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Amin A, Naim MD, Islam N, Mollah MNH. Genome-wide identification and characterization of DTX family genes highlighting their locations, functions, and regulatory factors in banana (Musa acuminata). PLoS One 2024; 19:e0303065. [PMID: 38843276 PMCID: PMC11156367 DOI: 10.1371/journal.pone.0303065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Accepted: 04/19/2024] [Indexed: 06/09/2024] Open
Abstract
The detoxification efflux carriers (DTX) are a significant group of multidrug efflux transporter family members that play diverse functions in all kingdoms of living organisms. However, genome-wide identification and characterization of DTX family transporters have not yet been performed in banana, despite its importance as an economic fruit plant. Therefore, a detailed genome-wide analysis of DTX family transporters in banana (Musa acuminata) was conducted using integrated bioinformatics and systems biology approaches. In this study, a total of 37 DTX transporters were identified in the banana genome and divided into four groups (I, II, III, and IV) based on phylogenetic analysis. The gene structures, as well as their proteins' domains and motifs, were found to be significantly conserved. Gene ontology (GO) annotation revealed that the predicted DTX genes might play a vital role in protecting cells and membrane-bound organelles through detoxification mechanisms and the removal of drug molecules from banana cells. Gene regulatory analyses identified key transcription factors (TFs), cis-acting elements, and post-transcriptional regulators (miRNAs) of DTX genes, suggesting their potential roles in banana. Furthermore, the changes in gene expression levels due to pathogenic infections and non-living factor indicate that banana DTX genes play a role in responses to both biotic and abiotic stresses. The results of this study could serve as valuable tools to improve banana quality by protecting them from a range of environmental stresses.
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Affiliation(s)
- Al Amin
- Department of Statistics, Bioinformatics Laboratory, Faculty of Science, University of Rajshahi, Rajshahi, Bangladesh
- Department of Zoology, Faculty of Biological Sciences, University of Rajshahi, Rajshahi, Bangladesh
| | - Md. Darun Naim
- Department of Botany, Faculty of Biological Sciences, University of Rajshahi, Rajshahi, Bangladesh
| | - Nurul Islam
- Department of Zoology, Faculty of Biological Sciences, University of Rajshahi, Rajshahi, Bangladesh
| | - Md. Nurul Haque Mollah
- Department of Statistics, Bioinformatics Laboratory, Faculty of Science, University of Rajshahi, Rajshahi, Bangladesh
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Balamurugan A, Mallikarjuna MG, Bansal S, Nayaka SC, Rajashekara H, Chellapilla TS, Prakash G. Genome-wide identification and characterization of NBLRR genes in finger millet (Eleusine coracana L.) and their expression in response to Magnaporthe grisea infection. BMC PLANT BIOLOGY 2024; 24:75. [PMID: 38281915 PMCID: PMC10823742 DOI: 10.1186/s12870-024-04743-z] [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: 08/16/2023] [Accepted: 01/11/2024] [Indexed: 01/30/2024]
Abstract
BACKGROUND The nucleotide binding site leucine rich repeat (NBLRR) genes significantly regulate defences against phytopathogens in plants. The genome-wide identification and analysis of NBLRR genes have been performed in several species. However, the detailed evolution, structure, expression of NBLRRs and functional response to Magnaporthe grisea are unknown in finger millet (Eleusine coracana (L.) Gaertn.). RESULTS The genome-wide scanning of the finger millet genome resulted in 116 NBLRR (EcNBLRRs1-116) encompassing 64 CC-NB-LRR, 47 NB-LRR and 5 CCR-NB-LRR types. The evolutionary studies among the NBLRRs of five Gramineae species, viz., purple false brome (Brachypodium distachyon (L.) P.Beauv.), finger millet (E. coracana), rice (Oryza sativa L.), sorghum (Sorghum bicolor L. (Moench)) and foxtail millet (Setaria italica (L.) P.Beauv.) showed the evolution of NBLRRs in the ancestral lineage of the target species and subsequent divergence through gene-loss events. The purifying selection (Ka/Ks < 1) shaped the expansions of NBLRRs paralogs in finger millet and orthologs among the target Gramineae species. The promoter sequence analysis showed various stress- and phytohormone-responsive cis-acting elements besides growth and development, indicating their potential role in disease defence and regulatory mechanisms. The expression analysis of 22 EcNBLRRs in the genotypes showing contrasting responses to Magnaporthe grisea infection revealed four and five EcNBLRRs in early and late infection stages, respectively. The six of these nine candidate EcNBLRRs proteins, viz., EcNBLRR21, EcNBLRR26, EcNBLRR30, EcNBLRR45, EcNBLRR55 and EcNBLRR76 showed CC, NB and LRR domains, whereas the EcNBLRR23, EcNBLRR32 and EcNBLRR83 showed NB and LRR somains. CONCLUSION The identification and expression analysis of EcNBLRRs showed the role of EcNBLRR genes in assigning blast resistance in finger millet. These results pave the foundation for in-depth and targeted functional analysis of EcNBLRRs through genome editing and transgenic approaches.
