Abstract
Oropetium thomaeum is an emerging model for desiccation tolerance and genome size evolution in grasses. A draft genome of Oropetium was recently sequenced, but the lack of a chromosome‐scale assembly has hindered comparative analyses and downstream functional genomics. Here, we reassembled Oropetium, and anchored the genome into 10 chromosomes using high‐throughput chromatin conformation capture (Hi‐C) based chromatin interactions. A combination of high‐resolution RNAseq data and homology‐based gene prediction identified thousands of new, conserved gene models that were absent from the V1 assembly. This includes thousands of new genes with high expression across a desiccation timecourse. Comparison between the Sorghum and Oropetium genomes revealed a surprising degree of chromosome‐level collinearity, and several chromosome pairs have near perfect synteny. Other chromosomes are collinear in the gene rich chromosome arms but have experienced pericentric translocations. Together, these resources will be useful for the grass‐comparative genomic community and further establish Oropetium as a model resurrection plant.
Highlights
Desiccation tolerance evolved as an adaptation to extreme and prolonged drying, and resurrection plants are among the most resilient plants on the planet
More intact long terminal repeat retrotransposons (LTR-RTs) and centromere specific repeat arrays were identified in Oropetium
The updated annotation includes thousands of new genes with differential expression related to desiccation tolerance
Summary
Desiccation tolerance evolved as an adaptation to extreme and prolonged drying, and resurrection plants are among the most resilient plants on the planet. The molecular basis of desiccation tolerance is still largely unknown, but a number of models have emerged to dissect the genetic control of this trait (Hoekstra et al, 2001; Zhang and Bartels, 2018). No chromosome scale assembles are available for these species, limiting large-scale quantitative genetics and comparative genomics based approaches. Many resurrection plants are polyploidy or have prohibitively large genomes including those in the genera Boea, Xerophyta, Eragostis, Sporobolus, and Craterostigma. This complexity complicates genome assembly and gene redundancy in the polyploid species hinders downstream functional genomics work
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