摘要: |
中甸刺玫(Rosa praelucens Byhouwer)是云南香格里拉县的特有“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,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、组装和比较分析,结果表明:(1)中甸刺玫的基因组序列长157 173~157 261bp,植株间仅相差88bp,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,后者大部分为单核苷酸SSRs,主要位于大单拷贝区的基因间隔区。(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,核酸多态性为0.00012;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。研究结果表明中甸刺玫种内在叶绿体基因组大小、序列和基因结构等方面均高度保守,其种内丰富的表型多样性不是由于叶绿体基因组的变异。 |
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 |
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基金项目:国家自然科学基金(31972443);云南省高层次科技人才及创新团队选拔专项(202305AS350002)。第一作者:王其刚 (1977 - ),硕士,研究员,研究方向为月季遗传育种,(E-mail)171068976@qq.com。*通信作者:蹇洪英 (1976 - ),博士,研究员,研究方向为月季种质资源研究与利用,(E-mail)ynwildflower@aliyun.com。 * |
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Chloroplast genome features and intraspecific variation of Rosa praelucens Byhouwer |
WANG Qigang1, CAO Shirui1, WANG Huichun1, MA Changle2, YAN Huijun1, QIU Xianqin1, JIN Weikun1, JIAN Hongying3,4,5
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Abstract: |
Rosa praelucens Byhouwer is a critically endangered alpine wild flower endemic to Shangrila County 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 individual plants representing different phenotypes within the species were sequenced by using the Illumina HiSeq 2000 platform, and then assembled, annotated and compared. 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 genes, mainly related with photosynthesis and self-replication. 27 155 codons, preferring using codon ending of A or U, were found in all the coding sequences. (2) Thirty six repeats and 73 simple sequence repeats (SSRs) were detected in the chloroplast genome of R. praelucens. Most of the cpSSRs were mononucleotide type and located in the intergenic region of LSC region. (3) The haplotype diversity (Hd) among the 40 chloroplast genomes was 0.928±0.027, and the nucleotide diversity (Pi)was 0.00012. 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 cp genomes of different individuals. These results suggest that the chloroplast genomes are highly conserved in size, sequence and structure within R. praelucens. The rich intraspecific phenotypic diversity was not directly caused by the variation of chloroplast genomes among different individual plants. |
Key words: Rosa praelucens Byhouwer, chloroplast, comparative genomics, simple sequence repeats (SSRs), nucleotide diversity (Pi), codon preference |