@ARTICLE{TreeBASE2Ref29357, author = {Lauren M Orton and Sean V Burke and Melvin R Duvall}, title = {Plastome phylogenomics and characterization of rare genomic changes as taxonomic markers in plastome groups 1 and 2 Poeae (Pooideae; Poaceae)}, year = {2019}, keywords = {chloroplast, Poeae, phylogenomics, rare genomic changes, intrastrand deletion, taxonomic markers}, doi = {}, url = {http://}, pmid = {}, journal = {PeerJ}, volume = {}, number = {}, pages = {}, 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. Three data partitions: complete plastomes, rare genomic changes (RGC), and a combined plastome and 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, and 27 were synapomorphic among the Group 2 subtribes: Loliinae, Ammochloinae, 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. } }

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