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Affiliation(s)
- Alexander Balamurugan
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | | | - Shilpi Bansal
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
- Department of Science and Humanities, SRM Institute of Science and Technology, Modinagar, Uttar Pradesh, 201204, India
| | - S Chandra Nayaka
- Department of Studies in Applied Botany and Biotechnology, University of Mysore, Mysore, 570005, India
| | | | | | - Ganesan Prakash
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India.
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Lei G, Zhou KH, Chen XJ, Huang YQ, Yuan XJ, Li GG, Xie YY, Fang R. Transcriptome and metabolome analyses revealed the response mechanism of pepper roots to Phytophthora capsici infection. BMC Genomics 2023; 24:626. [PMID: 37864214 PMCID: PMC10589972 DOI: 10.1186/s12864-023-09713-7] [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: 05/12/2023] [Accepted: 10/03/2023] [Indexed: 10/22/2023] Open
Abstract
BACKGROUND Phytophthora root rot caused by the oomycete Phytophthora capsici is the most devastating disease in pepper production worldwide, and current management strategies have not been effective in preventing this disease. Therefore, the use of resistant varieties was regarded as an important part of disease management of P. capsici. However, our knowledge of the molecular mechanisms underlying the defense response of pepper roots to P. capsici infection is limited. METHODS A comprehensive transcriptome and metabolome approaches were used to dissect the molecular response of pepper to P. capsici infection in the resistant genotype A204 and the susceptible genotype A198 at 0, 24 and 48 hours post-inoculation (hpi). RESULTS More genes and metabolites were induced at 24 hpi in A204 than A198, suggesting the prompt activation of defense responses in the resistant genotype, which can attribute two proteases, subtilisin-like protease and xylem cysteine proteinase 1, involved in pathogen recognition and signal transduction in A204. Further analysis indicated that the resistant genotype responded to P. capsici with fine regulation by the Ca2+- and salicylic acid-mediated signaling pathways, and then activation of downstream defense responses, including cell wall reinforcement and defense-related genes expression and metabolites accumulation. Among them, differentially expressed genes and differentially accumulated metabolites involved in the flavonoid biosynthesis pathways were uniquely activated in the resistant genotype A204 at 24 hpi, indicating a significant role of the flavonoid biosynthesis pathways in pepper resistance to P. capsici. CONCLUSION The candidate transcripts may provide genetic resources that may be useful in the improvement of Phytophthora root rot-resistant characters of pepper. In addition, the model proposed in this study provides new insight into the defense response against P. capsici in pepper, and enhance our current understanding of the interaction of pepper-P. capsici.
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Affiliation(s)
- Gang Lei
- Institute of Vegetables and Flowers, Jiangxi Academy of Agricultural Sciences, Nanchang, 330200, China
| | - Kun-Hua Zhou
- Institute of Vegetables and Flowers, Jiangxi Academy of Agricultural Sciences, Nanchang, 330200, China
| | - Xue-Jun Chen
- Institute of Vegetables and Flowers, Jiangxi Academy of Agricultural Sciences, Nanchang, 330200, China
| | - Yue-Qin Huang
- Institute of Vegetables and Flowers, Jiangxi Academy of Agricultural Sciences, Nanchang, 330200, China
| | - Xin-Jie Yuan
- Institute of Vegetables and Flowers, Jiangxi Academy of Agricultural Sciences, Nanchang, 330200, China
| | - Ge-Ge Li
- Institute of Vegetables and Flowers, Jiangxi Academy of Agricultural Sciences, Nanchang, 330200, China
| | - Yuan-Yuan Xie
- Institute of Vegetables and Flowers, Jiangxi Academy of Agricultural Sciences, Nanchang, 330200, China
| | - Rong Fang
- Institute of Vegetables and Flowers, Jiangxi Academy of Agricultural Sciences, Nanchang, 330200, China.
