Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, Hubei, People's Republic of China.
University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China.
BMC Plant Biol. 2022 Feb 26;22(1):88. doi: 10.1186/s12870-022-03480-5.
The large and diverse Coffeeae alliance clade of subfamily Ixoroideae (Rubiaceae) consists of 10 tribes, > 90 genera, and > 2000 species. Previous molecular phylogenetics using limited numbers of markers were often unable to fully resolve the phylogenetic relationships at tribal and generic levels. Also, the structural variations of plastomes (PSVs) within the Coffeeae alliance tribes have been poorly investigated in previous studies. To fully understand the phylogenetic relationships and PSVs within the clade, highly reliable and sufficient sampling with superior next-generation analysis techniques is required. In this study, 71 plastomes (40 newly sequenced and assembled and the rest from the GenBank) were comparatively analyzed to decipher the PSVs and resolve the phylogenetic relationships of the Coffeeae alliance using four molecular data matrices.
All plastomes are typically quadripartite with the size ranging from 153,055 to 155,908 bp and contained 111 unique genes. The inverted repeat (IR) regions experienced multiple contraction and expansion; five repeat types were detected but the most abundant was SSR. The size of the Coffeeae alliance clade plastomes and its elements are affected by the IR boundary shifts and the repeat types. However, the emerging PSVs had no taxonomic and phylogenetic implications. Eight highly divergent regions were identified within the plastome regions ndhF, ccsA, ndhD, ndhA, ndhH, ycf1, rps16-trnQ-UUG, and psbM-trnD. These highly variable regions may be potential molecular markers for further species delimitation and population genetic analyses for the clade. Our plastome phylogenomic analyses yielded a well-resolved phylogeny tree with well-support at the tribal and generic levels within the Coffeeae alliance.
Plastome data could be indispensable in resolving the phylogenetic relationships of the Coffeeae alliance tribes. Therefore, this study provides deep insights into the PSVs and phylogenetic relationships of the Coffeeae alliance and the Rubiaceae family as a whole.
亚科茜草族（茜草科）的大而多样的咖啡属联盟包括 10 个部落、>90 个属和>2000 个物种。以前使用有限数量标记的分子系统发育学研究往往无法完全解决部落和属级别的系统发育关系。此外，咖啡属联盟部落内质体基因组（PSVs）的结构变异在以前的研究中也没有得到很好的研究。为了充分了解该分支内的系统发育关系和 PSVs，需要使用高度可靠和充足的采样以及卓越的下一代分析技术。在这项研究中，比较分析了 71 个质体基因组（40 个新测序和组装，其余来自 GenBank），以破译 PSVs 并使用四个分子数据矩阵解析咖啡属联盟的系统发育关系。
所有质体基因组通常都是四分体，大小范围为 153055 到 155908bp，包含 111 个独特基因。反转重复（IR）区域经历了多次收缩和扩张；检测到五种重复类型，但最丰富的是 SSR。咖啡属联盟的质体基因组及其元素的大小受到 IR 边界移动和重复类型的影响。然而，新兴的 PSVs 没有分类学和系统发育意义。在质体区域 ndhF、ccsA、ndhD、ndhA、ndhH、ycf1、rps16-trnQ-UUG 和 psbM-trnD 中鉴定出八个高度分化的区域。这些高度变异的区域可能是该分支进一步物种划分和种群遗传分析的潜在分子标记。我们的质体基因组系统发育分析产生了一个分辨率良好的系统发育树，在咖啡属联盟的部落和属级别的支持率很高。
质体数据对于解决咖啡属联盟部落的系统发育关系至关重要。因此，本研究为咖啡属联盟及其整个茜草科的 PSVs 和系统发育关系提供了深入的见解。
