Comparative Analysis of the Complete Chloroplast Genomes in Allium Subgenus Cyathophora (Amaryllidaceae): Phylogenetic Relationship and Adaptive Evolution

Abstract

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.

Comparative Chloroplast Genomics of Corydalis Species (Papaveraceae): Evolutionary Perspectives on Their Unusual Large Scale Rearrangements

“…The pairwise Ka/Ks ratios were widely used as an effective way to detect positive selection or adaptive evolution in plant species ( Wang et al, 2010 ; Gao et al, 2019 ). For the protein-coding genes in the Corydalis plastomes, the majority (85.1%) of Ka/Ks ratios obtained in our analyses were between 0 and 0.5, which was consistent with the result of previous researches ( Nei et al, 2010 ; Yang et al, 2020 ). This suggests that the majority of genes in the Corydalis plastomes were probably under purifying selection.…”

Complete plastid genome of Angelica, Ostericum and related species (Apiaceae): genomic evolution and phylogenetic implications

“…chinense and O. sieboldii) had hexanucleotide SSRs (Figure 4). This is consistent with other Apiaceae species [34,37,40,41] and Allium [35,36,42], but dinucleotide repeats are most numerous in Forthysia [43], and trinucleotide repeats are most abundant in Nitotiana [44].…”

“…The most abundant SSRs were mononucleotide in our studied species, followed by (in decreasing abundance) dinucleotide, tetranucleotide, trinucleotide, pentanucleotide, and hexanucleotide repeats. This phenomenon is common in Allium [35,36,42] and Apiaceae [34,37,40,41]. In our species, mononucleotide and dinucleotide compositions were similar, but trinucleotide, tetranucleotide and pentanucleotide were different across clades.…”

Initial Complete Chloroplast Genomes of Alchemilla (Rosaceae): Comparative Analysis and Phylogenetic Relationships

“…In order to understand the evolutionary relationship among Rosaceae species, complete cp genome sequences and 78 PCGs in 27 species of subfamily Rosoideae and Amygdaloideae were used to infer the phylogenetic position of A. argyrophylla and A. pedata with Elaeagnus macrophylla (Elaeagnaceae) and Morus indica (Moraceae) as outgroups. The cp genome sequences and its PCGs provide precise and systematic genomic information for phylogenetic and evolutionary relationship reconstruction ( Yang X. et al, 2020 ). Phylogenetic analysis was conducted using ML, BI, and PhyML methods ( Figures 5 , 6 ).…”

“…The contention requires the separation of the Alchemilla into Eualchemilla and Afromilla clade, which has been restrained due to lack of substantial morphological borderlines despite extensive and significant studies ( Notov and Kusnetzova, 2004 ; Gehrke et al, 2008 ; Lundberg et al, 2009 ). The emergence and rapid development in cp genome sequencing technologies have been essential in providing resourceful genomic information that has been fundamental for the reconstruction of lower and higher plant phylogenies as well as evolutionary trends ( Daniell et al, 2016 ; Yang X. et al, 2020 ). Significantly, the cp genome sequences have been proven effective in eliminating phylogenetic incongruences arising from incomplete lineage sorting (ILS) and hybridization ( Lundberg et al, 2009 ; Morales-Briones et al, 2018 ).…”