板栗线粒体基因组的组装与比较分析
Assembly and comparative analysis of the complete mitochondrial genome of Castanea mollissima Blume
[目的]板栗(Castanea mollissima Blume),壳斗科,是原产于中国和朝鲜的一种坚果树种,也是食用栗属品种改良的重要遗传资源,在了解栗属物种起源和进化方面具有重要地位。板栗叶绿体基因组已被测序,而线粒体基因组迄今尚未被探索。[方法]使用BGI的二代测序数据和Nanopore 的三代测序数据,采用混合组装的策略组装板栗线粒体基因组,并与其相关物种的线粒体基因组进行比较分析。[结果]板栗线粒体基因组是一个多环结构,有两个长度分别为 363,232 bp和 24,806 bp的环状分子。该基因组包括 35个蛋白质编码基因、19个tRNA基因和3个rRNA基因。在整个板栗线粒体基因组中共鉴定了139个SSRs.叶绿体和线粒体基因组之间同源片段的总长度为 5,766 bp,占线粒体基因组的 1.49%。共预测到 484 个RNA编辑位点,均为出C-U的编辑。[结论]系统发育分析发现,板栗与木姜叶柯(Lithocarpus litseifolius)和麻栎(Quercus acutissima)的亲缘关系较近。板栗、麻栎、木姜叶柯、欧洲水青冈(Fagus sylvatica)和胡桃楸(Juglans mandshurica)的线粒体基因组序列在排列顺序上极度不保守,经历了极其频繁的基因组重组。本研究首次报道了板栗的线粒体基因组,作为栗属重要经济植物的参考基因组,为分子育种研究提供一定的信息。
[Objective]The Chinese chestnut,Castanea mollissima Blume,is a nut-bearing tree belonging to the Fagaceae family and is native to China and North Korea.C.mollissima is an important genetic resource for the improvement of edible chestnut varieties and occupies an important position in understanding the origin and evolution of chestnut species.The C.mollissima chloroplast genome has been sequenced;however,the mitochondrial genome(mitogenome)is to date unexplored.[Method]We characterized the C.mollissima mitogenome,assembling it using reads from BGI and Nanopore sequencing platforms,and analyzed in comparison with mitochondrial genomes of closely related species.[Result]The C.mollissima mitogenome is a polycyclic structure with two circular molecules of 363,232 bp and 24,806 bp in length.The genome comprises 35 unique protein-coding genes,19 tRNA genes and 3 rRNA genes.We identified 139 SSRs across the whole C.mollissima mitogenome.The total length of homologous fragments between the chloroplast and mitochondrial genomes was 5,766 bp,accounting for 1.49%of the mitogenome.A total of 484 RNA editing sites were predicted in C.mollissima,all exhibiting C-to-U RNA editing.[Conclusion]Phylogenetic analysis of the mitogenomes of related species revealed that C.mollissima was closely related to Lithocarpus litseifolius(Hance)Chun and Quercus acutissima Carruth.The mitogenome sequences of C.mollissima,L.litseifolius,Q.acutissima,Fagus sylvatica L.,and Juglans mandshurica Maxim.are not conserved in their alignments,suggesting they have undergone frequent genome reorganization.In this study,we report for the first time the mitogenome of C.mollissima,which serves as a reference genome for economically important plants of the genus Castanea and also provides information to inform molecular breeding.
刘丹;
山东省林草种质资源中心 济南 250102;
Castanea mollissima mitogenome repeated sequences phylogenetic relationship.
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