KeyGene delivers first-ever fully phased red raspberry genome

KeyGene completed the assembly of the red raspberry genome this summer and delivered the final results to the BerryWorld Plus Ltd. berry breeding programme, offering its breeders a unique and practical genome resource. This high-quality reference genome was delivered after Berry World Plus won KeyGene’s Genome Insight event in March.

The phased raspberry genome shows that the long reads of the Oxford Nanopore platform combined with KeyGene’s expertise on plant DNA extraction and advanced data analysis now provide new ways to affordably map the genome of any crop.

KeyGene’s high molecular weight DNA extraction started with the harvesting of biological material. While isolating genomic DNA of good length and quality is challenging, KeyGene has already proven its expertise through work on a wide range of vegetable and field crops. Long fragment-size libraries were constructed from the genomic DNA. The library was sequenced using the PromethION platform of Oxford nanopore Technologies and generated >100X coverage of the genome with a 62 Kb N50 read.

These exceptionally long reads were used for an initial de novo assembly that generated a 1.2 Mb contig N50, which is around five times larger than a draft genome published earlier this year. Hi-C data was then used in conjunction with the Proximo™ Hi-C pipeline from Phase Genomics to phase, order and orient the contigs into chromosome-scale scaffolds. The final assembly resulted in two fully phased assemblies, each with seven scaffolds, which corresponds to the number of chromosomes raspberry has.

A high degree of collinearity was observed when the two phased assemblies were compared to the published raspberry genome, showing the structural correctness of the final assemblies. Gene completeness analysis of the assemblies using BUSCO assessment identified around 94% of the conserved set of genes.

A chromosome-scale reference genome is an important step for research into understanding biological processes and for breeding programs. Breeders can use it to select for traits like color or taste when crossing plants. In the case of heterozygous genomes, a phased genome provides critical information about gene-based haplotypes. Such information is especially useful for recessive traits. The mapping of this genome will help BerryWorld Plus develop high-quality varieties faster and more efficiently.

“Plant breeding is a numbers game.” commented raspberry molecular breeder Dr Guillaume Daverdin. “By using molecular tools and genomic insight, we will be able to significantly increase the number of plants screened each year and enhance the chance of identifying plants that present the ideal combination of traits we are looking for. Molecular screens will be especially important in quickly deselecting between hundreds and thousands of the least promising plants before the remainder are screened by our breeding team.”