Hein, I. | Search bioRxiv

bioRxiv2018

Tracking disease resistance deployment in potato breeding by enrichment sequencing

Following the molecular characterisation of functional disease resistance genes in recent years, methods to track and verify the integrity of multiple genes in varieties are needed for crop improvement through resistance stacking. Diagnostic resistance gene enrichment sequencing (dRenSeq) enables the high-confidence identification and complete sequence validation of known functional resistance genes in crops. As demonstrated for tetraploid potato varieties, the methodology is more robust and cost-effective in monitoring resistances than whole-genome sequencing and can be used to appraise (trans)gene integrity efficiently. All currently known NB-LRRs effective against viruses, nematodes and the late blight pathogen Phytophthora infestans can be tracked with dRenSeq in potato and hitherto unknown polymorphisms have been identified. The methodology provides a means to improve the speed and efficiency of future disease resistance breeding in crops by directing parental and progeny selection towards effective combinations of resistance genes.

plant biology↗

bioRxiv2017

A critical comparison of technologies for a plant genome sequencing project

A high quality genome sequence of your model organism is an essential starting point for many studies. Old clone based methods are slow and expensive, whereas faster, cheaper short read only assemblies can be incomplete and highly fragmented, which minimises their usefulness. The last few years have seen the introduction of many new technologies for genome assembly. These new technologies and new algorithms are typically benchmarked on microbial genomes or, if they scale appropriately, human. However, plant genomes can be much more repetitive and larger than human, and plant biology makes obtaining high quality DNA free from contaminants difficult. Reflecting their challenging nature we observe that plant genome assembly statistics are typically poorer than for vertebrates. Here we compare Illumina short read, PacBio long read, 10x Genomics linked reads, Dovetail Hi-C and BioNano Genomics optical maps, singly and combined, in producing high quality long range genome assemblies of the potato species S. verrucosum. We benchmark the assemblies for completeness and accuracy, as well as DNA, compute requirements and sequencing costs. We expect our results will be helpful to other genome projects, and that these datasets will be used in benchmarking by assembly algorithm developers.

genomics↗