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 |
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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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