Data from: Phased-genome assemblies of saltgrass reveal structural dynamics and genomic basis for extreme salt tolerance and dioecy

For agriculture, the climate crisis will center on the key resource of
fresh water. Understanding of halophytic adaptations for productivity
without fresh water will open possibilities for crop production through
neodomestication. Saltgrass (Distichlis spp.) is a unique genus of
dioecious halophytic C4 grasses found in the PACMAD clade. They grow in
tidal plains and salt marshes that often exceed seawater salinity, making
them among the most tolerant grasses to salinity. Here we provide an
in-depth study of the genomic structure of Distichlis, which gives insight
into its unique biology, including dioecy and halophytic growth. We
generated high-quality telomere-to-telomere phased genome assemblies of
four genets of saltgrass that range in size from 569 Mb to 609 Mb. We show
that saltgrass is an allotetraploid with two highly syntenic but
degenerate subgenomes. Projecting full-length gene sequencing and deep RNA
sequencing data onto these assemblies supported 58,590 to 61,079
high-confidence genes and uncovered massive gene loss between the two
subgenomes, with each subgenome losing more than 40% of the orthologous
genes. Comparing genets, we discovered a novel chromosome fusion between
chromosomes from different subgenomes that differentiates two species (D.
spicata, 2n=40 and D. stricta, 2n=38), opening investigation into the role
of genomic rearrangements in adaptation and speciation. We also report a B
chromosome of 7 Mb in size in two of the genets, showing consistent
features with sequenced B chromosomes in other species. Using k-mer
analyses of sex-typed populations, we identified an 8 Mb sex determining
region in female genets, confirming that Distichlis has a ZW type sex
determination, and 58 genes that are associated with sex expression.
Population genetics of 364 saltgrass genets from 35 diverse populations
provide insight into differentiation corresponding to geographical
distribution, and clear separation of D. stricta as a distinct species.
These genomic resources establish a foundation for neodomestication of
saltgrass for agroecosystems in saline environments and advance our
understanding of genetic structure in dioecious, halophytic grasses.