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

C Zhou; B Olukolu; DC Gemenet; S Wu; W Gruneberg; MD Cao; Z Fei; ZB Zeng; AW George; A Khan; GC Yencho; LJM Coin

Journal article

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

C Zhou, B Olukolu, DC Gemenet, S Wu, W Gruneberg, MD Cao, Z Fei, ZB Zeng, AW George, A Khan, GC Yencho, LJM Coin

Nature Genetics | NATURE PORTFOLIO | Published : 2020

DOI: 10.1038/s41588-020-00717-7

Abstract

Despite advances in sequencing technologies, assembly of complex plant genomes remains elusive due to polyploidy and high repeat content. Here we report PolyGembler for grouping and ordering contigs into pseudomolecules by genetic linkage analysis. Our approach also provides an accurate method with which to detect and fix assembly errors. Using simulated data, we demonstrate that our approach is of high accuracy and outperforms three existing state-of-the-art genetic mapping tools. Particularly, our approach is more robust to the presence of missing genotype data and genotyping errors. We used our method to construct pseudomolecules for allotetraploid lawn grass utilizing PacBio long reads i..

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University of Melbourne Researchers

Lachlan Coin Author

Grants

Awarded by Bill and Melinda Gates Foundation

Funding Acknowledgements

We thank F. Diaz for developing the M9 x M19 I. trifida mapping population and M. David for extracting and quantifying DNA from the M9 x M19 cross. The 12601ab1 x Stirling Infinium 8303 potato array data were provided by C. A. Hackett. This research was supported by grants from the Bill & Melinda Gates Foundation (OPP1052983) and Australian Research Council (DP170102626 awarded to L.J.M.C.). The work at the International Potato Center (CIP) was carried out as part of the Consultative Group for International Agricultural Research (CGIAR) Research Program on Roots, Tubers and Bananas, which is supported by CGIAR Fund Donors (http://www.cgiar.org/about-us/our-funders/).This research was also supported by use of the NeCTAR Research Cloud, by QCIF and by the University of Queensland's Research Computing Centre. The NeCTAR Research Cloud is a collaborative Australian research platform supported by the National Collaborative Research Infrastructure Strategy.