Complete plastome sequencing resolves taxonomic relationships among species of Calligonum L. (Polygonaceae) in China
Complete plastome sequencing resolves taxonomic relationships among species of Calligonum L. (Polygonaceae) in China
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完整的质体组测序解决了中国Calligonum L.（蓼科）物种之间的分类关系
DOI：
10.1186/s12870-020-02466-5
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发表时间：
2020-06-08
影响因子：
5.3
通讯作者：
Ge, Xue-Jun
中科院分区：
文献类型：
--
作者：
Song, Feng;Li, Ting;Ge, Xue-Jun
蓼科蓼属植物分布于欧洲南部、北非和中亚，通常生长在干旱的沙漠地区。先前的研究表明，标准的DNA条形码无法区分鳄鱼属。在本研究中，我们对21个caligonumspecies的32个种质的质体基因组（质体组）进行了测序，不仅生成了caligonumum属的第一个完整的质体组序列，而且还1)评估了完整的质体组序列在类群内识别物种的能力，2)筛选了质体组序列，为今后的研究提供了一种高性价比的DNA条形码，可用于解决类群内的分类关系。结果全质粒具有典型的四部结构。叶绿体的大小约为161千碱基对（kbp），编码113个基因，其中包括79个蛋白质编码基因、30个tRNA基因和4个rRNA基因。基于ML系统发育树分析，完整质体组的物种识别率（78%）高于标准DNA条形码组合（rbcL + matK + nrITS, 56%）。新筛选到的5个基因区（ndhF、trnS-G、trnC-petN、ndhF-rpl32、rpl32-trnL）具有较高的种分辨能力，其中hdhf - trns - g5个基因区分辨出的种数比例最高（56%）。结论整个质体基因组是金盏花属最有效的条形码，其他基因区域也有潜力作为金盏花属的分类特异性条形码。
BackgroundCalligonum(Polygonaceae) is distributed from southern Europe through northern Africa to central Asia, and is typically found in arid, desert regions. Previous studies have revealed that standard DNA barcodes fail to discriminateCalligonumspecies. In this study, the complete plastid genomes (plastome) for 32 accessions of 21Calligonumspecies is sequenced to not only generate the first complete plastome sequence for the genusCalligonumbut to also 1) Assess the ability of the complete plastome sequence to discern species within the group, and 2) screen the plastome sequence for a cost-effective DNA barcode that can be used in future studies to resolve taxonomic relationships within the group.ResultsThe whole plastomes ofCalligonumspecies possess a typical quadripartite structure. The size of theCalligonumplastome is approximately 161 kilobase pairs (kbp), and encodes 113 genes, including 79 protein-coding genes, 30 tRNA genes, and four rRNA genes. Based on ML phylogenetic tree analyses, the complete plastome has higher species identification (78%) than combinations of standard DNA barcodes (rbcL + matK + nrITS, 56%). Five newly screened gene regions (ndhF,trnS-G,trnC-petN,ndhF-rpl32,rpl32-trnL) had high species resolution, wherendhFandtrnS-Gwere able to distinguish the highest proportion ofCalligonumspecies (56%).ConclusionsThe entire plastid genome was the most effective barcode for the genusCalligonum, although other gene regions showed great potential as taxon-specific barcodes for species identification inCalligonum.