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科尔希小麦叶绿体全基因组的测序及其特征分析
Sequencing and Charac-terization of the Whole Chloroplast Genome of Triticum paleocolchicum Men.

DOI: 10.12677/HJCB.2019.92004, PP. 22-31

Keywords: 科尔希小麦，叶绿体，系统进化，RNA编辑
Triticum paleocolchicum, Chloroplast, Phylogenetic Relationship, RNA Editing

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Abstract:

科尔希小麦(Triticum paleocolchicum Men.)是一种特殊类型的四倍体小麦，作为小麦的原始类型，在普通六倍体小麦的起源、进化以及遗传改良中具有重要地位。目前，有关科尔希小麦的基因组信息及序列资源相当有限。为了丰富科尔希小麦的分子遗传信息，本研究利用Illumina Novaseq平台对科尔希小麦基因组DNA进行了测序，然后以中国春叶绿体基因组为参考，组装获得了科尔希小麦的叶绿体基因组全长序列。特征分析发现，科尔希小麦叶绿体基因组全长为136,445 bp，具有典型的高等植物叶绿体基因组环状四分体结构，由一个长度分别为79,993 bp的长单拷贝区(Large single copy, LSC)、一个12,832 bp的短单拷贝区(small single copy, SSC)和一对21,815 bp的反向重复序列(Inverted repeat, IR)构成；基因注释发现其编码了109个非冗余基因，包括76个蛋白编码基因，29个tRNA基因以及4个rRNA基因，其中19个位于IR区而具有两个拷贝；这些基因中，有16个基因具有内含子，其中ycf3含有2个内含子；进一步，对其RNA编辑位点进行了预测，发现15个基因存在RNA编辑，共预测到了35个RNA编辑位点，这些特征与其他小麦属物种的叶绿体基因组类似。最后，基于叶绿体全基因组序列构建了进化树，发现科尔希小麦与所有AABB型的小麦聚为一类，而AAGG型的提莫菲维小麦为单独一类，这与他们的亲缘关系一致。本研究丰富了科尔希小麦的序列资源，为其分子鉴定、标记开发以及系统发育的研究提供了重要数据。
 Triticum paleocolchicum Men. is one of the specific tetraploid wheats, which plays a vital role in the origin, domestication and evolution of common wheat as the primitive relatives. At present, the genetic information and sequence resource of it is very limited, hindering the further genetic and evolutionary research. To enrich the genetic sequences, we sequenced and assembled the complete chloroplast (cp) genome sequence of Triticum paleocolchicum using the Illumina sequencing. The assembled cp genome is 136,445 bp in size, consisting of four parts, namely LSC (79,993 bp), SSC (12,832 bp) and two IRs (21,815 bp). Gene annotation found that it encoded 109 non-redundant genes, including 76 protein-coding genes, 29 tRNA genes and 4 rRNA genes, 19 of which were located in the IR region with two copies. Of these genes, 16 have introns, of which ycf3 contains two introns. Furthermore, the RNA editing sites of this genome were also predicted and 15 genes were found to have RNA editing sites and a total of 35 RNA editing sites were predicted, which were similar to that of other wheat relatives. Finally, an evolutionary tree was constructed based on the whole chloroplast genome sequence and it showed that Triticum paleocolchicum and other species with AABB were clustered together, while separated with Triticum timopheevii wheat (AAGG). This study enriched the sequence resources of
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