Comparative Analysis of the Complete Chloroplast Genomes in Allium Subgenus Cyathophora (Amaryllidaceae): Phylogenetic Relationship and Adaptive Evolution
Joint Authors
Yang, Xin
Xie, Deng-Feng
Chen, Jun-Pei
Zhou, Song-Dong
Yu, Yan
He, Xing-Jin
Source
Issue
Vol. 2020, Issue 2020 (31 Dec. 2020), pp.1-17, 17 p.
Publisher
Hindawi Publishing Corporation
Publication Date
2020-01-17
Country of Publication
Egypt
No. of Pages
17
Main Subjects
Abstract EN
Recent advances in molecular phylogenetics provide us with information of Allium L.
taxonomy and evolution, such as the subgenus Cyathophora, which is monophyletic and contains five species.
However, previous studies detected distinct incongruence between the nrDNA and cpDNA phylogenies, and the interspecies relationships of this subgenus need to be furtherly resolved.
In our study, we newly assembled the whole chloroplast genome of four species in subgenus Cyathophora and two allied Allium species.
The complete cp genomes were found to possess a quadripartite structure, and the genome size ranged from 152,913 to 154,174 bp.
Among these cp genomes, there were subtle differences in the gene order, gene content, and GC content.
Seven hotspot regions (infA, rps16, rps15, ndhF, trnG-UCC, trnC-GCA, and trnK-UUU) with nucleotide diversity greater than 0.02 were discovered.
The selection analysis showed that some genes have elevated Ka/Ks ratios.
Phylogenetic analysis depended on the complete chloroplast genome (CCG), and the intergenic spacer regions (IGS) and coding DNA sequences (CDS) showed same topologies with high support, which revealed that subgenus Cyathophora was a monophyletic group, containing four species, and A.
cyathophorum var.
farreri was sister to A.
spicatum with 100% bootstrap value.
Our study revealed selective pressure may exert effect on several genes of the six Allium species, which may be useful for them to adapt to their specific living environment.
We have well resolved the phylogenetic relationship of species in the subgenus Cyathophora, which will contribute to future evolutionary studies or phylogeographic analysis of Allium.
American Psychological Association (APA)
Yang, Xin& Xie, Deng-Feng& Chen, Jun-Pei& Zhou, Song-Dong& Yu, Yan& He, Xing-Jin. 2020. Comparative Analysis of the Complete Chloroplast Genomes in Allium Subgenus Cyathophora (Amaryllidaceae): Phylogenetic Relationship and Adaptive Evolution. BioMed Research International،Vol. 2020, no. 2020, pp.1-17.
https://search.emarefa.net/detail/BIM-1131880
Modern Language Association (MLA)
Yang, Xin…[et al.]. Comparative Analysis of the Complete Chloroplast Genomes in Allium Subgenus Cyathophora (Amaryllidaceae): Phylogenetic Relationship and Adaptive Evolution. BioMed Research International No. 2020 (2020), pp.1-17.
https://search.emarefa.net/detail/BIM-1131880
American Medical Association (AMA)
Yang, Xin& Xie, Deng-Feng& Chen, Jun-Pei& Zhou, Song-Dong& Yu, Yan& He, Xing-Jin. Comparative Analysis of the Complete Chloroplast Genomes in Allium Subgenus Cyathophora (Amaryllidaceae): Phylogenetic Relationship and Adaptive Evolution. BioMed Research International. 2020. Vol. 2020, no. 2020, pp.1-17.
https://search.emarefa.net/detail/BIM-1131880
Data Type
Journal Articles
Language
English
Notes
Includes bibliographical references
Record ID
BIM-1131880