OctoSEQ- Sequencing the octoploid strawberry

Lead Research Organisation: Earlham Institute
Department Name: UNLISTED


The octoploid strawberry is compact (800Mb) yet as a genome is complex due to the high levels of heterozygosity (and associated inbreeding depression) and the allo-octoploid nature of the genome. It behaves disomically and the latest evidence suggests that it arose due to the fusion of two allo-tetraploids, which themselves had a (A-B) (B' B'') genome structure. Second generation sequencing approaches using paired-end and mate jumping libraries have largely failed at resolving biologically meaningful contig lengths and it is clear that an alternative approach is required.
Using long-read paired end (450bp Hiseq sequenced illumina libraries) an assembly using Discovar and a novel haplotype selection procedure will be carried out (harnessing the heterozygosity). Following this, a step integrating low PCR bias mate jump libraries and local BAC sequences will be used to phase and extend the assembly (the hypothesis is that a minimum tiling path of BACs is not required due to the downstream use of other technologies). The massively parallel BAC sequencing approach allows the resolution of extremely long haplotypes, allowing the subgenome and heterozygosity assembly problems to be alleviated during the assembly step. This approach is possible due to the highly heterozygous and compact nature of the genome and is a novel approach to complex genome assembly. Further scaffolding and haplotyping is then accomplished by the use of a multi-user generated consensus SNP linkage map, generated by a novel mapping method, recently developed by a collaborator Dr Eric van de Weg and Dr Rob Vickerstaff (EMR PI's group) which allows an extremely accurate reconstruction of marker orders, integrating data from multiple biparental mapping populations.
Downstream feature calling and annotation will be generated along with a Web Apollo server instance for further collaboration. Resequencing of key germplasm will be contributed by partners for reference guided assembly.


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