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Genomic characterization of Cannabis sativa has accelerated rapidly in the last decade as sequencing costs have decreased and public and private interest in the species has increased. Here, we present seven new chromosome-level haplotype-phased genomes of C. sativa. All of these genotypes were alive at the time of publication, and several have numerous years of associated phenotype data. We performed a k-mer-based pangenome analysis to contextualize these assemblies within over 200 existing assemblies. This allowed us to identify unique haplotypes and genomic diversity among Cannabis sativa genotypes. We leveraged linkage maps constructed from F2 progeny of two of the assembled genotypes to characterize the recombination rate across the genome showing strong periphery-biased recombination. Lastly, we re-aligned a bulk segregant analysis dataset for the major-effect flowering locus Early1 to several of the new assemblies to evaluate the impact of reference bias on the mapping results and narrow the locus to a smaller region of the chromosome. These new assemblies, combined with the continued propagation of the genotypes, will contribute to the growing body of genomic resources for C. sativa to accelerate future research efforts.
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A Maize Practical Haplotype Graph Leverages Diverse NAM Assemblies
As a result of millions of years of transposon activity, multiple rounds of ancient polyploidization, and large populations that preserve diversity, maize has an extremely structurally diverse genome, evidenced by high-quality genome assemblies that capture substantial levels of both tropical and temperate diversity. We generated a pangenome representation (the Practical Haplotype Graph, PHG) of these assemblies in a database, representing the pangenome haplotype diversity and providing an initial estimate of structural diversity. We leveraged the pangenome to accurately impute haplotypes and genotypes of taxa using various kinds of sequence data, ranging from WGS to extremely-low coverage GBS. We imputed the genotypes of the recombinant inbred lines of the NAM population with over 99% mean accuracy, while unrelated germplasm attained a mean imputation accuracy of 92 or 95% when using GBS or WGS data, respectively. Most of the imputation errors occur in haplotypes within European or tropical germplasm, which have yet to be represented in the maize PHG database. Also, the PHG stores the imputation data in a 30,000-fold more space-efficient manner than a standard genotype file, which is a key improvement when dealing with large scale data.
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- Award ID(s):
- 1822330
- PAR ID:
- 10283585
- Date Published:
- Journal Name:
- bioRxiv
- ISSN:
- 2692-8205
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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Abstract Here the Human Pangenome Reference Consortium presents a first draft of the human pangenome reference. The pangenome contains 47 phased, diploid assemblies from a cohort of genetically diverse individuals 1 . These assemblies cover more than 99% of the expected sequence in each genome and are more than 99% accurate at the structural and base pair levels. Based on alignments of the assemblies, we generate a draft pangenome that captures known variants and haplotypes and reveals new alleles at structurally complex loci. We also add 119 million base pairs of euchromatic polymorphic sequences and 1,115 gene duplications relative to the existing reference GRCh38. Roughly 90 million of the additional base pairs are derived from structural variation. Using our draft pangenome to analyse short-read data reduced small variant discovery errors by 34% and increased the number of structural variants detected per haplotype by 104% compared with GRCh38-based workflows, which enabled the typing of the vast majority of structural variant alleles per sample.more » « less
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Abstract The current human reference genome, GRCh38, represents over 20 years of effort to generate a high-quality assembly, which has benefitted society 1,2 . However, it still has many gaps and errors, and does not represent a biological genome as it is a blend of multiple individuals 3,4 . Recently, a high-quality telomere-to-telomere reference, CHM13, was generated with the latest long-read technologies, but it was derived from a hydatidiform mole cell line with a nearly homozygous genome 5 . To address these limitations, the Human Pangenome Reference Consortium formed with the goal of creating high-quality, cost-effective, diploid genome assemblies for a pangenome reference that represents human genetic diversity 6 . Here, in our first scientific report, we determined which combination of current genome sequencing and assembly approaches yield the most complete and accurate diploid genome assembly with minimal manual curation. Approaches that used highly accurate long reads and parent–child data with graph-based haplotype phasing during assembly outperformed those that did not. Developing a combination of the top-performing methods, we generated our first high-quality diploid reference assembly, containing only approximately four gaps per chromosome on average, with most chromosomes within ±1% of the length of CHM13. Nearly 48% of protein-coding genes have non-synonymous amino acid changes between haplotypes, and centromeric regions showed the highest diversity. Our findings serve as a foundation for assembling near-complete diploid human genomes at scale for a pangenome reference to capture global genetic variation from single nucleotides to structural rearrangements.more » « less
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- Free Publicly Accessible Full Text
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Accepted Manuscript1.0
- Journal Article:
- https://doi.org/https://doi.org/10.1101/2020.08.31.268425
