Chloroplast genome features and intraspecific variation of Rosa praelucens

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(Pi)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.