ArticleGenome biology and evolution2021
Ultralong Oxford Nanopore Reads Enable the Development of a Reference-Grade Perennial Ryegrass Genome Assembly.
Article in Genome biology and evolution, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 30 papers.
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Who cites it
30 citing papers in PubMed.
- De novo genome assembly of Texas wintergrass [Nassella leucotricha {Trin. & Rupr.} Pohl] supports diagnostic marker development and phylogenetic analysis of species within the family Poaceae.G3 (Bethesda, Md.) · 2026Article
- Candidate genes for stem rust resistance in Italian ryegrass revealed by nested association mapping.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Article
- Chromosome-level haplotype-resolved assembly of highly heterozygous grass genomes with PhaseGrass.Nature communications · 2025Article
- The relationships among alkaloid concentration, endophyte mycelial concentration and host genetics in the tall fescue Epichloë symbiosis.BMC genomics · 2025Article
- Haplotype-resolved genome assembly of 'Manhattan' perennial ryegrass (Lolium perenne L.) and characterization of drought responsive late embryogenesis abundant genes.BMC genomics · 2025Article
- Genetic and genomic resources for turfgrasses: status, applications, and prospects.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2025Review
- Genome-wide analysis of the AP2/ERF transcription factor superfamily in perennial ryegrass.BMC genomics · 2025Article
- Chromosome-level haplotype-resolved genome assembly provides insights into the highly heterozygous genome of Italian ryegrass (Lolium multiflorum Lam.).The plant genome · 2025Article
- VULGARE ROW-TYPE SIX 5 binds to the promoter of tillering and floral homeotic genes to regulate their expression.Plant physiology · 2025Article
- The Genome of Lolium multiflorum Reveals the Genetic Architecture of Paraquat Resistance.Molecular ecology · 2025Article
- Estimation of ryegrass (Frontiers in plant science · 2025Article
- Isolation and transformation of perennial ryegrass (Frontiers in plant science · 2025Article
- Machine learning solutions for integrating partially overlapping genetic datasets and modelling host-endophyte effects in ryegrass (Frontiers in plant science · 2025Article
- The LpHsfA2-molecular module confers thermotolerance via fine tuning of its transcription in perennial ryegrass (Lolium perenne L.).Journal of integrative plant biology · 2024Article
- De novo diploid genome assembly using long noisy reads.Nature communications · 2024Article
- An improved chromosome-level genome assembly of perennial ryegrass (GigaByte (Hong Kong, China) · 2024Article
- DeepSelectNet: deep neural network based selective sequencing for oxford nanopore sequencing.BMC bioinformatics · 2023Article
- Fine-Mapping and Comparative Genomic Analysis Reveal the Gene Composition at the S and Z Self-incompatibility Loci in Grasses.Molecular biology and evolution · 2023Article
- Development of genomic resources for Rhodes grass (Frontiers in plant science · 2023Article
- IsolatingInternational journal of molecular sciences · 2022Article
Corrections and comments
- Erratum issued
Authors and funding
11 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Despite the progress made in DNA sequencing over the last decade, reconstructing telomere-to-telomere genome assemblies of large and repeat-rich eukaryotic genomes is still difficult. More accurate basecalls or longer reads could address this issue, but no current sequencing platform can provide both simultaneously. Perennial ryegrass (Lolium perenne L.) is an example of an important species for which the lack of a reference genome assembly hindered a swift adoption of genomics-based methods into breeding programs. To fill this gap, we optimized the Oxford Nanopore Technologies' sequencing protocol, obtaining sequencing reads with an N50 of 62 kb-a very high value for a plant sample. The assembly of such reads produced a highly complete (2.3 of 2.7 Gb), correct (QV 45), and contiguous (contig N50 and N90 11.74 and 3.34 Mb, respectively) genome assembly. We show how read length was key in determining the assembly contiguity. Sequence annotation revealed the dominance of transposable elements and repeated sequences (81.6% of the assembly) and identified 38,868 protein coding genes. Almost 90% of the bases could be anchored to seven pseudomolecules, providing the first high-quality haploid reference assembly for perennial ryegrass. This protocol will enable producing longer Oxford Nanopore Technology reads for more plant samples and ushering forage grasses into modern genomics-assisted breeding programs.
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