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Fu J, McKinley B, James B, Chrisler W, Markillie LM, Gaffrey MJ, Mitchell HD, Riaz MR, Marcial B, Orr G, Swaminathan K, Mullet J, Marshall-Colon A. Cell-type-specific transcriptomics uncovers spatial regulatory networks in bioenergy sorghum stems. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:1668-1688. [PMID: 38407828 DOI: 10.1111/tpj.16690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 12/17/2023] [Accepted: 02/07/2024] [Indexed: 02/27/2024]
Abstract
Bioenergy sorghum is a low-input, drought-resilient, deep-rooting annual crop that has high biomass yield potential enabling the sustainable production of biofuels, biopower, and bioproducts. Bioenergy sorghum's 4-5 m stems account for ~80% of the harvested biomass. Stems accumulate high levels of sucrose that could be used to synthesize bioethanol and useful biopolymers if information about cell-type gene expression and regulation in stems was available to enable engineering. To obtain this information, laser capture microdissection was used to isolate and collect transcriptome profiles from five major cell types that are present in stems of the sweet sorghum Wray. Transcriptome analysis identified genes with cell-type-specific and cell-preferred expression patterns that reflect the distinct metabolic, transport, and regulatory functions of each cell type. Analysis of cell-type-specific gene regulatory networks (GRNs) revealed that unique transcription factor families contribute to distinct regulatory landscapes, where regulation is organized through various modes and identifiable network motifs. Cell-specific transcriptome data was combined with known secondary cell wall (SCW) networks to identify the GRNs that differentially activate SCW formation in vascular sclerenchyma and epidermal cells. The spatial transcriptomic dataset provides a valuable source of information about the function of different sorghum cell types and GRNs that will enable the engineering of bioenergy sorghum stems, and an interactive web application developed during this project will allow easy access and exploration of the data (https://mc-lab.shinyapps.io/lcm-dataset/).
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Affiliation(s)
- Jie Fu
- Department of Plant Biology, University of Illinois Urbana-Champaign, Urbana, Illinois, 61801, USA
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, Urbana, Illinois, 61801, USA
| | - Brian McKinley
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, 77843, USA
- DOE Great Lakes Bioenergy Resource Center, Madison, Wisconsin, 53726, USA
| | - Brandon James
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, Urbana, Illinois, 61801, USA
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, 35806, USA
| | - William Chrisler
- Pacific Northwest National Laboratory, Richland, Washington, 99354, USA
| | | | - Matthew J Gaffrey
- Pacific Northwest National Laboratory, Richland, Washington, 99354, USA
| | - Hugh D Mitchell
- Pacific Northwest National Laboratory, Richland, Washington, 99354, USA
| | - Muhammad Rizwan Riaz
- Department of Plant Biology, University of Illinois Urbana-Champaign, Urbana, Illinois, 61801, USA
| | - Brenda Marcial
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, Urbana, Illinois, 61801, USA
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, 35806, USA
| | - Galya Orr
- Pacific Northwest National Laboratory, Richland, Washington, 99354, USA
| | - Kankshita Swaminathan
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, Urbana, Illinois, 61801, USA
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, 35806, USA
| | - John Mullet
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, 77843, USA
- DOE Great Lakes Bioenergy Resource Center, Madison, Wisconsin, 53726, USA
| | - Amy Marshall-Colon
- Department of Plant Biology, University of Illinois Urbana-Champaign, Urbana, Illinois, 61801, USA
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, Urbana, Illinois, 61801, USA
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Hu Z, Chen J, Olatoye MO, Zhang H, Lin Z. Transcriptome-wide expression landscape and starch synthesis pathway co-expression network in sorghum. THE PLANT GENOME 2024:e20448. [PMID: 38602082 DOI: 10.1002/tpg2.20448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2024]
