山雀科鸟类高海拔物种免疫基因的趋同放松选择研究

批准号:
32000290
项目类别:
青年科学基金项目
资助金额:
24.0 万元
负责人:
季妍竹
依托单位:
学科分类:
动物进化与发育
结题年份:
2023
批准年份:
2020
项目状态:
已结题
项目参与者:
季妍竹
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中文摘要
由于高寒、缺氧及强紫外线辐射,青藏高原的病原微生物多样性及数量可能降低,加上病原微生物与宿主免疫功能的协同演化的现象,在长期演化中高原适应物种有可能伴随免疫功能的弱化,在基因组层面,可表现为高原物种MHC基因遗传多样性的减少,和免疫系统信号转导基因的松弛选择。山雀科鸟类在高低海拔均有分布,是研究高原适应的良好实验对象。为获得山雀科物种的MHC序列,本研究对5个山雀科物种的基因组进行三代测序,注释和提取MHC基因序列,并以此设计引物,在19个山雀科鸟类的种群层面进行MHC基因的扩增子测序,深入挖掘各物种MHC基因遗传多样性。同时利用已有数据,在全基因组水平获得19个山雀科物种的免疫系统信号转导基因的松弛选择强度。最后,利用统计模型,对于这19个山雀科物种,在考虑有效种群大小的前提下,探究MHC基因的遗传多样性与免疫系统基因的松弛选择强度是否和海拔相关,揭示高海拔鸟类免疫系统是否有弱化的特点。
英文摘要
Characterized by low temperature, hypoxia, and strong ultraviolet radiation, Qinghai-Tibet Plateau may have fewer and lower number of pathogens compared to those of lowland area of the same latitude. The Red Queen Hypothesis, which describes the co-evolution between hosts and pathogens, predicts that species interacting with few pathogens may have weakened immune system. This means the immune genes in QTP species may evolve under low level of natural selection. Specifically, for genes such as MHC, low level of natural selection is equivalent to few alleles and low level of genetic diversity. For signaling genes of the immune system, low level of selection may correspond to relaxed selection. Here we will focus on the molecular evolution of immune genes in the genus Paridae, of which several species are distributed on the QTP whereas others distributed in low-altitude area or in between. To facilitate MHC characterization, we will first generate high-quality genome assemblies of five representative parid species using PacBio sequencing platform with the addition of available Illumina data in the lab. The sequence and copy number of MHC will be characterized from genome assemblies. Furthermore, to genotype MHC genes in other parid species, primers will be designed based on third-gen genome assemblies. With the primers, amplicon sequencing will be carried out to genotype MHCs in multiple individuals for each of 19 parid species. We will also identify signaling genes of the immune system in 19 parid species using available Illumina data. Strength of relaxed selection of each gene will be calculated using RELAX. Lastly, we will use multiple regression models to predict whether MHC diversity and the strength of relaxed selection in immune signaling genes are correlated with altitude and effective population size in the 19 parid species.
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专利列表
Orthologous microsatellites, transposable elements, and DNA deletions correlate with generation time and body mass in neoavian birds.
直系同源微卫星、转座元件和 DNA 缺失与新鸟类的世代时间和体重相关
DOI:10.1126/sciadv.abo0099
发表时间:2022-09-02
期刊:Science advances
影响因子:13.6
作者:
通讯作者:
DOI:10.1073/pnas.2023918118
发表时间:2021-12-14
期刊:Proceedings of the National Academy of Sciences of the United States of America
影响因子:11.1
作者:Cheng Y;Miller MJ;Zhang D;Xiong Y;Hao Y;Jia C;Cai T;Li SH;Johansson US;Liu Y;Chang Y;Song G;Qu Y;Lei F
通讯作者:Lei F
DOI:10.1016/j.isci.2022.103899
发表时间:2022-03-18
期刊:iScience
影响因子:5.8
作者:Chen X;Ji Y;Cheng Y;Hao Y;Lei X;Song G;Qu Y;Lei F
通讯作者:Lei F
国内基金
海外基金
