Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China.
University of Chinese Academy of Sciences, Beijing, 100049, China.
BMC Genomics. 2024 Feb 22;25(1):203. doi: 10.1186/s12864-024-10046-2.
Firmiana danxiaensis is a critically endangered and ecologically important tree currently only found in four locations in Danxia or Karst habitats in northern Guangdong Province, China. The specialized habitat preference makes it an ideal model species for study of adaptive evolution. Meanwhile, the phylogenetic relationships of F. danxiaensis in four locations under two landforms are unclear. Therefore, we sequenced its complete chloroplast (cp.) genomes and conducted comprehensive interspecific and intrageneric plastome studies.
The F. danxiaensis plastomes in four locations showed a typical quadripartite and circular structure that ranged from 160,832 to 161,206 bp in size, with 112 unique genes encoded. Comparative genomics showed that the plastomes of F. danxiaensis were relatively conserved with high similarity of genome organization, gene number, GC content and SSRs. While the genomes revealed higher biased codon preferences in Karst habitat than those in Danxia habitats. Eighteen and 11 divergent hotpots were identified at interspecific and intrageneric levels for species identification and further phylogenetic studies. Seven genes (clpP, accD, ccsA, ndhH, rpl20, rpoC2, and rps4) were under positive selection and may be related to adaptation. Phylogenetic analysis revealed that F. danxiaensis is sister to F. major and F. simplex. However, the interspecific relationships are not consistent with the habitat types.
The characteristics and interspecific relationship of F. danxiaensis plastomes provide new insights into further integration of geographical factors, environmental factors, and genetic variations on the genomic study of F. danxiaensis. Together, our study will contribute to the study of species identification, population genetics, and conservation biology of F. danxiaensis.
Firmiana danxiaensis 是一种濒危且生态重要的树种,目前仅在中国广东省北部丹霞或喀斯特生境的四个地点发现。其特殊的生境偏好使其成为适应进化研究的理想模式物种。同时,四个地点的 F. danxiaensis 与两种地貌的系统发育关系尚不清楚。因此,我们对其进行了完整的叶绿体(cp.)基因组测序,并进行了广泛的种间和属内质体研究。
四个地点的 F. danxiaensis 质体基因组显示出典型的四分体和圆形结构,大小在 160832 到 161206bp 之间,编码 112 个独特的基因。比较基因组学表明,F. danxiaensis 的质体基因组相对保守,基因组组织、基因数量、GC 含量和 SSR 高度相似。然而,基因组显示喀斯特生境的密码子偏好性高于丹霞生境。在种间和属内水平上,确定了 18 个和 11 个发散热点,用于物种鉴定和进一步的系统发育研究。七个基因(clpP、accD、ccsA、ndhH、rpl20、rpoC2 和 rps4)受到正选择,可能与适应有关。系统发育分析表明,F. danxiaensis 与 F. major 和 F. simplex 互为姐妹种。然而,种间关系与生境类型不一致。
F. danxiaensis 质体基因组的特征和种间关系为进一步整合地理因素、环境因素和遗传变异提供了新的见解,有助于对 F. danxiaensis 的基因组研究、物种鉴定、种群遗传学和保护生物学的研究。