Abstract
The gene expression landscape across different tissues and developmental stages reflects their biological functions and evolutionary patterns. Integrative and comprehensive analyses of all transcriptomic data in an organism are instrumental to obtaining a comprehensive picture of gene expression landscape. Such studies are still very limited in sorghum, which limits the discovery of the genetic basis underlying complex agricultural traits in sorghum. We characterized the genome-wide expression landscape for sorghum using 873 RNA-sequencing (RNA-seq) datasets representing 19 tissues. Our integrative analysis of these RNA-seq data provides the most comprehensive transcriptomic atlas for sorghum, which will be valuable for the sorghum research community for functional characterizations of sorghum genes. Based on the transcriptome atlas, we identified 595 housekeeping genes (HKGs) and 2080 tissue-specific expression genes (TEGs) for the 19 tissues. We identified different gene features between HKGs and TEGs, and we found that HKGs have experienced stronger selective constraints than TEGs. Furthermore, we built a transcriptome-wide co-expression network (TW-CEN) comprising 35 modules with each module enriched in specific Gene Ontology terms. High-connectivity genes in TW-CEN tend to express at high levels while undergoing intensive selective pressure. We also built global and seed-preferential co-expression networks of starch synthesis pathways, which indicated that photosynthesis and microtubule-based movement play important roles in starch synthesis. The global transcriptome atlas of sorghum generated by this study provides an important functional genomics resource for trait discovery and insight into starch synthesis regulation in sorghum.
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Affiliation(s)
- Zhenbin Hu
- Department of Biology, Saint Louis University, Saint Louis, Missouri, USA
| | - Junhao Chen
- Department of Biology, Saint Louis University, Saint Louis, Missouri, USA
| | - Marcus O Olatoye
- USDA-ARS, Forage Seed and Cereal Research Unit, Prosser, Washington, USA
| | - Hengyou Zhang
- State Key Laboratory of Black Soils Conservation and Utilization, Key Laboratory of Soybean Molecular Design and Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - Zhenguo Lin
- Department of Biology, Saint Louis University, Saint Louis, Missouri, USA
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Costes C, Navarro Sanz S, Calatayud C, Soriano A, Mameri H, Terrier N, Francin-Allami M. Transcriptomic analysis of developing sorghum grains to detect genes related to cell wall biosynthesis and remodelling. BMC Genom Data 2024; 25:14. [PMID: 38321382 PMCID: PMC10848504 DOI: 10.1186/s12863-024-01198-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 01/24/2024] [Indexed: 02/08/2024] Open
Abstract
OBJECTIVE Sorghum (Sorghum bicolor (L.) Moench) is the fifth most important grain produced in the world. Interest for cultivating sorghum is increasing all over the world in the context of climate change, due to its low input and water requirements. Like other cultivated cereals, sorghum has significant nutritional value thanks to its protein, carbohydrate and dietary fiber content, these latter mainly consisting of cell wall polysaccharides. This work describes for the first time a transcriptomic analysis dedicated to identify the genes involved in the biosynthesis and remodelling of cell walls both in the endosperm and outer layers of sorghum grain during its development. Further analysis of these transcriptomic data will improve our understanding of cell wall assembly, which is a key component of grain quality. DATA DESCRIPTION This research delineates the steps of our analysis, starting with the cultivation conditions and the grain harvest at different stages of development, followed by the laser microdissection applied to separate the endosperm from the outer layers. It also describes the procedures implemented to generate RNA libraries and to obtain a normalized and filtered table of transcript counts, and finally determine the number of putative cell wall-related genes already listed in literature.
