鱼类功能基因组学研究组
研究组组长：夏晓勤研究员
研究组成员：汪亚平 研究员 廖兰杰 高级实验师 黄容 副研究员 何利波 副研究员 吴南 副研究员 石米娟 副研究员 杨诚 助理研究员 李勇明 实验师 程莹寅 实验师 张婉婷 实验师
联系方式：
电话:027-68780119;68780916
电子邮箱:ljliao@ihb.ac.cn;xqxia@ihb.ac.cn
研究组介绍：
本研究组主要开展鱼类和甲壳类等水产动物抗病、生长、性控等经济性状遗传机制解析，关键分子标记挖掘，重要功能基因作用机理分析，新品种（系）培育等方面的研究工作，包括以下三个研究方向：
（1） 遗传育种相关基础数据整合与技术平台创新。开展遗传多样性种质收集、基因组测序、组装与注释；组学数据库与生物信息学分析平台建设；高通量低成本基因分型技术创新、种质鉴定，以及基于机器视觉的表型快速鉴定技术研发。
（2） 性状相关分子靶标精确定位与新品种（系）高效培育。针对抗病、生长、性控等经济性状，开展基于人工智能技术平台的基因型表型关联分析，精确定位性状相关分子标记和功能基因，用于鱼类、甲壳类优良养殖新品种（系）的高效培育。
（3） 经济性状网络调控机制精准解析与药物研发。聚焦水产病毒感染与免疫逃逸、宿主黏膜免疫反应与应答机制研究，精准解析经济性状网络调控分子机理，研发替抗中草药添加剂，绿色防控水产养殖病害。
学科组得到国家重点研发计划、科技创新-2030重大科技项目、国家自然科学基金项目、中国科学院战略性科技先导专项等项目支持。近5年发表SCI论文80余篇，获发明专利授权10余项。
代表性研究论文（#：并列第一作者，*：通讯作者）：
一、基因组学与转录组学基础研究
[1] Wang YP*, Lu Y, Zhang Y, Ning ZM, Li Y, Zhao Q, Lu HY, Huang R, Xia XQ, Feng Q, Liang XF, Liu KY, Zhang L, Lu TT, Huang T, Fan DL, Weng QJ, Zhu CR, Lu YQ, Li WJ, Wen ZR, Zhou CC, Tian QL, Kang XJ, Shi MJ, Zhang WT, Jang SH, Du FK, He S, Liao LJ, Li YM, Gui B, He HH, Ning Z, Yang C, He LB, Luo LF, Yang R, Luo Q, Liu XC, Li SS, Huang W, Xiao L, Lin HR*, Han B*, Zhu ZY*. The draft genome of the grass carp (Ctenopharyngodon idellus) provides genomic insights into its evolution and vegetarian diet adaptation. Nature Genetics, 2015, 47: 625-631.
[2] He W#,Shi M#,Xia X-Q,Zhang W,Yao W,Gao T. The chromosome-level genome assembly of goldstripe ponyfish (Karalla daura) reveals its similarity to Chinese sillago on contracted immune gene families. Frontiers in Marine Science,2022,9: 1049138.
[3] Duan Y,Zhang Q,Jiang Y,Zhang W,Cheng Y,Shi M*,Xia X-Q*. Dynamic transcriptional landscape of grass carp (Ctenopharyngodon idella) reveals key transcriptional features involved in fish development. International Journal of Molecular Sciences,2022,23: 11547.
[4] Yang C#,Chen L#,Huang R*,Gui B,Li YYu,Li YY,Li YM,Liao L,Zhu Z,Wang Y. Screening of genes related to sex determination and differentiation in mandarin fish (Siniperca chuatsi). International Journal of Molecular Sciences,2022,23(14):7692.
[5] He L#,Zhu D,Liang X,Li Y,Liao L,Yang C,Huang R,Zhu Z,Wang Y*. Multi-omics sequencing provides insights into age-dependent susceptibility of grass carp (Ctenopharyngodon idellus) to Reovirus. Frontiers in Immunology. 2021,12: 694965.
[6] Huang R#,Shi M#,Luo L,Yang C,Ou M,Zhang W,Liao L,Li Y,Xia X,Zhu Z,Wang Y*. De novo screening of disease-resistant genes from the chromosome-level genome of rare minnow using CRISPR-cas9 random mutation. GigaScience,2021,10(11):giab075.
