞,马兴宇. 2014

[11]不同规格黄鳍金枪鱼红肌转录组比较分析. 闫路路,郭杰匀,赵超,王鹏飞,张博,邱丽华,陈作志. 2024

[12]黑斑原鮡（Glyptosternum maculatum）皮肤RNA-Seq数据中补体样组分分析. 张颖,马波,李宝海,尹家胜,储明星. 2022

[13]Development of 15 novel dinucleotide microsatellite markers in the Senegalese sole Solea senegalensis. Chen, Song-Lin,Shao, Chang-Wei,Xu, Gen-Bo,Liao, Xiao-Lin,Tian, Yong-Sheng. 2008

[14]Rapid isolation and characterization of microsatellites from the genome of pearl oyster (Pinctada martensi Dunker). Kuang, Youyi,Tong, Guangxiang,Yan, Xuechun,Sun, Xiaowen. 2009

[15]Development of polymorphic microsatellite markers in Sardinella aurita by 5 '-anchored PCR technique. Ma, Chunyan,Jiang, Wei,Ma, Hongyu,Feng, Chunlei,Zhang, Xun,Ma, Lingbo. 2015

[16]Development and testing of 13 polymorphic microsatellite markers in Larimichthys polyactis (Sciaenidae) using 5 ' anchored PCR. Ma, C. Y.,Ma, H. Y.,Ma, L. B.. 2011

[17]Isolation and characterization of 31 polymorphic microsatellite markers in barfin flounder (Verasper moseri) and the cross-species amplification in spotted halibut (Verasper variegatus). Ma, Hongyu,Chen, Songlin,Ma, Hongyu. 2009

[18]Polymorphic microsatellite markers in the false kelpfish Sebastiscus marmoratus: isolation, characterization, and cross-species amplification. Liu, H. B.,Liu, H. B.,Liu, S. F.,Ye, J. B.,Yuan, Y. J.,Zhuang, Z. M.,Yuan, Y. J.,Ding, S. X.. 2014

[19]Development of thirty-four novel polymorphic microsatellite markers in Coilia ectenes (Clupeiformes: Engraulidae) and cross-species amplification in two closely related taxa. Chen, Fang,Zeng, Liyan,Cheng, Qiqun,Chen, Fang. 2012

[20]Development and characterization of twelve microsatellite markers for miiuy croaker. Ma, Chunyan,Ma, Hongyu,Ma, Lingbo,Li, Shujuan,Jiang, Wei. 2013

作者其他论文更多>>

Assessment of the bioflocculant production and safety properties of Metabacillus hrfriensis sp. nov. based on phenotypic and whole-genome sequencing analysis

作者：Zhang, Rui;Zhao, Zhigang;Luo, Liang;Wang, Shihui;Guo, Kun;Xu, Wei;Zhang, Rui;Zhao, Zhigang;Luo, Liang;Wang, Shihui;Guo, Kun;Xu, Wei

关键词：Bioflocculants; EPS; Bioflocculant-production bacteria; Safety assessment; Metabacillus
Application and evaluation of biochar/attapulgite composites for controlling nitrogen pollution and ecological response in a small lentic system: Implications water/sediment quality management in standing water bodies

作者：Huang, Xiaoli;Zhou, Wenjing;Cui, Kanli;Huo, Tangbin;Geng, Longwu;Xu, Wei;Huang, Xiaoli;Liu, Shouxin;Huang, Xiaoli;Huo, Tangbin;Zhou, Wenjing;Hu, Qi;Cui, Kanli;Hao, Qirui;Zhao, Xinyue;Wang, Yumei

关键词：Biochar-attapulgite composite; Ammonia nitrogen; Water quality; Plankton; Microbial community structure; Pond restoration
Dietary creatine improves the growth performance, antioxidant capacity and energy metabolism of common carp (Cyprinus carpio) by activating glucose metabolism and the Nrf2-Keap1 pathway

