ArticleNature genetics2020
Assembly of whole-chromosome pseudomolecules for polyploid plant genomes using outbred mapping populations.
Article in Nature genetics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
What it found
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
7 citing papers in PubMed, 18 citations in OpenAlex.
- Beef Cattle Genome Project: Advances in Genome Sequencing, Assembly, and Functional Genes Discovery.International journal of molecular sciences · 2024Review
- Recent Advances in Assembly of Complex Plant Genomes.Genomics, proteomics & bioinformatics · 2023Review
- Chromosome-scale and haplotype-resolved genome assembly of a tetraploid potato cultivar.Nature genetics · 2022Article
- Quinoa genome assembly employing genomic variation for guided scaffolding.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2021Article
- Using probabilistic genotypes in linkage analysis of polyploids.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2021Article
- High-Frequency Homologous Recombination Occurred Preferentially inFrontiers in genetics · 2021Article
- Genetic Diversity and Population Structure of the USDA Sweetpotato (Frontiers in plant science · 2018Article
Corrections and comments
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Authors and funding
12 authors at 5 institutions in 4 countries.
Funding
No grant is acknowledged in the PubMed record.
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 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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.