PT  - JOURNAL ARTICLE
AU  - Chenxi Zhou
AU  - Bode Olukolu
AU  - Dorcus C. Gemenet
AU  - Shan Wu
AU  - Wolfgang Gruneberg
AU  - Minh Duc Cao
AU  - Zhangjun Fei
AU  - Zhao-Bang Zeng
AU  - Andrew W. George
AU  - Awais Khan
AU  - G. Craig Yencho
AU  - Lachlan J.M. Coin
TI  - Assembly of whole-chromosome pseudomolecules for polyploid plant genomes using outcrossed mapping populations
AID  - 10.1101/119271
DP  - 2017 Jan 01
TA  - bioRxiv
PG  - 119271
4099  - http://biorxiv.org/content/early/2017/03/22/119271.short
4100  - http://biorxiv.org/content/early/2017/03/22/119271.full
AB  - 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 accuracy on both grouping and ordering, and is robust to the presence of substantial amounts of missing data and genotyping errors. We applied our method to three real datasets including a diploid Ipomoea trifida and two tetraploid potato mapping populations. The linkage maps show significant concordance with the reference chromosomes. We resolved seven assembly errors for the published Ipomoea trifida genome assembly as well as anchored an unplaced scaffold in the published potato genome.