Haplotype-resolved genome assembly of 'Manhattan' perennial ryegrass (Lolium perenne L.) and characterization of drought responsive late embryogenesis abundant genes

<h4>Background</h4>Perennial ryegrass is a premier forage and turf grass, a genomic model organism for cool-season perennial grasses, but has relatively poor persistence under drought stress. The cultivar 'Manhattan' is an heirloom turf-type cultivar, and ancestral to many current turf cultivars and breeding lines in the USA. To improve turf-type perennial ryegrass genome resources, we assembled and compared two haplotypes of 'Manhattan' and extracted late embryogenesis abundant (LEA) gene families.<h4>Results</h4>Both haplotypes resolved into 2.3 Gb genome assemblies of 7 chromosomes each, with Gypsy-like retrotransposon concentrations in putative centromere regions. Repeat content was 83%, and the two haplotypes were syntenic with each other as well as published forage-type perennial ryegrass genomes. Annotations resulted in 43,000 genes for each haplotype with over 95% complete, 89% as single copy genes, and 86% with functional annotation. Seventy-two LEA genes were identified in haplotype-1 and fitted into 8 Pfam-based families, with 46 exhibiting expression evidence in vegetative tissues and 39 showing differential expression upon drought stress.<h4>Conclusions</h4>Broad synteny but high heterozygosity characterized the 'Manhattan' perennial ryegrass genome haplotypes. Repeat content, including long terminal repeat genes with annotation support, were high and indicative of cool-season Poaceae grasses. The identification of LEA genes differentially expressed upon drought stress provide candidate genes for further drought tolerance studies.