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Franzoni G, Spadafora ND, Sirangelo TM, Ferrante A, Rogers HJ. Biochemical and molecular changes in peach fruit exposed to cold stress conditions. MOLECULAR HORTICULTURE 2023; 3:24. [PMID: 37953307 PMCID: PMC10641970 DOI: 10.1186/s43897-023-00073-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 10/26/2023] [Indexed: 11/14/2023]
Abstract
Storage or transportation temperature is very important for preserving the quality of fruit. However, low temperature in sensitive fruit such as peach can induce loss of quality. Fruit exposed to a specific range of temperatures and for a longer period can show chilling injury (CI) symptoms. The susceptibility to CI at low temperature varies among cultivars and genetic backgrounds. Along with agronomic management, appropriate postharvest management can limit quality losses. The importance of correct temperature management during postharvest handling has been widely demonstrated. Nowadays, due to long-distance markets and complex logistics that require multiple actors, the management of storage/transportation conditions is crucial for the quality of products reaching the consumer.Peach fruit exposed to low temperatures activate a suite of physiological, metabolomic, and molecular changes that attempt to counteract the negative effects of chilling stress. In this review an overview of the factors involved, and plant responses is presented and critically discussed. Physiological disorders associated with CI generally only appear after the storage/transportation, hence early detection methods are needed to monitor quality and detect internal changes which will lead to CI development. CI detection tools are assessed: they need to be easy to use, and preferably non-destructive to avoid loss of products.
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Affiliation(s)
- Giulia Franzoni
- Department of Agricultural and Environmental Sciences, University of Milan, Via Celoria 2, 20133, Milan, Italy
| | - Natasha Damiana Spadafora
- Department of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, 44121, Ferrara, Italy.
| | - Tiziana Maria Sirangelo
- ENEA-Italian National Agency for New Technologies, Energy and Sustainable Economic Development-Division Biotechnologies and Agroindustry, 00123, Rome, Italy
| | - Antonio Ferrante
- Department of Agricultural and Environmental Sciences, University of Milan, Via Celoria 2, 20133, Milan, Italy
| | - Hilary J Rogers
- School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff, CF10 3AX, UK
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2
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Paull RE, Ksouri N, Kantar M, Zerpa‐Catanho D, Chen NJ, Uruu G, Yue J, Guo S, Zheng Y, Wai CMJ, Ming R. Differential gene expression during floral transition in pineapple. PLANT DIRECT 2023; 7:e541. [PMID: 38028646 PMCID: PMC10644199 DOI: 10.1002/pld3.541] [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: 12/18/2022] [Revised: 09/20/2023] [Accepted: 09/26/2023] [Indexed: 12/01/2023]
Abstract
Pineapple (Ananas comosus var. comosus) and ornamental bromeliads are commercially induced to flower by treatment with ethylene or its analogs. The apex is transformed from a vegetative to a floral meristem and shows morphological changes in 8 to 10 days, with flowers developing 8 to 10 weeks later. During eight sampling stages ranging from 6 h to 8 days after treatment, 7961 genes were found to exhibit differential expression (DE) after the application of ethylene. In the first 3 days after treatment, there was little change in ethylene synthesis or in the early stages of the ethylene response. Subsequently, three ethylene response transcription factors (ERTF) were up-regulated and the potential gene targets were predicted to be the positive flowering regulator CONSTANS-like 3 (CO), a WUSCHEL gene, two APETALA1/FRUITFULL (AP1/FUL) genes, an epidermal patterning gene, and a jasmonic acid synthesis gene. We confirm that pineapple has lost the flowering repressor FLOWERING LOCUS C. At the initial stages, the SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (SOC1) was not significantly involved in this transition. Another WUSCHEL gene and a PHD homeobox transcription factor, though not apparent direct targets of ERTF, were up-regulated within a day of treatment, their predicted targets being the up-regulated CO, auxin response factors, SQUAMOSA, and histone H3 genes with suppression of abscisic acid response genes. The FLOWERING LOCUS T (FT), TERMINAL FLOWER (TFL), AGAMOUS-like APETELAR (AP2), and SEPETALA (SEP) increased rapidly within 2 to 3 days after ethylene treatment. Two FT genes were up-regulated at the apex and not at the leaf bases after treatment, suggesting that transport did not occur. These results indicated that the ethylene response in pineapple and possibly most bromeliads act directly to promote the vegetative to flower transition via APETALA1/FRUITFULL (AP1/FUL) and its interaction with SPL, FT, TFL, SEP, and AP2. A model based on AP2/ERTF DE and predicted DE target genes was developed to give focus to future research. The identified candidate genes are potential targets for genetic manipulation to determine their molecular role in flower transition.
