title: Phylogenomics and Plastome Evolution of Tropical Forest Grasses (Leptaspis, Streptochaeta: Poaceae).
abstract: Studies of complete plastomes have proven informative for our understanding of the molecular evolution and phylogenomics of grasses. In this study, a plastome phylogenomic analysis sampled species from lineages of deeply diverging grasses includingStreptochaeta spicata(Anomochlooideae),Leptaspis banksii, andL.zeylanica(both Pharoideae). Plastomes from next generation sequences for three species were assembled byde novomethods. The unambiguously aligned coding and non-coding sequences of the entire plastomes were aligned with those from 43 other grasses and the outgroupJoinvillea ascendens. Outgroup sampling of grasses has previously posed a challenge for plastome phylogenomic studies because of major rearrangements of the plastome. Here, over 81,000 bases of homologous sequence were aligned for phylogenomic and divergence estimation analyses. Rare genomic changes, including persistently long ψycf1and ψycf2loci, the loss of therpoC1intron, and a 21 base tandem repeat insert in the coding sequence forrps19defined branch points in the grass phylogeny. Marked differences were seen in the topologies inferred from the complete plastome and two gene matrices, and mean maximum likelihood support values for the former were 10% higher. In the full plastome phylogenomic analyses, the two species of Anomochlooideae were monophyletic.LeptaspisandPharuswere found to be reciprocally monophyletic, with the estimated divergence of twoLeptaspisspecies preceding those ofPharusby over 14 Ma, consistent with historical biogeography. Our estimates for deep divergences among grasses were older than previous such estimates, likely influenced by more complete taxonomic and molecular sampling and the use of recently available or previously unused fossil calibration points.
authors.affiliation: Department of Biological Sciences, Northern Illinois University, DeKalb IL, USA.
authors.forename: Sean V
authors.initials: SV
authors.lastname: Burke
authors.affiliation: Plant Tech Core Unit, Agricultural Biotechnology Research Center, Academia Sinica Taipei, Taiwan.
authors.forename: Choun-Sea
authors.initials: CS
authors.lastname: Lin
authors.affiliation: Department of Biological Sciences, Northern Illinois University, DeKalb IL, USA.
authors.forename: William P
authors.initials: WP
authors.lastname: Wysocki
authors.affiliation: Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames IA, USA.
authors.forename: Lynn G
authors.initials: LG
authors.lastname: Clark
authors.affiliation: Department of Biological Sciences, Northern Illinois University, DeKalb IL, USA.
authors.forename: Melvin R
authors.initials: MR
authors.lastname: Duvall
keywords: Anomochlooideae; Pharoideae; Poaceae; plastid genome; plastome phylogenomics