ArticlePloS one2014
De novo assembly of the perennial ryegrass transcriptome using an RNA-Seq strategy.
Article in PloS one, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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Who cites it
33 citing papers in PubMed.
- Genome-wide identification and expression patterns analysis of the DREB gene family under various abiotic stress in Lolium perenne.BMC plant biology · 2025Article
- Combined genomic and transcriptomic analysis reveals the contribution of tandem duplication genes to low-temperature adaptation in perennial ryegrass.Frontiers in plant science · 2023Article
- Article
- Chromosome-scale assembly and annotation of the perennial ryegrass genome.BMC genomics · 2022Article
- Elucidating the Molecular Mechanisms by which Seed-Borne Endophytic Fungi,International journal of molecular sciences · 2021Article
- Article
- Strategies for Efficient Gene Editing in Protoplasts of Solanum tuberosum Theme: Determining gRNA Efficiency Design by Utilizing Protoplast (Research).Frontiers in genome editing · 2021Article
- Overcoming challenges in variant calling: exploring sequence diversity in candidate genes for plant development in perennial ryegrass (Lolium perenne).DNA research : an international journal for rapid publication of reports on genes and genomes · 2019Article
- Exploitation of data from breeding programs supports rapid implementation of genomic selection for key agronomic traits in perennial ryegrass.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2018Article
- Genetic Loci Governing Androgenic Capacity in Perennial Ryegrass (G3 (Bethesda, Md.) · 2018Article
- Transcriptome profiling of fully open flowers in a frost-tolerant almond genotype in response to freezing stress.Molecular genetics and genomics : MGG · 2018Article
- De novo transcriptome assembly analysis of weed Apera spica-venti from seven tissues and growth stages.BMC genomics · 2017Article
- De novo assembly, functional annotation, and analysis of the giant reed (Biotechnology for biofuels · 2017Article
- Article
- Differential Gene Expression Analysis inFrontiers in plant science · 2017Article
- Transcriptional Profiling and Identification of Heat-Responsive Genes in Perennial Ryegrass by RNA-Sequencing.Frontiers in plant science · 2017Article
- Article
- Genomics-assisted characterization of a breeding collection of Apios americana, an edible tuberous legume.Scientific reports · 2016Article
- An ultra-high density genetic linkage map of perennial ryegrass (Lolium perenne) using genotyping by sequencing (GBS) based on a reference shotgun genome assembly.Annals of botany · 2016Article
- Global transcriptome changes in perennial ryegrass during early infection by pink snow mould.Scientific reports · 2016Article
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundPerennial ryegrass is a highly heterozygous outbreeding grass species used for turf and forage production. Heterozygosity can affect de-Bruijn graph assembly making de novo transcriptome assembly of species such as perennial ryegrass challenging. Creating a reference transcriptome from a homozygous perennial ryegrass genotype can circumvent the challenge of heterozygosity. The goals of this study were to perform RNA-sequencing on multiple tissues from a highly inbred genotype to develop a reference transcriptome. This was complemented with RNA-sequencing of a highly heterozygous genotype for SNP calling.
resultDe novo transcriptome assembly of the inbred genotype created 185,833 transcripts with an average length of 830 base pairs. Within the inbred reference transcriptome 78,560 predicted open reading frames were found of which 24,434 were predicted as complete. Functional annotation found 50,890 transcripts with a BLASTp hit from the Swiss-Prot non-redundant database, 58,941 transcripts with a Pfam protein domain and 1,151 transcripts encoding putative secreted peptides. To evaluate the reference transcriptome we targeted the high-affinity K+ transporter gene family and found multiple orthologs. Using the longest unique open reading frames as the reference sequence, 64,242 single nucleotide polymorphisms were found. One thousand sixty one open reading frames from the inbred genotype contained heterozygous sites, confirming the high degree of homozygosity.
conclusionOur study has developed an annotated, comprehensive transcriptome reference for perennial ryegrass that can aid in determining genetic variation, expression analysis, genome annotation, and gene mapping.
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