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.

Long-reads reveal that Rhododendron delavayi plastid genome contains extensive repeat sequences, and recombination exists among plastid genomes of photosynthetic Ericaceae

“…By contrast, the plastid genomes of photosynthetic Ericaceae are usually long: they are 150,897 bp for A. unedo (Martinez-Alberola et al, 2013), 168,995 bp for P. rotundifolia (Logacheva et al, 2016), 176,045 bp for Vaccinium macrocarpon (Fajardo et al, 2013), and 202, 169 bp for R. delavayi in this study. However, most of the reported conserved plastid genomes are usually 120-160 kb in length (Orton, Burke & Duvall, 2019;Twyford & Ness, 2017;Xue et al, 2019). In addition, ycf1, which is common in conserved plastid genomes, is missing from R. delavayi, and from other photosynthetic Ericaceae (Kim et al, 2019;Logacheva et al, 2016;Martinez-Alberola et al, 2013).…”

Phylogenetic lineages and the role of hybridization as driving force of evolution in grass supertribe Poodae

“…1-3 for lemma and awn shapes in exemplary species), were summarized in Genera graminum (Clayton & Renvoize, 1986), which served as an important basis for later molecular phylogenetic studies. Since then, due to the sheer size of the group, usually representative genera were selected for comparative studies to gain an overview on the whole Poodae and their major groupings using morphological data, plastid DNA restriction site analysis, traditional Sanger and, more recently, plastid genome sequencing (Soreng & Davis, 2000;Quintanar & al., 2007;Schneider & al., 2009;Saarela & al., 2015Saarela & al., , 2018Pimentel & al., 2017;Orton & al., 2019). Other studies focused on special groups using an in-depth sampling of taxa, for example, within traditional Aveneae (Grebenstein & al., 1998;Saarela & al., 2010Saarela & al., , 2017Wölk & Röser, 2014 and Poeae Birch & al., 2014Birch & al., , 2017, in which especially the subtribes Poinae (Hunter & al., 2004;Gillespie & Soreng, 2005;Gillespie & al., 2007Gillespie & al., , 2009Gillespie & al., , 2018Refulio-Rodríguez & al., 2012;Hoffmann & al., 2013;Soreng & al., , 2015a, Loliinae (Torrecilla & Catalán, 2002Inda & al., 2008;Cheng & al., 2016;, Sesleriinae (Kuzmanović & al., 2017), Brizinae and Calothecinae (Essi & al., 2008;Persson & Rydin, 2016;Silva & al., 2020) were studied.…”

Genetic diversity and taxonomic issues inGastridiumP.Beauv (Poaceae) inferred from plastid and nuclear DNA sequence analysis

“…G. scabrum and G. lainzii from G. ventricosum and G. phleoides ), and trnH-psbA further increased their genetic distance. Plastid intergenic spacers are prone to develop high numbers of insertion/deletion mutations (indels) and other microstructural genomic changes with potential phylogenetic utility (Orton et al, 2019). At this regard, no evidence of synapomorphic changes at the inter-/intrageneric level could be identified (cf.…”

“…At this regard, no evidence of synapomorphic changes at the inter-/intrageneric level could be identified (cf. Orton et al, 2019), likely due to limited sampling. Likewise, the apomorphic or homoplasious state of the 21-bp indel separating G. scabrum and G. lainzii from the “major” species cannot be inferred with the available data.…”