A haplotype-resolved chromosome-level genome assembly of Urochloa decumbens cv. Basilisk resolves its allopolyploid ancestry and composition

Ryan, Camilla, Fraser, Fiona, Irish, Naomi, Barker, Tom, Knitlhoffer, Vanda, Durrant, Alex, Reynolds, Gillian, Kaithakottil, Gemy, Swarbreck, David and De Vega, Jose J. (2025) A haplotype-resolved chromosome-level genome assembly of Urochloa decumbens cv. Basilisk resolves its allopolyploid ancestry and composition. G3: Genes, Genomes, Genetics, 15 (4). ISSN 2160-1836

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Abstract

Haplotyped-resolved phased assemblies aim to capture the full allelic diversity in heterozygous and polyploid species to enable accurate genetic analyses. However, building non-collapsed references still presents a challenge. Here, we used long-range interaction Hi-C reads (high-throughput chromatin conformation capture) and HiFi PacBio reads to assemble the genome of the apomictic cultivar Basilisks from Urochloa decumbens (2n = 4x = 36), an outcrossed tetraploid Paniceae grass widely cropped to feed livestock in the tropics. We identified and removed Hi-C reads between homologous unitigs to facilitate their scaffolding and employed methods for the manual curation of rearrangements and misassemblies. Our final phased assembly included the 4 haplotypes in 36 chromosomes. We found that 18 chromosomes originated from diploid Urochloa brizantha and the other 18 from either Urochloa ruziziensis or diploid U. decumbens. We also identified a chromosomal translocation between chromosomes 5 and 32, as well as evidence of pairing exclusively within subgenomes, except for a homoeologous exchange in chromosome 21. Our results demonstrate that haplotype-aware assemblies accurately capture the allelic diversity in heterozygous species, making them the preferred option over collapsed-haplotype assemblies.

Item Type: Article
Additional Information: Data availability: Raw reads are deposited in the SRA under accession PRJEB73762. The genome assembly, together with its gene annotation, was deposited in ENA with accession GCA_964030465.3 (https://www.ebi.ac.uk/ena/browser/view/GCA_964030465.3). The scripts used in this study are publicly available in GitHub (https://github.com/DeVegaGroup/HaplotypeAwareChromosomeLevelAssemblyUrochloaDecumbens). Supplemental material available at G3 online. Funding: This study was partially funded by the Biotechnology and Biological Sciences Research Council (BBSRC), part of UK Research and Innovation (UKRI), via Earlham Institute’s Strategic Programme Grant (Decoding Biodiversity) BBX011089/1, and its constituent work package BBS/E/ER/230002B (WP2 Genome Enabled Analysis of Diversity to Identify Gene Function, Biosynthetic Pathways, and Variation in Agri/Aquacultural Traits). Funding was also received from the BBSRCs funded "Core Strategic Programme Grant" (Genomes to Food Security) BB/CSP1720/1 and its constituent work package BBS/E/T/000PR9818 (WP1 Signatures of Domestication and Adaptation), as well as BB/X011089/1. Funding was also received from the Biotechnology and Biological Sciences Research Council (BBSRC) as part of UK Research and Innovation, Core Capability Grant BB/CCG1720/1. This study was partially funded by the Biotechnology and Biological Sciences Research Council (BBSRC), part of UK Research and Innovation (UKRI), via Earlham Institute’s Strategic Programme Grant (Decoding Biodiversity) BBX011089/1, and its constituent work package BBS/E/ER/230002B (WP2 Genome Enabled Analysis of Diversity to Identify Gene Function, Biosynthetic Pathways, and Variation in Agri/Aquacultural Traits). Funding was also received from the BBSRCs funded "Core Strategic Programme Grant" (Genomes to Food Security) BB/CSP1720/1 and its constituent work package BBS/E/T/000PR9818 (WP1 Signatures of Domestication and Adaptation), as well as BB/X011089/1. Funding was also received from the Biotechnology and Biological Sciences Research Council (BBSRC) as part of UK Research and Innovation, Core Capability Grant BB/CCG1720/1.
Uncontrolled Keywords: genome assembly,hi-c,hifi,polyploid,urochloa decumbens,molecular biology,genetics,genetics(clinical) ,/dk/atira/pure/subjectarea/asjc/1300/1312
Faculty \ School: Faculty of Science > School of Biological Sciences
Related URLs:
Depositing User: LivePure Connector
Date Deposited: 20 Aug 2025 13:30
Last Modified: 24 Aug 2025 06:30
URI: https://ueaeprints.uea.ac.uk/id/eprint/100173
DOI: 10.1093/g3journal/jkaf005

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