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

Authors

Daniel S. Carvalho, University of Nebraska - LincolnFollow
Aime Nishimwe, University of Nebraska - LincolnFollow
James Schnable, University of Nebraska-LincolnFollow

Document Type

Article

Date of this Version

2020

Citation

Plant Direct. 2020;4:1–10.

DOI: 10.1002/pld3.203

Comments

This is an open access article under the terms of the Creative Commons Attribution License. © 2020 The Authors

Abstract

The number of plant species with genomic and transcriptomic data has been increasing rapidly. The grasses—Poaceae—have been well represented among species with published reference genomes. However, as a result the genomes of wild grasses are less frequently targeted by sequencing efforts. Sequence data from wild relatives of crop species in the grasses can aid the study of domestication, gene discovery for breeding and crop improvement, and improve our understanding of the evolution of C₄ photosynthesis. Here, we used long-read sequencing technology to characterize the transcriptomes of three C₃ panicoid grass species: Dichanthelium oligosanthes, Chasmanthium laxum, and Hymenachne amplexicaulis. Based on alignments to the sorghum genome, we estimate that assembled consensus transcripts from each species capture between 54.2% and 65.7% of the conserved syntenic gene space in grasses. Genes co-opted into C₄ were also well represented in this dataset, despite concerns that because these genes might play roles unrelated to photosynthesis in the target species, they would be expressed at low levels and missed by transcript-based sequencing. A combined analysis using syntenic orthologous genes from grasses with published reference genomes and consensus long-read sequences from these wild species was consistent with previously published phylogenies. It is hoped that these data, targeting underrepresented classes of species within the PACMAD grasses— wild species and species utilizing C₃ photosynthesis—will aid in future studies of domestication and C₄ evolution by d ecreasing t he evolutionary d istance b etween C₄ and C₃ species within this clade, enabling more accurate comparisons associated with evolution of the C₄ pathway.