中甸刺玫的叶绿体基因组特征及种内变异

Rosa praelucens is a critically endangered alpine wild flower endemic to ShangrilaCounty of Yunnan Province. Rich in phenotypic diversity and with a high ploidy level ofdecaploid, R. praelucens is a very important rose germplasm resource. In order to clarify thegenetic background of its phenotypic variation, the chloroplast genomes of 40 individual plantsrepresenting different phenotypes within the species were sequenced by using the Illumina HiSeq2000 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 differenceof 88 bp among different individual plants. The genomes encoded 132 genes, mainly related withphotosynthesis 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 weremononucleotide type and located in the intergenic region of LSC region. (3) The haplotypediversity (Hd) among the 40 chloroplast genomes was 0.9280.027, and the nucleotide diversity(Piwas 0.00012. The intergenic region of petN-trnD and psaA-ycf3, gene rps16 and ycf1 wererelatively more divergent. No reverse or loss of large DNA fragments and genes were foundamong the cp genomes of different individuals. These results suggested that the chloroplastgenomes were highly conserved in size, sequence and structure within R. praelucens. The richintraspecific phenotypic diversity was not directly caused by the variation of chloroplast genomesamong different individual plants.