Progress on the development of a genome sequence for red raspberry Rubus idaeus

A draft pseudo chromosome assembly of the highly heterozygous diploid red raspberry variety ‘Heritage’ (R. idaeus subsp. vulgatus Arrhen. x R. idaeus subsp. strigosus Michx) is presented. Approximately 90x coverage of the genome (~6x in pairs with insert greater than 2 kb) was used to assemble the sequence into 11,502 scaffolds. Detailed internal analysis of the assembly reveals two highly divergent haplotypes, consistent with previous linkage studies in raspberry, which likely contribute to the relatively high number of scaffolds. A genetic map was created using Genotyping by Sequencing and approximately 3400 markers from the map were used to assign scaffolds to linkage groups. Large‐scale agreement between the scaffolds and the genetic map is apparent and only 0.2 percent of the scaffolds are mapped to by markers from more than one linkage group. Despite the high density of the genetic map it allowed assignment of only 60% of bases to pseudomolecules due to the relatively high number of scaffolds produced by the assembly. Efforts are now underway to improve the pseudomolecule assembly by incorporating synteny with the Fragaria vesca genome and additional paired data to assign more scaffolds to linkage groups. Gene finding with GeneMark ES+ estimates a gene content of 36009, which is approximately 1,200 more than F. vesca. Gene‐family analysis and comparison to strawberry continues

A draft assembly and analysis of the highly heterozygous diploid red raspberry genome (Rubus idaeus cv. Heritage)

An improved draft genome sequence of the highly heterozygous diploid red raspberry variety ‘Heritage’ (R. idaeus subsp. vulgatus Arrhen. x R. idaeus subsp. strigosus Michx) is presented. Fragments from 400 bp to 20,000 bp in length were sequenced using a combination of 454 and Illumina technologies. The reads were assembled using Newbler to produce 14,867 scaffolds containing a total of 252,359,088 bases (Ns included) with an N50 scaffold size of 218,942 bp. The internal contig graph structure of the assembly confirms genetic linkage studies suggesting an extremely high rate of heterozygosity. This extreme heterozygosity places several interesting demands on the assembly including 1) distinguishing between sequences that are in both chromosomes of a homologous pair and sequence variants that may be present in only one and 2) ensuring that the contigs are a consistently phased for a given chromosome. Efforts have been made to fill the intrascaffold gaps though use of syntenic evidence from the closely related Fragaria vesca genome, additional paired-end reads, and high-density linkage maps. Preliminary gene finding with GeneMark ES+ estimates a gene content of 37,803, which is close to the estimated 34,809 genes of F. vesca. Annotation of predicted gene models demonstrates that most genes from conserved metabolic pathways such as the tricarboxylic acid cycle and glycolysis are present in scaffolds. Novel algorithms being developed for this assembly will be of value for the assembly of other highly heterozygous genomes