Trifolium pratense, L. variety Milvus genome
Red clover (Trifolium pratense) is a globally important legume in pastoral livestock farming systems. It has been used as a cattle feed because of its nutritional value, high yield and protein content. A good biomass yield for two or three seasons represents a secure and good feed resource for the farmers. It is also an excellent transitional crop used to fix nitrogen in the soil. The diverse uses of this plant increase the need to learn about the differences between populations that generate a diversity of gene pool.   However, its high level of heterozygosity makes genetic and genomic analyses challenging. One of the two existing genomes is a short reads-based assembly, fragmented into > 135.000 contigs and with some orientation errors because gametophytic self-incompatibility (GSI) system resulting in inherent high heterozygosity  This highlights the need for a new reference based on long read assembly. For that purpose, HiFi reads have been used to detect all types of variants with high precision, even in hard-to-sequence regions of the genome. As a result, we obtained a high-quality primary assembly with 98.5% completed genes and less than 0.5% of fragmented regions calculated using BUSCO. Our assembly statistics are similar to the last published genome of red clover in 2021, but a smaller number of contigs than the oldest version. However, we present the longest assembly of 423 Mb, an alternative genome which includes all the haplotypes identified and an entire annotated genome generated using the novel REAT pipeline. This is a robust genome annotation toolkit for turning high-quality genome assembly into usable and informative resources. As a result, we have identified 45,549 genes and 65,157 transcripts. We are currently using this genome to generate a pan-genome for Red Clover, thus allowing us to identify the core and variable genome. We plan to study the core and variable genome to gain insight in to genomic difference between red clover crops corresponding to their various uses which can explain the differences between red clover crops.