A pan-transcriptome describes the transcriptional and post-transcriptional consequences of genome diversity from multiple individuals within a species. We developed a barley pan-transcriptome using 20 inbred genotypes representing domesticated barley diversity by generating and analyzing short- and long-read RNA-sequencing datasets from multiple tissues. To overcome single reference bias in transcript quantification, we constructed genotype-specific reference transcript datasets (RTDs) and integrated these into a linear pan-genome framework to create a pan-RTD, allowing transcript categorization as core, shell or cloud. Focusing on the core (expressed in all genotypes), we observed significant transcript abundance variation among tissues and between genotypes driven partly by RNA processing, gene copy number, structural rearrangements and conservation of promotor motifs. Network analyses revealed conserved co-expression module::tissue correlations and frequent functional diversification. To complement the pan-transcriptome, we constructed a comprehensive cultivar (cv.) Morex gene-expression atlas and illustrate how these combined datasets can be used to guide biological inquiry.

Carlsberg Research Laboratory Copenhagen Denmark

Chair of Crop Plant Genetics Institute of Agricultural and Nutritional Sciences Martin Luther University Halle Wittenberg Halle Germany

Chair of Plant Breeding Institute of Agricultural and Nutritional Sciences Martin Luther University Halle Wittenberg Halle Germany

College of Agriculture and Biotechnology Zhejiang University Hangzhou China

College of Agriculture Yangtze University Jinzhou China

Council for Agriculture Research and Economics Research Centre for Genomics and Bioinformatics Fiorenzuola d'Arda Italy

CREA Research Centre for Olive Fruit and Citrus Crops Forlì Italy

Department of Agronomy and Plant Genetics University of Minnesota St Paul MN USA

Department of Molecular Life Sciences Computational Plant Biology School of Life Sciences Technical University of Munich Freising Germany

Department of Plant Breeding Swedish University of Agricultural Sciences Uppsala Sweden

Department of Plant Sciences and Crop Development Centre University of Saskatchewan Saskatoon Saskatchewan Canada

Department of Primary Industry and Regional Development Western Australia South Perth Western Australia Australia

Department of Soil and Crop Sciences Texas A and M University College Station TX USA

DLF Roskilde Denmark

Higentec Breeding Innovation Co Ltd Lishui China

Institute of Experimental Botany of the Czech Academy of Sciences Olomouc Czech Republic

Institute of Plant Science and Resources Okayama University Kurashiki Japan

International Barley Hub Dundee Scotland

Kazusa DNA Research Institute Kisarazu Japan

Leibniz Institute of Plant Genetics and Crop Plant Research Gatersleben Seeland Germany

Minnesota Supercomputing Institute University of Minnesota Minneapolis MN USA

Plant Genome and Systems Biology Helmholtz Center Munich German Research Center for Environmental Health Neuherberg Germany

School of Agriculture Food and Wine University of Adelaide Waite Campus Urrbrae South Australia Australia

School of Life Sciences Technical University of Munich Freising Germany

School of Life Sciences University of Dundee Dundee UK

Texas A and M AgriLife Research Center at Dallas Texas A and M University System Dallas TX USA

Western Crop Genetics Alliance Food Futures Institute School of Agriculture Murdoch University Murdoch Western Australia Australia

Zobrazit více v PubMed

Verstegen, H., Köneke, O., Korzun, V. & von Broock, R. in

Langridge, P. in

Harwood, W. A. in

Von Bothmer, R., van Hintum, T., Knüpffer, H. & Sato, K.

Komatsuda, T. et al. Six-rowed barley originated from a mutation in a homeodomain-leucine zipper I-class homeobox gene. PubMed DOI PMC

Russell, J. et al. Exome sequencing of geographically diverse barley landraces and wild relatives gives insights into environmental adaptation. PubMed DOI

Taketa, S. et al. Barley grain with adhering hulls is controlled by an ERF family transcription factor gene regulating a lipid biosynthesis pathway. PubMed DOI PMC

Jayakodi, M. et al. The barley pan-genome reveals the hidden legacy of mutation breeding. PubMed DOI PMC

Jayakodi, M. et al. Structural variation in the pangenome of wild and domesticated barley. PubMed DOI PMC