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Affiliation(s)
| | - Sergi Navarro Sanz
- CIRAD, UMR AGAP Institut, 34398, Montpellier, France
- CIRAD, INRAE, UMR AGAP Institut, Univ Montpellier, Institut Agro, Montpellier, France
- Montpellier Ressources Imagerie, BioCampus, University of Montpellier, CNRS, INSERM, Montpellier, France
| | - Caroline Calatayud
- CIRAD, UMR AGAP Institut, 34398, Montpellier, France
- CIRAD, INRAE, UMR AGAP Institut, Univ Montpellier, Institut Agro, Montpellier, France
| | - Alexandre Soriano
- CIRAD, UMR AGAP Institut, 34398, Montpellier, France
- CIRAD, INRAE, UMR AGAP Institut, Univ Montpellier, Institut Agro, Montpellier, France
| | - Hamza Mameri
- UMR IATE, Univ Montpellier, INRAE, Institut-Agro Montpellier, 34060, Montpellier, France
| | - Nancy Terrier
- CIRAD, INRAE, UMR AGAP Institut, Univ Montpellier, Institut Agro, Montpellier, France.
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4
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Khasin M, Bernhardson LF, O'Neill PM, Palmer NA, Scully ED, Sattler SE, Sarath G, Funnell-Harris DL. Phenylpropanoids Following Wounding and Infection of Sweet Sorghum Lines Differing in Responses to Stalk Pathogens. PHYTOPATHOLOGY 2024; 114:177-192. [PMID: 37486162 DOI: 10.1094/phyto-12-22-0459-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/25/2023]
Abstract
Sweet sorghum (Sorghum bicolor) lines M81-E and Colman were previously shown to differ in responses to Fusarium thapsinum and Macrophomina phaseolina, stalk rot pathogens that can reduce the yields and quality of biomass and extracted sugars. Inoculated tissues were compared for transcriptomic, phenolic metabolite, and enzymatic activity during disease development 3 and 13 days after inoculation (DAI). At 13 DAI, M81-E had shorter mean lesion lengths than Colman when inoculated with either pathogen. Transcripts encoding monolignol biosynthetic and modification enzymes were associated with transcriptional wound (control) responses of both lines at 3 DAI. Monolignol biosynthetic genes were differentially coexpressed with transcriptional activator SbMyb76 in all Colman inoculations, but only following M. phaseolina inoculation in M81-E, suggesting that SbMyb76 is associated with lignin biosynthesis during pathogen responses. In control inoculations, defense-related genes were expressed at higher levels in M81-E than Colman. Line, treatment, and timepoint differences observed in phenolic metabolite and enzyme activities did not account for observed differences in lesions. However, generalized additive models were able to relate metabolites, but not enzyme activities, to lesion length for quantitatively modeling disease progression: in M81-E, but not Colman, sinapic acid levels positively predicted lesion length at 3 DAI when cell wall-bound syringic acid was low, soluble caffeic acid was high, and lactic acid was high, suggesting that sinapic acid may contribute to responses at 3 DAI. These results provide potential gene targets for development of sweet sorghum varieties with increased stalk rot resistance to ensure biomass and sugar quality.
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Affiliation(s)
- Maya Khasin
- Wheat, Sorghum, and Forage Research Unit, U.S. Department of Agriculture-Agricultural Research Service, Lincoln, NE 68583
- Department of Plant Pathology, University of Nebraska, Lincoln, NE 68583
| | - Lois F Bernhardson
- Wheat, Sorghum, and Forage Research Unit, U.S. Department of Agriculture-Agricultural Research Service, Lincoln, NE 68583
- Department of Plant Pathology, University of Nebraska, Lincoln, NE 68583
| | - Patrick M O'Neill
- Wheat, Sorghum, and Forage Research Unit, U.S. Department of Agriculture-Agricultural Research Service, Lincoln, NE 68583
- Department of Plant Pathology, University of Nebraska, Lincoln, NE 68583
| | - Nathan A Palmer
- Wheat, Sorghum, and Forage Research Unit, U.S. Department of Agriculture-Agricultural Research Service, Lincoln, NE 68583
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE 68583
| | - Erin D Scully
- Stored Product Insect and Engineering Research Unit, U.S. Department of Agriculture-Agricultural Research Service Center for Grain and Animal Health Research, Manhattan, KS 66502
| | - Scott E Sattler
- Wheat, Sorghum, and Forage Research Unit, U.S. Department of Agriculture-Agricultural Research Service, Lincoln, NE 68583
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE 68583
| | - Gautam Sarath
- Wheat, Sorghum, and Forage Research Unit, U.S. Department of Agriculture-Agricultural Research Service, Lincoln, NE 68583
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE 68583
| | - Deanna L Funnell-Harris
- Wheat, Sorghum, and Forage Research Unit, U.S. Department of Agriculture-Agricultural Research Service, Lincoln, NE 68583
- Department of Plant Pathology, University of Nebraska, Lincoln, NE 68583
