Dataset Information

The complete chloroplast genome of Allium wallichii Kunth (Amaryllidaceae).

ABSTRACT: Allium wallichii Kunth is a herb species with potentially extensive applications because of its edible, ornamental, and pharmaceutical values. The structural characteristics and phylogenetic relationships of its chloroplast genome were determined here for the first time. The complete cp genome was found to be 152,496 bp long, with a GC content of 37.04%. It consists of four distinct regions: a large single copy (LSC) region of 82,510 bp, a small single copy (SSC) region of 17,460 bp, and two inverted repeat (IR) regions of 26,263 bp each. The genome encodes 129 genes, including 86 protein-coding genes, 37 tRNA genes, and six rRNA genes. Our phylogenetic analysis revealed that A. wallichii was closely related to Allium wallichii var. platyphyllum, which are included in the section Bromatorrhiza, subgenus Amerallium Traub of the genus Allium. Our report provides valuable information on the genetic diversity of Allium species.

SUBMITTER: Zhao J

PROVIDER: S-EPMC10557535 | biostudies-literature | 2023

REPOSITORIES: biostudies-literature

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The complete chloroplast genome of <i>Allium wallichii</i> Kunth (Amaryllidaceae).

Zhao Jin J Huang Miao M Ni Rui R Peng Ting T Chen Xiaoyulong X Nan Hong H

Mitochondrial DNA. Part B, Resources 20231005 10

<i>Allium wallichii</i> Kunth is a herb species with potentially extensive applications because of its edible, ornamental, and pharmaceutical values. The structural characteristics and phylogenetic relationships of its chloroplast genome were determined here for the first time. The complete cp genome was found to be 152,496 bp long, with a GC content of 37.04%. It consists of four distinct regions: a large single copy (LSC) region of 82,510 bp, a small single copy (SSC) region of 17,460 bp, and ...[more]

PMID: 37810614

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Project description:The genus Allium (Amaryllidaceae, Allioideae) is one of the largest monocotyledonous genera and it includes many economically important crops that are cultivated for consumption or medicinal uses. Recent advances in molecular phylogenetics have revolutionized our understanding of Allium taxonomy and evolution. However, the phylogenetic relationships in some Allium sections (such as the Allium section Daghestanica) and the genetic bases of adaptative evolution, remain poorly understood. Here, we newly assembled six chloroplast genomes from Chinese endemic species in Allium section Daghestanica and by combining these genomes with another 35 allied species, we performed a series of analyses including genome structure, GC content, species pairwise Ka/Ks ratios, and the SSR component, nucleotide diversity and codon usage. Positively selected genes (PSGs) were detected in the Allium lineage using the branch-site model. Comparison analysis of Bayesian and ML phylogeny on CCG (complete chloroplast genome), SCG (single copy genes) and CDS (coding DNA sequences) produced a well-resolved phylogeny of Allioideae plastid lineages, which illustrated several novel relationships with the section Daghestanica. In addition, six species in section Daghestanica showed highly conserved structures. The GC content and the GC3s content in Allioideae species exhibited lower values than studied non-Allioideae species, along with elevated pairwise Ka/Ks ratios. The rps2 gene was lost in all examined Allioideae species, and 10 genes with significant posterior probabilities for codon sites were identified in the positive selection analysis, seven of them are associated with photosynthesis. Our study uncovered a new species relationship in section Daghestanica and suggested that the selective pressure has played an important role in Allium adaptation and evolution, these results will facilitate our further understanding of evolution and adaptation of species in the genus Allium.

Dataset Information

The complete chloroplast genome of Allium wallichii Kunth (Amaryllidaceae).

Publications

The complete chloroplast genome of <i>Allium wallichii</i> Kunth (Amaryllidaceae).

Similar Datasets

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