An haplotype aware, chromosome level assembly of Urochloa decumbens

Haplotyped-resolved phased assemblies capture the allelic diversity that exists in heterozygous and polyploid species and enable the genetic analysis of complex traits and efficient breeding. However, building allele-aware references still represents a significant challenge due to the difficulty of differentiating among homologues during assembly and scaffolding and a limited number of polyploid aware software. Recent advances in sequencing technology such as highly accurate long reads and long-range interaction data can combat these challenges. Here, we exploited Hi-C (high-throughput chromatin conformation capture) data and PacBio HiFi reads to assemble the genome of the outcrossed tetraploid Urochloa decumbens (2n = 4x = 36), a tropical forage Paniceae grass used to feed livestock. Our pipeline leveraged gene alleles to identify homologous unitigs, optimised scaffolding tools, and enabled manual curation of chromosomal rearrangements and mis-assemblies. The final phased assembly of the tetraploid U. decumbens included all 36 chromosomes and has enabled identification of structural re-arrangements and clarified the ancestry of this important crop.