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Chemelewski R, McKinley BA, Finlayson S, Mullet JE. Epicuticular wax accumulation and regulation of wax pathway gene expression during bioenergy Sorghum stem development. FRONTIERS IN PLANT SCIENCE 2023; 14:1227859. [PMID: 37936930 PMCID: PMC10626490 DOI: 10.3389/fpls.2023.1227859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 09/11/2023] [Indexed: 11/09/2023]
Abstract
Bioenergy sorghum is a drought-tolerant high-biomass C4 grass targeted for production on annual cropland marginal for food crops due primarily to abiotic constraints. To better understand the overall contribution of stem wax to bioenergy sorghum's resilience, the current study characterized sorghum stem cuticular wax loads, composition, morphometrics, wax pathway gene expression and regulation using vegetative phase Wray, R07020, and TX08001 genotypes. Wax loads on sorghum stems (~103-215 µg/cm2) were much higher than Arabidopsis stem and leaf wax loads. Wax on developing sorghum stem internodes was enriched in C28/30 primary alcohols (~65%) while stem wax on fully developed stems was enriched in C28/30 aldehydes (~80%). Scanning Electron Microscopy showed minimal wax on internodes prior to the onset of elongation and that wax tubules first appear associated with cork-silica cell complexes when internode cell elongation is complete. Sorghum homologs of genes involved in wax biosynthesis/transport were differentially expressed in the stem epidermis. Expression of many wax pathway genes (i.e., SbKCS6, SbCER3-1, SbWSD1, SbABCG12, SbABCG11) is low in immature apical internodes then increases at the onset of stem wax accumulation. SbCER4 is expressed relatively early in stem development consistent with accumulation of C28/30 primary alcohols on developing apical internodes. High expression of two SbCER3 homologs in fully elongated internodes is consistent with a role in production of C28/30 aldehydes. Gene regulatory network analysis aided the identification of sorghum homologs of transcription factors that regulate wax biosynthesis (i.e., SbSHN1, SbWRI1/3, SbMYB94/96/30/60, MYS1) and other transcription factors that could regulate and specify expression of the wax pathway in epidermal cells during cuticle development.
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Affiliation(s)
- Robert Chemelewski
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, TX, United States
| | - Brian A. McKinley
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, TX, United States
| | - Scott Finlayson
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, United States
| | - John E. Mullet
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, TX, United States
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6
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Yang L, Zhou Q, Sheng X, Chen X, Hua Y, Lin S, Luo Q, Yu B, Shao T, Wu Y, Chang J, Li Y, Tu M. Harnessing the Genetic Basis of Sorghum Biomass-Related Traits to Facilitate Bioenergy Applications. Int J Mol Sci 2023; 24:14549. [PMID: 37833996 PMCID: PMC10573072 DOI: 10.3390/ijms241914549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 09/18/2023] [Accepted: 09/21/2023] [Indexed: 10/15/2023] Open
Abstract
The extensive use of fossil fuels and global climate change have raised ever-increasing attention to sustainable development, global food security and the replacement of fossil fuels by renewable energy. Several C4 monocot grasses have excellent photosynthetic ability, stress tolerance and may rapidly produce biomass in marginal lands with low agronomic inputs, thus representing an important source of bioenergy. Among these grasses, Sorghum bicolor has been recognized as not only a promising bioenergy crop but also a research model due to its diploidy, simple genome, genetic diversity and clear orthologous relationship with other grass genomes, allowing sorghum research to be easily translated to other grasses. Although sorghum molecular genetic studies have lagged far behind those of major crops (e.g., rice and maize), recent advances have been made in a number of biomass-related traits to dissect the genetic loci and candidate genes, and to discover the functions of key genes. However, molecular and/or targeted breeding toward biomass-related traits in sorghum have not fully benefited from these pieces of genetic knowledge. Thus, to facilitate the breeding and bioenergy applications of sorghum, this perspective summarizes the bioenergy applications of different types of sorghum and outlines the genetic control of the biomass-related traits, ranging from flowering/maturity, plant height, internode morphological traits and metabolic compositions. In particular, we describe the dynamic changes of carbohydrate metabolism in sorghum internodes and highlight the molecular regulators involved in the different stages of internode carbohydrate metabolism, which affects the bioenergy utilization of sorghum biomass. We argue the way forward is to further enhance our understanding of the genetic mechanisms of these biomass-related traits with new technologies, which will lead to future directions toward tailored designing sorghum biomass traits suitable for different bioenergy applications.