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Jimmy JL, Karn R, Kumari S, Sruthilaxmi CB, Pooja S, Emerson IA, Babu S. Rice WRKY13 TF protein binds to motifs in the promoter region to regulate downstream disease resistance-related genes. Funct Integr Genomics 2023; 23:249. [PMID: 37474674 DOI: 10.1007/s10142-023-01167-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 06/22/2023] [Accepted: 07/03/2023] [Indexed: 07/22/2023]
Abstract
In plants, pathogen resistance is brought about by the binding of certain transcription factor (TF) proteins to the cis-elements of certain target genes. These cis-elements are present upstream in the motif of the promoters of each gene. This ensures the binding of a specific TF to a specific promoter, therefore regulating the expression of that gene. Therefore, the study of each promoter sequence of all the rice genes would help identify the target genes of a specific TF. Rice 1 kb upstream promoter sequences of 55,986 annotated genes were analyzed using the Perl program algorithm to detect WRKY13 binding motifs (bm). The resulting genes were grouped using Gene Ontology and gene set enrichment analysis. A gene with more than 4 TF bm in their promoter was selected. Ten genes reported to have a role in rice disease resistance were selected for further analysis. Cis-acting regulatory element analysis was carried out to find the cis-elements and confirm the presence of the corresponding motifs in the promoter sequences of these genes. The 3D structure of WRKY13 TF and the corresponding ten genes were built, and the interacting residues were determined. The binding capacity of WRKY13 to the promoter of these selected genes was analyzed using docking studies. WRKY13 was considered for docking analysis based on the prior reports of autoregulation. Molecular dynamic simulations provided more details regarding the interactions. Expression data revealed the expression of the genes that helped provide the mechanism of interaction. Further co-expression network helped to characterize the interaction of these selected disease resistance-related genes with the WRKY13 TF protein. This study suggests downstream target genes that are regulated by the WRKY13 TF. The molecular mechanism involving the gene network regulated by WRKY13 TF in disease resistance against rice fungal pathogens is explored.
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Affiliation(s)
- John Lilly Jimmy
- School of Bio Science and Technology, Vellore Institute of Technology, Vellore, 632014, India.
| | - Rohit Karn
- School of Bio Science and Technology, Vellore Institute of Technology, Vellore, 632014, India
| | - Sweta Kumari
- School of Bio Science and Technology, Vellore Institute of Technology, Vellore, 632014, India
| | | | - Singh Pooja
- School of Science, Monash University Malaysia, Bandar Sunway, Selangor, Malaysia
| | - Isaac Arnold Emerson
- School of Bio Science and Technology, Vellore Institute of Technology, Vellore, 632014, India
| | - Subramanian Babu
- VIT School of Agricultural Innovations and Advanced Learning, Vellore Institute of Technology, Vellore, 632014, India
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Dong W, Xie Q, Liu Z, Han Y, Wang X, Xu R, Gao C. Genome-wide identification and expression profiling of the bZIP gene family in Betula platyphylla and the functional characterization of BpChr04G00610 under low-temperature stress. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 198:107676. [PMID: 37060866 DOI: 10.1016/j.plaphy.2023.107676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 03/17/2023] [Accepted: 03/29/2023] [Indexed: 05/07/2023]
Abstract
The basic leucine zipper (bZIP) gene, which plays a significant role in the regulation of tolerance to biotic/abiotic stresses, has been characterized in many plant species. Betula platyphylla is a significant afforestation species. To elucidate the stress resistance mechanism of birch, previous studies identified some stress resistance genes. However, the genome-wide identification and characterization of bZIP gene family in the birch have not been reported. Here, the 56 BpbZIP genes were identified and classified into 13 groups in birch. Cis-element analysis showed that the promoters of 56 family genes contained 108 elements, of which 16 were shared by 13 groups. There were 8 pairs of fragment repeats and 1 pair of tandem repeats, indicating that duplication may be the major reason for the amplification of the BpbZIP gene family. Tissue-specific of BpbZIP genes showed 18 genes with the highest expression in roots, 15 in flowers, 11 in xylem and 9 in leaves. In addition, five differentially expressed bZIP genes were identified from the RNA-seq data of birch under low-temperature stress, and the co-expressed differentially expressed genes were further screened. The analysis of gene ontology (GO) enrichment of each co-expression regulatory network showed that they were related to membrane lipids and cell walls. Furthermore, the transient overexpression of BpChr04G00610 decreased the ROS scavenging ability of birch under low-temperature stress, suggesting that it may be more sensitive to low-temperature. In conclusion, this study provides a basis for the study of the function of BpbZIP genes.
