Genome-Guided Phylo-Transcriptomic Methods and the Nuclear Phylogenetic 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.

From cacti to carnivores: Improved phylotranscriptomic sampling and hierarchical homology inference provide further insight into the evolution of Caryophyllales

“…Transcriptomics has emerged as a powerful tool for phylogenomics. The ever‐decreasing costs of sequencing combined with improved methods for collecting plant material (Yang et al., ) and downstream data analysis (Dunn et al., ; Kocot et al., ; Yang and Smith, ; Emms and Kelly, ; Washburn et al., ) have made this a cost‐efficient means for investigating systematic and evolutionary questions. To date, phylotranscriptomic analyses have been used at multiple phylogenetic levels, from genera (Pease et al., ; Yu et al., ) and large clades (Yang et al., , Yang et al., ; McKain et al., ), to across all land plants (Wickett et al., ).…”

Surprising amount of stasis in repetitive genome content across the Brassicales

“…To produce an ultrametric tree necessary for comparative genomic analyses, final alignments were concatenated (those without paralogous genes) using scripts from the Washburn et al (2017) Genome-Guided Phylo-Transcriptomic pipeline ('concatenate_matrices.py'), followed by tree estimation in RAxML v8 (Stamatakis 2014) To test for the placement and magnitude of possible adaptive shifts in the data, Bayou v 2.0 was used (https://github.com/uyedaj/bayou/blob/master/tutorial.md; Uyeda and Harmon, 2014). Cleomella serrulata was again dropped from analyses due to lack of DNA sequence data for this sample.…”

IsoSeq transcriptome assembly of C3 panicoid grasses provides tools to study evolutionary change in the Panicoideae

“…D. oligosanthes is the only PACMAD species exclusively utilizing C 3 photosynthesis with a published genome sequence to date (Studer et al, ). It is a member of the grass tribe Paniceae, a group which also includes foxtail millet, proso millet, and switchgrass, but is an outgroup to the MPC C 4 subclade of exclusively C 4 ‐utilizing species within that tribe (Giussani, Cota‐Sánchez, Zuloaga, & Kellogg, ; GPWG II, ; Washburn et al, ; Washburn, Schnable, Davidse, & Pires, ). As the published D. oligosanthes reference genome was constructed utilizing short‐read sequencing, the inclusion of D. oligosanthes provided an opportunity to improve the proportion of genes with full‐length sequences from this lineage available for comparative analyses.…”

“…D. oligosanthes is the only PACMAD species exclusively utilizing C 3 photosynthesis with a published genome sequence to date . It is a member of the grass tribe Paniceae, a group which also includes foxtail millet, proso millet, and switchgrass, but is an outgroup to the MPC C 4 subclade of exclusively C 4 -utilizing species within that tribe (Giussani, Cota-Sánchez, Zuloaga, & Kellogg, 2001;GPWG II, 2012;Washburn et al, 2017;Washburn, Schnable, Davidse, & Pires, 2015). As the…”