Comparative analyses of chloroplast genomes from 22 Lythraceae species: inferences for phylogenetic relationships and genome evolution within Myrtales
Comparative analyses of chloroplast genomes from 22 Lythraceae species: inferences for phylogenetic relationships and genome evolution within Myrtales
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DOI：
10.1186/s12870-019-1870-3
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发表时间：
2019-06-26
影响因子：
5.3
通讯作者：
Wang, Yixiang
中科院分区：
文献类型：
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作者：
Gu, Cuihua;Ma, Li;Wang, Yixiang
桃金娘科属于桃金娘目，是石竹科的一部分。该科有31属，包含约620种草本植物、灌木和乔木。在这31个属中，有5个大属各有35种以上。他们是Lythrum，有35个；罗塔拉，45人；尼西亚，50人；紫薇，56分；和Cuphea，有275种。结果报道了6个新测序的叶绿体基因组（Duabanga grandflora、Trapa natans、Lythrum salicaria、Lawsonia inermis、Woodfordia fruticosa和Rotala rotundifolia），并与其他16个lythaceae物种的叶绿体基因组进行了比较。22种石蒜科植物的cp基因组长度在152049 ~ 160769 bp之间。在每个蓟科植物中，cp基因组包含112个基因，其中包括78个蛋白质编码基因、4个核糖体rna和30个转移rna。在6个分类中检测到211 ~ 332个简单重复序列（SSRs），在4个分类中检测到7 ~ 27个长重复序列（long repeats）。我们从22种蓟科植物中选择了10个不同的热点（ndhF、matK、ycf1、rpl22、rpl32、trnK-rps16、trnR-atpA、rpl32- trnl、trnH-psbA和trg - trnr）作为潜在的分子标记。以42株桃金娘属植物和8株香叶属植物为类群构建了系统发育树。利用66个蛋白编码基因构建的最大似然树（ML）、最大简约树（MP）和贝叶斯推理树（BI），有效区分了桃金娘属植物间的亲缘关系。一般来说，22种Lythraceae植物聚集在一个分支中，该分支被分解为三个onagracae物种的姐妹。与蜜桃科和桃金娘科相比，桃金娘科和月桂科在桃金娘科中分化较晚。结论本研究为桃金娘提供了10个潜在的分子标记作为候选DNA条形码，为桃金娘进一步研究提供了cp基因组资源。
BackgroundLythraceae 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.ResultsWe 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 152,049bp to 160,769bp. 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.ConclusionsThe study provided ten potential molecular markers as candidate DNA barcodes and contributed cp genome resources within Myrtales for further study.