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Affiliation(s)
- Wenfang Dong
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), Harbin, 150040, China
| | - Qingjun Xie
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), Harbin, 150040, China
| | - Zhongyuan Liu
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), Harbin, 150040, China
| | - Yating Han
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), Harbin, 150040, China
| | - Xinyu Wang
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), Harbin, 150040, China
| | - Ruiting Xu
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), Harbin, 150040, China
| | - Caiqiu Gao
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), Harbin, 150040, China.
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Mapping Genetic Variation in Arabidopsis in Response to Plant Growth-Promoting Bacterium Azoarcus olearius DQS-4T. Microorganisms 2023; 11:microorganisms11020331. [PMID: 36838296 PMCID: PMC9961961 DOI: 10.3390/microorganisms11020331] [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: 11/16/2022] [Revised: 01/26/2023] [Accepted: 01/27/2023] [Indexed: 02/03/2023] Open
Abstract
Plant growth-promoting bacteria (PGPB) can enhance plant health by facilitating nutrient uptake, nitrogen fixation, protection from pathogens, stress tolerance and/or boosting plant productivity. The genetic determinants that drive the plant-bacteria association remain understudied. To identify genetic loci highly correlated with traits responsive to PGPB, we performed a genome-wide association study (GWAS) using an Arabidopsis thaliana population treated with Azoarcus olearius DQS-4T. Phenotypically, the 305 Arabidopsis accessions tested responded differently to bacterial treatment by improving, inhibiting, or not affecting root system or shoot traits. GWA mapping analysis identified several predicted loci associated with primary root length or root fresh weight. Two statistical analyses were performed to narrow down potential gene candidates followed by haplotype block analysis, resulting in the identification of 11 loci associated with the responsiveness of Arabidopsis root fresh weight to bacterial inoculation. Our results showed considerable variation in the ability of plants to respond to inoculation by A. olearius DQS-4T while revealing considerable complexity regarding statistically associated loci with the growth traits measured. This investigation is a promising starting point for sustainable breeding strategies for future cropping practices that may employ beneficial microbes and/or modifications of the root microbiome.
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Guo X, Li Q, Yan B, Wang Y, Wang S, Xiong F, Zhang C, Zhang Y, Guo L. Mild shading promotes sesquiterpenoid synthesis and accumulation in Atractylodes lancea by regulating photosynthesis and phytohormones. Sci Rep 2022; 12:21648. [PMID: 36522369 PMCID: PMC9755305 DOI: 10.1038/s41598-022-25494-7] [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: 05/04/2022] [Accepted: 11/30/2022] [Indexed: 12/23/2022] Open
Abstract
Atractylodes lancea rhizome (AR) has high medicinal and economic value. A previous study has reported that the accumulation of sesquiterpenoids in AR has obvious advantages under bamboo canopy. A concrete shade value to promote the cultivation of high-quality AR has not been established. In this study, 80% shading was screened at six different light intensities (100%, 80%, 60%, 40%, 20%, 7%), and the mechanism was explored in terms of photosynthetic efficiency and phytohormones levels. The results indicated that the total sesquiterpenoid content of 80% mild shading increased by 58%, 52%, and 35%, respectively, compared to 100% strong light in seedling, expansion, and harvest stages and increased by 144%, 178%, and 94%, respectively, compared with 7% low light. The sesquiterpenoids hinesol and β-eudesmol contributed approximately 70% to the differential contribution ratio between mild shading and strong light (100%) or between mild shading and low light (7%). Furthermore, HMGR, DXR, and FPPS genes, which regulate sesquiterpenoid synthesis, were significantly upregulated in 80% mild shading. Transpiration rate; the intercellular CO2 concentration; net photosynthetic rate; and levels of jasmonic acid, abscisic acid, and gibberellin were strongly correlated (r > 0.85) with sesquiterpenoid accumulation. Cis-acting elements responding to light and phytohormones were present within the promoter regions of HMGR, DXR, and FPPS. Therefore, 80% shading promotes the synthesis and accumulation of sesquiterpenoids in AR by regulating photosynthetic efficiency and phytohormone production, thereby promoting transcriptional expression.