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Affiliation(s)
- Robert E. Paull
- Tropical Plant & Soil SciencesUniversity of Hawaii at ManoaHonoluluHawaiiUSA
| | - Najla Ksouri
- Laboratory of Genomics, Genetics and Breeding of Fruits and Grapevine, Experimental Aula Dei‐CSICZaragozaSpain
| | - Michael Kantar
- Tropical Plant & Soil SciencesUniversity of Hawaii at ManoaHonoluluHawaiiUSA
| | | | - Nancy Jung Chen
- Tropical Plant & Soil SciencesUniversity of Hawaii at ManoaHonoluluHawaiiUSA
| | - Gail Uruu
- Tropical Plant & Soil SciencesUniversity of Hawaii at ManoaHonoluluHawaiiUSA
| | - Jingjing Yue
- Center for Genomics and BiotechnologyFujian Agriculture and Forestry UniversityFuzhouChina
| | - Shiyong Guo
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational MedicineKunming University of Science and TechnologyKunmingYunnanChina
| | - Yun Zheng
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational MedicineKunming University of Science and TechnologyKunmingYunnanChina
| | | | - Ray Ming
- Department of Plant BiologyUniversity of Illinois at Urbana‐ChampaignUrbanaIllinoisUSA
- Center for Genomics and BiotechnologyFujian Agriculture and Forestry UniversityFuzhouChina
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3
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Rodríguez Del Río Á, Monteagudo A, Contreras-Moreira B, Kiss T, Mayer M, Karsai I, Igartua E, Casas AM. Diversity of gene expression responses to light quality in barley. Sci Rep 2023; 13:17143. [PMID: 37816785 PMCID: PMC10564772 DOI: 10.1038/s41598-023-44263-8] [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: 01/06/2023] [Accepted: 10/05/2023] [Indexed: 10/12/2023] Open
Abstract
Light quality influence on barley development is poorly understood. We exposed three barley genotypes with either sensitive or insensitive response to two light sources producing different light spectra, fluorescent bulbs, and metal halide lamps, keeping constant light intensity, duration, and temperature. Through RNA-seq, we identified the main genes and pathways involved in the genotypic responses. A first analysis identified genotypic differences in gene expression of development-related genes, including photoreceptors and flowering time genes. Genes from the vernalization pathway of light quality-sensitive genotypes were affected by fluorescent light. In particular, vernalization-related repressors reacted differently: HvVRN2 did not experience relevant changes, whereas HvOS2 expression increased under fluorescent light. To identify the genes primarily related to light quality responses, and avoid the confounding effect of plant developmental stage, genes influenced by development were masked in a second analysis. Quantitative expression levels of PPD-H1, which influenced HvVRN1 and HvFT1, explained genotypic differences in development. Upstream mechanisms (light signaling and circadian clock) were also altered, but no specific genes linking photoreceptors and the photoperiod pathway were identified. The variety of light-quality sensitivities reveals the presence of possible mechanisms of adaptation of winter and facultative barley to latitudinal variation in light quality, which deserves further research.
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Affiliation(s)
- Álvaro Rodríguez Del Río
- Department of Genetics and Plant Breeding, Aula Dei Experimental Station, CSIC, Avda Montañana 1005, 50059, Zaragoza, Spain
- Centro de Biotecnología y Genómica de Plantas, UPM/INIA-CSIC, Madrid, Spain
| | - Arantxa Monteagudo
- Department of Genetics and Plant Breeding, Aula Dei Experimental Station, CSIC, Avda Montañana 1005, 50059, Zaragoza, Spain
| | - Bruno Contreras-Moreira
- Department of Genetics and Plant Breeding, Aula Dei Experimental Station, CSIC, Avda Montañana 1005, 50059, Zaragoza, Spain
- Fundación ARAID, Zaragoza, Spain
| | - Tibor Kiss
- Centre for Agriculture Research ELKH (ATK), Martonvásár, Hungary
- Center for Research and Development, Food and Wine Center of Excellence, Eszterházy Károly Catholic University, Eger, Hungary
| | - Marianna Mayer
- Centre for Agriculture Research ELKH (ATK), Martonvásár, Hungary
| | - Ildikó Karsai
- Centre for Agriculture Research ELKH (ATK), Martonvásár, Hungary
| | - Ernesto Igartua
- Department of Genetics and Plant Breeding, Aula Dei Experimental Station, CSIC, Avda Montañana 1005, 50059, Zaragoza, Spain.
