Genome-Guided Phylo-Transcriptomic Methods and the Nuclear Phylogentic Tree of the Paniceae Grasses

Abstract

The past few years have witnessed a paradigm shift in molecular systematics from phylogenetic methods (using one or a few genes) to those that can be described as phylogenomics (phylogenetic inference with entire genomes). One approach that has recently emerged is phylo-transcriptomics (transcriptome-based phylogenetic inference). As in any phylogenetics experiment, accurate orthology inference is critical to phylo-transcriptomics. To date, most analyses have inferred orthology based either on pure sequence similarity or using gene-tree approaches. The use of conserved genome synteny in orthology detection has been relatively under-employed in phylogenetics, mainly due to the cost of sequencing genomes. While current trends focus on the quantity of genes included in an analysis, the use of synteny is likely to improve the quality of ortholog inference. In this study, we combine de novo transcriptome data and sequenced genomes from an economically important group of grass species, the tribe Paniceae, to make phylogenomic inferences. This method, which we call "genome-guided phylo-transcriptomics", is compared to other recently published orthology inference pipelines, and benchmarked using a set of sequenced genomes from across the grasses. These comparisons provide a framework for future researchers to evaluate the costs and benefits of adding sequenced genomes to transcriptome data sets.

Figure 1

Genome-guided phylo-transcriptomics workflow. Illustration of the workflow followed to produce the genome-guided phylogenies in this study.

Figure 2

Genome-guided concatenation-based phylogeny of the tribe Paniceae. Phylogenetic tree of the tribe Paniceae (Poaceae) built using RAxML based on a concatenated matrix with 90% gene occupancy. Branches are labeled with maximum likelihood bootstrap values; unlabeled branches have values of 100.

Figure 3

(a) Primary nuclear topology found using all methods, (b) Secondary nuclear topology, (c) Chloroplast topology based on Washburn, et al.. (d) An ideogram of the Setaria italica chromosomes with conserved syntenic blocks between S. italica and Sorghum bicolor demarcated. Syntenic blocks are colored based on the phylogenetic patterns from a-c that each block supports. Gray indicates areas of the chromosomes not covered by our blocks. Asterisks below the blocks indicate significance level for pairwise Robinson-Foulds distance tests: ***0.001, **0.01, *0.05.

Figure 4

A Venn Diagram comparing the Poaceae gene sets derived from whole genomes, the genome-guided approach, and the Yang & Smith MO pipeline (the 1to1 pipeline is not shown because of large overlap with MO). Diagram created using Inkscape and the R package Vennerable^,.