ArticlePloS one2013
Large-scale collection and analysis of full-length cDNAs from Brachypodium distachyon and integration with Pooideae sequence resources.
Article in PloS one, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers, 1 of them a synthesis that pooled it.
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Who cites it
15 citing papers in PubMed, 1 synthesis or guideline pooled it.
- The Brachypodium distachyon cold-acclimated plasma membrane proteome is primed for stress resistance.G3 (Bethesda, Md.) · 2021Pooled it
- Targeted and Untargeted Metabolomic Analyses Reveal Organ Specificity of Specialized Metabolites in the Model GrassMolecules (Basel, Switzerland) · 2022Article
- Rapid sequence and functional diversification of a miRNA superfamily targeting calcium signaling components in seed plants.The New phytologist · 2022Article
- Salicylic acid-dependent immunity contributes to resistance against Rhizoctonia solani, a necrotrophic fungal agent of sheath blight, in rice and Brachypodium distachyon.The New phytologist · 2018Article
- Long noncoding RNAs in the model species Brachypodium distachyon.Scientific reports · 2017Article
- Analysis of single nucleotide polymorphisms based on RNA sequencing data of diverse bio-geographical accessions in barley.Scientific reports · 2016Article
- Expression profiling of marker genes responsive to the defence-associated phytohormones salicylic acid, jasmonic acid and ethylene in Brachypodium distachyon.BMC plant biology · 2016Article
- Gene Overexpression Resources in Cereals for Functional Genomics and Discovery of Useful Genes.Frontiers in plant science · 2016Review
- Transcriptome analysis of hormone-induced gene expression in Brachypodium distachyon.Scientific reports · 2015Article
- Evaluation of Brachypodium distachyon L-Tyrosine Decarboxylase Using L-Tyrosine Over-Producing Saccharomyces cerevisiae.PloS one · 2015Article
- Systematic analysis and identification of stress-responsive genes of the NAC gene family in Brachypodium distachyon.PloS one · 2015Article
- MOROKOSHI: transcriptome database in Sorghum bicolor.Plant & cell physiology · 2015Article
- Full-length enriched cDNA libraries and ORFeome analysis of sugarcane hybrid and ancestor genotypes.PloS one · 2014Article
- Unlocking Triticeae genomics to sustainably feed the future.Plant & cell physiology · 2013Review
- Genome-wide landscape of alternative splicing events in Brachypodium distachyon.DNA research : an international journal for rapid publication of reports on genes and genomes · 2013Article
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Authors and funding
6 authors.
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No grant is acknowledged in the PubMed record.
Abstract
A comprehensive collection of full-length cDNAs is essential for correct structural gene annotation and functional analyses of genes. We constructed a mixed full-length cDNA library from 21 different tissues of Brachypodium distachyon Bd21, and obtained 78,163 high quality expressed sequence tags (ESTs) from both ends of ca. 40,000 clones (including 16,079 contigs). We updated gene structure annotations of Brachypodium genes based on full-length cDNA sequences in comparison with the latest publicly available annotations. About 10,000 non-redundant gene models were supported by full-length cDNAs; ca. 6,000 showed some transcription unit modifications. We also found ca. 580 novel gene models, including 362 newly identified in Bd21. Using the updated transcription start sites, we searched a total of 580 plant cis-motifs in the -3 kb promoter regions and determined a genome-wide Brachypodium promoter architecture. Furthermore, we integrated the Brachypodium full-length cDNAs and updated gene structures with available sequence resources in wheat and barley in a web-accessible database, the RIKEN Brachypodium FL cDNA database. The database represents a "one-stop" information resource for all genomic information in the Pooideae, facilitating functional analysis of genes in this model grass plant and seamless knowledge transfer to the Triticeae crops.
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