De novo transcriptome assembly and analysis of differentially expressed genes of two barley genotypes reveal root-zone-specific responses to salt exposure
暂无分享,去创建一个
Monika S. Doblin | U. Roessner | A. Bacic | C. Hill | M. Doblin | G. Keeble-Gagnère | Andrew M. Cassin
[1] U. Roessner,et al. Root spatial metabolite profiling of two genotypes of barley (Hordeum vulgare L.) reveals differences in response to short-term salt stress , 2016, Journal of experimental botany.
[2] U. Roessner,et al. Salt-stress induced alterations in the root lipidome of two barley genotypes with contrasting responses to salinity. , 2016, Functional plant biology : FPB.
[3] S. Kelly,et al. OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy , 2015, Genome Biology.
[4] Chengzhang Wang,et al. De Novo Characterization of Fall Dormant and Nondormant Alfalfa (Medicago sativa L.) Leaf Transcriptome and Identification of Candidate Genes Related to Fall Dormancy , 2015, PloS one.
[5] H. Piepho,et al. A High-Resolution Tissue-Specific Proteome and Phosphoproteome Atlas of Maize Primary Roots Reveals Functional Gradients along the Root Axes1[OPEN] , 2015, Plant Physiology.
[6] Peter B. McGarvey,et al. UniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches , 2014, Bioinform..
[7] Richard D. Hayes,et al. The genome of Eucalyptus grandis , 2014, Nature.
[8] Amborella Genome. The Amborella Genome and the Evolution of Flowering Plants , 2013, Science.
[9] Colin N. Dewey,et al. De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis , 2013, Nature Protocols.
[10] Michael Ott,et al. De novo transcript sequence reconstruction from RNA-Seq: reference generation and analysis with Trinity , 2013 .
[11] R. E. Sharp,et al. Genetic variation in the root growth response of barley genotypes to salinity stress. , 2013, Functional plant biology : FPB.
[12] Roger P. Hellens,et al. De Novo Transcriptome Sequence Assembly and Analysis of RNA Silencing Genes of Nicotiana benthamiana , 2013, PloS one.
[13] P. Benfey,et al. High-resolution metabolic mapping of cell types in plant roots , 2013, Proceedings of the National Academy of Sciences.
[14] M. Delledonne,et al. De novo transcriptome characterization of Vitis vinifera cv. Corvina unveils varietal diversity , 2013, BMC Genomics.
[15] L. Hennighausen,et al. Comprehensive meta-analysis of Signal Transducers and Activators of Transcription (STAT) genomic binding patterns discerns cell-specific cis-regulatory modules , 2013, BMC Genomics.
[16] Mihaela M. Martis,et al. A physical, genetic and functional sequence assembly of the barley genome. , 2022 .
[17] Tim H. Brom,et al. A Reference-Free Algorithm for Computational Normalization of Shotgun Sequencing Data , 2012, 1203.4802.
[18] Steven L Salzberg,et al. Fast gapped-read alignment with Bowtie 2 , 2012, Nature Methods.
[19] J. Abadía,et al. Spatially resolved analysis of small molecules by matrix-assisted laser desorption/ionization mass spectrometric imaging (MALDI-MSI). , 2012, The New phytologist.
[20] Davis J. McCarthy,et al. Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation , 2012, Nucleic acids research.
[21] Tanya Z. Berardini,et al. The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools , 2011, Nucleic Acids Res..
[22] David M. Goodstein,et al. Phytozome: a comparative platform for green plant genomics , 2011, Nucleic Acids Res..
[23] Alvaro J. González,et al. The Medicago Genome Provides Insight into the Evolution of Rhizobial Symbioses , 2011, Nature.
[24] Colin N. Dewey,et al. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome , 2011, BMC Bioinformatics.
[25] Matko Bosnjak,et al. REVIGO Summarizes and Visualizes Long Lists of Gene Ontology Terms , 2011, PloS one.
[26] N. Friedman,et al. Trinity: reconstructing a full-length transcriptome without a genome from RNA-Seq data , 2011, Nature Biotechnology.
[27] N. Friedman,et al. Trinity : reconstructing a full-length transcriptome without a genome from RNA-Seq data , 2016 .
[28] M. Hrmova,et al. A SOS3 homologue maps to HvNax4, a barley locus controlling an environmentally sensitive Na+ exclusion trait , 2010, Journal of experimental botany.
[29] B. Baum,et al. Control of somatic embryogenesis and embryo development by AP2 transcription factors , 2010, Plant Molecular Biology.
[30] E. Tavakkoli,et al. The response of barley to salinity stress differs between hydroponic and soil systems , 2010 .
[31] Sai Guna Ranjan Gurazada,et al. Genome sequencing and analysis of the model grass Brachypodium distachyon , 2010, Nature.
[32] Dawn H. Nagel,et al. The B73 Maize Genome: Complexity, Diversity, and Dynamics , 2009, Science.
[33] Mark D. Robinson,et al. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data , 2009, Bioinform..
[34] Hadley Wickham,et al. ggplot2 - Elegant Graphics for Data Analysis (2nd Edition) , 2017 .
[35] Widodo,et al. Metabolic responses to salt stress of barley (Hordeum vulgare L.) cultivars, Sahara and Clipper, which differ in salinity tolerance , 2009, Journal of experimental botany.
[36] Mihaela M. Martis,et al. The Sorghum bicolor genome and the diversification of grasses , 2009, Nature.