| | - Ana M Casas
- Department of Genetics and Plant Breeding, Aula Dei Experimental Station, CSIC, Avda Montañana 1005, 50059, Zaragoza, Spain
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Yang R, Wang Z, Zhao L, Liu J, Meng J, Luan Y. Secreted Peptide SpPIP1 Modulates Disease Resistance and Salt Tolerance in Tomato. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:12264-12279. [PMID: 37535837 DOI: 10.1021/acs.jafc.3c03412] [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: 08/05/2023]
Abstract
Tomato is a globally important horticultural and economic crop, but its productivity is severely affected by various stresses. Plant small secretory peptides have been identified as crucial mediators in plant resistance. Here, we conducted a comparative transcriptome analysis and identified the prePIP1 gene from Solanum pimpinellifolium (SpprePIP1), as an ortholog of Arabidopsis prePIP1 encoding the precursor protein of PAMP-induced SSP 1. The expression level of SpprePIP1 is transcriptionally induced in tomato upon infection with Phytophthora infestans (P. infestans), the pathogen responsible for late blight. Overexpression of SpprePIP1 resulted in enhanced tomato resistance to P. infestans. In addition, exogenous application of SpPIP1, whether through spraying or irrigation, improved tomato resistance by enhancing the transcript accumulations of pathogenesis-related proteins, as well as reactive oxygen species and the jasmonic acid (JA) levels. Integrated analysis of transcriptomics and metabolomics revealed the potential contributions of JA and phenylpropanoid biosynthesis to SpPIP1-induced tomato immunity. Additionally, SpPIP1 may strengthen tomato resistance to salt stress through the ABA signaling pathway. Overall, our findings demonstrate that SpPIP1 positively regulates tomato tolerance to P. infestans and salt stress, making it a potential plant elicitor for crop protection in an environmentally friendly way.
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Affiliation(s)
- Ruirui Yang
- School of Bioengineering, Dalian University of Technology, Dalian 116024, China
| | - Zhicheng Wang
- School of Bioengineering, Dalian University of Technology, Dalian 116024, China
| | - Lei Zhao
- Institute of Environmental Systems Biology, College of Environmental Science and Engineering, Dalian Maritime University, Dalian 116026, China
| | - Jie Liu
- School of Bioengineering, Dalian University of Technology, Dalian 116024, China
| | - Jun Meng
- School of Computer Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Yushi Luan
- School of Bioengineering, Dalian University of Technology, Dalian 116024, China
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Yasmeen E, Wang J, Riaz M, Zhang L, Zuo K. Designing artificial synthetic promoters for accurate, smart, and versatile gene expression in plants. PLANT COMMUNICATIONS 2023:100558. [PMID: 36760129 PMCID: PMC10363483 DOI: 10.1016/j.xplc.2023.100558] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 01/30/2023] [Accepted: 02/06/2023] [Indexed: 06/18/2023]
Abstract
With the development of high-throughput biology techniques and artificial intelligence, it has become increasingly feasible to design and construct artificial biological parts, modules, circuits, and even whole systems. To overcome the limitations of native promoters in controlling gene expression, artificial promoter design aims to synthesize short, inducible, and conditionally controlled promoters to coordinate the expression of multiple genes in diverse plant metabolic and signaling pathways. Synthetic promoters are versatile and can drive gene expression accurately with smart responses; they show potential for enhancing desirable traits in crops, thereby improving crop yield, nutritional quality, and food security. This review first illustrates the importance of synthetic promoters, then introduces promoter architecture and thoroughly summarizes advances in synthetic promoter construction. Restrictions to the development of synthetic promoters and future applications of such promoters in synthetic plant biology and crop improvement are also discussed.
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Affiliation(s)
- Erum Yasmeen
- Single Cell Research Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jin Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Muhammad Riaz
- Single Cell Research Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Lida Zhang
- Single Cell Research Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Kaijing Zuo
- Single Cell Research Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China.
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6
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Nora LC, Cassiano MHA, Santana ÍP, Guazzaroni ME, Silva-Rocha R, da Silva RR. Mining novel cis-regulatory elements from the emergent host Rhodosporidium toruloides using transcriptomic data. Front Microbiol 2023; 13:1069443. [PMID: 36687612 PMCID: PMC9853887 DOI: 10.3389/fmicb.2022.1069443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 12/14/2022] [Indexed: 01/07/2023] Open
Abstract
The demand for robust microbial cell factories that produce valuable biomaterials while resisting stresses imposed by current bioprocesses is rapidly growing. Rhodosporidium toruloides is an emerging host that presents desirable features for bioproduction, since it can grow in a wide range of substrates and tolerate a variety of toxic compounds. To explore R. toruloides suitability for application as a cell factory in biorefineries, we sought to understand the transcriptional responses of this yeast when growing under experimental settings that simulated those used in biofuels-related industries. Thus, we performed RNA sequencing of the oleaginous, carotenogenic yeast in different contexts. The first ones were stress-related: two conditions of high temperature (37 and 42°C) and two ethanol concentrations (2 and 4%), while the other used the inexpensive and abundant sugarcane juice as substrate. Differential expression and functional analysis were implemented using transcriptomic data to select differentially expressed genes and enriched pathways from each set-up. A reproducible bioinformatics workflow was developed for mining new regulatory elements. We then predicted, for the first time in this yeast, binding motifs for several transcription factors, including HAC1, ARG80, RPN4, ADR1, and DAL81. Most putative transcription factors uncovered here were involved in stress responses and found in the yeast genome. Our method for motif discovery provides a new realm of possibilities in studying gene regulatory networks, not only for the emerging host R. toruloides, but for other organisms of biotechnological importance.