作者：Xing, Meiqi;Shang, Xinchi;Geng, Longwu;Wei, Haijun;Che, Xinghua;Shi, Xiaodan;Xu, Wei;Xing, Meiqi;Shang, Xinchi;Geng, Longwu;Wei, Haijun;Che, Xinghua;Shi, Xiaodan;Xu, Wei;Shang, Xinchi;Li, Zhengwei;He, Hailong

关键词：Creatine; Growth performance; Energy metabolism; Antioxidant
Transcriptome analysis reveals the candidate genes associated with skin color variation in Luciobarbus capito

作者：Geng, Longwu;Shang, Xinchi;Wei, Haijun;Tong, Guangxiang;Xu, Wei;Kuang, Youyi;Geng, Longwu;Shang, Xinchi;Wei, Haijun;Tong, Guangxiang;Xu, Wei;Kuang, Youyi

关键词：Transcriptomics; Pigmentation; Melanin; Carotenoids; Luciobarbus capito
Chronic Cr(VI) exposure-induced biotoxicity involved in liver microbiota-gut axis disruption in Phoxinus lagowskii Dybowski based on multi-omics technologies

作者：Shang, Xinchi;Che, Xinghua;Ma, Kai;Sun, Zhi Peng;Xu, Wei;Zhang, Yongquan;Guo, Wenxue;Wang, Shanshan;Shang, Xinchi

关键词：Hepatic metabolome; Cr(VI) stress; Gut microbial; LPS; Antioxidant
Transcriptomic analysis reveals that selenium-enriched Lactobacillus plantarum alleviates high -salinity stress in common carp through lipid metabolism and ferroptosis signalling pathways

作者：Shang, Xinchi;Che, Xinghua;Geng, Longwu;Zhang, Qing;Wei, Haijun;Li, Wang;Shi, Xiaodan;Xu, Wei;Shang, Xinchi;Che, Xinghua;Geng, Longwu;Zhang, Qing;Wei, Haijun;Li, Wang;Shi, Xiaodan;Xu, Wei;Shang, Xinchi;Che, Xinghua;Geng, Longwu;Zhang, Qing;Wei, Haijun;Li, Wang;Shi, Xiaodan;Xu, Wei;Shang, Xinchi

关键词：High salinity stress; Selenium-enriched Lactobacillus plantarum; Oxidative stress; Ferroptosis; Cysteine/glutamate antiporter system (Xc(-)); Glutathione peroxidase 4 (GPX4)
Effects of dietary Lycium barbarum polysaccharide on the growth, antioxidant, immunity response, and intestinal microbiota in Bulatmai barbel (Luciobarbus capito)

作者：Luo, Liang;Meng, Xianwei;Wang, Shihui;Zhang, Rui;Guo, Kun;Xu, Wei;Zhao, Zhigang;Luo, Liang;Wang, Wei

关键词：Bulatmai barbel; Growth; Immunity; Intestinal flora; Lycium barbarum

De novo assembly and characterization of the Hucho taimen transcriptome

作者其他论文 更多>>

Assessment of the bioflocculant production and safety properties of Metabacillus hrfriensis sp. nov. based on phenotypic and whole-genome sequencing analysis

Application and evaluation of biochar/attapulgite composites for controlling nitrogen pollution and ecological response in a small lentic system: Implications water/sediment quality management in standing water bodies

Dietary creatine improves the growth performance, antioxidant capacity and energy metabolism of common carp (Cyprinus carpio) by activating glucose metabolism and the Nrf2-Keap1 pathway

Transcriptome analysis reveals the candidate genes associated with skin color variation in Luciobarbus capito

Chronic Cr(VI) exposure-induced biotoxicity involved in liver microbiota-gut axis disruption in Phoxinus lagowskii Dybowski based on multi-omics technologies

Transcriptomic analysis reveals that selenium-enriched Lactobacillus plantarum alleviates high -salinity stress in common carp through lipid metabolism and ferroptosis signalling pathways

Effects of dietary Lycium barbarum polysaccharide on the growth, antioxidant, immunity response, and intestinal microbiota in Bulatmai barbel (Luciobarbus capito)

意 见 箱

作者其他论文更多>>

意见箱