We have sequenced four different red clover breeding accessions using PacBio HiFi long read sequencing technology, Hi-C sequencing, and PacBio-Isoseq sequencing patforms to generate high-quality red clover genome assemblies and improved reference annotation. HiFi reads, HiFi + Hi-C reads will be used to generate haplotype resolved genome assemblies for all four red clover materials. De novo transcript assembly and annotation will be performed using PacBio Isoseq reads. Illumina RNA-Seq short reads generated from our previous red clover- root rot and clover rot pathogen interaction studies will be integrated to produce more accurate genome annotation. Also, two alsike clover accessions will be sequenced (on-going) using long-read PacBio HiFi technology. Genome assembly will follow similar procedures. Comparative genomics will be performed at both intra-species and inter-species levels. Comparative analysis among the four red clover accessions and Cross-species comparison between red clover, other forage legume species, including Medicago truncatula, white clover, alsike clover and model plant Arabidopsis thaliana will identify conserved and species-specific genes related to agronomically important traits.