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Affiliation(s)
- Xiuzhi Guo
- grid.410318.f0000 0004 0632 3409State Key Laboratory and Breeding Base of Dao-Di Herbs, Resource Center of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700 China
| | - Qiang Li
- grid.410318.f0000 0004 0632 3409State Key Laboratory and Breeding Base of Dao-Di Herbs, Resource Center of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700 China
| | - Binbin Yan
- grid.410318.f0000 0004 0632 3409State Key Laboratory and Breeding Base of Dao-Di Herbs, Resource Center of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700 China
| | - Yuefeng Wang
- grid.410318.f0000 0004 0632 3409State Key Laboratory and Breeding Base of Dao-Di Herbs, Resource Center of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700 China
| | - Sheng Wang
- grid.410318.f0000 0004 0632 3409State Key Laboratory and Breeding Base of Dao-Di Herbs, Resource Center of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700 China
| | - Feng Xiong
- grid.410318.f0000 0004 0632 3409State Key Laboratory and Breeding Base of Dao-Di Herbs, Resource Center of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700 China
| | - Chengcai Zhang
- grid.410318.f0000 0004 0632 3409State Key Laboratory and Breeding Base of Dao-Di Herbs, Resource Center of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700 China
| | - Yan Zhang
- grid.410318.f0000 0004 0632 3409State Key Laboratory and Breeding Base of Dao-Di Herbs, Resource Center of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700 China
| | - Lanping Guo
- grid.410318.f0000 0004 0632 3409State Key Laboratory and Breeding Base of Dao-Di Herbs, Resource Center of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700 China
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Khandagale K, Roylawar P, Kulkarni O, Khambalkar P, Ade A, Kulkarni A, Singh M, Gawande S. Comparative Transcriptome Analysis of Onion in Response to Infection by Alternaria porri (Ellis) Cifferi. FRONTIERS IN PLANT SCIENCE 2022; 13:857306. [PMID: 35481153 PMCID: PMC9036366 DOI: 10.3389/fpls.2022.857306] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 03/08/2022] [Indexed: 06/14/2023]
Abstract
Purple blotch (PB) is one of the most destructive foliar diseases of onion and other alliums, caused by a necrotrophic fungal pathogen Alternaria porri. There are no reports on the molecular response of onion to PB infection. To elucidate the response of onion to A. porri infection, we consequently carried out an RNAseq analysis of the resistant (Arka Kalyan; AK) and susceptible (Agrifound rose; AFR) genotype after an artificial infection. Through differential expression analyses between control and pathogen-treated plants, we identified 8,064 upregulated and 248 downregulated genes in AFR, while 832 upregulated and 564 downregulated genes were identified in AK. A further significant reprogramming in the gene expression profile was also demonstrated by a functional annotation analysis. Gene ontology (GO) terms, which are particularly involved in defense responses and signaling, are overrepresented in current analyses such as "oxidoreductase activity," "chitin catabolic processes," and "defense response." Several key plant defense genes were differentially expressed on A. porri infection, which includes pathogenesis-related (PR) proteins, receptor-like kinases, phytohormone signaling, cell-wall integrity, cytochrome P450 monooxygenases, and transcription factors. Some of the genes were exclusively overexpressed in resistant genotype, namely, GABA transporter1, ankyrin repeat domain-containing protein, xyloglucan endotransglucosylase/hydrolase, and PR-5 (thaumatin-like). Antioxidant enzyme activities were observed to be increased after infection in both genotypes but higher activity was found in the resistant genotype, AK. This is the first report of transcriptome profiling in onion in response to PB infection and will serve as a resource for future studies to elucidate the molecular mechanism of onion-A. porri interaction and to improve PB resistance in onions.
