College of Forestry and Biotechnology, Zhejiang A&F University, Lin'an, 311300, Hangzhou, China.
Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China.
Sci Rep. 2024 Sep 4;14(1):20577. doi: 10.1038/s41598-024-71838-w.
Chloroplast (cp) genome sequences have been extensively used for phylogenetic and evolutionary analyses, as many have been sequenced in recent years. Identification of Quercus is challenging because many species overlap phenotypically owing to interspecific hybridization, introgression, and incomplete lineage sorting. Therefore, we wanted to gain a better understanding of this genus at the level of the maternally inherited chloroplast genome. Here, we sequenced, assembled, and annotated the cp genomes of the threatened Quercus marlipoensis (160,995 bp) and Q. kingiana (161,167 bp), and mined these genomes for repeat sequences and codon usage bias. Comparative genomic analyses, phylogenomics, and selection pressure analysis were also performed in these two threatened species along with other species of Quercus. We found that the guanine and cytosine content of the two cp genomes were similar. All 131 annotated genes, including 86 protein-coding genes, 37 transfer RNA genes, and 8 ribosomal RNA genes, had the same order in the two species. A strong A/T bias was detected in the base composition of simple sequence repeats. Among the 59 synonymous codons, the codon usage pattern of the cp genomes in these two species was more inclined toward the A/U ending. Comparative genomic analyses indicated that the cp genomes of Quercus section Ilex are highly conserved. We detected eight highly variable regions that could be used as molecular markers for species identification. The cp genome structure was consistent and different within and among the sections of Quercus. The phylogenetic analysis showed that section Ilex was not monophyletic and was divided into two groups, which were respectively nested with section Cerris and section Cyclobalanopsis. The two threatened species sequenced in this study were grouped into the section Cyclobalanopsis. In conclusion, the analyses of cp genomes of Q. marlipoensis and Q. kingiana promote further study of the taxonomy, phylogeny and evolution of these two threatened species and Quercus.
叶绿体（cp）基因组序列在近年来已被广泛用于系统发育和进化分析，许多序列已经被测定。栎属的鉴定具有挑战性，因为许多物种由于种间杂交、基因渐渗和不完全谱系分选而在表型上重叠。因此，我们希望在母系遗传的叶绿体基因组水平上更好地了解这个属。在这里，我们对受威胁的麻栎（Quercus marlipoensis）（160995 bp）和栓皮栎（Q. kingiana）（161167 bp）的 cp 基因组进行了测序、组装和注释，并从这些基因组中挖掘了重复序列和密码子使用偏好。比较基因组分析、系统发育基因组学和选择压力分析也在这两个受威胁的物种以及其他栎属物种中进行。我们发现，这两个 cp 基因组的鸟嘌呤和胞嘧啶含量相似。在这两个物种中，所有 131 个注释基因，包括 86 个蛋白质编码基因、37 个转移 RNA 基因和 8 个核糖体 RNA 基因，都具有相同的顺序。在简单序列重复的碱基组成中检测到强烈的 A/T 偏倚。在 59 个同义密码子中，这两个物种 cp 基因组的密码子使用模式更倾向于 A/U 结尾。比较基因组分析表明，栎属 Ilex 节的 cp 基因组高度保守。我们检测到了 8 个高度可变区域，这些区域可以作为物种鉴定的分子标记。cp 基因组结构在栎属的内部和各节之间是一致的，但不同。系统发育分析表明，Ilex 节不是单系的，分为两组，分别嵌套在 Cerris 节和 Cyclobalanopsis 节中。本研究中测序的两个受威胁物种被归入 Cyclobalanopsis 节。总之，对 Q. marlipoensis 和 Q. kingiana 的 cp 基因组分析促进了对这两个受威胁物种和栎属的分类学、系统发育和进化的进一步研究。
