板栗和猕猴桃NBS-encoding基因家族的全基因组分析
发布时间：2018-12-21 15:25
【摘要】：NBS-encoding基因家族包括NBS-only类型和NBS-LRR类型的基因,且NBS-LRR基因家族是植物中最大的抗病基因家族之一,在抵御病原体的侵染过程中起到重要的作用。对NBS-encoding基因家族的分析研究对植物抗病基因的鉴定和筛选具有重要的意义。板栗和猕猴桃是我国重要的经济果树,都含有较高的营养价值,但是病害严重制约板栗和猕猴桃产业的发展。所以,对板栗和猕猴桃的抗病基因的研究对于优化农业生产显得尤为重要。本研究利用生物信息学的方法,从基因鉴定、家族划分、复制时间、复制方式、选择压和启动子区域的顺式调控元件分析等几个方面,对板栗和猕猴桃的NBS-encoding基因进行了分析。1、本研究中我们从板栗全基因组中鉴定出519个NBS-encoding基因,其中含有374个NBS-LRR基因,复制时间相对古老,且复制方式为物种内特异性复制。我们计算了Ka/K 来判断基因受到的选择压作用,结果表明:大部分家族受到纯化选择,也有小部分家族受到了正选择压力。以Ks = 0.4～0.5为界,越新近和越古老的基因受到越大的选择压力作用。另外,我们发现RPW8-NBS-encoding基因群体是独立于non-TIR-NBS-encoding基因的群体,且位于进化树相对基部的位置。此外,NBS-encoding家族基因的启动子区域含有很多与植物抗性防御相关的顺式调控元件。2、我们利用同样的方法,在猕猴桃基因组中共鉴定出96个NBS-encoding基因,其中含有74个NBS-LRR基因。Ks频率分布显示,该家族的复制时间是新近的,而且越新近的基因在进化过程中受到越小的选择压作用。绝大多数的基因家族的Ka/Ks小于1,说明纯化选择起重要的作用;同时,鉴定出6个基因家族中125个氨基酸位点受到正选择作用。
[Abstract]:NBS-encoding gene family includes NBS-only type and NBS-LRR type gene, and NBS-LRR gene family is one of the largest resistance genes in plants, which plays an important role in resisting pathogen infection. The analysis of NBS-encoding gene family plays an important role in the identification and screening of plant disease resistance genes. Chinese chestnut and kiwifruit are important economic fruit trees in China, both of which contain high nutritional value, but the disease seriously restricts the development of Chinese chestnut and kiwifruit industry. Therefore, the study of resistance genes of Chinese chestnut and kiwifruit is particularly important for optimizing agricultural production. In this study, bioinformatics was used to analyze gene identification, family division, replication time, replication mode, selection of pressure and analysis of cis regulatory elements in promoter regions. The NBS-encoding genes of Chinese chestnut and kiwifruit were analyzed. 1. In this study, 519 NBS-encoding genes were identified from the whole genome of Chinese chestnut, including 374 NBS-LRR genes. And the way of replication is specific within species. We calculated Ka/K to determine the selection pressure of genes. The results showed that most families were selected for purification and a few families were under positive selection pressure. The more recent and the older the gene is, the greater the selection pressure is when the Ks = 0. 4 ~ 0. 5 is used as the boundary. In addition, we found that the RPW8-NBS-encoding gene population is independent of the non-TIR-NBS-encoding gene and is located at the base of the evolutionary tree. In addition, the promoter region of the NBS-encoding family gene contains many cis-regulatory elements related to plant resistance defense. 2. Using the same method, 96 NBS-encoding genes were identified in kiwifruit genome. The Ks frequency distribution showed that the replication time of the family was recent and the more recent genes were subjected to less selective pressure during evolution. The Ka/Ks of most gene families was less than 1, which indicated that purification selection played an important role, and 125 amino acid sites in 6 gene families were positively selected.
【学位授予单位】：南京农业大学
【学位级别】：硕士
【学位授予年份】：2016
【分类号】：S664.2;S663.4
本文编号：2389095
[Abstract]:NBS-encoding gene family includes NBS-only type and NBS-LRR type gene, and NBS-LRR gene family is one of the largest resistance genes in plants, which plays an important role in resisting pathogen infection. The analysis of NBS-encoding gene family plays an important role in the identification and screening of plant disease resistance genes. Chinese chestnut and kiwifruit are important economic fruit trees in China, both of which contain high nutritional value, but the disease seriously restricts the development of Chinese chestnut and kiwifruit industry. Therefore, the study of resistance genes of Chinese chestnut and kiwifruit is particularly important for optimizing agricultural production. In this study, bioinformatics was used to analyze gene identification, family division, replication time, replication mode, selection of pressure and analysis of cis regulatory elements in promoter regions. The NBS-encoding genes of Chinese chestnut and kiwifruit were analyzed. 1. In this study, 519 NBS-encoding genes were identified from the whole genome of Chinese chestnut, including 374 NBS-LRR genes. And the way of replication is specific within species. We calculated Ka/K to determine the selection pressure of genes. The results showed that most families were selected for purification and a few families were under positive selection pressure. The more recent and the older the gene is, the greater the selection pressure is when the Ks = 0. 4 ~ 0. 5 is used as the boundary. In addition, we found that the RPW8-NBS-encoding gene population is independent of the non-TIR-NBS-encoding gene and is located at the base of the evolutionary tree. In addition, the promoter region of the NBS-encoding family gene contains many cis-regulatory elements related to plant resistance defense. 2. Using the same method, 96 NBS-encoding genes were identified in kiwifruit genome. The Ks frequency distribution showed that the replication time of the family was recent and the more recent genes were subjected to less selective pressure during evolution. The Ka/Ks of most gene families was less than 1, which indicated that purification selection played an important role, and 125 amino acid sites in 6 gene families were positively selected.
【学位授予单位】：南京农业大学
【学位级别】：硕士
【学位授予年份】：2016
【分类号】：S664.2;S663.4
【参考文献】
相关期刊论文 前1条
1 刘金灵;刘雄伦;戴良英;王国梁;;植物抗病基因结构、功能及其进化机制研究进展(英文)[J];遗传学报;2007年09期
，本文编号：2389095
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