光亮橡胶树叶绿体基因组测序组装与注释  

Sequencing,assembly and annotation of chloroplast genome of Hevea nitida

作　　者：牛迎凤 李国华[1] 刘紫艳 郑诚 柳觐[1] NIU Yingfeng;LI Guohua;LIU Ziyan;ZHENG Cheng;LIU Jin(Yunnan Institute of Tropical Crops,Xishuangbanna 666100,Yunnan,China)

机构地区：[1]云南省热带作物科学研究所,云南景洪666100

出　　处：《经济林研究》2020年第4期62-71,共10页Non-wood Forest Research

基　　金：国家自然科学基金项目(32060347);云南省现代农业橡胶产业技术体系项目(2020KJTX008-01);云南省热带作物科技创新体系建设项目(RF2020)。

摘　　要：【目的】为了研究光亮橡胶树叶绿体基因组序列特征,从基因组层面评价光亮橡胶树的育种可利用性,从而为橡胶树近缘野生种的深度评价和有效利用提供参考依据。【方法】以光亮橡胶树嫩叶为材料,通过提取高质量基因组DNA、构建测序文库、illumina HiSeq 2000测序、叶绿体基因组拼接组装、生物信息学注释,获得了完整的光亮橡胶树叶绿体基因组图谱,并将其与大戟科其他12个已完成叶绿体基因组测序的物种进行了进化分析。【结果】光亮橡胶树叶绿体基因组为典型的双链环状结构,其大小为161124 bp,由1个大单拷贝区域、1个小单拷贝区域和2个反向重复区域这4个区域组成;光亮橡胶树叶绿体基因组包含A碱基51495个、T碱基52022个、G碱基28915个、C碱基28692个,GC含量为35.75%;通过生物信息学注释共得到134个基因,其中,86个为蛋白编码基因,4个为假基因,36个为tRNA基因,8个为rRNA基因;从基因功能来看,86个蛋白编码基因主要参与光合系统Ⅰ、光合系统Ⅱ、细胞色素b/f复合体、ATP合成酶、NADH脱氢酶、核糖体蛋白、RNA聚合酶等生物学过程;利用叶绿体基因组蛋白编码序列与大戟科中其他12种植物构建了系统发育树,结果发现,橡胶树属4个种之间的亲缘关系非常密切。【结论】对于橡胶树远缘杂交育种而言,光亮橡胶树具有潜在的利用价值。【Objective】The characteristics of chloroplast genome sequence of Hevea nitida was studied,and its breeding availability was evaluated based on genome in order to provide a reference for further evaluation and effective utilization of wild relative species of H.brasiliensis.【Method】The complete chloroplast genome map of H.nitida was obtained for the first time in the world by extracting high quality genomic DNA,constructing sequencing library,Illumina HiSeq 2000 sequencing,and bioinformatics assembly and annotation.The phylogenetic relationship among H.nitida and 12 other Euphorbiaceae species which chloroplast genomes being sequenced were analyzed.【Result】The chloroplast genome of H.nitida was a typical double-stranded ring with 161124 bp in size and 4 regions:one large single-copy region,one small single-copy region and two inverted repeats regions.The chloroplast genome including 51495 A,52022 T,28915 G and 28692 C,with the GC content of 35.75%.A total of 134 genes were annotated by bioinformatics,including 86 protein-coding genes,4 pseudogenes,36 tRNA genes and 8 rRNA genes.According to gene function,86 protein coding genes mainly involved in Photosynthetic systemⅠ,Photosynthetic systemⅡ,Cytochrome B/f complex,ATP synthase,NADH dehydrogenase,Ribosomal proteins,RNA polymerase and other biological processes.A phylogenetic tree was constructed among H.nitida and 12 other Euphorbiaceae species using the protein coding sequence of chloroplast genome,it was found that the genetic relationship among these four species of Hevea genus was very close.【Conclusion】H.nitida has a potential value for distant hybridization breeding of H.brasiliensis.

关 键 词：光亮橡胶树 叶绿体基因组 测序 进化分析 

分 类 号：S602.4[农业科学—园艺学] S794.1