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Affiliation(s)
- Lin Yang
- School of Chemical and Environmental Engineering, Wuhan Polytechnic University, Wuhan 430023, China (Y.W.)
| | - Qin Zhou
- School of Chemical and Environmental Engineering, Wuhan Polytechnic University, Wuhan 430023, China (Y.W.)
| | - Xuan Sheng
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan 430023, China
| | - Xiangqian Chen
- School of Chemical and Environmental Engineering, Wuhan Polytechnic University, Wuhan 430023, China (Y.W.)
| | - Yuqing Hua
- School of Chemical and Environmental Engineering, Wuhan Polytechnic University, Wuhan 430023, China (Y.W.)
| | - Shuang Lin
- School of Chemical and Environmental Engineering, Wuhan Polytechnic University, Wuhan 430023, China (Y.W.)
| | - Qiyun Luo
- School of Chemical and Environmental Engineering, Wuhan Polytechnic University, Wuhan 430023, China (Y.W.)
| | - Boju Yu
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, The Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science & Technology, Wuhan 430074, China; (B.Y.); (T.S.); (J.C.)
| | - Ti Shao
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, The Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science & Technology, Wuhan 430074, China; (B.Y.); (T.S.); (J.C.)
| | - Yixiao Wu
- School of Chemical and Environmental Engineering, Wuhan Polytechnic University, Wuhan 430023, China (Y.W.)
| | - Junli Chang
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, The Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science & Technology, Wuhan 430074, China; (B.Y.); (T.S.); (J.C.)
| | - Yin Li
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, The Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science & Technology, Wuhan 430074, China; (B.Y.); (T.S.); (J.C.)
| | - Min Tu
- School of Chemical and Environmental Engineering, Wuhan Polytechnic University, Wuhan 430023, China (Y.W.)
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7
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Tu M, Zeng J, Zhang J, Fan G, Song G. Unleashing the power within short-read RNA-seq for plant research: Beyond differential expression analysis and toward regulomics. FRONTIERS IN PLANT SCIENCE 2022; 13:1038109. [PMID: 36570898 PMCID: PMC9773216 DOI: 10.3389/fpls.2022.1038109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 11/21/2022] [Indexed: 06/17/2023]
Abstract
RNA-seq has become a state-of-the-art technique for transcriptomic studies. Advances in both RNA-seq techniques and the corresponding analysis tools and pipelines have unprecedently shaped our understanding in almost every aspects of plant sciences. Notably, the integration of huge amount of RNA-seq with other omic data sets in the model plants and major crop species have facilitated plant regulomics, while the RNA-seq analysis has still been primarily used for differential expression analysis in many less-studied plant species. To unleash the analytical power of RNA-seq in plant species, especially less-studied species and biomass crops, we summarize recent achievements of RNA-seq analysis in the major plant species and representative tools in the four types of application: (1) transcriptome assembly, (2) construction of expression atlas, (3) network analysis, and (4) structural alteration. We emphasize the importance of expression atlas, coexpression networks and predictions of gene regulatory relationships in moving plant transcriptomes toward regulomics, an omic view of genome-wide transcription regulation. We highlight what can be achieved in plant research with RNA-seq by introducing a list of representative RNA-seq analysis tools and resources that are developed for certain minor species or suitable for the analysis without species limitation. In summary, we provide an updated digest on RNA-seq tools, resources and the diverse applications for plant research, and our perspective on the power and challenges of short-read RNA-seq analysis from a regulomic point view. A full utilization of these fruitful RNA-seq resources will promote plant omic research to a higher level, especially in those less studied species.
