柑橘特异基因的鉴定及其起源方式分析

发布时间：2018-04-20 12:15

本文选题：柑橘 + 特异基因　；参考：《华中农业大学》2016年硕士论文

【摘要】：甜橙(Citrus sinensis)所在的柑橘属(Citrus L)共有几十个物种。随着甜橙基因组草图的完成,越来越多的柑橘属基因组序列被测定,如克里曼丁(C.clemetina)、蚝壳刺(Severinia buxifolia)、枸橼(C.medica)、宜昌橙(C.ichangenisis)、晚白柚(Citrus maxima)等。这些工作对于推进柑橘属基因组的比较基因组学、功能基因组学和进化基因组学研究有重要作用。通过比较基因组学分析,找到一些物种中的特异基因,将有助于理解柑橘属种间差异以及相关特异性状产生的方式;对柑橘属不同物种及其近缘物种间特异基因的进化和功能等研究,可为揭示柑橘属不同物种间表型和适应性差异的分子基础提供依据。在这个基础上,为了进一步从生物信息学的角度探索柑橘特异基因的物种特异性,本论文主要包括三个方面内容:柑橘特异蛋白编码基因的鉴定及特征分析;柑橘特异蛋白编码基因的起源研究;柑橘特异mi RNA的起源研究。主要结果如下:(1)柑橘特异蛋白编码基因的鉴定及特征分析。通过比较基因组学的分析方法,结合已经测序的41个植物物种基因组数据和已公布的EST数据库筛选出柑橘特异基因,在甜橙基因组中鉴定了296个保守柑橘特异基因(CCSG)和1039个甜橙特异蛋白编码基因(CSG)。相对于柑橘进化保守基因(CEC),它们具有基因序列短,外显子少,高GC含量,较少转录本支持,较少功能注释结果等特征。(2)柑橘特异蛋白编码基因的起源研究。新基因起源的分子机制主要有基因复制(GD)、外显子重排(EDS)、可移动元件(TE)等。参考这些机制,本文对柑橘特异基因的起源问题进行了初步探索。得到的102对大片段复制(LSG)中分别包含了45个CCSG和162个CSG,猜测其可能的起源方式是GD;得到71个CCSG和119个CSG显示其产生可能与TE相关;得到1个CCSG和8个CSG显示经历了EDS事件。(3)柑橘特异mi RNA的起源研究。根据甜橙全基因组mi RNA的鉴定结果及其相应物种特异的38个mi RNA家族,探索了其基因家族的扩张模式,其中13个基因家族显示有串联重复(TD)事件发生,10个基因家族显示有大片段复制(LSD)事件,为研究柑橘新起源的mi RNA基因家族的进化和功能提供参考。
[Abstract]:There are dozens of species in Citrus L., home to Citrus Sinensis. With the completion of the complete genome sketch of sweet orange, more and more citrus genome sequences have been sequenced, such as C. clemetina, Severinia buxifolia, C. medica, C. ichangeniensis, Citrus Maxima and so on. These works play an important role in promoting comparative genomics, functional genomics and evolutionary genomics of citrus genomes. By comparative genomics analysis, the identification of specific genes in some species will help to understand the differences among citrus species and the ways in which specific traits are produced. Studies on the evolution and function of specific genes among different species and their close relatives of Citrus may provide a basis for revealing the molecular basis of phenotypic and adaptive differences among different species of Citrus. On this basis, in order to further explore the species specificity of citrus specific genes from the perspective of bioinformatics, this paper mainly includes three aspects: identification and characterization of citrus specific protein coding genes; Studies on the origin of citrus specific protein encoding gene and the origin of citrus specific mi RNA. The main results are as follows: 1) Identification and characterization of citrus specific protein coding gene. Citrus specific genes were screened by comparative genomics analysis, combined with genomic data of 41 plant species that had been sequenced and published EST database. A total of 296 conserved citrus specific genes (CCSGG) and 1039 orange-specific protein encoding genes (CSGG) were identified in the genome of sweet orange. Compared with the conserved citrus gene (CECN), they have the characteristics of short sequence, less exons, higher GC content, less transcripts, less functional annotation, etc.) the origin of citrus specific protein coding genes is studied. The molecular mechanisms of the origin of the new gene include gene replication, exon rearrangement, and transportable elements, etc. Referring to these mechanisms, the origin of citrus specific genes was preliminarily explored. The 102 pairs of LSGs contained 45 CCSG and 162 CSGs respectively, and 71 CCSG and 119 CSG showed that they might be related to te. One CCSG and eight CSG were obtained to show the origin of citrus specific mi RNA. Based on the identification of the whole genome mi RNA of sweet orange and the 38 species specific mi RNA families, the expansion pattern of its gene family was explored. Among them, 13 gene families showed tandem repeat (td) events, and 10 showed large fragment replicas (LSD) events, which provided a reference for studying the evolution and function of the mi RNA gene family of citrus.
【学位授予单位】：华中农业大学
【学位级别】：硕士
【学位授予年份】：2016
【分类号】：S666

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