Key Laboratory of Forest Genetics & Biotechnology of Educational Department of China and of Jiangsu Province, College of Forestry, Nanjing Forestry University, Nanjing 210037, China.
Biomed Res Int. 2019 Jul 15;2019:5190425. doi: 10.1155/2019/5190425. eCollection 2019.
is an important ornamental willow tree widely distributed in China. In this study, an integrated circular chloroplast genome was reconstructed for based on the chloroplast reads screened from the whole-genome sequencing data generated with the PacBio RSII platform. The obtained pseudomolecule was 155,750 bp long and had a typical quadripartite structure, comprising a large single copy region (LSC, 84,638 bp) and a small single copy region (SSC, 16,282 bp) separated by two inverted repeat regions (IR, 27,415 bp). The chloroplast genome encoded 115 unique genes, including four rRNA genes, 30 tRNA genes, 78 protein-coding genes, and three pseudogenes. Repetitive sequence analysis identified 32 tandem repeats, 22 forward repeats, two reverse repeats, and five palindromic repeats. Additionally, a total of 118 perfect microsatellites were detected, with mononucleotide repeats being the most common (89.83%). By comparing the chloroplast genome with those of other rosid plant species, significant contractions or expansions were identified at the IR-LSC/SSC borders. Phylogenetic analysis of 17 willow species confirmed that was most closely related to and revealed the monophyly of the genus . The complete chloroplast genome provides an additional sequence-based resource for studying the evolution of organelle genomes in woody plants.
是一种在中国广泛分布的重要观赏柳树。在这项研究中,基于 PacBio RSII 平台生成的全基因组测序数据中筛选出的叶绿体reads,我们为 构建了一个整合的圆形叶绿体基因组。获得的假分子长 155750bp,具有典型的四分体结构,由一个大的单拷贝区(LSC,84638bp)和一个小的单拷贝区(SSC,16282bp)组成,它们被两个反向重复区(IR,27415bp)隔开。 叶绿体基因组编码 115 个独特的基因,包括四个 rRNA 基因、30 个 tRNA 基因、78 个蛋白质编码基因和三个假基因。重复序列分析鉴定出 32 个串联重复序列、22 个正向重复序列、两个反向重复序列和五个回文重复序列。此外,总共检测到 118 个完美的微卫星,其中单核苷酸重复最常见(89.83%)。通过将 叶绿体基因组与其他蔷薇科植物的基因组进行比较,在 IR-LSC/SSC 边界处发现了明显的收缩或扩张。对 17 种柳树物种的系统发育分析证实, 与 最为密切相关,并揭示了属 的单系性。完整的 叶绿体基因组为研究木本植物细胞器基因组的进化提供了额外的基于序列的资源。