Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, 510275, China.
Faculty of Health and Life Sciences, INTI International University, 71800, Nilai, Malaysia.
BMC Genomics. 2022 Mar 14;23(1):203. doi: 10.1186/s12864-022-08397-9.
Ilex (Aquifoliaceae) are of great horticultural importance throughout the world for their foliage and decorative berries, yet a dearth of genetic information has hampered our understanding of phylogenetic relationships and evolutionary history. Here, we compare chloroplast genomes from across Ilex and estimate phylogenetic relationships.
We sequenced the chloroplast genomes of seven Ilex species and compared them with 34 previously published Ilex plastomes. The length of the seven newly sequenced Ilex chloroplast genomes ranged from 157,182 bp to 158,009 bp, and contained a total of 118 genes, including 83 protein-coding, 31 rRNA, and four tRNA genes. GC content ranged from 37.6 to 37.69%. Comparative analysis showed shared genomic structures and gene rearrangements. Expansion and contraction of the inverted repeat regions at the LSC/IRa and IRa/SSC junctions were observed in 22 and 26 taxa, respectively; in contrast, the IRb boundary was largely invariant. A total of 2146 simple sequence repeats and 2843 large repeats were detected in the 41 Ilex plastomes. Additionally, six genes (psaC, rbcL, trnQ, trnR, trnT, and ycf1) and two intergenic spacer regions (ndhC-trnV and petN-psbM) were identified as hypervariable, and thus potentially useful for future phylogenetic studies and DNA barcoding. We recovered consistent phylogenetic relationships regardless of inference methodology or choice of loci. We recovered five distinct, major clades, which were inconsistent with traditional taxonomic systems.
Our findings challenge traditional circumscriptions of the genus Ilex and provide new insights into the evolutionary history of this important clade. Furthermore, we detail hypervariable and repetitive regions that will be useful for future phylogenetic and population genetic studies.
冬青属（冬青科）因其叶和装饰性浆果而在全球范围内具有重要的园艺价值，但由于遗传信息的缺乏，阻碍了我们对系统发育关系和进化历史的理解。在这里，我们比较了来自冬青属的叶绿体基因组，并估计了系统发育关系。
我们对 7 种冬青属植物的叶绿体基因组进行了测序，并与 34 个先前发表的冬青属质体基因组进行了比较。新测序的 7 个冬青属叶绿体基因组的长度范围为 157182bp 至 158009bp，共包含 118 个基因，包括 83 个蛋白质编码基因、31 个 rRNA 基因和 4 个 tRNA 基因。GC 含量范围为 37.6%至 37.69%。比较分析表明具有共享的基因组结构和基因重排。在 LSC/IRa 和 IRa/SSC 连接处的反向重复区分别观察到 22 和 26 个分类群的扩张和收缩；相比之下，IRb 边界基本不变。在 41 个冬青属质体基因组中检测到 2146 个简单重复序列和 2843 个大重复序列。此外，鉴定出 6 个基因（psaC、rbcL、trnQ、trnR、trnT 和 ycf1）和 2 个基因间间隔区（ndhC-trnV 和 petN-psbM）为高变区，因此可能对未来的系统发育研究和 DNA 条形码有用。无论推理方法或基因座选择如何，我们都恢复了一致的系统发育关系。我们恢复了五个不同的主要分支，这与传统的分类系统不一致。
我们的研究结果挑战了冬青属的传统范围，并为这个重要分支的进化历史提供了新的见解。此外，我们详细介绍了高变区和重复区，这将对未来的系统发育和群体遗传研究有用。