Mascher, M. et al. A chromosome conformation capture ordered sequence of the barley genome. PubMed DOI

Lundqvist, U. Scandinavian mutation research in barley—a historical review. PubMed DOI

Guo, W., Coulter, M., Waugh, R. & Zhang, R. The value of genotype-specific reference for transcriptome analyses in barley. PubMed DOI PMC

Brown, J. W. S., Calixto, C. P. G. & Zhang, R. High-quality reference transcript datasets hold the key to transcript-specific RNA-sequencing analysis in plants. PubMed DOI

Zhang, R. et al. A high quality PubMed DOI PMC

Rapazote-Flores, P. et al. BaRTv1.0: an improved barley reference transcript dataset to determine accurate changes in the barley transcriptome using RNA-seq. PubMed DOI PMC

Coulter, M. et al. BaRTv2: a highly resolved barley reference transcriptome for accurate transcript‐specific RNA‐seq quantification. PubMed DOI PMC

Wang, J. et al. A pangenome analysis pipeline provides insights into functional gene identification in rice. PubMed DOI PMC

Aleksander, S. A. et al. The Gene Ontology knowledgebase in 2023. PubMed DOI PMC

Francia, E. et al. Copy number variation at the HvCBF4–HvCBF2 genomic segment is a major component of frost resistance in barley. PubMed DOI

Jeknić, Z. et al. Hv-CBF2A overexpression in barley accelerates COR gene transcript accumulation and acquisition of freezing tolerance during cold acclimation. PubMed DOI

Schreiber, M. et al. Genomic resources for a historical collection of cultivated two-row European spring barley genotypes. PubMed DOI PMC

Shrestha, A. et al. The double round-robin population unravels the genetic architecture of grain size in barley. PubMed DOI PMC

Cu, S. T. et al. Genetic analysis of grain and malt quality in an elite barley population. DOI

Genievskaya, Y., Almerekova, S., Abugalieva, A. & Abugalieva, S. Genome-wide association study of grain quality traits in spring barley collection grown in Kyzylorda region.

Pasam, R. K. et al. Genome-wide association studies for agronomical traits in a world wide spring barley collection. PubMed DOI PMC

Elía, M. et al. A model of the genetic differences in malting quality between European and North American barley cultivars based on a QTL study of the cross Triumph x Morex. DOI

Du, B. et al. Detection of consensus genomic regions and candidate genes for quality traits in barley using QTL meta-analysis. PubMed DOI PMC

Collins, H. M. et al. Genes that mediate starch metabolism in developing and germinated barley grain. PubMed DOI PMC

Franco-Zorrilla, J. M. et al. DNA-binding specificities of plant transcription factors and their potential to define target genes. PubMed DOI PMC

Spitz, F. & Furlong, E. E. M. Transcription factors: from enhancer binding to developmental control. PubMed DOI

Ricci, W. A. et al. Widespread long-range PubMed DOI PMC

Langfelder, P. & Horvath, S. WGCNA: an R package for weighted correlation network analysis. PubMed DOI PMC

Patro, R., Duggal, G., Love, M. I., Irizarry, R. A. & Kingsford, C. Salmon provides fast and bias-aware quantification of transcript expression. PubMed DOI PMC

Milne, L. et al. EORNA, a barley gene and transcript abundance database. PubMed DOI PMC

Peng, J. et al. ‘Green revolution’ genes encode mutant gibberellin response modulators. PubMed DOI

Betts, N. S. et al. Transcriptional and biochemical analyses of gibberellin expression and content in germinated barley grain. PubMed DOI PMC

Cheng, J. et al. Diversity of gibberellin 2-oxidase genes in the barley genome offers opportunities for genetic improvement. PubMed DOI PMC

Potokina, E. et al. Gene expression quantitative trait locus analysis of 16000 barley genes reveals a complex pattern of genome-wide transcriptional regulation. PubMed DOI

Druka, A. et al. Expression quantitative trait loci analysis in plants. PubMed DOI

Wonneberger, R. et al. Major chromosome 5H haplotype switch structures the European two-rowed spring barley germplasm of the past 190 years. PubMed DOI PMC

Harper, A. L. et al. Associative transcriptomics of traits in the polyploid crop species PubMed DOI

Jin, M. et al. Maize pan-transcriptome provides novel insights into genome complexity and quantitative trait variation. PubMed DOI PMC

