ArticleBMC genomics2019
A pan-transcriptome analysis shows that disease resistance genes have undergone more selection pressure during barley domestication.
Article in BMC genomics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- Domestication Reduces Plant Immune Receptor Gene Repertoires Across Lineages.Genome biology and evolution · 2025Article
- A barley pan-transcriptome reveals layers of genotype-dependent transcriptional complexity.Nature genetics · 2025Article
- Direct RNA sequencing in plants: Practical applications and future perspectives.Plant communications · 2024Review
- Comparative Transcriptomic Analysis Reveals Domestication and Improvement Patterns of Broomcorn Millet (International journal of molecular sciences · 2024Article
- An Integrated Multi-Omics and Artificial Intelligence Framework for Advance Plant Phenotyping in Horticulture.Biology · 2023Review
- Transcriptome profiling of barley in response to mineral and organic fertilizers.BMC plant biology · 2023Article
- Does one subgenome become dominant in the formation and evolution of a polyploid?Annals of botany · 2023Article
- Rewiring of the seed metabolome during Tartary buckwheat domestication.Plant biotechnology journal · 2023Article
- Individual Genetic Heterogeneity.Genes · 2022Review
- Pan-transcriptome assembly combined with multiple association analysis provides new insights into the regulatory network of specialized metabolites in the tea plantHorticulture research · 2022Article
- Plant NLR diversity: the known unknowns of pan-NLRomes.The Plant cell · 2021Review
- Modern Approaches for Transcriptome Analyses in Plants.Advances in experimental medicine and biology · 2021Article
- Genetic Diversity, Nitrogen Fixation, and Water Use Efficiency in a Panel of Honduran Common Bean (Plants (Basel, Switzerland) · 2020Article
- Identifying barley pan-genome sequence anchors using genetic mapping and machine learning.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2020Article
- Understanding the Plant-microbe Interactions in CRISPR/CAS9 Era: Indeed a Sprinting Start in Marathon.Current genomics · 2020Review
- Pan-genomics in the human genome era.Nature reviews. Genetics · 2020Review
- Grape-RNA: A Database for the Collection, Evaluation, Treatment, and Data Sharing of Grape RNA-Seq Datasets.Genes · 2020Article
- The draft genome of a wild barley genotype reveals its enrichment in genes related to biotic and abiotic stresses compared to cultivated barley.Plant biotechnology journal · 2020Article
- Transcriptomic and presence/absence variation in the barley genome assessed from multi-tissue mRNA sequencing and their power to predict phenotypic traits.BMC genomics · 2019Article
- Variation in Recombination Rate Is Shaped by Domestication and Environmental Conditions in Barley.Molecular biology and evolution · 2019Article
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4 authors.
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Abstract
backgroundIt has become clear in recent years that many genes in a given species may not be found in a single genotype thus using sequences from a single genotype as reference may not be adequate for various applications.
resultsIn this study we constructed a pan-transcriptome for barley by de novo assembling 288 sets of RNA-seq data from 32 cultivated barley genotypes and 31 wild barley genotypes. The pan-transcriptome consists of 756,632 transcripts with an average N50 length of 1240 bp. Of these, 289,697 (38.2%) were not found in the genome of the international reference genotype Morex. The novel transcripts are enriched with genes associated with responses to different stresses and stimuli. At the pan-transcriptome level, genotypes of wild barley have a higher proportion of disease resistance genes than cultivated ones.
conclusionsWe demonstrate that the use of the pan-transcriptome dramatically improved the efficiency in detecting variation in barley. Analysing the pan-transcriptome also found that, compared with those in other categories, disease resistance genes have gone through stronger selective pressures during domestication.
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