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Adaptation Evolution and Phylogenetic Analyses of Species in Chinese Allium Section Pallasia and Related Species Based on Complete Chloroplast Genome Sequences.

ABSTRACT: The section Pallasia is one of the components of the genus Allium subgenus Allium (Amaryllidaceae), and species relationship in this section is still not resolved very well, which hinders further evolutionary and adaptive studies. Here, the complete chloroplast genomes of five sect. Pallasia species were reported, and a comparative analysis was performed with other three related Allium species. The genome size of the eight species ranged from 151,672 bp to 153,339 bp in length, GC content changed from 36.7% to 36.8%, and 130 genes (except Allium pallasii), 37 tRNA, and 8 rRNA were identified in each genome. By analyzing the IR/LSC and IR/SSC boundary, A. pallasii exhibited differences compared with other seven species. Phylogenetic analysis achieved high supports in each branch, seven of the eight Allium species cluster into a group, and A. pallasii exhibit a close relationship with A. obliquum. Higher pairwise Ka/Ks ratios were found in A. schoenoprasoides compared to A. caeruleum and A. macrostemon while a lower value of Ka/Ks ratios was detected between A. caeruleum and A. macrostemon. This study will be a great contribution to the future phylogenetic and adaptive research in Allium.

SUBMITTER: Xie FM

PROVIDER: S-EPMC7306069 | biostudies-literature |

REPOSITORIES: biostudies-literature

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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

Adaptation Evolution and Phylogenetic Analyses of Species in Chinese Allium Section Pallasia and Related Species Based on Complete Chloroplast Genome Sequences.

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