[7] Ou M#,Huang R#,Yang C,Gui B,Luo Q,Zhao J,Li Y,Liao L,Zhu Z,Wang Y*,Chen K*. Chromosome-level genome assemblies of Channa argus and Channa maculata and comparative analysis of their temperature adaptability. GigaScience,2021;10: 1-11.
二、生物信息学工具与数据库开发
[8] Zhang L#,Li H#,Shi M*,Ren K,Zhang W,Cheng Y,Wang Y,Xia X-Q*. FishSNP: a high quality cross-species SNP database of fishes. Scientific Data,2024,11:286.
[9] Xia L#,Shi M#,Li H,Zhang W,Cheng Y,Xia X-Q*. PMSeeker: a scheme based on the greedy algorithm and the exhaustive algorithm to screen low-redundancy marker sets for large-scale parentage assignment with full parental genotyping. Biology,2024,13(2):100.
[10] Guo C#,Ye W#,Cao D,Shi M*,Zhang W,Cheng Y,Wang Y,Xia X-Q*. Unraveling the stereoscopic gene transcriptional landscape of zebrafish using FishSED,a fish spatial expression database with multispecies scalability. Science China Life Sciences,2023. DOI: 10.1007/s11427-023-2418-2.
[11] Guo C#,Duan Y#,Ye W,Zhang W,Cheng Y,Shi M*,Xia X-Q*,FishGET: a fish gene expression and transcriptome database with improved accuracy and visualization. iScience,2023,26: 106539.
[12] Guo C#,Ye W#,Shi M*,Duan Y,Zhang W,Cheng Y,Xia X-Q*. FishSCT: a zebrafish-centric database for exploration and visualization of fish single-cell transcriptome. Science China Life Sciences,2023,66(9):2185-2188.
[13] Li H,Shi M*,Ren K,Zhang L,Ye W,Zhang W,Cheng Y,Xia X-Q*. Visual Omics: a web-based platform for omics data analysis and visualization with rich graph-tuning capabilities. Bioinformatics,2023,39(1):btac777.
[14] Yang C#,Huang R*,Ou M,Gui B,Zhao J,He L,Li Y,Liao L,Chen K,Wang Y*. A rapid method of sex-marker discovery based on NGS and determination of the XX / XY sex-determination type in Channa maculate. Aquaculture,2020;528: 735499.
三、抗病毒、黏膜免疫以及其它疾病研究
[15] Liang X#,Wang Q,Wang H,Wang X,Chu P,Yang C,Li Y,Liao L,Zhu Z,Wang Y,He L*. Grass carp superoxide dismutases exert antioxidant function and inhibit autophagy to promote grass carp reovirus (GCRV) replication. International Journal of Biological Macromolecules,2024,256(Pt 2):128454.
[16] Liu Y#,Cao D#,Wu N*,Zhao X,Zhu Q,Su L,Altaf F,Zhang Q,Liu H,Li Y,Unger BH,Cheng Y,Zhang W,Li A,Wang Y,Xia X-Q*. Sinomenine improves resistance to foodborne enteritis and anti-bacteria mucosal immunity in grass carp. Aquaculture,2024,581: 740364.
[17] Zhao X#,Zhang L#,Wu N*,Liu Y,Xie J,Su L,Zhu Q,Unger BH,Altaf F,Hu Y,Ye W,Qiao Z,Cheng Y,Zhang W,Wang Y,Xia X-Q*. Gallic acid acts as an anti-inflammatory agent via PPARγ-mediated immunomodulation and antioxidation in fish gut-liver axis. Aquaculture,2024,578: 740142.
[18] Ouyang G,Yuan L,Xia X-Q,Zhang W,Shi M*. Transcriptomes of zebrafish in early stages of multiple viral invasions reveal the role of sterols in innate immune switch-on. International Journal of Molecular Sciences,2023,24: 4427.
[19] Zhao X#,Liu Y#,Xie J,Guo C,Li H,Cheng Y,Zhang W,Su L,Wu N*,Xia X-Q*. The manipulation of cell suspensions from zebrafish intestinal mucosa contributes to understanding enteritis. Frontiers in Immunology,2023,14: 1193977.
