Plastome phylogenomics and characterization of rare genomic changes as taxonomic markers in plastome groups 1 and 2 Poeae (Pooideae; Poaceae)

Abstract

A phylogenomic analysis of 42 complete plastid genomes (plastomes), including 16 that were newly sequenced, was conducted. Plastomes were sampled from 19 subtribes of Pooideae, to investigate relationships within and between Chloroplast Group 1 (Aveneae) and Group 2 (Poeae) species. Two data partitions: complete plastomes, and a combined plastome and rare genomic change (RGC) data matrix, were analyzed. Overall, 156 non-ambiguous RGC were identified, of which homology was inferred for 38 RGC. Among the 38 RGC identified, six were synapomorphic among the Group 1 subtribes: Aveninae, Agrostidinae, and Anthoxanthinae, (Phalaridinae + Torreyochloinae), and 27 were synapomorphic among the Group 2 subtribes: Loliinae, (Ammochloinae + Parapholiinae + Dactylidinae), Parapholiinae, Dactylidinae, Poinae, and Coleanthinae. Four RGC were determined to be homoplasious in Groups 1 and 2. Two other RGC originated through intrastrand deletion events. The remaining RGC events likely originated through recombination given their size and lack of sequence evidence for other types of mutations. This study also determined that relationships between taxa, even those only weakly supported in previous studies, could be inferred with strong support when utilizing complete plastomes.

Keywords: Chloroplast; Intrastrand deletion; Phylogenomics; Poeae; Rare genomic changes; Taxonomic markers.

Figure 1. Phylogeny of Poeae group 1 and 2 species included in this study.

ML cladogram showing relationships between both Group 1 and Group 2 taxa. Bracketed clades correspond to taxa sensu Soreng et al. (2017). GenBank accession number indicates the previously published species of F. ovina. Supersubtribe designations are shown in bolded text. Subtribe designations are shown in standard text.

Figure 2. ML sequence and RGC BS consensus for group 1 and 2 taxa.

ML consensus cladogram of sequence and rare genomic change (RGC) data for Group 1 and Group 2 taxa with bootstrap support (BS) values noted. Nodes without values are at maximum support. Support values within circles correspond to sequence only analyses. Support values within squares correspond to sequence + RGC analyses. GenBank accession number indicates the previously published species of F. ovina. A. brachychaeta and K. melanthera serve as outgroup comparisons.

Figure 3. ML BS consensus tree of Group 1 species.

ML BS tree of Group 1 species inferred from aligned sequences. The support values of two nodes, which are less than maximum, are indicated. Support values within circles correspond to sequence only analyses. Support values within squares correspond to sequence + rare genomic change (RGC) analyses. A. brachychaeta serves as the outgroup comparison. Supersubtribe designations are shown in bolded text. Subtribe designations are shown in standard text. Bracketed clades correspond to taxa sensu Soreng et al. (2017).

Figure 4. ML BS tree of Group 2 species inferred from aligned sequences.

The support values of three nodes, which are less than maximum, are indicated. Support values within circles correspond to sequence only analyses. Support values within squares correspond to sequence + rare genomic change (RGC) analyses. GenBank accession number indicates the previously published species of F. ovina. K. melanthera serves as the outgroup comparison. Supersubtribe designations are shown in bolded text. Subtribe designations are shown in standard text. Bracketed clades correspond to taxa sensu Soreng et al. (2017).

Figure 5. Taxonomic markers identified for Group 1 & Group 2 taxa.

(A) Taxonomic markers including the unique intrastrand deletion (ISD) event in P. fugax and B. maxima, are superimposed onto a ML phylogram for Group 1. Scale bar length is 0.003. Letter-number codes correspond to “Taxonomic Markers” found in Table S2 for Group 1 taxa. Subtribes are designated by dashed-line or bracket and bolded text; supersubtribes are designated by bold dashed-line/bracket and capitalized text. Bracketed clades correspond to taxa sensu Soreng et al. (2017). One rare genomic change (RGC) (F1) appears as homoplasious in both Phalaris arundinacea and Avena sativa. † Indicates a unique ISD event in the designated taxa. These ISD events are synapomorphic. (B) Taxonomic markers including the ISD event in F. ovina, are superimposed onto a ML phylogram for Group 2. Scale bar length is 0.003. GenBank accession number indicates the previously published species of F. ovina. Letter-number codes correspond to “Taxonomic Markers” found in Table S1 for Group 2 taxa. Subtribes are designated by dashed-line or bracket and bolded text; supersubtribes are designated by bold dashed-line/bracket and capitalized text. Bracketed clades correspond to taxa sensu Soreng et al. (2017). ‡ Indicates the unique ISD event seen in the previously published F. ovina (NC_019649); see Table 5 for sequence evidence of this ISD event.