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

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 decreasing the evolutionary distance between C4 and C3 species within this clade, enabling more accurate comparisons associated with evolution of the C4 pathway.

A long-read and short-read transcriptomics approach provides the first high-quality reference transcriptome and genome annotation for Pseudotsuga menziesii (Douglas-fir)

“…2019 ). Well-represented reference genomes were used as a guide for LR transcriptome assembly for grapes ( Vitis vinifera ; Minio et al ., 2019 ) and Panicoid grasses ( Carvalho et al . 2020 ).…”

“…2020 ) and grapes ( Minio et al . 2019 ), and the evolution of photosynthesis in grass ( Carvalho et al . 2020 ).…”