Abstract - Sweetpotato [Ipomoea batatas (L.) Lam.] is a globally important staple food crop, especially for sub-Saharan Africa. Agronomic improvement of sweetpotato has lagged behind other major food crops partially due to a lack of genomic and genetic resources. In this talk I will present work we have carried out as part of the GT4SP (genomic tools for sweet potato) consortium towards building a genome assembly for hexaploid sweet potato. I will describe algorithms we have developed for using genotype-by-sequence data from a F1 cross to scaffold and phase polyploid genome assemblies. I will describe application of this tool to build a high quality genome assembly for two diploid wild relatives, Ipomoea trifida and Ipomoea triloba. I will also describe sequencing of hexaploid sweet potato using linked-reads (10X genomics) as well as Oxford Nanopore technologies MinION sequencer. Using low coverage nanopore sequence data, we have been able to assemble a high quality chloroplast genome for hexaploid sweetpotato, and to use this to study the evolutionary relationships between different cultivars. Finally I will describe integrating multiple technologies, including Illumina sequencing, linked-read sequencing, long-reads and genotype-by-sequence data to assemble a hexaploid sweetpotato genome.
Biography - Lachlan completed a Bachelor of Science at ANU, majoring in Mathematics. After several years out of science working in consulting, he went to the Wellcome Trust Sanger Institute to do a PhD in bioinformatics. Lachlan was a research fellow at the School of Public Health, Imperial College London, largely working on methodology for genome-wide association studies. He returned to Australia in 2012 to start a group at the Institute for Molecular Bioscience, University of Queensland where his group works on developing genomics and bioinformatics tools with application in plant sciences, cancer, infectious disease.
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