Li Zhiyuan, Zhang Yunyan, Tng David Y P, Chen Qixun, Wang Yahong, Tian Yongjing, Zhou Jingbo, Wang Zhongsheng
College of Life Sciences, Nanjing University, Nanjing 210023, China.
Centre for Rainforest Studies, The School for Field Studies, Yungaburra, QLD 4884, Australia.
Int J Mol Sci. 2025 Jul 30;26(15):7357. doi: 10.3390/ijms26157357.
In the traditional classification system of the Lauraceae family based on morphology and anatomy, the phylogenetic position of the genus has long been controversial. Chloroplast (cp) evolution of has not yet been illuminated. In this study, we first sequenced and assembled the complete cp genomes of , and conducted the comparative cp genomics, phylogenomics, and divergence time estimation of this ecological and economic important genus. The whole length of cp genomes of the 10 ranged from 151,970 bp to 154,011 bp with typical quadripartite structure, conserved gene arrangements and contents. Variations in length of cp were observed in the inverted repeat regions (IRs) and a relatively high usage frequency of codons ending with T/A was detected. Four hypervariable intergenic regions (A-D, H-A, 15-1, and A-J) and 672 cp microsatellites were identified for . Phylogenetic analysis based on 106 cp genomes from 30 genera within the Lauraceae family demonstrated that constituted a monophyletic clade and grouped a sister branch with the sect. within the tribe Cinnamomeae. Divergence time between and its East Asian siblings was estimated at the Middle Miocene (16.98 Mya), diverged from at the Pleistocene epoch (3.63 Mya). Combined with fossil evidence, our results further revealed the crucial role of the Bering Land Bridge and glacial refugia in the speciation and differentiation of . Overall, our study clarified the evolution pattern of cp genomes and elucidated the phylogenetic position and divergence time framework of .
在基于形态学和解剖学的樟科传统分类系统中，该属的系统发育位置长期以来一直存在争议。其叶绿体（cp）进化尚未得到阐明。在本研究中，我们首先对该属的完整cp基因组进行了测序和组装，并对这个具有生态和经济重要性的属进行了比较cp基因组学、系统发育基因组学和分歧时间估计。10个该属物种的cp基因组全长在151,970 bp至154,011 bp之间，具有典型的四分体结构、保守的基因排列和内容。在反向重复区域（IRs）观察到cp长度的变化，并检测到以T/A结尾的密码子使用频率相对较高。为该属鉴定出四个高变基因间隔区（A-D、H-A、15-1和A-J）和672个cp微卫星。基于樟科30个属的106个cp基因组的系统发育分析表明，该属构成一个单系类群，并与樟族肉桂亚族的某组形成姐妹分支。该属与其东亚近缘种之间的分歧时间估计在中新世中期（1698万年前），该属在更新世时期（363万年前）与某属分化。结合化石证据，我们的结果进一步揭示了白令陆桥和冰川避难所在该属物种形成和分化中的关键作用。总体而言，我们的研究阐明了该属cp基因组的进化模式，并阐明了该属的系统发育位置和分歧时间框架。
