{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"submitter":["Bickhart DM"],"funding":["USDA-ARS"],"pagination":["gigabyte42"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC9650271"],"repository":["biostudies-literature"],"omics_type":["Unknown"],"volume":["2022"],"pubmed_abstract":["Relative to other crops, red clover (<i>Trifolium pratense</i> L.) has various favorable traits making it an ideal forage crop. Conventional breeding has improved varieties, but modern genomic methods could accelerate progress and facilitate gene discovery. Existing short-read-based genome assemblies of the ∼420 megabase pair (Mbp) genome are fragmented into >135,000 contigs, with numerous order and orientation errors within scaffolds, probably associated with the plant's biology, which displays gametophytic self-incompatibility resulting in inherent high heterozygosity. Here, we present a high-quality long-read-based assembly of red clover with a more than 500-fold reduction in contigs, improved per-base quality, and increased contig N50 by three orders of magnitude. The 413.5 Mbp assembly is nearly 20% longer than the 350 Mbp short-read assembly, closer to the predicted genome size. We also present quality measures and full-length isoform RNA transcript sequences for assessing accuracy and future genome annotation. The assembly accurately represents the seven main linkage groups in an allogamous (outcrossing), highly heterozygous plant genome."],"journal":["GigaByte (Hong Kong, China)"],"pubmed_title":["Chromosome-scale assembly of the highly heterozygous genome of red clover (<i>Trifolium pratense</i> L.), an allogamous forage crop species."],"pmcid":["PMC9650271"],"funding_grant_id":["3040-31000-100-00D","5090-21000-071-00D","5090-21000-001-00D","5090-31000-026-00D"],"pubmed_authors":["Sullivan ML","Riday H","Koch LM","Smith TPL","Bickhart DM"],"additional_accession":[]},"is_claimable":false,"name":"Chromosome-scale assembly of the highly heterozygous genome of red clover (<i>Trifolium pratense</i> L.), an allogamous forage crop species.","description":"Relative to other crops, red clover (<i>Trifolium pratense</i> L.) has various favorable traits making it an ideal forage crop. Conventional breeding has improved varieties, but modern genomic methods could accelerate progress and facilitate gene discovery. Existing short-read-based genome assemblies of the ∼420 megabase pair (Mbp) genome are fragmented into >135,000 contigs, with numerous order and orientation errors within scaffolds, probably associated with the plant's biology, which displays gametophytic self-incompatibility resulting in inherent high heterozygosity. Here, we present a high-quality long-read-based assembly of red clover with a more than 500-fold reduction in contigs, improved per-base quality, and increased contig N50 by three orders of magnitude. The 413.5 Mbp assembly is nearly 20% longer than the 350 Mbp short-read assembly, closer to the predicted genome size. We also present quality measures and full-length isoform RNA transcript sequences for assessing accuracy and future genome annotation. The assembly accurately represents the seven main linkage groups in an allogamous (outcrossing), highly heterozygous plant genome.","dates":{"release":"2022-01-01T00:00:00Z","publication":"2022","modification":"2025-04-04T14:17:53.803Z","creation":"2025-02-19T02:24:08.269Z"},"accession":"S-EPMC9650271","cross_references":{"pubmed":["36824517"],"doi":["10.46471/gigabyte.42"]}}