Journal article

Assembly of whole-chromosome pseudomolecules for polyploid plant genomes using outcrossed mapping populations

Chenxi Zhou, Bode Olukolu, Dorcus Gemenet, Shan Wu, Wolfgang Gruneberg, Minh Duc Cao, Zhangjun Fei, Zhao-Bang Zeng, Andrew George, Awais Khan, Craig Yencho, Lachlan JM Coin

Published : 2017

Abstract

ABSTRACT The assembly of whole-chromosome pseudomolecules for plant genomes remains challenging due to polyploidy and high repeat content. We developed an approach for constructing complete pseudomolecules for polyploid species using genotyping-by-sequencing data from outcrossing mapping populations coupled with high coverage whole genome sequence data of a reference genome. Our approach combines de novo assembly with linkage mapping to arrange scaffolds into pseudomolecules. We show that the method is able to reconstruct simulated chromosomes for both diploid and tetraploid genomes. Comparisons to three existing genetic mapping tools show that our method outperforms the other methods in acc..

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University of Melbourne Researchers