Supporting data for "Genome assembly of an Australian native grass species reveals a recent whole genome duplication and biased gene retention of genes involved in stress response"

The adaptive significance of polyploidy has been extensively debated and chromosome-level genome assemblies of polyploids can provide insight into this topic. The Australian grass, Bothriochloa decipiens, belongs to the BCD clade, a group with a complex history of hybridization and polyploidy. This is the first genome assembly and annotation of a species that belongs to this fascinating yet complex group.
Using a combination of Illumina short reads, 10X Genomics linked reads and Hi-C sequencing data we assembled a highly contiguous genome of Bothriochloa decipiens, with a total length of 1,218.22 Mb and scaffold N50 of 42.637 Mb. Comparative analysis revealed that the species is a diploidized allotetraploid. We clustered the 20 major scaffolds, representing the 20 chromosomes, into the two subgenomes of the parental species using unique repeat signatures. We found evidence of biased fractionation and differences in the activity of transposable elements between the subgenomes prior to hybridization. Duplicates were enriched for genes involved in transcription and response to external stimuli like drought, supporting a biased retention of duplicated genes following whole genome duplication.
Our results support hypotheses explaining the biased retention of duplicated genes following polyploidy and point to differences in repeat activity associated with subgenome dominance. Bothriochloa decipiens is a widespread species with the ability to establish across many soil types, making it useful for ecological restoration of Australian grasslands. This reference genome is a valuable resource for future population genomic research involving Australian grasses which may be helpful in ecological restoration projects.