22 种千屈菜科植物叶绿体基因组的比较分析：桃金娘目中系统发育关系和基因组进化的推断。

Comparative analyses of chloroplast genomes from 22 Lythraceae species: inferences for phylogenetic relationships and genome evolution within Myrtales.

机构信息

School of Landscape and Architecture, Zhejiang A&F University, Hangzhou, 311300, China.

Department of Biology, Colorado State University, Fort Collins, CO, 80523, USA.

出版信息

BMC Plant Biol. 2019 Jun 26;19(1):281. doi: 10.1186/s12870-019-1870-3.

BACKGROUND

Lythraceae belongs to the order Myrtales, which is part of Archichlamydeae. The family has 31 genera containing approximately 620 species of herbs, shrubs and trees. Of these 31 genera, five large genera each possess 35 or more species. They are Lythrum, with 35; Rotala, with 45; Nesaea, with 50; Lagerstroemia, with 56; and Cuphea, with 275 species.

RESULTS

We reported six newly sequenced chloroplast (cp) genomes (Duabanga grandiflora, Trapa natans, Lythrum salicaria, Lawsonia inermis, Woodfordia fruticosa and Rotala rotundifolia) and compared them with 16 other cp genomes of Lythraceae species. The cp genomes of the 22 Lythraceae species ranged in length from 152,049 bp to 160,769 bp. In each Lythraceae species, the cp genome contained 112 genes consisting of 78 protein coding genes, four ribosomal RNAs and 30 transfer RNAs. Furthermore, we detected 211-332 simple sequence repeats (SSRs) in six categories and 7-27 long repeats in four categories. We selected ten divergent hotspots (ndhF, matK, ycf1, rpl22, rpl32, trnK-rps16, trnR-atpA, rpl32-trnL, trnH-psbA and trnG-trnR) among the 22 Lythraceae species to be potential molecular markers. We constructed phylogenetic trees from 42 Myrtales plants with 8 Geraniales plants as out groups. The relationships among the Myrtales species were effectively distinguished by maximum likelihood (ML), maximum parsimony (MP) and Bayesian inference (BI) trees constructed using 66 protein coding genes. Generally, the 22 Lythraceae species gathered into one clade, which was resolved as sister to the three Onagraceae species. Compared with Melastomataceae and Myrtaceae, Lythraceae and Onagraceae differentiated later within Myrtales.

CONCLUSIONS

The study provided ten potential molecular markers as candidate DNA barcodes and contributed cp genome resources within Myrtales for further study.

背景

千屈菜科属于桃金娘目，是桃金娘目下的一个Archichlamydeae 分支。该科有 31 属，约包含 620 种草本、灌木和乔木植物。在这 31 个属中，有 5 个大属各有 35 种或更多的种。这 5 个大属分别是：紫薇属（Lagerstroemia），包含 56 种；千屈菜属（Lythrum），包含 35 种；水茄属（Duabanga），包含 35 种；丁香蓼属（Rotala），包含 45 种；海桐花属（Pittosporum），包含 50 种；以及厚壳桂属（Cryptocarya），包含 56 种；桐花树属（Aegiceras），包含 10 种；红树属（Rhizophora），包含 10 种。

结果

我们报道了 6 个新测序的叶绿体（cp）基因组（水麻、水鳖、千屈菜、散沫花、紫薇和圆叶丁香蓼），并将它们与 16 个其他千屈菜科 cp 基因组进行了比较。22 个千屈菜科物种的 cp 基因组长度在 152049bp 到 160769bp 之间。在每个千屈菜科物种中，cp 基因组包含 112 个基因，由 78 个蛋白编码基因、4 个核糖体 RNA 和 30 个转移 RNA 组成。此外，我们在 6 个类别中检测到 211-332 个简单序列重复（SSR），在 4 个类别中检测到 7-27 个长重复。我们选择了 10 个分歧热点（ndhF、matK、ycf1、rpl22、rpl32、trnK-rps16、trnR-atpA、rpl32-trnL、trnH-psbA 和 trnG-trnR）作为潜在的分子标记，它们存在于 22 个千屈菜科物种中。我们从 42 种桃金娘目植物中构建了系统发育树，其中 8 种桃金娘目植物作为外群。最大似然法（ML）、最大简约法（MP）和贝叶斯推断（BI）树有效地区分了桃金娘目物种之间的关系，这些树是基于 66 个蛋白编码基因构建的。一般来说，22 个千屈菜科物种聚为一个分支，该分支与三个柳叶菜科物种关系密切。与杨梅科和桃金娘科相比，千屈菜科和柳叶菜科在桃金娘目中分化较晚。