[20] Shan J#,Wang G#,Li H,Zhao X,Ye W,Su L,Zhu Q,Liu Y,Cheng Y,Zhang W,Wu N*,Xia X-Q*. The immunoregulatory role of fish specific type II SOCS via inhibiting metaflammation in gut-liver axis. Water Biology and Security,2023,2(2):100131.
[21] He L*,Wang Q,Liang X,Wang H,Chu P,Yang C,Li Y,Liao L,Zhu Z,Wang Y*. Grass carp reovirus induces formation of lipid droplets as sites for its replication and assembly. mBio. 2022,13(6):e0229722.
[22] He L*,Liang X,Wang Q,Yang C,Li Y,Liao L,Zhu Z,Wang Y*. Genome-wide DNA methylation reveals potential epigenetic mechanism of age-dependent viral susceptibility in grass carp. Immunity & Ageing. 2022,19(1):28.
[23] Xie J#,Li M#,Ye W,Shan J,Zhao X,Duan Y,Liu Y,Unger BH,Cheng Y,Zhang W,Wu N*,Xia X-Q*. Sinomenine hydrochloride ameliorates fish foodborne enteritis via α7nAchR mediated anti-inflammatory effect whilst altering microbiota composition. Frontiers in Immunology,2021,12: 766845.
[24] Li M#,Zhao X#,Xie J,Tong X,Shan J,Shi M,Wang G,Ye W,Liu Y,Unger BH,Cheng Y,Zhang W,Wu N*,Xia X-Q*. Dietary inclusion of seabuckthorn (Hippophae rhamnoides) mitigates foodborne enteritis in zebrafish through the gut-liver immune axis. Frontiers in Physiology,2022,13:831226.
[25] Chu P,He L*,Huang R,Liao L,Li Y,Zhu Z,Hu W,Wang Y*. Autophagy inhibits grass carp reovirus (gcrv) replication and protects Ctenopharyngodon idella kidney (CIK) cells from excessive inflammatory responses after gcrv infection. Biomolecules,2020,10: 1296-1318.
[26] Li Y,Huang R*,Chen L,Li Y,Li YM,Liao L,He L,Zhu Z,Wang Y. Characterization of SR-B2a and SR-B2b genes and their ability to promote GCRV infection in grass carp (Ctenopharyngodon idellus). Developmental & Comparative Immunology 2021;124: 104202.
[27] Chen L,Huang R*,Li Y,Li YM,Liao L,He L,Zhu Z,Wang Y. Genome-wide identification,evolution of Krüppel-like factors (klfs) and their expressions during GCRV challenge in grass carp (Ctenopharyngodon idella). Developmental & Comparative Immunology 2021;120: 104062.
四、生长与其它经济性状研究
[28] Ye W,Shi M*,Chen S,Duan Y,Jiang Y,Cheng Y,Zhang W,Chen J,Wang Y,Xia X-Q*. Transcriptome analysis revealed the existence of family-specific regulation of growth traits in grass carp. Genomics,2023,115(5):110706.
[29] Ye W,Shi M*,Ren K,Liu Y,Duan Y,Cheng Y,Zhang W,Xia X-Q*. Profiling the spatial expression pattern and ceRNA network of lncRNA,miRNA,and mRNA associated with the development of intermuscular bones in zebrafish. Biology,2023,12(1):75.
[30] Shi M#,Luo H#,Zhang W,Jiang Y,Chen J,Cheng Y,Hu W*,Xia X-Q*. A genome-wide linkage map and QTL mapping for growth traits of Asian rice-field eel (Monopterus albus). Aquaculture,2021,536: 736394.
[31] Huang X#,Jiang Y#,Zhang W,Cheng Y,Wang Y,Ma X,Duan Y,Xia L,Chen Y,Wu N,Shi M*,Xia X-Q*. Construction of a high-density genetic map and mapping of growth related QTLs in the grass carp (Ctenopharyngodon idellus). BMC Genomics,2020,21:313.
[32] Ye W,Duan Y,Zhang W,Cheng Y,Shi M*,Xia X-Q*. Comprehensive analysis of hub mRNA,lncRNA and miRNA,and associated ceRNA networks implicated in grass carp (Ctenopharyngodon idella) growth traits. Genomics,2021,113(6):4004-4014.
