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

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Title Assembly of whole-chromosome pseudomolecules for polyploid plant genomes using outbred mapping populations
 
Creator Zhou, C.
Olukolu, B.
Gemenet, D.
Wu, S.
Gruneberg, W.J.
Cao, M.D.
Fei, Z.
Zeng, Z.B.
George, A.W.
Khan, A.
Yencho, G.C.
Coin, L.J.M.
 
Subject genetic linkage
genomes
software
polyploidy
plant genetics
 
Description 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 in combination with restriction site-associated DNA sequencing, and for diploid Ipomoea trifida and autotetraploid potato utilizing contigs assembled from Illumina reads in combination with genotype data generated by single-nucleotide polymorphism arrays and genotyping by sequencing, respectively. We resolved 13 assembly errors for a published I. trifida genome assembly and anchored eight unplaced scaffolds in the published potato genome.
 
Date 2020-10
2020-11-09T20:29:02Z
2020-11-09T20:29:02Z
 
Type Journal Article
 
Identifier Zhou, C., Olukolu, B., Gemenet, D., Wu, S., Gruneberg, W.J., Cao, M.D., Fei, Z., Zeng, Z.B., George, A.W., Khan, A.,Yencho, G.C. and Coin, L.J.M. (2020). Assembly of whole-chromosome pseudomolecules for polyploid plant genomes using outbred mapping populations. Nature Genetics. ISSN 1546-1718. v52: 1256–1264
1546-1718
https://hdl.handle.net/10568/110094
https://doi.org/10.1038/s41588-020-00717-7
 
Language en
 
Rights Copyrighted; all rights reserved
Limited Access
 
Format 1256–1264
 
Source Nature Genetics