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Affiliation(s)
- Luísa Czamanski Nora
- Cell and Molecular Biology Department, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil,*Correspondence: Luísa Czamanski Nora,
| | | | - Ítalo Paulino Santana
- Faculty of Philosophy, Sciences and Letters of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - María-Eugenia Guazzaroni
- Faculty of Philosophy, Sciences and Letters of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Rafael Silva-Rocha
- Cell and Molecular Biology Department, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Ricardo Roberto da Silva
- Faculty of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, Brazil,Ricardo Roberto da Silva,
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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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Kitchen SA, Jiang D, Harii S, Satoh N, Weis VM, Shinzato C. Coral larvae suppress heat stress response during the onset of symbiosis decreasing their odds of survival. Mol Ecol 2022; 31:5813-5830. [PMID: 36168983 DOI: 10.1111/mec.16708] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 09/06/2022] [Accepted: 09/15/2022] [Indexed: 01/13/2023]
Abstract
The endosymbiosis between most corals and their photosynthetic dinoflagellate partners begins early in the host life history, when corals are larvae or juvenile polyps. The capacity of coral larvae to buffer climate-induced stress while in the process of symbiont acquisition could come with physiological trade-offs that alter behaviour, development, settlement and survivorship. Here we examined the joint effects of thermal stress and symbiosis onset on colonization dynamics, survival, metamorphosis and host gene expression of Acropora digitifera larvae. We found that thermal stress decreased symbiont colonization of hosts by 50% and symbiont density by 98.5% over 2 weeks. Temperature and colonization also influenced larval survival and metamorphosis in an additive manner, where colonized larvae fared worse or prematurely metamorphosed more often than noncolonized larvae under thermal stress. Transcriptomic responses to colonization and thermal stress treatments were largely independent, while the interaction of these treatments revealed contrasting expression profiles of genes that function in the stress response, immunity, inflammation and cell cycle regulation. The combined treatment either cancelled or lowered the magnitude of expression of heat-stress responsive genes in the presence of symbionts, revealing a physiological cost to acquiring symbionts at the larval stage with elevated temperatures. In addition, host immune suppression, a hallmark of symbiosis onset under ambient temperature, turned to immune activation under heat stress. Thus, by integrating the physical environment and biotic pressures that mediate presettlement event in corals, our results suggest that colonization may hinder larval survival and recruitment under projected climate scenarios.
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Affiliation(s)
- Sheila A Kitchen
- Department of Integrative Biology, Oregon State University, Corvallis, Oregon, USA
| | - Duo Jiang
- Statistics Department, Oregon State University, Corvallis, Oregon, USA
| | - Saki Harii
- Tropical Biosphere Research Center, University of the Ryukyus, Okinawa, Japan
| | - Noriyuki Satoh
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Virginia M Weis
- Department of Integrative Biology, Oregon State University, Corvallis, Oregon, USA
| | - Chuya Shinzato
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
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Rozière J, Guichard C, Brunaud V, Martin ML, Coursol S. A comprehensive map of preferentially located motifs reveals distinct proximal cis-regulatory sequences in plants. FRONTIERS IN PLANT SCIENCE 2022; 13:976371. [PMID: 36311095 PMCID: PMC9597372 DOI: 10.3389/fpls.2022.976371] [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: 06/23/2022] [Accepted: 09/21/2022] [Indexed: 06/16/2023]
Abstract
Identification of cis-regulatory sequences controlling gene expression is an arduous challenge that is being actively explored to discover key genetic factors responsible for traits of agronomic interest. Here, we used a genome-wide de novo approach to investigate preferentially located motifs (PLMs) in the proximal cis-regulatory landscape of Arabidopsis thaliana and Zea mays. We report three groups of PLMs in both the 5'- and 3'-gene-proximal regions and emphasize conserved PLMs in both species, particularly in the 3'-gene-proximal region. Comparison with resources from transcription factor and microRNA binding sites shows that 79% of the identified PLMs are unassigned, although some are supported by MNase-defined cistrome occupancy analysis. Enrichment analyses further reveal that unassigned PLMs provide functional predictions that differ from those derived from transcription factor and microRNA binding sites. Our study provides a comprehensive map of PLMs and demonstrates their potential utility for future characterization of orphan genes in plants.
