Table 1.
List of materials used in the present study including species, haplomes, accession number, origin, the number of sequenced clones, abbreviation displayed in MJ network, and the sequence number in Genbank (https://www.ncbi.nlm.nih.gov).
Fig 1.
(A) Partial alignment of the amplified Pgk1 gene of Avena species (B) Secondary structure of the deletion sequence between the A and C genomes.
Fig 2.
Saturation plot for transition and transversion of Pgk1 gene sequences.
The crosses are the number of transition events; the triangles are the number of transversion events. The x axis shows the genetic distance based on the TN93 model; the y axis is the proportion of transitions or tansversions, which was calculated by using the number of transitions or transversions divided by the sequence length. The curves show the trends of the variance of transitions and transversions with the genetic distance increasing.
Fig 3.
Maximum parsimony tree derived from Pgk1 sequence data.
The tree was constructed using a heuristic search with TBR branch swapping. Numbers above the branches are bootstrap support (BS) values ≥50%. Accession number, species name and haplome are indicated for each taxon.
Fig 4.
Median-joining networks based on 41 Pgk1 gene haplotypes of intron regions derived from 26 Avena species.
Each circular node represents a single haplotype, with relative size being proportional to the frequency of that haplotype. Distinct colors in the same haplotype node represent different species sharing the same haplotype (colors are arbitrary). Median vectors (mv) represent the putative missing intermediates. Numbers along network branches indicate the number of bases involved in mutations between two nodes. Clusters (surrounded by dashed lines) are named based on clade names shown in the MP tree (Fig 3). Three-letter abbreviations of species names are listed in Table 1. The numbers immediately after each species abbreviation represent different accessions of the same species, and the number following the underscore identifies different haplotypes from the same accession.