Abstract
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.
Highlights
Allium L. is the single genus of Allieae and belongs to the subfamily Allioideae (Amaryllidaceae) as per update APG IV (Chase et al, 2016)
The complete cp genomes of six Allium species ranged from 153,605 bp (A. herderianum) to 153,710 bp (A. chrysocephalum) in length, with the minimum and maximum differences being
We found that five parameters involved in codon usage bias were lower in Allium (Allioideae) species than non-Allioideae species, except the codon adaptation index (CAI) that was lower in the family Asparagaceae (Figure 5)
Summary
Allium L. is the single genus of Allieae and belongs to the subfamily Allioideae (Amaryllidaceae) as per update APG IV (Chase et al, 2016) It is one of the largest genera of the monocotyledons (∼ 920 species) and includes many economically important crops (Herden et al, 2016; Zhu et al, 2017). Daghestanica according to molecular phylogenetic analyses, and was confirmed by morphological evidences produced by Yu et al (2018). These previous studies have significantly advanced the phylogeny and taxonomy of the six species, yet a consensus of the six species’ exact relationships have not been reached. Uncertainties remain because A. herderianum was not sampled in previous phylogenetic studies (Li et al, 2010)
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