Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing, China.
College of Horticulture, Jinling Institute of Technology, Nanjing City, Jiangsu Province, P.R. China.
PLoS One. 2022 May 19;17(5):e0268679. doi: 10.1371/journal.pone.0268679. eCollection 2022.
Ilex dabieshanensis K. Yao & M. B. Deng is not only a highly valued tree species for landscaping, it is also a good material for making kuding tea due to its anti-inflammatory and lipid-lowering medicinal properties. Utilizing next-generation and long-read sequencing technologies, we assembled the whole chloroplast genome of I. dabieshanensis. The genome was 157,218 bp in length, exhibiting a typical quadripartite structure with a large single copy (LSC: 86,607 bp), a small single copy (SSC: 18,427 bp) and a pair of inverted repeat regions (IRA and IRB: each of 26,092 bp). A total of 121 predicted genes were encoded, including 113 distinctive (79 protein-coding genes, 30 tRNAs, and 4 rRNAs) and 8 duplicated (8 protein-coding genes) located in the IR regions. Overall, 132 SSRs and 43 long repeats were detected and could be used as potential molecular markers. Comparative analyses of four traditional Ilex tea species (I. dabieshanensis, I. paraguariensis, I. latifolia and I. cornuta) revealed seven divergent regions: matK-rps16, trnS-psbZ, trnT-trnL, atpB-rbcL, petB-petD, rpl14-rpl16, and rpl32-trnL. These variations might be applicable for distinguishing different species within the genus Ilex. Phylogenetic reconstruction strongly suggested that I. dabieshanensis formed a sister clade to I. cornuta and also showed a close relationship to I. latifolia. The generated chloroplast genome information in our study is significant for Ilex tea germplasm identification, phylogeny and genetic improvement.
大别山冬青不仅是一种极具观赏价值的树种，还具有抗炎和降脂的药用特性，因此也是制作苦丁茶的好材料。利用新一代和长读测序技术，我们组装了大别山冬青的整个叶绿体基因组。该基因组长 157218bp，具有典型的四分体结构，包括一个大单拷贝区（LSC：86607bp）、一个小单拷贝区（SSC：18427bp）和一对反向重复区（IRA 和 IRB：各 26092bp）。共预测到 121 个基因，包括 113 个独特的（79 个蛋白编码基因、30 个 tRNA 和 4 个 rRNA）和 8 个位于 IR 区的重复基因（8 个蛋白编码基因）。总共检测到 132 个 SSRs 和 43 个长重复序列，可作为潜在的分子标记。对四个传统的冬青茶物种（大别山冬青、巴拉圭冬青、冬青和cornuta 冬青）进行比较分析，发现了 7 个分化区域：matK-rps16、trnS-psbZ、trnT-trnL、atpB-rbcL、petB-petD、rpl14-rpl16 和 rpl32-trnL。这些变异可能适用于区分冬青属不同物种。系统发育重建强烈表明，大别山冬青与 cornuta 冬青形成姐妹分支，与 latifolia 冬青也有密切关系。本研究生成的叶绿体基因组信息对冬青茶种质资源鉴定、系统发育和遗传改良具有重要意义。
