PS Seminar Series: Assembly of hexaploid sweet potato genome

Description

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.

Please use this LINK for more details on Assoc Prof Lanchal Coin's profile.

Date & time

1–2pm 4 April 2018

Location

Eucalyptus Room (S2.05), Level 2, RN Robertson Building (46), ANU

Speakers

Assoc Prof Lachlan Coin, Univesity of Queensland

Contacts

 Gagan Bhardwaj
 02 6125 9395

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