Jiangxi Provincial Key Laboratory of Silviculture, College of Forestry, Jiangxi Agricultural University, Nanchang, China.
PLoS One. 2019 Jul 30;14(7):e0212325. doi: 10.1371/journal.pone.0212325. eCollection 2019.
Castanopsis sclerophylla (Lindl.) Schott is an important species of evergreen broad-leaved tree in subtropical areas and has high ecological and economic value. However, there are few studies on its chloroplast genome. In this study, the complete chloroplast genome sequence of C. sclerophylla was determined using the Illumina HiSeq 2500 platform. The complete chloroplast genome of C. sclerophylla is 160,497 bp long, including a pair of inverted repeat (IR) regions (25,675 bp) separated by a large single-copy (LSC) region of 90,255 bp and a small single-copy (SSC) region of 18,892 bp. The overall GC content of the chloroplast genome is 36.82%. A total of 131 genes were found; of these, 111 genes are unique and annotated, including 79 protein-coding genes, 27 transfer RNA genes (tRNAs), and four ribosomal RNA genes (rRNAs). Twenty-one genes were found to be duplicated in the IR regions. Comparative analysis indicated that IR contraction might be the reason for the smaller chloroplast genome of C. sclerophylla compared to three congeneric species. Sequence analysis indicated that the LSC and SSC regions are more divergent than IR regions within Castanopsis; furthermore, greater divergence was found in noncoding regions than in coding regions. The maximum likelihood phylogenetic analysis showed that four species of the genus Castanopsis form a monophyletic clade and that C. sclerophylla is closely related to Castanopsis hainanensis with strong bootstrap values. These results not only provide a basic understanding of Castanopsis chloroplast genomes, but also illuminate Castanopsis species evolution within the Fagaceae family. Furthermore, these findings will be valuable for future studies of genetic diversity and enhance our understanding of the phylogenetic evolution of Castanopsis.
锥栗（Castanopsis sclerophylla (Lindl.) Schott）是亚热带地区一种重要的常绿阔叶树种，具有很高的生态和经济价值。然而，目前对其叶绿体基因组的研究较少。本研究采用 Illumina HiSeq 2500 平台测定了锥栗的完整叶绿体基因组序列。锥栗的完整叶绿体基因组序列长 160497bp，包括一对长为 25675bp 的反向重复（IR）区，由长为 90255bp 的大单拷贝区（LSC）和长为 18892bp 的小单拷贝区（SSC）隔开。叶绿体基因组的 GC 含量总体为 36.82%。共发现 131 个基因；其中 111 个为注释的独特基因，包括 79 个蛋白编码基因、27 个转移 RNA 基因（tRNA）和 4 个核糖体 RNA 基因（rRNA）。在 IR 区发现有 21 个基因发生了倍增。比较分析表明，IR 收缩可能是锥栗叶绿体基因组比三个同属物种小的原因。序列分析表明，在锥栗中，LSC 和 SSC 区比 IR 区更具多态性；此外，非编码区的变异大于编码区。最大似然系统发育分析表明，四个锥栗属种形成一个单系分支，并且锥栗与海南锥栗具有很强的bootstrap 值，亲缘关系较近。这些结果不仅为了解锥栗叶绿体基因组提供了基础，也阐明了壳斗科中锥栗属的进化关系。此外，这些发现将有助于今后对遗传多样性的研究，并加深我们对锥栗属系统发育进化的认识。
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