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Affiliation(s)
- Min Tu
- School of Chemical and Environmental Engineering, Wuhan Polytechnic University, Wuhan, China
| | - Jian Zeng
- Guangdong Provincial Key Laboratory of Utilization and Conservation of Food and Medicinal Resources in Northern Region, Shaoguan University, Shaoguan, Guangdong, China
| | - Juntao Zhang
- School of Chemical and Environmental Engineering, Wuhan Polytechnic University, Wuhan, China
| | - Guozhi Fan
- School of Chemical and Environmental Engineering, Wuhan Polytechnic University, Wuhan, China
| | - Guangsen Song
- School of Chemical and Environmental Engineering, Wuhan Polytechnic University, Wuhan, China
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8
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Ferreira SS, Goeminne G, Simões MS, Pina AVDA, Lima LGAD, Pezard J, Gutiérrez A, Rencoret J, Mortimer JC, Del Río JC, Boerjan W, Cesarino I. Transcriptional and metabolic changes associated with internode development and reduced cinnamyl alcohol dehydrogenase activity in sorghum. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:6307-6333. [PMID: 35788296 DOI: 10.1093/jxb/erac300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 07/04/2022] [Indexed: 06/15/2023]
Abstract
The molecular mechanisms associated with secondary cell wall (SCW) deposition in sorghum remain largely uncharacterized. Here, we employed untargeted metabolomics and large-scale transcriptomics to correlate changes in SCW deposition with variation in global gene expression profiles and metabolite abundance along an elongating internode of sorghum, with a major focus on lignin and phenolic metabolism. To gain deeper insight into the metabolic and transcriptional changes associated with pathway perturbations, a bmr6 mutant [with reduced cinnamyl alcohol dehydrogenase (CAD) activity] was analyzed. In the wild type, internode development was accompanied by an increase in the content of oligolignols, p-hydroxybenzaldehyde, hydroxycinnamate esters, and flavonoid glucosides, including tricin derivatives. We further identified modules of genes whose expression pattern correlated with SCW deposition and the accumulation of these target metabolites. Reduced CAD activity resulted in the accumulation of hexosylated forms of hydroxycinnamates (and their derivatives), hydroxycinnamaldehydes, and benzenoids. The expression of genes belonging to one specific module in our co-expression analysis correlated with the differential accumulation of these compounds and contributed to explaining this metabolic phenotype. Metabolomics and transcriptomics data further suggested that CAD perturbation activates distinct detoxification routes in sorghum internodes. Our systems biology approach provides a landscape of the metabolic and transcriptional changes associated with internode development and with reduced CAD activity in sorghum.