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Affiliation(s)
- Julien Rozière
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Gif sur Yvette, France
- Université de Paris Cité, Institute of Plant Sciences Paris-Saclay (IPS2), Gif sur Yvette, France
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Versailles, France
| | - Cécile Guichard
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Gif sur Yvette, France
- Université de Paris Cité, Institute of Plant Sciences Paris-Saclay (IPS2), Gif sur Yvette, France
| | - Véronique Brunaud
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Gif sur Yvette, France
- Université de Paris Cité, Institute of Plant Sciences Paris-Saclay (IPS2), Gif sur Yvette, France
| | - Marie-Laure Martin
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Gif sur Yvette, France
- Université de Paris Cité, Institute of Plant Sciences Paris-Saclay (IPS2), Gif sur Yvette, France
- Université Paris-Saclay, INRAE, AgroParisTech, UMR MIA-Paris-Saclay, Palaiseau, France
| | - Sylvie Coursol
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Versailles, France
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10
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Sancho R, Catalán P, Contreras‐Moreira B, Juenger TE, Des Marais DL. Patterns of pan-genome occupancy and gene coexpression under water-deficit in Brachypodium distachyon. Mol Ecol 2022; 31:5285-5306. [PMID: 35976181 PMCID: PMC9804473 DOI: 10.1111/mec.16661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 07/29/2022] [Accepted: 08/11/2022] [Indexed: 01/05/2023]
Abstract
Natural populations are characterized by abundant genetic diversity driven by a range of different types of mutation. The tractability of sequencing complete genomes has allowed new insights into the variable composition of genomes, summarized as a species pan-genome. These analyses demonstrate that many genes are absent from the first reference genomes, whose analysis dominated the initial years of the genomic era. Our field now turns towards understanding the functional consequence of these highly variable genomes. Here, we analysed weighted gene coexpression networks from leaf transcriptome data for drought response in the purple false brome Brachypodium distachyon and the differential expression of genes putatively involved in adaptation to this stressor. We specifically asked whether genes with variable "occupancy" in the pan-genome - genes which are either present in all studied genotypes or missing in some genotypes - show different distributions among coexpression modules. Coexpression analysis united genes expressed in drought-stressed plants into nine modules covering 72 hub genes (87 hub isoforms), and genes expressed under controlled water conditions into 13 modules, covering 190 hub genes (251 hub isoforms). We find that low occupancy pan-genes are under-represented among several modules, while other modules are over-enriched for low-occupancy pan-genes. We also provide new insight into the regulation of drought response in B. distachyon, specifically identifying one module with an apparent role in primary metabolism that is strongly responsive to drought. Our work shows the power of integrating pan-genomic analysis with transcriptomic data using factorial experiments to understand the functional genomics of environmental response.
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Affiliation(s)
- Rubén Sancho
- Department of Agricultural and Environmental Sciences, High Polytechnic School of HuescaUniversity of ZaragozaHuescaSpain,Unidad Associada al CSIC, Grupo de BioquímicaGrupo de Bioquímica, Biofísica y Biología Computacional (BIFI, UNIZAR)ZaragozaSpain
| | - Pilar Catalán
- Department of Agricultural and Environmental Sciences, High Polytechnic School of HuescaUniversity of ZaragozaHuescaSpain,Unidad Associada al CSIC, Grupo de BioquímicaGrupo de Bioquímica, Biofísica y Biología Computacional (BIFI, UNIZAR)ZaragozaSpain
| | - Bruno Contreras‐Moreira
- Unidad Associada al CSIC, Grupo de BioquímicaGrupo de Bioquímica, Biofísica y Biología Computacional (BIFI, UNIZAR)ZaragozaSpain,Estación Experimental de Aula Dei‐Consejo Superior de Investigaciones CientíficasZaragozaSpain,Fundación ARAIDZaragozaSpain
| | - Thomas E. Juenger
- Department of Integrative BiologyThe University of Texas at AustinAustinTexasUSA
| | - David L. Des Marais
- Department of Civil and Environmental EngineeringMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
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11
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Yao Y, Dong L, Fu X, Zhao L, Wei J, Cao J, Sun Y, Liu J. HrTCP20 dramatically enhance drought tolerance of sea buckthorn (Hippophae rhamnoides L). by mediating the JA signaling pathway. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2022; 174:51-62. [PMID: 35144110 DOI: 10.1016/j.plaphy.2022.01.026] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 01/04/2022] [Accepted: 01/24/2022] [Indexed: 06/14/2023]
Abstract
Sea buckthorn, an important ecological and economical tree species, have remarkable drought and salt resistance. The plant-specific transcription factor TCPs play important roles in plant growth, development, and stress responses. However, in sea buckthorn, the molecular mechanism of TCP proteins and their involvement in drought stress are unknown. Here, we found that the expression of HrTCP20 was significantly up-regulated in sea buckthorn under drought stress. Overexpression of HrTCP20 in Arabidopsis thaliana showed that the superoxide dismutase (SOD), polyphenol oxidase (POD), and chlorophyll (SPAD) content was significantly increased by 1.37 and 1.35 times. However, the malondialdehyde (MDA) content decreased by 0.51 times. Our studies further confirmed that silencing HrTCP20 by virus-induced gene silencing (VIGS) led to a decrease in the content of defense enzymes, relative water content (RWC), and an increase of relative electrical conductivity (REC). Silencing HrTCP20 also caused the jasmonic acid (JA) content to decrease in the VIGS-treated tree. Interestingly, we found that JA accumulation content and the expression of HrLOX2, an essential enzyme for JA synthesis, was significantly inhibited in HrTCP20-silenced sea buckthorn under drought stress. Yeast two-hybrid analysis also showed that HrTCP20 is directly bound to HrLOX2. Taken together, the HrTCP20 transcription factor was a positive regulator in drought resistance of sea buckthorn. Further, our findings will provide comprehensive insights into the forest tree defence system of drought stress.
