Jeon Ji-Hyeon, Maki Masayuki, Chiang Yu-Chung, Kim Seung-Chul
Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Republic of Korea.
Department of Ecological Developmental Adaptability Life Sciences, Tohoku University, Sendai, 980-8577, Japan.
Bot Stud. 2025 Jun 13;66(1):17. doi: 10.1186/s40529-025-00466-y.
The section Synstylae of the genus Rosa (Rosaceae) is predominantly distributed across the Eastern Asiatic Floristic Region and is characterized by increased species diversity and natural hybrids. These characteristics render species within this section exemplary for studying phenotypic variability and easy crossbreeding, which hold potential for advancements in the rose-breeding industry. However, genetic introgression and hybridization have posed challenges to our understanding of their phylogenetic relationships. Despite recurrent interspecific introgression, chloroplast DNA can still aid in phylogenetic inference within the section Synstylae due to its uniparental inheritance and high conservation.
Phylogenetic inferences and haplotype network analysis identified seven distinct chloroplast haplotype groups within the East Asian Synstylae. Clear differentiation was observed between the chloroplast haplotypes of the Sino-Himalayan series Brunonianae and Sino-Japanese series Multiflorae lineages. The chloroplast haplotypes within each lineage aligned more closely with geographic gradients than with species boundaries. Consequently, various chloroplast haplotypes were shared among Sino-Japanese Synstylae species with broader distributions, whereas unique haplotypes were found in the species with restricted distribution ranges. Similarly, geographically specific haplotype groups were identified in the Japanese Archipelago, Taiwan, and Eastern China of the Sino-Japanese Subregion, respectively.
The chloroplast genomes of Sino-Japanese Synstylae species may have diverged along geographic gradients, influenced by the geographical and ecological complexity of East Asia and the climate oscillations during the Pleistocene. The recurring cycles of fragmentation and rejoining in Sino-Japanese Synstylae populations have allowed founder effects and genetic drift to drive divergence and diversification of their chloroplast genomes along these geographic gradients. The substantial incongruence between the chloroplast and nuclear phylogenies evidenced the prevalent genetic introgression within the Sino-Japanese Synstylae lineage. Additionally, two putative hybrid speciation events highlighted the role of genetic introgression in species diversification of the East Asian Synstylae lineage. This study substantiates the value of chloroplast genomes in elucidating genetic introgression and the unique evolutionary history of recently diverged and closely related East Asian Synstylae species.
蔷薇属（蔷薇科）的合柱组主要分布于东亚植物区，其特点是物种多样性增加且存在自然杂交种。这些特征使该组内的物种成为研究表型变异和易于杂交的典范，这对玫瑰育种产业的发展具有潜在意义。然而，基因渗入和杂交给我们理解它们的系统发育关系带来了挑战。尽管存在种间反复渗入，但叶绿体DNA因其单亲遗传和高度保守性，仍有助于合柱组内的系统发育推断。
系统发育推断和单倍型网络分析在东亚合柱组中确定了七个不同的叶绿体单倍型组。在中喜马拉雅的短脚蔷薇系和中日的野蔷薇系叶绿体单倍型之间观察到明显分化。每个谱系内的叶绿体单倍型与地理梯度的一致性比与物种边界的一致性更高。因此，分布较广的中日合柱组物种共享了各种叶绿体单倍型，而分布范围受限的物种则发现了独特的单倍型。同样，在中日次区域的日本群岛、台湾和中国东部分别鉴定出了地理特异性单倍型组。
中日合柱组物种的叶绿体基因组可能沿着地理梯度发生了分化，这受到东亚地理和生态复杂性以及更新世期间气候振荡的影响。中日合柱组种群中反复出现的分裂和重新连接循环，使得奠基者效应和遗传漂变推动其叶绿体基因组沿着这些地理梯度发生分化和多样化。叶绿体和核系统发育之间的显著不一致证明了中日合柱组谱系中普遍存在基因渗入。此外，两个推定的杂交物种形成事件突出了基因渗入在东亚合柱组谱系物种多样化中的作用。这项研究证实了叶绿体基因组在阐明基因渗入以及最近分化且密切相关的东亚合柱组物种独特进化历史方面的价值。
