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 including Streptochaeta spicata (Anomochlooideae), Leptaspis banksii, and L. zeylanica (both Pharoideae). Plastomes from next generation sequences for three species were assembled by de novo methods. The unambiguously aligned coding and non-coding sequences of the entire plastomes were aligned with those from 43 other grasses and the outgroup Joinvillea 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 ψycf1 and ψycf2 loci, the loss of the rpoC1 intron, and a 21 base tandem repeat insert in the coding sequence for rps19 defined 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. Leptaspis and Pharus were found to be reciprocally monophyletic, with the estimated divergence of two Leptaspis species preceding those of Pharus by 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.

Keywords: Anomochlooideae; Pharoideae; Poaceae; plastid genome; plastome phylogenomics.

FIGURE 1

Maximum likelihood phylogram inferred from 47 complete plastomes. Branch lengths are proportional to the number of substitutions per site along the branch and are indicated on the branches. Newly sequenced species of Anomochlooideae and Pharoideae are emphasized with a larger font. The crown grass clade (CGC) and spikelet clades are indicated. Note that the Bayesian inference (BI) analysis produced a topology that was identical to the maximum likelihood (ML) topology. All depicted nodes are supported with 100% ML bootstrap values and PP = 1.0. The orange highlight indicates a New World modern distribution, while the blue indicates an Old World modern distribution. Numbers in circles identify six rare genomic changes (RGCs) denoted as: 1, large ψycf1 and ψycf2; 2, loss of rpoC1 intron; 3, rps19 insertion; 4, atpB-rbcL intergenic spacer (IGS) 75 base inversion; 5, loss of ψrpl23; and 6, ψrpl33 + ψrps18 dual pseudogenization.

FIGURE 2

Chronogram determined from divergence date estimation analysis using the complete plastome and the same species included in the tree of Figure 1. Branch lengths are proportional to the amount of time since divergence, as indicated on the scale at the bottom of the figure. Fossil calibration nodes are represented with letters (Table 1). Bars illustrate the 95% highest posterior density (HPD) interval for clades of interest. Newly sequenced taxa are in bold.