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De novo transcriptome assembly and analyses of gene expression during photomorphogenesis in diploid wheat Triticum monococcum.
PLoS One. 2014; 9(5):e96855.Plos

Abstract

BACKGROUND

Triticum monococcum (2n) is a close ancestor of T. urartu, the A-genome progenitor of cultivated hexaploid wheat, and is therefore a useful model for the study of components regulating photomorphogenesis in diploid wheat. In order to develop genetic and genomic resources for such a study, we constructed genome-wide transcriptomes of two Triticum monococcum subspecies, the wild winter wheat T. monococcum ssp. aegilopoides (accession G3116) and the domesticated spring wheat T. monococcum ssp. monococcum (accession DV92) by generating de novo assemblies of RNA-Seq data derived from both etiolated and green seedlings.

PRINCIPAL FINDINGS

The de novo transcriptome assemblies of DV92 and G3116 represent 120,911 and 117,969 transcripts, respectively. We successfully mapped ∼90% of these transcripts from each accession to barley and ∼95% of the transcripts to T. urartu genomes. However, only ∼77% transcripts mapped to the annotated barley genes and ∼85% transcripts mapped to the annotated T. urartu genes. Differential gene expression analyses revealed 22% more light up-regulated and 35% more light down-regulated transcripts in the G3116 transcriptome compared to DV92. The DV92 and G3116 mRNA sequence reads aligned against the reference barley genome led to the identification of ∼500,000 single nucleotide polymorphism (SNP) and ∼22,000 simple sequence repeat (SSR) sites.

CONCLUSIONS

De novo transcriptome assemblies of two accessions of the diploid wheat T. monococcum provide new empirical transcriptome references for improving Triticeae genome annotations, and insights into transcriptional programming during photomorphogenesis. The SNP and SSR sites identified in our analysis provide additional resources for the development of molecular markers.

Authors+Show Affiliations

Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America.Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America; Molecular and Cellular Biology Graduate Program, Oregon State University, Corvallis, Oregon, United States of America.Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America.Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America; Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon, United States of America.Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America; Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon, United States of America.Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America.Department of Crop and Soil Science, Oregon State University, Corvallis, Oregon, United States of America.Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America.Department of Crop and Soil Science, Oregon State University, Corvallis, Oregon, United States of America.Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America.Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi State, Mississippi, United States of America.European Bioinformatics Institute, Hinxton, Cambridge, United Kingdom.European Bioinformatics Institute, Hinxton, Cambridge, United Kingdom.School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, Arizona, United States of America.European Bioinformatics Institute, Hinxton, Cambridge, United Kingdom.USDA-ARS, Western Regional Research Center, Albany, California, United States of America.Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America; Department of Crop and Soil Science, Oregon State University, Corvallis, Oregon, United States of America.

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

24821410

Citation

Fox, Samuel E., et al. "De Novo Transcriptome Assembly and Analyses of Gene Expression During Photomorphogenesis in Diploid Wheat Triticum Monococcum." PloS One, vol. 9, no. 5, 2014, pp. e96855.
Fox SE, Geniza M, Hanumappa M, et al. De novo transcriptome assembly and analyses of gene expression during photomorphogenesis in diploid wheat Triticum monococcum. PLoS One. 2014;9(5):e96855.
Fox, S. E., Geniza, M., Hanumappa, M., Naithani, S., Sullivan, C., Preece, J., Tiwari, V. K., Elser, J., Leonard, J. M., Sage, A., Gresham, C., Kerhornou, A., Bolser, D., McCarthy, F., Kersey, P., Lazo, G. R., & Jaiswal, P. (2014). De novo transcriptome assembly and analyses of gene expression during photomorphogenesis in diploid wheat Triticum monococcum. PloS One, 9(5), e96855. https://doi.org/10.1371/journal.pone.0096855
Fox SE, et al. De Novo Transcriptome Assembly and Analyses of Gene Expression During Photomorphogenesis in Diploid Wheat Triticum Monococcum. PLoS One. 2014;9(5):e96855. PubMed PMID: 24821410.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - De novo transcriptome assembly and analyses of gene expression during photomorphogenesis in diploid wheat Triticum monococcum. AU - Fox,Samuel E, AU - Geniza,Matthew, AU - Hanumappa,Mamatha, AU - Naithani,Sushma, AU - Sullivan,Chris, AU - Preece,Justin, AU - Tiwari,Vijay K, AU - Elser,Justin, AU - Leonard,Jeffrey M, AU - Sage,Abigail, AU - Gresham,Cathy, AU - Kerhornou,Arnaud, AU - Bolser,Dan, AU - McCarthy,Fiona, AU - Kersey,Paul, AU - Lazo,Gerard R, AU - Jaiswal,Pankaj, Y1 - 2014/05/12/ PY - 2013/11/05/received PY - 2014/04/12/accepted PY - 2014/5/14/entrez PY - 2014/5/14/pubmed PY - 2015/1/24/medline SP - e96855 EP - e96855 JF - PloS one JO - PLoS One VL - 9 IS - 5 N2 - BACKGROUND: Triticum monococcum (2n) is a close ancestor of T. urartu, the A-genome progenitor of cultivated hexaploid wheat, and is therefore a useful model for the study of components regulating photomorphogenesis in diploid wheat. In order to develop genetic and genomic resources for such a study, we constructed genome-wide transcriptomes of two Triticum monococcum subspecies, the wild winter wheat T. monococcum ssp. aegilopoides (accession G3116) and the domesticated spring wheat T. monococcum ssp. monococcum (accession DV92) by generating de novo assemblies of RNA-Seq data derived from both etiolated and green seedlings. PRINCIPAL FINDINGS: The de novo transcriptome assemblies of DV92 and G3116 represent 120,911 and 117,969 transcripts, respectively. We successfully mapped ∼90% of these transcripts from each accession to barley and ∼95% of the transcripts to T. urartu genomes. However, only ∼77% transcripts mapped to the annotated barley genes and ∼85% transcripts mapped to the annotated T. urartu genes. Differential gene expression analyses revealed 22% more light up-regulated and 35% more light down-regulated transcripts in the G3116 transcriptome compared to DV92. The DV92 and G3116 mRNA sequence reads aligned against the reference barley genome led to the identification of ∼500,000 single nucleotide polymorphism (SNP) and ∼22,000 simple sequence repeat (SSR) sites. CONCLUSIONS: De novo transcriptome assemblies of two accessions of the diploid wheat T. monococcum provide new empirical transcriptome references for improving Triticeae genome annotations, and insights into transcriptional programming during photomorphogenesis. The SNP and SSR sites identified in our analysis provide additional resources for the development of molecular markers. SN - 1932-6203 UR - https://www.unboundmedicine.com/medline/citation/24821410/De_novo_transcriptome_assembly_and_analyses_of_gene_expression_during_photomorphogenesis_in_diploid_wheat_Triticum_monococcum_ L2 - https://dx.plos.org/10.1371/journal.pone.0096855 DB - PRIME DP - Unbound Medicine ER -