Meng Danni, Lu Tianxin, He Meng, Ren Yuze, Fu Mumei, Zhang Yuxiao, Yang Peifeng, Lin Xinyu, Yang Yong, Zhang Ying, Yang Yuchen, Jin Xiang
Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Haikou, China.
Hainan Observation and Research Station of Dongzhaigang Mangrove Wetland Ecosystem, Hainan Normal University, Haikou, China.
Front Plant Sci. 2025 Apr 24;16:1587750. doi: 10.3389/fpls.2025.1587750. eCollection 2025.
Chloroplast and mitochondrial genomes harbor crucial information that can be utilized for elucidating plant evolution and environmental adaptation. The organellar genomic characteristics of Goodeniaceae, a sister family to Asteraceae, remain unexplored. Here, using a combination of short-read and long-read sequencing technologies, we successfully assembled the complete organellar genomes of two Goodeniaceae species native to China, and . Chloroplast genome collinearity analysis revealed that expanded its genome length through inverted repeat expansion and large single copy fragment duplication, resulting in 181,022 bp () and 182,726 bp (), ~30 kb increase compared to its related species. Mitochondrial genomes of two species exhibit multi-ring topology, forming dual mitochondrial chromosomes of 314,251 bp () and 276,175 bp (). Sequence variation analysis demonstrated substantial chloroplast sequence divergence (Pi = 0.45) and an increase in gene copy number within the genus. Relative synonymous codon usage (RSCU) analysis revealed that chloroplast has a higher bias for A/U-ending codons than mitochondria, with chloroplasts RSCU values ranging from 0.32 to 1.94, whereas mitochondrial RSCU values ranging from 0.38 to 1.62. Phylogenetic analyses support the monophyly of the Asteraceae-Goodeniaceae sister group, whereas the extended evolutionary branches of , coupled with mitochondrial collinearity analysis, indicate rapid organellar genome evolution of . Organellar-nuclear horizontal gene transfer analysis identified specific increased in the copy numbers of photosynthesis-related genes and chloroplast-nuclear transfer events in . Our study not only provides insights for understanding environmental adaptation mechanisms of coastal plants, but also contributes to elucidating organellar genome evolution in and Goodeniaceae.
叶绿体和线粒体基因组包含可用于阐明植物进化和环境适应性的关键信息。菊科的姐妹科——草海桐科的细胞器基因组特征尚未得到探索。在这里，我们结合短读长和长读长测序技术，成功组装了两种原产于中国的草海桐科植物的完整细胞器基因组。叶绿体基因组共线性分析表明，[物种名称1]通过反向重复序列扩增和大单拷贝片段重复扩展了其基因组长度，导致基因组长度为181,022 bp（[物种名称1]）和182,726 bp（[物种名称2]），与其相关物种相比增加了约30 kb。两种[物种名称]的线粒体基因组呈现多环拓扑结构，形成了314,251 bp（[物种名称1]）和276,175 bp（[物种名称2]）的双线粒体染色体。序列变异分析表明，叶绿体序列存在显著差异（Pi = 0.45），且该属内基因拷贝数增加。相对同义密码子使用情况（RSCU）分析显示，[物种名称]的叶绿体比线粒体对以A/U结尾的密码子有更高的偏好，叶绿体的RSCU值范围为0.32至1.94，而线粒体的RSCU值范围为0.38至1.62。系统发育分析支持菊科 - 草海桐科姐妹群的单系性，而[物种名称]的进化分支扩展，再加上线粒体共线性分析，表明[物种名称]的细胞器基因组进化迅速。细胞器 - 核水平基因转移分析确定了[物种名称]中光合作用相关基因拷贝数的特定增加以及叶绿体 - 核转移事件。我们的研究不仅为理解沿海植物的环境适应机制提供了见解，也有助于阐明[物种名称]和草海桐科的细胞器基因组进化。