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Affiliation(s)
- Ying Yao
- College of Life Science, Institute of Life Science and Green Development, Hebei University, Baoding, China
| | - Lijun Dong
- College of Life Science, Institute of Life Science and Green Development, Hebei University, Baoding, China
| | - Xiaohong Fu
- College of Life Science, Institute of Life Science and Green Development, Hebei University, Baoding, China
| | - Lin Zhao
- College of Life Science, Institute of Life Science and Green Development, Hebei University, Baoding, China
| | - Jianrong Wei
- College of Life Science, Institute of Life Science and Green Development, Hebei University, Baoding, China
| | - Jinfeng Cao
- Hebei Key Laboratory of Crop Salt-Alkali Stress Tolerance Evaluation and Genetic Improvement, Cangzhou, China
| | - Yongyuan Sun
- Hebei Key Laboratory of Crop Salt-Alkali Stress Tolerance Evaluation and Genetic Improvement, Cangzhou, China.
| | - Jianfeng Liu
- College of Life Science, Institute of Life Science and Green Development, Hebei University, Baoding, China.
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12
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Santana-Garcia W, Castro-Mondragon JA, Padilla-Gálvez M, Nguyen NT, Elizondo-Salas A, Ksouri N, Gerbes F, Thieffry D, Vincens P, Contreras-Moreira B, van Helden J, Thomas-Chollier M, Medina-Rivera A. OUP accepted manuscript. Nucleic Acids Res 2022; 50:W670-W676. [PMID: 35544234 PMCID: PMC9252783 DOI: 10.1093/nar/gkac312] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 04/12/2022] [Accepted: 04/20/2022] [Indexed: 11/12/2022] Open
Abstract
RSAT (Regulatory Sequence Analysis Tools) enables the detection and the analysis of cis-regulatory elements in genomic sequences. This software suite performs (i) de novo motif discovery (including from genome-wide datasets like ChIP-seq/ATAC-seq) (ii) genomic sequences scanning with known motifs, (iii) motif analysis (quality assessment, comparisons and clustering), (iv) analysis of regulatory variations and (v) comparative genomics. RSAT comprises 50 tools. Six public Web servers (including a teaching server) are offered to meet the needs of different biological communities. RSAT philosophy and originality are: (i) a multi-modal access depending on the user needs, through web forms, command-line for local installation and programmatic web services, (ii) a support for virtually any genome (animals, bacteria, plants, totalizing over 10 000 genomes directly accessible). Since the 2018 NAR Web Software Issue, we have developed a large REST API, extended the support for additional genomes and external motif collections, enhanced some tools and Web forms, and developed a novel tool that builds or refine gene regulatory networks using motif scanning (network-interactions). The RSAT website provides extensive documentation, tutorials and published protocols. RSAT code is under open-source license and now hosted in GitHub. RSAT is available at http://www.rsat.eu/.