[37] K. Kosová,et al. Expression of dehydrin 5 during the development of frost tolerance in barley (Hordeum vulgare). , 2008, Journal of plant physiology.
[38] Daniel L. Mace,et al. Cell Identity Mediates the Response of Arabidopsis Roots to Abiotic Stress , 2008, Science.
[39] M. Tester,et al. Mechanisms of salinity tolerance. , 2008, Annual review of plant biology.
[40] Daniel L. Mace,et al. A High-Resolution Root Spatiotemporal Map Reveals Dominant Expression Patterns , 2007, Science.
[41] V. Lumbreras,et al. Overexpression of wheat dehydrin DHN-5 enhances tolerance to salt and osmotic stress in Arabidopsis thaliana , 2007, Plant Cell Reports.
[42] David W Mount,et al. Using the Basic Local Alignment Search Tool (BLAST). , 2007, CSH protocols.
[43] Yiyue Zhang,et al. SDIR1 Is a RING Finger E3 Ligase That Positively Regulates Stress-Responsive Abscisic Acid Signaling in Arabidopsis[W] , 2007, The Plant Cell Online.
[44] Keith Bradnam,et al. CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes , 2007, Bioinform..
[45] Z. Fei,et al. Identification of early salt stress response genes in tomato root by suppression subtractive hybridization and microarray analysis. , 2007, Journal of experimental botany.
[46] John A. Hamilton,et al. The TIGR Rice Genome Annotation Resource: improvements and new features , 2006, Nucleic Acids Res..
[47] A. Harfouche,et al. The Arabidopsis Tetratricopeptide Repeat-Containing Protein TTL1 Is Required for Osmotic Stress Responses and Abscisic Acid Sensitivity1[W] , 2006, Plant Physiology.
[48] M. Gribskov,et al. The Genome of Black Cottonwood, Populus trichocarpa (Torr. & Gray) , 2006, Science.
[49] Shuhei Yamamoto,et al. Abscisic acid-activated SNRK2 protein kinases function in the gene-regulation pathway of ABA signal transduction by phosphorylating ABA response element-binding factors. , 2005, The Plant journal : for cell and molecular biology.
[50] Frédérique Bitton,et al. Genome-wide expression profiling of the host response to root-knot nematode infection in Arabidopsis. , 2005, The Plant journal : for cell and molecular biology.
[51] T. Koshiba,et al. A novel rice PR10 protein, RSOsPR10, specifically induced in roots by biotic and abiotic stresses, possibly via the jasmonic acid signaling pathway. , 2004, Plant & cell physiology.
[52] M. Sauer,et al. Genetic dissection of root formation in maize (Zea mays) reveals root-type specific developmental programmes. , 2004, Annals of botany.
[53] F. Menting,et al. Chapter 12 – Diversity in ex situ genebank collections of barley , 2003 .
[54] P. Langridge,et al. Mapping and QTL analysis of the barley population Clipper × Sahara , 2003 .
[55] P. A. Davies,et al. Mapping and QTL analysis of the barley population Amagi Nijo × WI2585 , 2003 .
[56] D. Shasha,et al. A Gene Expression Map of the Arabidopsis Root , 2003, Science.
[57] Mario Stanke,et al. Gene prediction with a hidden Markov model and a new intron submodel , 2003, ECCB.
[58] A. Miyao,et al. Three Distinct Rice Cellulose Synthase Catalytic Subunit Genes Required for Cellulose Synthesis in the Secondary Wall1 , 2003, Plant Physiology.
[59] Ulrich Schurr,et al. Expansion dynamics, metabolite composition and substance transfer of the primary root growth zone of Zea mays L. grown in different external nutrient availabilities , 2003 .
[60] J. Delcour,et al. TAXI type endoxylanase inhibitors in different cereals. , 2003, Journal of agricultural and food chemistry.
[61] V. Sharma,et al. Ectopic Expression of BABY BOOM Triggers a Conversion from Vegetative to Embryonic Growth Article, publication date, and citation information can be found at www.plantcell.org/cgi/doi/10.1105/tpc.001941. , 2002, The Plant Cell Online.
[62] W. J. Kent,et al. BLAT--the BLAST-like alignment tool. , 2002, Genome research.
[63] P. Proost,et al. Isolation and characterization of a jacalin-related mannose-binding lectin from salt-stressed rice (Oryza sativa) plants , 2000, Planta.
[64] C. Kim,et al. The Arabidopsis thaliana SOS2 gene encodes a protein kinase that is required for salt tolerance. , 2000, Proceedings of the National Academy of Sciences of the United States of America.
[65] Edward P. Glenn,et al. Salt Tolerance and Crop Potential of Halophytes , 1999 .
[66] M. Evans,et al. Specialized Zones of Development in Roots , 1995, Plant physiology.
[67] N. Raikhel,et al. Lectins, lectin genes, and their role in plant defense. , 1991, The Plant cell.
[68] C. Pikaard,et al. Molecular characterization of the patatin multigene family of potato. , 1988, Gene.
[69] E. Maas,et al. CROP SALT TOLERANCE–CURRENT ASSESSMENT , 1977 .
[70] Yutaka Sato,et al. Genome-wide transcriptome dissection of the rice root system: implications for developmental and physiological functions. , 2012, The Plant journal : for cell and molecular biology.
[71] Ute Baumann,et al. Root-specific transcript profiling of contrasting rice genotypes in response to salinity stress. , 2011, Molecular plant.