Comparative chloroplast genome analyses of Avena: insights into evolutionary dynamics and phylogeny

Abstract

Background Oat ( Avena sativa L.) is a recognized health-food, and the contributions of its different candidate A-genome progenitor species remain inconclusive. Here, we report chloroplast genome sequences of eleven Avena species, to examine the plastome evolutionary dynamics and analyze phylogenetic relationships between oat and its congeneric wild related species. Results The chloroplast genomes of eleven Avena species (size range of 135,889–135,998 bp) share quadripartite structure, comprising of a large single copy (LSC; 80,014–80,132 bp), a small single copy (SSC; 12,575–12,679 bp) and a pair of inverted repeats (IRs; 21,603–21,614 bp). The plastomes contain 131 genes including 84 protein-coding genes, eight ribosomal RNAs and 39 transfer RNAs. The nucleotide sequence diversities (Pi values) range from 0.0036 ( rps19 ) to 0.0093 ( rpl32 ) for ten most polymorphic genes and from 0.0084 ( psbH-petB ) to 0.0240 ( petG-trnW-CCA ) for ten most polymorphic intergenic regions. Gene selective pressure analysis shows that all protein-coding genes have been under purifying selection. The adjacent position relationships between tandem repeats, insertions/deletions and single nucleotide polymorphisms support the evolutionary importance of tandem repeats in causing plastome mutations in Avena . Phylogenomic analyses, based on the complete plastome sequences and the LSC intermolecular recombination sequences, support the monophyly of Avena with two clades in the genus. Conclusions Diversification of Avena plastomes is explained by the presence of highly diverse genes and intergenic regions, LSC intermolecular recombination, and the co-occurrence of tandem repeat and indels or single nucleotide polymorphisms. The study demonstrates that the A-genome diploid-polyploid lineage maintains two subclades derived from different maternal ancestors, with A. longiglumis as the first diverging species in clade I. These genome resources will be helpful in elucidating the chloroplast genome structure, understanding the evolutionary dynamics at genus Avena and family Poaceae levels, and are potentially useful to exploit plastome variation in making hybrids for plant breeding.

Reference genome assemblies reveal the origin and evolution of allohexaploid oat

“…To determine the maternal origin of hexaploid oat, we assembled approximately complete plastid genomes of 136 kb for each Avena species. Phylogenetic analysis of 18 complete Avena plastid genomes together with the previous 26 Avena chloroplast genomes (Supplementary Tables 14-15) 24,25 showed that the C genome was undoubtedly the male parent in polyploid formation and that the D genome, rather than the A genome, was the maternal donor of hexaploid oat. The evolutionary order of the different A genome subtypes was Ac-Ad-Al-As (Fig 3e, Supplementary Fig.…”

“…The chloroplast genomes of all sequenced taxa were assembled using the clean short reads with NOVOPlasty 63 . Another 26 Avena chloroplast genomes previously published by Fu et al 24 and Liu et al 25 were also downloaded (Supplementary Table 15). Multiple sequence alignments were performed using MUSCLE 64 , and the identified informative sites were used for phylogenetic tree construction using RAxML with 100 bootstrap replicates under the GTR+I+Γ evolutionary model, where the chloroplast genome sequence from Triticum aestivum was used as the outgroup.…”

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

“…), Plantaginaceae ( Zhu et al, 2016 ; Kwon et al, 2019 ; Asaf et al, 2020 , etc. ), and Poaceae ( Palmer and Thompson, 1982 ; Doyle et al, 1992 ; Michelangeli et al, 2003 ; Burke et al, 2016 ; Liu et al, 2020 , etc.). Given that the structure of the two already known plastomes from the genus Corydalis was highly variable ( Wu et al, 2020 ; Xu and Wang, 2020 ), this genus is expected to represent an overlooked lineage with extensive large-scale plastome rearrangements.…”

Characteristics of the completed chloroplast genome sequence of Xanthium spinosum: comparative analyses, identification of mutational hotspots and phylogenetic implications

“…With the emergence of next-generation sequencing technology [ 3 ], complete cp genome sequences are being extensively used to improve phylogenetic resolution at the interspecific level [ 4 ]. In addition, cp genomes have been found to contain polymorphic regions generated through genomic expansion, contraction, inversion, or gene rearrangement, and such sequences have been widely used as an effective tool for plant phylogenomic analyses [ 5 ].…”