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Affiliation(s)
| | | | - Mónica Padilla-Gálvez
- Laboratorio Internacional de Investigación sobre el Genoma Humano, Universidad Nacional Autónoma de México, Campus Juriquilla, Blvd Juriquilla 3001, 76230 Santiago de Querétaro, México
| | - Nga Thi Thuy Nguyen
- Institut de biologie de l’Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, PSL Université Paris, 75005 Paris, France
| | - Ana Elizondo-Salas
- Laboratorio Internacional de Investigación sobre el Genoma Humano, Universidad Nacional Autónoma de México, Campus Juriquilla, Blvd Juriquilla 3001, 76230 Santiago de Querétaro, México
| | - Najla Ksouri
- Estación Experimental de Aula Dei-CSIC, 50059 Zaragoza, Spain
| | - François Gerbes
- CNRS, Institut Français de Bioinformatique, IFB-core, UMS 3601, Evry, France
| | - Denis Thieffry
- Institut de biologie de l’Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, PSL Université Paris, 75005 Paris, France
| | - Pierre Vincens
- Institut de biologie de l’Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, PSL Université Paris, 75005 Paris, France
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13
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Decena MA, Gálvez-Rojas S, Agostini F, Sancho R, Contreras-Moreira B, Des Marais DL, Hernandez P, Catalán P. Comparative Genomics, Evolution, and Drought-Induced Expression of Dehydrin Genes in Model Brachypodium Grasses. PLANTS (BASEL, SWITZERLAND) 2021; 10:2664. [PMID: 34961135 PMCID: PMC8709310 DOI: 10.3390/plants10122664] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 11/25/2021] [Accepted: 11/27/2021] [Indexed: 06/14/2023]
Abstract
Dehydration proteins (dehydrins, DHNs) confer tolerance to water-stress deficit in plants. We performed a comparative genomics and evolutionary study of DHN genes in four model Brachypodium grass species. Due to limited knowledge on dehydrin expression under water deprivation stress in Brachypodium, we also performed a drought-induced gene expression analysis in 32 ecotypes of the genus' flagship species B. distachyon showing different hydric requirements. Genomic sequence analysis detected 10 types of dehydrin genes (Bdhn) across the Brachypodium species. Domain and conserved motif contents of peptides encoded by Bdhn genes revealed eight protein architectures. Bdhn genes were spread across several chromosomes. Selection analysis indicated that all the Bdhn genes were constrained by purifying selection. Three upstream cis-regulatory motifs (BES1, MYB124, ZAT) were detected in several Bdhn genes. Gene expression analysis demonstrated that only four Bdhn1-Bdhn2, Bdhn3, and Bdhn7 genes, orthologs of wheat, barley, rice, sorghum, and maize genes, were expressed in mature leaves of B. distachyon and that all of them were more highly expressed in plants under drought conditions. Brachypodium dehydrin expression was significantly correlated with drought-response phenotypic traits (plant biomass, leaf carbon and proline contents and water use efficiency increases, and leaf water and nitrogen content decreases) being more pronounced in drought-tolerant ecotypes. Our results indicate that dehydrin type and regulation could be a key factor determining the acquisition of water-stress tolerance in grasses.
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Affiliation(s)
- Maria Angeles Decena
- Escuela Politécnica Superior de Huesca, Universidad de Zaragoza, Ctra. Cuarte km 1, 22071 Huesca, Spain; (M.A.D.); (R.S.)
| | - Sergio Gálvez-Rojas
- ETSI Informática, Universidad de Málaga, Blvr Louis Pasteur 35, 29071 Málaga, Spain; (S.G.-R.); (F.A.)
| | - Federico Agostini
- ETSI Informática, Universidad de Málaga, Blvr Louis Pasteur 35, 29071 Málaga, Spain; (S.G.-R.); (F.A.)
- Instituto de Botánica del Nordeste, UNNE-CONICET, Corrientes W3402, Argentina
| | - Ruben Sancho
- Escuela Politécnica Superior de Huesca, Universidad de Zaragoza, Ctra. Cuarte km 1, 22071 Huesca, Spain; (M.A.D.); (R.S.)
- Grupo de Bioquímica, Biofísica y Biología Computacional (BIFI, UNIZAR), Unidad Asociada al CSIC, 50018 Zaragoza, Spain;
| | - Bruno Contreras-Moreira
- Grupo de Bioquímica, Biofísica y Biología Computacional (BIFI, UNIZAR), Unidad Asociada al CSIC, 50018 Zaragoza, Spain;
- Estación Experimental de Aula Dei-Consejo Superior de Investigaciones Científicas, Av. Montañana 1005, 50059 Zaragoza, Spain
| | - David L. Des Marais
- Civil and Environmental Engineering Department, Faculty of Environmental and Life Science, Massachusetts Institute of Technology, 15 Vassar Street, Cambridge, MA 02139, USA;
| | - Pilar Hernandez
- Instituto de Agricultura Sostenible, IAS-CSIC, Menendez Pidal Ave, 14004 Córdoba, Spain
| | - Pilar Catalán
- Escuela Politécnica Superior de Huesca, Universidad de Zaragoza, Ctra. Cuarte km 1, 22071 Huesca, Spain; (M.A.D.); (R.S.)
- Grupo de Bioquímica, Biofísica y Biología Computacional (BIFI, UNIZAR), Unidad Asociada al CSIC, 50018 Zaragoza, Spain;
- Departamento de Ciencias Agrarias y del Medio Natural, Tomsk State University, 36 Lenin Ave, 634050 Tomsk, Russia
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14
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Contreras-Moreira B, Filippi CV, Naamati G, Girón CG, Allen JE, Flicek P. K-mer counting and curated libraries drive efficient annotation of repeats in plant genomes. THE PLANT GENOME 2021; 14:e20143. [PMID: 34562304 PMCID: PMC7614178 DOI: 10.1002/tpg2.20143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 07/06/2021] [Indexed: 06/13/2023]
Abstract
The annotation of repetitive sequences within plant genomes can help in the interpretation of observed phenotypes. Moreover, repeat masking is required for tasks such as whole-genome alignment, promoter analysis, or pangenome exploration. Although homology-based annotation methods are computationally expensive, k-mer strategies for masking are orders of magnitude faster. Here, we benchmarked a two-step approach, where repeats were first called by k-mer counting and then annotated by comparison to curated libraries. This hybrid protocol was tested on 20 plant genomes from Ensembl, with the k-mer-based Repeat Detector (Red) and two repeat libraries (REdat, last updated in 2013, and nrTEplants, curated for this work). Custom libraries produced by RepeatModeler were also tested. We obtained repeated genome fractions that matched those reported in the literature but with shorter repeated elements than those produced directly by sequence homology. Inspection of the masked regions that overlapped genes revealed no preference for specific protein domains. Most Red-masked sequences could be successfully classified by sequence similarity, with the complete protocol taking less than 2 h on a desktop Linux box. A guide to curating your own repeat libraries and the scripts for masking and annotating plant genomes can be obtained at https://github.com/Ensembl/plant-scripts.
