Shi Shi, Zhang Ziyan, Lin Xinhao, Lu Linjing, Fu Keyi, He Miaoxin, Lee Shiou Yih, Yin Hui, Yu Jingwei
Guangdong Provincial Key Laboratory of Pharmaceutical Bioactive Substances, Guangdong Pharmaceutical University, Guangzhou 510006, China.
South China Limestone Plants Research Center, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China.
Genes (Basel). 2025 May 22;16(6):616. doi: 10.3390/genes16060616.
: In South China, species dominate mixed evergreen broadleaf forests, forming symbiotic relationships with ectomycorrhizal fungi and serving as food resources for diverse fauna, including frugivorous birds and mammals. The limited understanding of chloroplast genomes in this genus restricts our insights into its species diversity. This study investigates the chloroplast genome (cp genome) sequences from seven species, aims to elucidate their structural variation, evolutionary relationships, and functional gene content to provide effective support for future genetic conservation and breeding efforts. : We isolated total DNA from fresh leaves and sequenced the complete cp genomes of these samples. To develop a genomic resource and clarify the evolutionary relationships within species, comparative chloroplast genome studies and phylogenetic investigations were performed. : All studied species exhibited a conserved quadripartite chloroplast genome structure, with sizes ranging from 161,495 to 163,880 bp. Genome annotation revealed 130 functional genes and a GC content of 36.72-37.76%. Codon usage analysis showed a predominance of leucine-encoding codons. Our analysis identified 322 simple sequence repeats (SSRs), which were predominantly palindromic in structure (82.3%). All eight species exhibited the same 19 SSR categories in similar proportions. Eight highly variable regions (ndhF, ycf1, trnS-trnG-exon1, trnk(exon1)-rps16(exon2), rps16(exon2), rbcL-accD, and ccsA-ndh) have been identified, which could be valuable as molecular markers in future studies on the population genetics and phylogeography of this genus. The phylogeny tree provided critical insights into the evolutionary trajectory of Fagaceae, suggesting that was strongly supported as monophyletic, while Quercus was inferred to be polyphyletic, showing a significant cytonuclear discrepancy. : We characterized and compared the chloroplast genome features across eight species, followed by comprehensive phylogenetic analyses. These findings provide critical insights for resolving taxonomic uncertainties and advancing systematic research in this genus.
在华南地区，该属物种在常绿阔叶林混交林中占主导地位，与外生菌根真菌形成共生关系，并作为包括食果鸟类和哺乳动物在内的多种动物的食物资源。目前对该属叶绿体基因组的了解有限，这限制了我们对其物种多样性的认识。本研究调查了七个该属物种的叶绿体基因组（cp基因组）序列，旨在阐明其结构变异、进化关系和功能基因内容，为未来的遗传保护和育种工作提供有效支持。：我们从新鲜叶片中分离出总DNA，并对这些样本的完整cp基因组进行测序。为了开发基因组资源并阐明该属物种内部的进化关系，我们进行了叶绿体基因组比较研究和系统发育调查。：所有研究物种均呈现出保守的四分体叶绿体基因组结构，大小在161,495至163,880 bp之间。基因组注释显示有130个功能基因，GC含量为36.72 - 37.76%。密码子使用分析表明，编码亮氨酸的密码子占主导地位。我们的分析确定了322个简单序列重复（SSR），其结构主要为回文结构（82.3%）。所有八个物种都表现出相同的19种SSR类别，比例相似。已鉴定出八个高度可变区域（ndhF、ycf1、trnS - trnG - exon1、trnk(exon1) - rps16(exon2)、rps16(exon2)、rbcL - accD和ccsA - ndh），这些区域在未来该属的种群遗传学和系统地理学研究中作为分子标记可能具有重要价值。系统发育树为壳斗科的进化轨迹提供了关键见解，表明该属得到了强烈的单系支持，而栎属被推断为多系，显示出明显的细胞核与细胞质差异。：我们对八个该属物种的叶绿体基因组特征进行了表征和比较，随后进行了全面的系统发育分析。这些发现为解决分类学上的不确定性和推进该属的系统研究提供了关键见解。
