Curation of Bioenergy-Relevant Families in the Switchgrass Genome

Switchgrass (Panicum virgatum L.) is a large-stature, stress-tolerant bioenergy crop. The reference genotype, AP13, is of the lowland ecotype with an allotetraploid genome (1n=2x= 1.4 Gbp) estimated to have resulted from hybridization of two related Panicum species approximately 1 M years ago. This project provides expert curation of the switchgrass genome, version 3.1 of which is now available on the DOE Joint Genome Institute’s Phytozome portal (https://phytozome.jgi.doe.gov/pz/portal.html). It contains 1.16 Gbp of sequence, 88% of which is assembled into the 18 chromosomes. Goals include gauging the quality of the genome and facilitating switchgrass functional genomics analyses. The current project focuses on several gene families relevant to bioenergy crop characteristics, including transcription factors in the R2R3-MYB and NAC/NAM families; cell wall biosynthesis and remodeling enzymes, including those of lignin, acyltransferases, glycosyltransferases, and glycosylhydrolases; and NBS-LRR disease resistance proteins. The project uses hidden Markov models to identify proteins from the genome annotation and phylogentic reconstruction of subfamilies of greatest interest. For smaller protein families, the project includes phylogenetic comparisons with proteins from selected dicots and grasses and gene expression visualization via the switchgrass gene atlas project. Analyses reveal that most genes of interest are in the assembled chromosomes. For example, for a subfamily of BAHD acyltransferases implicated in esterifying cell wall components with phenolic acids, 42 of 44 clade members are on the assembled chromosomes. Comparison of the BAHDs from switchgrass and rice reveals that most acyltransferases in subclade i, which includes all the characterized proteins, are conserved, with each gene from rice corresponding to two switchgrass members located on homoeologous chromosomes. Conversely, subclade ii is more rapidly evolving with different expansions in the rice and switchgrass lineages. Some of these genes are not located on pairs of homoeologs, consistent with rapid divergence of the switchgrass or parental genomes and/or challenges to accurate assembly of parts of the genome.