IsoSeq transcriptome assembly of C₃panicoid grasses provides tools to study evolutionary change in the Panicoideae

Abstract

7The number of plant species with genomic and transcriptomic data has been increasing 8 rapidly. The grasses -Poaceae -have been well represented among species with published 9 reference genomes. However, as a result the genomes of wild grasses are less frequently tar-10 geted by sequencing efforts. Sequence data from wild relatives of crop species in the grasses 11 can aid the study of domestication, gene discovery for breeding and crop improvement, and 12 improve our understanding of the evolution of C4 photosynthesis. Here we used long read 13 sequencing technology to characterize the transcriptomes of three C3 panicoid grass species: 14Dichanthelium oligosanthes, Chasmanthium laxum, and Hymenachne amplexicaulis. Based on 15 alignments to the sorghum genome we estimate that assembled consensus transcripts from 16 each species capture between 54.2 and 65.7% of the conserved syntenic gene space in grasses. 17Genes co-opted into C4 were also well represented in this dataset, despite concerns that, be-18 cause these genes might play roles unrelated to photosynthesis in the target species, they 19 would be expressed at low levels and missed by transcript-based sequencing. A combined 20 analysis using syntenic orthologous genes from grasses with published reference genomes and 21 consensus long read sequences from these wild species was consistent with previously pub-22 lished phylogenies. It is hoped that this data, targeting under represented classes of species 23 within the PACMAD grasses -wild species and species utilizing C3 photosynthesis -will aid 24 in futurue studies of domestication and C4 evolution by decreasing the evolutionary distance 25 between C4 and C3 species within this clade, enabling more accurate comparisons associated 26