Complete chloroplast genome sequences of four Allium species: comparative and phylogenetic analyses
文献类型： 外文期刊
作者： Huo, YuMeng 1 ; Gao, LiMin 1 ; Liu, BingJiang 1 ; Yang, YanYan 1 ; Kong, SuPing 1 ; Sun, YuQing 2 ; Yang, YaHui 3 ; Wu, Xiong 1 ;
作者机构： 1.Shandong Acad Agr Sci, Key Lab Biol Greenhouse Vegetable Shandong Prov, Natl Ctr Vegetable Improvement, Shandong Branch,Vegetable & Flower Res Inst, Jinan 250100, Shandong, Peoples R China
2.Northeast Agr Univ, Coll Hort & Landscape Architecture, Harbin 150030, Heilongjiang, Peoples R China
3.Shandong Agr Univ, Coll Hort Sci & Engn, Tai An 271018, Shandong, Peoples R China
期刊名称：SCIENTIFIC REPORTS （ 影响因子：4.379； 五年影响因子：5.133 ）
ISSN： 2045-2322
年卷期： 2019 年 9 卷
页码：
收录情况： SCI
摘要： The genus Allium is one of the largest monocotyledonous genera, containing over 850 species, and most of these species are found in temperate climates of the Northern Hemisphere. Furthermore, as a large number of new Allium species continue to be identified, phylogenetic classification based on morphological characteristics and a few genetic markers will gradually exhibit extremely low discriminatory power. In this study, we present the use of complete chloroplast genome sequences in genome-scale phylogenetic studies of Allium. We sequenced and assembled four Allium chloroplast genomes and retrieved five published chloroplast genomes from GenBank. All nine chloroplast genomes were used for genomic comparison and phylogenetic inference. The chloroplast genomes, ranging from 152,387 bp to 154,482 bp in length, exhibited conservation of genomic structure, and gene organization and order. Subsequently, we observed the expansion of IRs from the basal monocot Acorus americanus to Allium, identified 814 simple sequence repeats, 131 tandem repeats, 154 dispersed repeats and 109 palindromic repeats, and found six highly variable regions. The phylogenetic relationships of the Allium species inferred from the chloroplast genomes obtained high support, indicating that chloroplast genome data will be useful for further resolution of the phylogeny of the genus Allium.
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