Comparative and phylogenetic analysis of the complete chloroplast genome sequences of Allium mongolicum

Abstract

Allium mongolicum Regel is a wild and sandy vegetable with unique flavours. In this study, a complete chloroplast (cp) genome of A. mongolicum was obtained (Genbank accession number: OM630416), and contained 153,609 base pairs with the GC ratio as 36.8%. 130 genes were annotated including 84 protein-coding genes, 38 tRNA, and 8 rRNA genes. The large single-copy (LSC) region was 82,644 bp, and a small single-copy (SSC) region was 18,049 bp, which were separated by two inverted repeats (IRs, including IRa and IRb) of 26,458 bp. Comparative genome analyses of 55 Allium species suggested that genomic structure of genus Allium was conserved, and LSC and SSC regions were outstanding with high variability. Among them, more divergent loci were in the SSC region covering ycf1-rrn4.5 and ndhF-ccsA. Phylogenetic analysis on cp genomes of 55 Allium determined that all members were clustered into 13 clades, and A. mongolicum had close relationship with A. senescens. Corresponding analyses of four protein-coding genes (ycf1, ndhF, rpl32, and ccsA) in aforementioned divergent loci confirmed that ycf1 was finally chosen as the candidate gene for species identification and evolutionary classification of genus Allium. These data provide valuable genetic resources for future research on Allium.

New insights into the phylogenetic relationships among wild onions (Allium, Amaryllidaceae), with special emphasis on the subgenera Anguinum and Rhizirideum, as revealed by plastomes

“…Although concatenated chloroplast non-coding region sequences had limited values, complete plastome sequences have been treasured and used recently to reveal the evolutionary history and adaptive evolution of the genus Allium and related genera ( Huo et al., 2019 ; Xie D.-F. et al., 2019 , Xie et al., 2020 ; Yang et al., 2020 ; Namgung et al., 2021 ; Scobeyeva et al., 2021 ; Chen et al., 2022 ; Jin et al., 2022 ). In particular, a total of 39 complete plastomes of Allium , covering 12 subgenera, provided well-supported phylogenetic relationships, identified numerous positively selected genes, and confirmed the monophyly of the genus and the three evolutionary lines ( Xie et al., 2020 ).…”

Comparative study on chloroplast genomes of three Hansenia forbesii varieties (Apiaceae)

“…The cp genome is slow evolving [10] and inherited from a single parent: maternally in most angiosperms [11] and paternally in some gymnosperms [12]. It is widely used in the study of plant molecular evolution and phylogeny, as well as in genetic transformation, genetic engineering, and molecular breeding [13][14][15]. Recently, with the gradual popularization and low cost of high-throughput sequencing technology, some scientists have proposed that cp genome data can be used for species identification and interspecific differentiation research [16][17][18][19][20].…”