Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China.
BMC Evol Biol. 2014 Jul 7;14:151. doi: 10.1186/1471-2148-14-151.
Camellia is an economically and phylogenetically important genus in the family Theaceae. Owing to numerous hybridization and polyploidization, it is taxonomically and phylogenetically ranked as one of the most challengingly difficult taxa in plants. Sequence comparisons of chloroplast (cp) genomes are of great interest to provide a robust evidence for taxonomic studies, species identification and understanding mechanisms that underlie the evolution of the Camellia species.
The eight complete cp genomes and five draft cp genome sequences of Camellia species were determined using Illumina sequencing technology via a combined strategy of de novo and reference-guided assembly. The Camellia cp genomes exhibited typical circular structure that was rather conserved in genomic structure and the synteny of gene order. Differences of repeat sequences, simple sequence repeats, indels and substitutions were further examined among five complete cp genomes, representing a wide phylogenetic diversity in the genus. A total of fifteen molecular markers were identified with more than 1.5% sequence divergence that may be useful for further phylogenetic analysis and species identification of Camellia. Our results showed that, rather than functional constrains, it is the regional constraints that strongly affect sequence evolution of the cp genomes. In a substantial improvement over prior studies, evolutionary relationships of the section Thea were determined on basis of phylogenomic analyses of cp genome sequences.
Despite a high degree of conservation between the Camellia cp genomes, sequence variation among species could still be detected, representing a wide phylogenetic diversity in the genus. Furthermore, phylogenomic analysis was conducted using 18 complete cp genomes and 5 draft cp genome sequences of Camellia species. Our results support Chang's taxonomical treatment that C. pubicosta may be classified into sect. Thea, and indicate that taxonomical value of the number of ovaries should be reconsidered when classifying the Camellia species. The availability of these cp genomes provides valuable genetic information for accurately identifying species, clarifying taxonomy and reconstructing the phylogeny of the genus Camellia.
山茶属在山茶科中具有重要的经济和系统发育意义。由于大量的杂交和多倍化，它在分类学和系统发育上被认为是植物中最具挑战性的类群之一。叶绿体（cp）基因组序列比较对于提供分类学研究、物种鉴定以及理解山茶属物种进化机制的有力证据具有重要意义。
利用 Illumina 测序技术，通过从头组装和参考指导组装相结合的策略，测定了 8 个山茶属物种的完整 cp 基因组和 5 个 cp 基因组草图序列。山茶属 cp 基因组表现出典型的圆形结构，在基因组结构和基因顺序的同源性方面相对保守。进一步比较了 5 个完整 cp 基因组中重复序列、简单重复序列、插入缺失和替换的差异，代表了该属广泛的系统发育多样性。鉴定了 15 个分子标记，这些标记的序列差异超过 1.5%，可能对进一步的山茶属系统发育分析和物种鉴定有用。结果表明，不是功能约束，而是区域约束强烈影响 cp 基因组的序列进化。在对 cp 基因组序列进行系统发育分析的基础上，对茶组的进化关系进行了深入研究。
尽管山茶属 cp 基因组高度保守，但仍能检测到种间序列变异，代表了该属广泛的系统发育多样性。此外，对 18 个完整的 cp 基因组和 5 个山茶属 cp 基因组草图序列进行了基因组分析。研究结果支持 Chang 的分类处理，即 C. pubicosta 可能被归类为茶组，并表明在分类山茶属物种时，应重新考虑子房数目的分类学价值。这些 cp 基因组的获得为准确鉴定物种、阐明分类学和重建山茶属的系统发育提供了有价值的遗传信息。
