中甸刺玫的叶绿体基因组特征及种内变异

Chloroplast genome features and intraspecific variation of Rosa praelucens

关键词:  中甸刺玫, 叶绿体基因组, 比较基因组, 简单重复序列, 核酸多态性, 密码子偏好

Key words:  Rosa praelucens, chloroplast genome, comparative genome, simple sequence repeats(SSRs), nucleotide polymorphism(P_i), codon preference

摘要:

中甸刺玫(Rosa praelucens)是云南香格里拉市的特有“极危”植物和国家二级重点保护植物,也是著名的高山花卉和重要的十倍体月季种质资源,种内存在丰富的表型多样性。为了澄清中甸刺玫种内表型变异的遗传背景,该文利用二代测序技术对40个不同表型的中甸刺玫代表性个体的叶绿体基因组进行测序、组装注释和比较分析。结果表明:(1)中甸刺玫的基因组序列长157 173～157 261 bp,植株间仅相差88 bp,共编码132个功能基因,主要为与光合作用和自我复制相关的基因。全部基因共由27 155个密码子编码,以A-和U-为末端的密码子较常见。(2)中甸刺玫的叶绿体基因组共鉴定出36个重复序列和73个简单重复序列(SSRs),后者大部分为单核苷酸SSRs,主要位于大单拷贝(LSC)区的基因间隔区。(3)中甸刺玫种内叶绿体全基因组的单倍型多样性为0.928±0.027,核酸多态性(P_i)为0.000 12; 位于LSC的petN-trnD、psaA-ycf3等基因间隔区,以及rps16和ycf1等基因的核酸多态性相对较高; 不同表型的代表性个体的叶绿体基因组间在结构上不存在大片段或基因的逆转或者丢失。该研究结果表明,中甸刺玫种内在叶绿体基因组大小、序列和结构等方面均高度保守,其种内丰富的表型多样性并非由叶绿体基因组变异而引起。

Abstract:

Rosa praelucens is a critically endangered alpine wild flower endemic to Shangri-La City of Yunnan Province. Rich in phenotypic diversity and with a high ploidy level of decaploid, R. praelucens is a very important rose germplasm resource. In order to clarify the genetic background of its phenotypic variation, the chloroplast genomes of 40 R. praelucens individual plants representing different phenotypes within the species were sequenced by using the Illumina HiSeq 2000 platform, and then assembled, annotated, compared and analyzed. The results were as follows:(1)Chloroplast genomes of R. praelucens were 157 173 - 157 261 bp in length, with a size difference of 88 bp among different individual plants. The genomes encoded 132 function genes, mainly related with photosynthesis and self-replication. A total of 27 155 codons, preferring using codon ending of A or U, were found in all the coding sequences.(2)A total of 36 repeats and 73 simple sequence repeats(SSRs)were detected in the chloroplast genome of R. praelucens. Most of the SSRs were mononucleotide type and located in the intergenic region of large single scale(LSC).(3)The haplotype diversity among the 40 chloroplast genomes was 0.928±0.027, and the nucleotide polymorphism(P_i)was 0.000 12. The intergenic region of petN-trnD and psaA-ycf3, gene rps16 and ycf1 were relatively more divergent. No reverse or loss of large DNA fragments and genes were found among the chloroplast genomes of different individuals. These results indicate that the chloroplast genomes are highly conserved in size, sequence and structure within R. praelucens. The rich intraspecific phenotypic diversity is not caused by the variation of chloroplast genomes among different individual plants.