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Affiliation(s)
- Bruno Contreras-Moreira
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Carla V Filippi
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
- Instituto de Biotecnología, Centro de Investigaciones en Ciencias Veterinarias y Agronómicas (CICVyA), Instituto Nacional de Tecnología Agropecuaria (INTA); Instituto de Agrobiotecnología y Biología Molecular (IABIMO), INTA-Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) Nicolas Repetto y Los Reseros s/n (1686), Hurlingham, Buenos Aires, Argentina
- CONICET, Av Rivadavia 1917, C1033AAJ Ciudad de Buenos Aires, Argentina
| | - Guy Naamati
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Carlos García Girón
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - James E Allen
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
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15
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Kakei Y, Masuda H, Nishizawa NK, Hattori H, Aung MS. Elucidation of Novel cis-Regulatory Elements and Promoter Structures Involved in Iron Excess Response Mechanisms in Rice Using a Bioinformatics Approach. FRONTIERS IN PLANT SCIENCE 2021; 12:660303. [PMID: 34149757 PMCID: PMC8207140 DOI: 10.3389/fpls.2021.660303] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 04/06/2021] [Indexed: 05/24/2023]
Abstract
Iron (Fe) excess is a major constraint on crop production in flooded acidic soils, particularly in rice cultivation. Under Fe excess, plants activate a complex mechanism and network regulating Fe exclusion by roots and isolation in various tissues. In rice, the transcription factors and cis-regulatory elements (CREs) that regulate Fe excess response mechanisms remain largely elusive. We previously reported comprehensive microarray analyses of several rice tissues in response to various levels of Fe excess stress. In this study, we further explored novel CREs and promoter structures in rice using bioinformatics approaches with this microarray data. We first performed network analyses to predict Fe excess-related CREs through the categorization of the gene expression patterns of Fe excess-responsive transcriptional regulons, and found four major expression clusters: Fe storage type, Fe chelator type, Fe uptake type, and WRKY and other co-expression type. Next, we explored CREs within these four clusters of gene expression types using a machine-learning method called microarray-associated motif analyzer (MAMA), which we previously established. Through a comprehensive bioinformatics approach, we identified a total of 560 CRE candidates extracted by MAMA analyses and 42 important conserved sequences of CREs directly related to the Fe excess response in various rice tissues. We explored several novel cis-elements as candidate Fe excess CREs including GCWGCWGC, CGACACGC, and Myb binding-like motifs. Based on the presence or absence of candidate CREs using MAMA and known PLACE CREs, we found that the Boruta-XGBoost model explained expression patterns with high accuracy of about 83%. Enriched sequences of both novel MAMA CREs and known PLACE CREs led to high accuracy expression patterns. We also found new roles of known CREs in the Fe excess response, including the DCEp2 motif, IDEF1-, Zinc Finger-, WRKY-, Myb-, AP2/ERF-, MADS- box-, bZIP and bHLH- binding sequence-containing motifs among Fe excess-responsive genes. In addition, we built a molecular model and promoter structures regulating Fe excess-responsive genes based on new finding CREs. Together, our findings about Fe excess-related CREs and conserved sequences will provide a comprehensive resource for discovery of genes and transcription factors involved in Fe excess-responsive pathways, clarification of the Fe excess response mechanism in rice, and future application of the promoter sequences to produce genotypes tolerant of Fe excess.
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Affiliation(s)
- Yusuke Kakei
- Institute of Vegetable and Floriculture Science, Research Center for Agricultural Information Technology, National Agriculture and Food Research Organization, Ibaraki, Japan
| | - Hiroshi Masuda
- Faculty of Bioresource Sciences, Department of Biological Production, Akita Prefectural University, Akita, Japan
| | - Naoko K. Nishizawa
- Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, Ishikawa, Japan
| | - Hiroyuki Hattori
- Faculty of Bioresource Sciences, Department of Biological Production, Akita Prefectural University, Akita, Japan
| | - May Sann Aung
- Faculty of Bioresource Sciences, Department of Biological Production, Akita Prefectural University, Akita, Japan
- Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, Ishikawa, Japan
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