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Affiliation(s)
- Sávio Siqueira Ferreira
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, Rua do Matão, São Paulo, Brazil
| | - Geert Goeminne
- VIB Center for Plant Systems Biology, Ghent, Belgium
- VIB Metabolomics Core, Ghent, Belgium
| | - Marcella Siqueira Simões
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, Rua do Matão, São Paulo, Brazil
| | | | | | - Jade Pezard
- Joint BioEnergy Institute, Emeryville, CA, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Ana Gutiérrez
- Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), CSIC, Avenida de la Reina Mercedes, Seville, Spain
| | - Jorge Rencoret
- Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), CSIC, Avenida de la Reina Mercedes, Seville, Spain
| | - Jenny C Mortimer
- Joint BioEnergy Institute, Emeryville, CA, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - José C Del Río
- Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), CSIC, Avenida de la Reina Mercedes, Seville, Spain
| | - Wout Boerjan
- VIB Center for Plant Systems Biology, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Igor Cesarino
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, Rua do Matão, São Paulo, Brazil
- Synthetic and Systems Biology Center, InovaUSP, Avenida Professor Lucio Martins Rodrigues, São Paulo, Brazil
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9
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Zhou Y, Sukul A, Mishler-Elmore JW, Faik A, Held MA. PlantNexus: A Gene Co-expression Network Database and Visualization Tool for Barley and Sorghum. PLANT & CELL PHYSIOLOGY 2022; 63:565-572. [PMID: 35024864 PMCID: PMC9214644 DOI: 10.1093/pcp/pcac007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 01/03/2022] [Accepted: 01/10/2022] [Indexed: 06/14/2023]
Abstract
Global gene co-expression networks (GCNs) are powerful tools for functional genomics whereby putative functions and regulatory mechanisms can be inferred by gene co-expression. Cereal crops, such as Hordeum vulgare (barley) and Sorghum bicolor (sorghum), are among the most important plants to civilization. However, co-expression network tools for these plants are lacking. Here, we have constructed global GCNs for barley and sorghum using existing RNA-seq data sets. Meta-information was manually curated and categorized by tissue type to also build tissue-specific GCNs. To enable GCN searching and visualization, we implemented a website and database named PlantNexus. PlantNexus is freely available at https://plantnexus.ohio.edu/.
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Affiliation(s)
- Yadi Zhou
- Department of Chemistry and Biochemistry, Ohio University, Athens, OH 45701, USA
| | - Abhijit Sukul
- Department of Chemistry and Biochemistry, Ohio University, Athens, OH 45701, USA
| | | | - Ahmed Faik
- Department of Environmental and Plant Biology, Ohio University, Athens, OH 45701, USA
- Molecular and Cellular Biology Program, Ohio University, Athens, OH 45701, USA
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10
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Tu M, Li Y. Profiling Alternative 3' Untranslated Regions in Sorghum using RNA-seq Data. Front Genet 2020; 11:556749. [PMID: 33193635 PMCID: PMC7649775 DOI: 10.3389/fgene.2020.556749] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 09/30/2020] [Indexed: 12/18/2022] Open
Abstract
Sorghum is an important crop widely used for food, feed, and fuel. Transcriptome-wide studies of 3′ untranslated regions (3′UTR) using regular RNA-seq remain scarce in sorghum, while transcriptomes have been characterized extensively using Illumina short-read sequencing platforms for many sorghum varieties under various conditions or developmental contexts. 3′UTR is a critical regulatory component of genes, controlling the translation, transport, and stability of messenger RNAs. In the present study, we profiled the alternative 3′UTRs at the transcriptome level in three genetically related but phenotypically contrasting lines of sorghum: Rio, BTx406, and R9188. A total of 1,197 transcripts with alternative 3′UTRs were detected using RNA-seq data. Their categorization identified 612 high-confidence alternative 3′UTRs. Importantly, the high-confidence alternative 3′UTR genes significantly overlapped with the genesets that are associated with RNA N6-methyladenosine (m6A) modification, suggesting a clear indication between alternative 3′UTR and m6A methylation in sorghum. Moreover, taking advantage of sorghum genetics, we provided evidence of genotype specificity of alternative 3′UTR usage. In summary, our work exemplifies a transcriptome-wide profiling of alternative 3′UTRs using regular RNA-seq data in non-model crops and gains insights into alternative 3′UTRs and their genotype specificity.
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Affiliation(s)
- Min Tu
- Waksman Institute of Microbiology, Rutgers, The State University of New Jersey, Piscataway, NJ, United States
| | - Yin Li
- Waksman Institute of Microbiology, Rutgers, The State University of New Jersey, Piscataway, NJ, United States
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