A KBase case study on genome-wide transcriptomics and plant primary metabolism in response to drought stress in Sorghum.

Jenks, 2013 Ramiro, 2016, Expression of arabidopsis bax inhibitor-1 in transgenic sugarcane confers drought tolerance, Plant Biotechnol. J., 14, 1826, 10.1111/pbi.12540 Munemasa, 2015, Mechanisms of abscisic acid-mediated control of stomatal aperture, Curr. Opin. Plant Biol., 28, 154, 10.1016/j.pbi.2015.10.010 Tuteja, 2007, Abscisic acid and abiotic stress signaling, Plant Signal. Behav., 2, 135, 10.4161/psb.2.3.4156 Shinozaki, 2007, Gene networks involved in drought stress response and tolerance, J. Exp. Bot., 58, 221, 10.1093/jxb/erl164 Bohra, 2020, Genomic interventions for sustainable agriculture, Plant Biotechnol. J., 18, 2388, 10.1111/pbi.13472 Arkin, 2018, KBase: The United States department of energy systems biology knowledgebase, Nat. Biotechnol., 36, 566, 10.1038/nbt.4163 Aglawe, 2012, Quantitative RT-PCR analysis of 20 transcription factor genes of MADS, ARF, HAP2, MBF and HB families in moisture stressed shoot and root tissues of sorghum, Physiol. Mol. Biol. Plants., 18, 287, 10.1007/s12298-012-0135-5 Paterson, 2009, The Sorghum bicolor genome and the diversification of grasses, Nature, 457, 551, 10.1038/nature07723 McCormick, 2018, The Sorghum bicolor reference genome: improved assembly, gene annotations, a transcriptome atlas, and signatures of genome organization, Plant J., 93, 338, 10.1111/tpj.13781 Wang, 2019, Reviving the transcriptome studies: an insight into the emergence of single-molecule transcriptome sequencing, Front. Genet., 10, 384, 10.3389/fgene.2019.00384 Paterson, 2009, The Sorghum bicolor genome and the diversification of grasses, Nature, 457, 551, 10.1038/nature07723 Cooper, 2019, A new reference genome for Sorghum bicolor reveals high levels of sequence similarity between sweet and grain genotypes: implications for the genetics of sugar metabolism, BMC Genom., 20, 420, 10.1186/s12864-019-5734-x Deschamps, 2018, A chromosome-scale assembly of the sorghum genome using nanopore sequencing and optical mapping, Nat. Commun., 9, 4844, 10.1038/s41467-018-07271-1 Gelli, 2014, Identification of differentially expressed genes between sorghum genotypes with contrasting nitrogen stress tolerance by genome-wide transcriptional profiling, BMC Genom., 15, 179, 10.1186/1471-2164-15-179 Dugas, 2011, Functional annotation of the transcriptome of Sorghum bicolor in response to osmotic stress and abscisic acid, BMC Genom., 12, 514, 10.1186/1471-2164-12-514 Varoquaux, 2019, Transcriptomic analysis of field-droughted sorghum from seedling to maturity reveals biotic and metabolic responses, Proc. Natl. Acad. Sci. USA, 116, 27124, 10.1073/pnas.1907500116 Ogden, 2020, Distinct preflowering drought tolerance strategies of Sorghum bicolor genotype RTx430 revealed by subcellular protein profiling, Int. J. Mol. Sci., 21, 10.3390/ijms21249706 Emms, 2015, OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy, Genome Biol., 16, 157, 10.1186/s13059-015-0721-2 S. Andrews et al., FastQC: a quality control tool for high throughput sequence data. (2017). 2010. Bolger, 2014, Trimmomatic: a flexible trimmer for Illumina sequence data, Bioinformatics, 30, 2114, 10.1093/bioinformatics/btu170 Martin, 2011, Cutadapt removes adapter sequences from high-throughput sequencing reads, EMBnet J., 17, 10, 10.14806/ej.17.1.200 Trapnell, 2012, Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks, Nat. Protoc., 7, 562, 10.1038/nprot.2012.016 Pertea, 2016, Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown, Nat. Protoc., 11, 1650, 10.1038/nprot.2016.095 Kim, 2015, HISAT: a fast spliced aligner with low memory requirements, Nat. Methods, 12, 357, 10.1038/nmeth.3317 Kim, 2019, Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype, Nat. Biotechnol., 37, 907, 10.1038/s41587-019-0201-4 Pertea, 2015, StringTie enables improved reconstruction of a transcriptome from RNA-seq reads, Nat. Biotechnol., 33, 290, 10.1038/nbt.3122 Anders, 2010, Differential expression analysis for sequence count data, Genome Biol., 11, 106, 10.1186/gb-2010-11-10-r106 Love, 2013 Love, 2014, Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2, Genome Biol., 15, 550, 10.1186/s13059-014-0550-8 Seaver, 2018, PlantSEED enables automated annotation and reconstruction of plant primary metabolism with improved compartmentalization and comparative consistency, Plant J., 95, 1102, 10.1111/tpj.14003 King, 2015, Escher: a web application for building, sharing, and embedding data-rich visualizations of biological pathways, PLOS Comput. Biol., 11, 10.1371/journal.pcbi.1004321 Okonechnikov, 2016, Qualimap 2: advanced multi-sample quality control for high-throughput sequencing data, Bioinformatics, 32, 292, 10.1093/bioinformatics/btv566 Seaver, 2015, Improved