2020 journal article
Assembly of whole-chromosome pseudomolecules for polyploid plant genomes using outbred mapping populations
NATURE GENETICS, 52(11), 1256-+.
MeSH headings : Algorithms; Chromosomes, Plant; Computer Simulation; Genetic Linkage; Genome, Plant; Genotype; Ipomoea / genetics; Plant Breeding; Poaceae / genetics; Polyploidy; Protein Array Analysis; Solanum tuberosum / genetics
TL;DR:
PolyGembler, a method for grouping and ordering contigs into complete pseudomolecules by combining long-read sequencing and genotype information from an outbred mapping population, improves the accuracy for assembly of polyploidy plant genomes.
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UN Sustainable Development Goal Categories
13. Climate Action
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15. Life on Land
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Added: November 24, 2020
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.