Thirteen Camellia chloroplast genome sequences determined by high-throughput sequencing: genome structure and phylogenetic relationships.
Thirteen Camellia chloroplast genome sequences determined by high-throughput sequencing: genome structure and phylogenetic relationships.
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高通量测序确定的13个茶花叶绿体基因组序列：基因组结构和系统发育关系
DOI：
10.1186/1471-2148-14-151
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发表时间：
2014-07-07
影响因子：
3.4
通讯作者：
Gao LZ
中科院分区：
文献类型：
--
作者：
Huang H;Shi C;Liu Y;Mao SY;Gao LZ
背景：山茶属是山茶科植物中一个具有重要经济价值和系统发育价值的属。由于大量的杂交和多倍化，它在分类学和系统发育上被列为植物中最具挑战性的困难类群之一。茶树叶绿体(Cp)基因组的序列比较对于分类研究、物种鉴定和理解茶树物种进化的机制具有重要意义。结果：利用Illumina测序技术，通过从头开始和参考引导组装相结合的策略，获得了茶树属8个完整的cp基因组和5个粗略的cp基因组序列。茶树基因组具有典型的环状结构，在基因组结构和基因序列的共性上较为保守。进一步分析了5个完整的cp基因组在重复序列、简单序列重复、插入和替换等方面的差异，表明该属具有广泛的系统发育多样性。共鉴定出15个分子标记，序列差异大于1.5%，可用于山茶属进一步的系统发育分析和物种鉴定。我们的结果表明，对cp基因组序列进化有强烈影响的不是功能约束，而是区域约束。结论：尽管茶树cp基因组间高度保守，但仍可检测到物种间的序列差异，代表了该属广泛的系统发育多样性。此外，还利用18个茶树属植物完整的cp基因组和5个茶树属植物的cp基因组草图序列进行了系统发育分析。我们的结果支持Chang的分类观点，即普比科斯塔可能被归入Sect。Thea，并指出在对山茶属进行分类时，应重新考虑子房数目的分类价值。这些cp基因组的获得为准确鉴定物种、阐明分类和重建山茶属的系统发育提供了有价值的遗传信息。
Background: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.Results: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.Conclusions: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.
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影响因子：
3.4
作者：
Liu Y;Yang SX;Ji PZ;Gao LZ
通讯作者：
Gao LZ
影响因子：
7
作者：
Li, Ruiqiang;Zhu, Hongmei;Wang, Jun
通讯作者：
Wang, Jun
影响因子：
4.1
作者：
Asano, T;Tsudzuki, T;Kadowaki, K
通讯作者：
Kadowaki, K
影响因子：
4.1
作者：
Kim, KJ;Lee, HL
通讯作者：
Lee, HL
影响因子：
14.9
作者：
Katoh K;Kuma K;Toh H;Miyata T
通讯作者：
Miyata T