evidence-based genome-scale metabolic models for maize leaf, embryo, and endosperm, Front. Plant Sci., 6, 142, 10.3389/fpls.2015.00142 Buels, 2016, JBrowse: a dynamic web platform for genome visualization and analysis, Genome Biol., 17, 66, 10.1186/s13059-016-0924-1 Thorvaldsdottir, 2013, Integrative genomics viewer (IGV): high-performance genomics data visualization and exploration, Brief. Bioinform., 14, 178, 10.1093/bib/bbs017 Kavi Kishor, 1995, Overexpression of delta 1-pyrroline-5-carboxylate synthetase increases proline production and confers osmotolerance in transgenic plants, Plant Physiol., 108, 1387, 10.1104/pp.108.4.1387 Yoshiba, 1997, Regulation of levels of proline as an osmolyte in plants under water stress, Plant Cell Physiol., 38, 1095, 10.1093/oxfordjournals.pcp.a029093 Muzammil, 2018, An ancestral allele of pyrroline-5-carboxylate synthase1 promotes proline accumulation and drought adaptation in cultivated barley, Plant Physiol., 178, 771, 10.1104/pp.18.00169 Turchetto-Zolet, 2009, The evolution of pyrroline-5-carboxylate synthase in plants: a key enzyme in proline synthesis, Mol. Genet. Genom., 281, 87, 10.1007/s00438-008-0396-4 Strizhov, 1997, Differential expression of two P5CS genes controlling proline accumulation during salt‐stress requires ABA and is regulated by ABA1, ABI1 and AXR2 in Arabidopsis, Plant J., 12, 557, 10.1046/j.1365-313X.1997.00537.x Wyman, 2015, Lignin bioproducts to enable biofuels, Biofuels Bioprod. Biorefin., 9, 447, 10.1002/bbb.1582 Yan, 2018, Increased drought tolerance in plants engineered for low lignin and low xylan content, Biotechnol. Biofuels, 11, 195, 10.1186/s13068-018-1196-7 Bang, 2019, Overexpression of OsTF1L, a rice HD-Zip transcription factor, promotes lignin biosynthesis and stomatal closure that improves drought tolerance, Plant Biotechnol. J., 17, 118, 10.1111/pbi.12951 Geng, 2020, Regulation of phenylpropanoid biosynthesis by MdMYB88 and MdMYB124 contributes to pathogen and drought resistance in apple, Hortic Res., 7, 102, 10.1038/s41438-020-0324-2 Xu, 2020, SiMYB56 confers drought stress tolerance in transgenic rice by regulating lignin biosynthesis and ABA signaling pathway, Front. Plant Sci., 11, 785, 10.3389/fpls.2020.00785 Yan, 2021, MeRAV5 promotes drought stress resistance in cassava by modulating hydrogen peroxide and lignin accumulation, Plant J., 107, 847, 10.1111/tpj.15350 Vanholme, 2019, Lignin biosynthesis and its integration into metabolism, Curr. Opin. Biotechnol., 56, 230, 10.1016/j.copbio.2019.02.018 Barros, 2016, Role of bifunctional ammonia-lyase in grass cell wall biosynthesis, Nat. Plants, 2, 16050, 10.1038/nplants.2016.50 Barros, 2020, Plant phenylalanine/tyrosine ammonia-lyases, Trends Plant Sci., 25, 66, 10.1016/j.tplants.2019.09.011 Saito, 1976, Biosynthesis of stizolobinic acid and stizolobic acid in higher plants. An enzyme system(s) catalyzing the conversion of dihydroxyphenylalanine into stizolobinic acid and stizolobic acid from etiolated seedlings of Stizolobium hassjoo, Eur. J. Biochem., 68, 237, 10.1111/j.1432-1033.1976.tb10783.x Kasei, 2021, Comparative analysis of the extradiol ring-cleavage dioxygenase LigB from arabidopsis and 3,4-dihydroxyphenylalanine dioxygenase from betalain-producing plants, Plant Cell Physiol., 62, 732, 10.1093/pcp/pcab031 Xie, 2018, Regulation of lignin biosynthesis and its role in growth-defense tradeoffs, Front. Plant Sci., 9, 1427, 10.3389/fpls.2018.01427 Durbin, 1995, Evolution of the chalcone synthase gene family in the genus Ipomoea, Proc. Natl. Acad. Sci. USA, 92, 3338, 10.1073/pnas.92.8.3338 Burbulis, 1996, A null mutation in the first enzyme of flavonoid biosynthesis does not affect male fertility in Arabidopsis, Plant Cell, 8, 1013 Anguraj Vadivel, 2018, Genome-wide identification and localization of chalcone synthase family in soybean (Glycine max [L]Merr), BMC Plant Biol., 18, 325, 10.1186/s12870-018-1569-x Zhou, 2013, Chalcone synthase family genes have redundant roles in anthocyanin biosynthesis and in response to blue/UV-A light in turnip (Brassica rapa; Brassicaceae), Am. J. Bot., 100, 2458, 10.3732/ajb.1300305 Dao, 2011, Chalcone synthase and its functions in plant resistance, Phytochem. Rev., 10, 397, 10.1007/s11101-011-9211-7 Li, 2010, The growth reduction associated with repressed lignin biosynthesis in Arabidopsis thaliana is independent of flavonoids, Plant Cell, 22, 1620, 10.1105/tpc.110.074161 Zuk, 2016, Chalcone synthase (CHS) gene suppression in flax leads to changes in wall synthesis and sensing genes, cell wall chemistry and stem morphology parameters, Front. Plant Sci., 7, 894, 10.3389/fpls.2016.00894 Eloy, 2017, Silencing chalcone synthase in maize impedes the incorporation of tricin into lignin and increases lignin content, Plant Physiol., 173, 998, 10.1104/pp.16.01108