Kim Jong-Hwa, Lee Sung-Il, Kim Bo-Ram, Choi Ik-Young, Ryser Peter, Kim Nam-Soo
Department of Horticulture, Kangwon National University, Chuncheon, Korea.
Institute of Bioscience and Biomedical Sciences, Kangwon National University, Chuncheon, Korea.
PLoS One. 2017 Oct 24;12(10):e0186788. doi: 10.1371/journal.pone.0186788. eCollection 2017.
Chloroplast (cp) genomes of Lilium amabile, L. callosum, L. lancifolium, and L. philadelphicum were fully sequenced. Using these four novel cp genome sequences and five other previously sequenced cp genomes, features of the cp genomes were characterized in detail among species in the genus Lilium and other related genera in the order Liliales. The lengths and nucleotide composition showed little variation. No structural variation was found among the cp genomes in Liliales. Gene contents were conserved among four newly sequenced cp genome in Lilium species, the only differences being in two pseudogenes. We identified 112 genes in 13 functional categories, 18 of which carried introns that were conserved among the species in Liliales. There were 16-21 SSR loci (>12 bp, >3 repeats) in the cp genomes in Lilium and the genomic locations of these loci were highly variable among the species. Average mutations were 15 SNPs per 1kb and 5 indels per 1kb, respectively, in the cp genomes of the newly sequenced four Lilium species. Phylogenetic classifications revealed some discrepancies between trees based on the cp genomes and previous classifications based on the morphology and geographic distributions.
对天香百合、渥丹、卷丹和毛百合的叶绿体（cp）基因组进行了全序列测定。利用这四个新的cp基因组序列以及其他五个先前测序的cp基因组，详细表征了百合属物种以及百合目其他相关属物种cp基因组的特征。其长度和核苷酸组成变化不大。在百合目中，cp基因组之间未发现结构变异。百合属四个新测序的cp基因组中的基因含量保守，唯一的差异在于两个假基因。我们在13个功能类别中鉴定出112个基因，其中18个基因含有在百合目物种中保守的内含子。百合cp基因组中有16 - 21个SSR位点（>12 bp，>3个重复），这些位点的基因组位置在物种间高度可变。新测序的四个百合物种的cp基因组中，平均每1kb分别有15个SNP和5个插入缺失。系统发育分类显示，基于cp基因组构建的树与先前基于形态学和地理分布的分类之间存在一些差异。
