Isdale, D. | bioRxiv Science

bioRxiv2019

Integrating past, present and future wheat research with Pretzel

MotivationMajor advances have been made in the assembly of complex genomes such as wheat. Remaining challenges include linking these new resources to legacy research, as well as lowering the bar to entry for members of the research community who may lack specific bioinformatics skills.\n\nResultsPretzel aims to solve these problems by providing an interactive, online environment for data visualisation and analysis which, when loaded with appropriately curated data, can enable researchers with no bioinformatics training to exploit the latest genomic resources. We demonstrate that Pretzel can be used to answer common questions asked by researchers as well as for advanced curation of pseudomolecule structure.\n\nAvailabilityPretzel is implemented in JavaScript and is freely available under a GPLv3 license online at: https://github.com/plantinformatics/pretzel.\n\nContactgabriel.keeble-gagnere@ecodev.vic.gov.au

bioinformatics↗

bioRxiv2018

Optical and physical mapping with local finishing enables megabase-scale resolution of agronomically important regions in the wheat genome

BackgroundNumerous scaffold-level sequences for wheat are now being released and, in this context, we report on a strategy for improving the overall assembly to a level comparable to that of the human genome.\n\nResultsUsing chromosome 7A of wheat as a model, sequence-finished megabase scale sections of this chromosome were established by combining a new independent assembly based on a BAC-based physical map, BAC pool paired end sequencing, chromosome arm specific mate-pair sequencing and Bionano optical mapping with the IWGSC RefSeq v1.0 sequence and its underlying raw data. The combined assembly results in 18 super-scaffolds across the chromosome. The value of finished genome regions is demonstrated for two approximately 2.5 Mb regions associated with yield and the grain quality phenotype of fructan carbohydrate grain levels. In addition, the 50 Mb centromere region analysis incorporates cytological data highlighting the importance of non-sequence data in the assembly of this complex genome region.\n\nConclusionsSufficient genome sequence information is shown to be now available for the wheat community to produce sequence-finished releases of each chromosome of the reference genome. The high-level completion identified that an array of seven fructosyl transferase genes underpins grain quality and yield attributes are affected by five f-box-only-protein-ubiquitin ligase domain and four root-specific lipid transfer domain genes. The completed sequence also includes the centromere.

genomics↗