State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, People's Republic of China.
BMC Genet. 2019 Mar 12;20(1):33. doi: 10.1186/s12863-019-0733-0.
The genus Ostrya (Betulaceae) contains eight species and four of them are distributed in China. However, studies based on limited informative sites of several chloroplast markers failed to resolve interspecific delimitation and relationships among the four Chinese species. In this study, we aimed to use the whole chloroplast genomes to address these two issues.
We assembled and annotated 33 complete chloroplast genomes (plastomes) of the four Chinese species, representing 17 populations across most of their geographical distributions. Each species contained samples of several individuals that cover most of geographic distributions of the species. All plastomes are highly conserved in genome structure and gene order, with a total length of 158-159 kb and 122 genes. Phylogenetic analyses of whole plastomes, non-coding regions and protein-coding genes produced almost the same topological relationships. In contrast to the well-delimitated species boundary inferred from the nuclear ITS sequence variations, three of the four species are non-monophyletic in the plastome trees, which is consistent with previous studies based on a few chloroplast markers.
The high incongruence between the ITS and plastome trees may suggest the widespread occurrences of hybrid introgression and incomplete lineage sorting during the divergence of these species. In addition, the plastomes with more informative sites compared with a few chloroplast markers still failed to resolve the phylogenetic relationships of the four species, and further studies involving population genomic data may be needed to better understand their evolutionary histories.
梣属（桦木科）包含 8 个物种，其中有 4 个分布在中国。然而，基于几个叶绿体标记物有限信息位点的研究未能解决种间界限和 4 个中国种之间的关系问题。在本研究中，我们旨在使用整个叶绿体基因组来解决这两个问题。
我们组装并注释了来自四个中国种的 33 个完整叶绿体基因组（质体基因组），代表了它们地理分布的大部分地区的 17 个种群。每个种都包含了覆盖大部分物种地理分布的几个个体的样本。所有质体基因组在基因组结构和基因顺序上高度保守，总长度为 158-159kb，包含 122 个基因。基于整个质体基因组、非编码区和蛋白编码基因的系统发育分析产生了几乎相同的拓扑关系。与核 ITS 序列变异推断出的明确物种界限相反，四个物种中的三个在质体树上不是单系的，这与以前基于少数几个叶绿体标记物的研究结果一致。
ITS 与质体树之间的高度不一致可能表明，在这些物种的分化过程中，广泛存在杂交渐渗和不完全谱系分选。此外，与少数几个叶绿体标记物相比，具有更多信息位点的质体基因组仍然未能解决四个物种的系统发育关系，可能需要进一步研究种群基因组数据，以更好地了解它们的进化历史。
