Complete chloroplast genome sequences of four Allium species: comparative and phylogenetic analyses
Autor: | Xiong Wu, Liu Bingjiang, Yang Yanyan, Limin Gao, Huo Yumeng, Sun Yuqing, Yahui Yang, Kong Suping |
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Jazyk: | angličtina |
Rok vydání: | 2019 |
Předmět: |
0301 basic medicine
Chloroplasts lcsh:Medicine Biology Genome Article Allium Evolution Molecular 03 medical and health sciences Plant evolution 0302 clinical medicine Tandem repeat Phylogenetics lcsh:Science Genome Chloroplast Phylogeny Multidisciplinary Phylogenetic tree lcsh:R DNA Chloroplast food and beverages biology.organism_classification 030104 developmental biology Genetic marker Evolutionary biology GenBank Molecular evolution lcsh:Q 030217 neurology & neurosurgery Genome Plant Phylogenetic nomenclature Microsatellite Repeats |
Zdroj: | Scientific Reports Scientific Reports, Vol 9, Iss 1, Pp 1-14 (2019) |
ISSN: | 2045-2322 |
Popis: | 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. |
Databáze: | OpenAIRE |
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