Nanopore and Hi-C produce a new fully-phased, chromosome-scale genome for the red raspberry.
On October 22, scientists at KeyGene revealed the first fully-phased, chromosome-scale reference genome for the red raspberry, sequenced with Oxford Nanopore long-read technology and scaffolded and phased into full chromosomes using Phase Genomics’ Proximo™ Hi-C method.
Assembling complex plant genomes used to be considered nearly impossible as they can be extremely large, polypoid, and contain highly repetitive regions. Long-read sequencing generates genomic data spanning very long regions, but still needs to be scaffolded, or “put together” into chromosomes. Proximo Hi-C not only helps guide the assembly to produce chromosome-level scaffolds but can also tell which sequences and mutations come from the maternal and paternal chromosome copies (this is called phasing). Our phasing method, FALCON-Phase was originally released in 2018 and was used in conjunction with the Proximo pipeline to generate this “platinum level” raspberry genome.
Read more about the assembly and future directions for the project here.