李属（蔷薇科）叶绿体基因组揭示了系统发育关系和分化时间。
The chloroplast genome of Amygdalus L. (Rosaceae) reveals the phylogenetic relationship and divergence time.
机构信息
College of life science, Shaanxi Key Laboratory of Ecological Restoration in Northern Shaanxi Mining Area, Yulin University, Yulin, China.
School of Ecology and environment, Breeding Base for State Key Laboratory of Land Degradation and Ecological Restoration in Northwest China, Ministry of Education Key Laboratory for Restoration and Reconstruction of Degraded Ecosystems in Northwest China, Ningxia University, Yinchuan, China.
出版信息
BMC Genomics. 2021 Sep 7;22(1):645. doi: 10.1186/s12864-021-07968-6.
BACKGROUND
Limited access to genetic information has greatly hindered our understanding of the molecular evolution, phylogeny, and differentiation time of subg. Amygdalus. This study reported complete chloroplast (cp) genome sequences of subg. Amygdalus, which further enriched the available valuable resources of complete cp genomes of higher plants and deepened our understanding of the divergence time and phylogenetic relationships of subg. Amygdalus.
RESULTS
The results showed that subg. Amygdalus species exhibited a tetrad structure with sizes ranging from 157,736 bp (P. kansuensis) to 158,971 bp (P. davidiana), a pair of inverted repeat regions (IRa/IRb) that ranged from 26,137-26,467 bp, a large single-copy region that ranged from 85,757-86,608 bp, and a small single-copy region that ranged from 19,020-19,133 bp. The average GC content of the complete cp genomes in the 12 species was 36.80%. We found that the structure of the subg. Amygdalus complete cp genomes was highly conserved, and the 12 subg. Amygdalus species had an rps19 pseudogene. There was not rearrangement of the complete cp genome in the 12 subg. Amygdalus species. All 12 subg. Amygdalus species clustered into one clade based on both Bayesian inference and maximum likelihood. The divergence time analyses based on the complete cp genome sequences showed that subg. Amygdalus species diverged approximately 15.65 Mya.
CONCLUSION
Our results provide data on the genomic structure of subg. Amygdalus and elucidates their phylogenetic relationships and divergence time.
背景
遗传信息获取的局限性极大地阻碍了我们对杏仁属的分子进化、系统发育和分化时间的理解。本研究报道了杏仁属的完整叶绿体（cp）基因组序列，进一步丰富了高等植物完整 cp 基因组的可用宝贵资源，并加深了我们对杏仁属的分化时间和系统发育关系的理解。
结果
结果表明，杏仁属物种表现出四联体结构，大小范围从 157736bp（P. kansuensis）到 158971bp（P. davidiana），一对反向重复区（IRa/IRb）范围从 26137-26467bp，大片段单拷贝区范围从 85757-86608bp，小片段单拷贝区范围从 19020-19133bp。12 种植物完整 cp 基因组的平均 GC 含量为 36.80%。我们发现，杏仁属完整 cp 基因组的结构高度保守，12 种杏仁属植物都有 rps19 假基因。12 种杏仁属植物的完整 cp 基因组没有发生重排。基于贝叶斯推断和最大似然法，12 种杏仁属植物都聚类到一个分支中。基于完整 cp 基因组序列的分化时间分析表明，杏仁属物种大约在 15.65 万年前分化。
结论
我们的研究结果提供了杏仁属基因组结构的数据，阐明了它们的系统发育关系和分化时间。
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