Chen, X. et al. An eQTL analysis of partial resistance to PubMed DOI PMC

Ma, Y., Liu, M., Stiller, J. & Liu, C. A pan-transcriptome analysis shows that disease resistance genes have undergone more selection pressure during barley domestication. PubMed DOI PMC

Ramírez-González, R. H. et al. The transcriptional landscape of polyploid wheat. PubMed DOI

Chen, S., Zhou, Y., Chen, Y. & Gu, J. fastp: an ultra-fast all-in-one FASTQ preprocessor. PubMed DOI PMC

Dobin, A. & Gingeras, T. R. Mapping RNA-seq reads with STAR. PubMed DOI PMC

Pertea, M. et al. StringTie enables improved reconstruction of a transcriptome from RNA-seq reads. PubMed DOI PMC

Shao, M. & Kingsford, C. Accurate assembly of transcripts through phase-preserving graph decomposition. PubMed DOI PMC

Li, H. Minimap2: pairwise alignment for nucleotide sequences. PubMed DOI PMC

Kuo, R. I. et al. Illuminating the dark side of the human transcriptome with long read transcript sequencing. PubMed DOI PMC

Zhang, R. et al. A high-resolution single-molecule sequencing-based PubMed DOI PMC

Entizne, J. C. et al. TranSuite: a software suite for accurate translation and characterization of transcripts. Preprint at

Quevillon, E. et al. InterProScan: protein domains identifier. PubMed DOI PMC

Guo, W. et al. 3D RNA-seq: a powerful and flexible tool for rapid and accurate differential expression and alternative splicing analysis of RNA-seq data for biologists. PubMed DOI PMC

Frazee, A. C., Jaffe, A. E., Langmead, B. & Leek, J. T. Polyester: simulating RNA-seq datasets with differential transcript expression. PubMed DOI PMC

Altschul, S. F., Gish, W., Miller, W., Myers, E. W. & Lipman, D. J. Basic local alignment search tool. PubMed DOI

Goel, M., Sun, H., Jiao, W. B. & Schneeberger, K. SyRI: finding genomic rearrangements and local sequence differences from whole-genome assemblies. PubMed DOI PMC

Goel, M. & Schneeberger, K. plotsr: visualizing structural similarities and rearrangements between multiple genomes. PubMed DOI PMC

Love, M. I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. PubMed DOI PMC

Lohse, M. et al. Mercator: a fast and simple web server for genome scale functional annotation of plant sequence data. PubMed DOI

Wu, T. et al. clusterProfiler 4.0: a universal enrichment tool for interpreting omics data. PubMed PMC

Hagberg, A. A., Schult, D. A. & Swart, P. J. Exploring network structure, dynamics, and function using NetworkX. In

De Meo, P., Ferrara, E., Fiumara, G. & Provetti, A. Generalized Louvain method for community detection in large networks. In

Brodersen, P. & Voinnet, O. Revisiting the principles of microRNA target recognition and mode of action. PubMed DOI

Sakai, H. et al. Rice Annotation Project Database (RAP-DB): an integrative and interactive database for rice genomics. PubMed DOI PMC

Cheng, C. Y. et al. Araport11: a complete reannotation of the PubMed DOI

Emms, D. M. & Kelly, S. OrthoFinder: phylogenetic orthology inference for comparative genomics. PubMed DOI PMC

Mascher, M. et al. Long-read sequence assembly: a technical evaluation in barley. PubMed DOI PMC

Knudsen, S. et al. FIND-IT: accelerated trait development for a green evolution. PubMed DOI PMC

Marosi, V., Bayer, M., & Guo, W. cropgeeks/barleyPantranscriptome: v1.0 (v1.0).

Marosi, V. vanda-marosi/PanBarleyNetworks: publication (1.0).

Viet, D., Brett, C., Yong, J., Chengdao, L., & Western Crop Genetics Alliance. WCGA-Murdoch/Barley-phenology-2023: barley phenology genes CNV analysis—2023 (v1.0).

Guo, W. et al. A barley pan-transcriptome reveals layers of genotype-dependent transcriptional complexity. PubMed PMC

A barley pan-transcriptome reveals layers of genotype-dependent transcriptional complexity