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Affiliation(s)
- Kiran Khandagale
- Department of Botany, Savitribai Phule Pune University, Pune, India
| | - Praveen Roylawar
- Department of Botany, Sangamner Nagarpalika Arts, D. J. Malpani Commerce, B. N. Sarda Science College, Sangamner, India
| | - Onkar Kulkarni
- Bioinformatics Centre, Savitribai Phule Pune University, Pune, India
| | | | - Avinash Ade
- Department of Botany, Savitribai Phule Pune University, Pune, India
| | - Abhijeet Kulkarni
- Bioinformatics Centre, Savitribai Phule Pune University, Pune, India
| | - Major Singh
- ICAR-Directorate of Onion and Garlic Research (DOGR), Pune, India
| | - Suresh Gawande
- ICAR-Directorate of Onion and Garlic Research (DOGR), Pune, India
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Escobar E, Oladzad A, Simons K, Miklas P, Lee RK, Schroder S, Bandillo N, Wunsch M, McClean PE, Osorno JM. New genomic regions associated with white mold resistance in dry bean using a MAGIC population. THE PLANT GENOME 2022; 15:e20190. [PMID: 35106945 DOI: 10.1002/tpg2.20190] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 12/16/2021] [Indexed: 06/14/2023]
Abstract
Dry bean (Phaseolus vulgaris L.) production in many regions is threatened by white mold (WM) [Sclerotinia sclerotiorum (Lib.) de Bary]. Seed yield losses can be up to 100% under conditions favorable for the pathogen. The low heritability, polygenic inheritance, and cumbersome screening protocols make it difficult to breed for improved genetic resistance. Some progress in understanding genetic resistance and germplasm improvement has been accomplished, but cultivars with high levels of resistance are yet to be released. A WM multiparent advanced generation inter-cross (MAGIC) population (n = 1060) was developed to facilitate mapping and breeding efforts. A seedling straw test screening method provided a quick assay to phenotype the population for response to WM isolate 1980. Nineteen MAGIC lines were identified with improved resistance. For genome-wide association studies (GWAS), the data was transformed into three phenotypic distributions-quantitative, polynomial, and binomial-and coupled with ∼52,000 single-nucleotide polymorphisms (SNPs). The three phenotypic distributions identified 30 significant genomic intervals [-log10 (P value) ≥ 3.0]. However, across distributions, four new genomic regions as well as two regions previously reported were found to be associated with resistance. Cumulative R2 values were 57% for binomial distribution using 13 genomic intervals, 41% for polynomial using eight intervals, and 40% for quantitative using 11 intervals. New resistant germplasm as well as new genomic regions associated with resistance are now available for further investigation.
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Affiliation(s)
- Edgar Escobar
- Dep. of Plant Sciences, North Dakota State Univ., Fargo, ND, 50108-6050, USA
| | - Atena Oladzad
- Dep. of Plant Sciences, North Dakota State Univ., Fargo, ND, 50108-6050, USA
- Genomics and Bioinformatics Program, North Dakota State Univ., Fargo, ND, 50108-6050, USA
| | - Kristin Simons
- Dep. of Plant Sciences, North Dakota State Univ., Fargo, ND, 50108-6050, USA
| | - Phillip Miklas
- Grain Legume Genetics and Physiology Research Unit, USDA-ARS, Prosser, WA, 99350, USA
| | - Rian K Lee
- Dep. of Plant Sciences, North Dakota State Univ., Fargo, ND, 50108-6050, USA
- Genomics and Bioinformatics Program, North Dakota State Univ., Fargo, ND, 50108-6050, USA
| | - Stephan Schroder
- Dep. of Plant Sciences, North Dakota State Univ., Fargo, ND, 50108-6050, USA
- Breeding Technology, Hazera, Netherlands
| | - Nonoy Bandillo
- Dep. of Plant Sciences, North Dakota State Univ., Fargo, ND, 50108-6050, USA
| | - Michael Wunsch
- Carrington Research and Extension Center, North Dakota State Univ, Carrington, ND, 58421-0219, USA
| | - Phillip E McClean
- Dep. of Plant Sciences, North Dakota State Univ., Fargo, ND, 50108-6050, USA
- Genomics and Bioinformatics Program, North Dakota State Univ., Fargo, ND, 50108-6050, USA
| | - Juan M Osorno
- Dep. of Plant Sciences, North Dakota State Univ., Fargo, ND, 50108-6050, USA
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Genome-Wide Characterization and Expression Analysis of KH Family Genes Response to ABA and SA in Arabidopsis thaliana. Int J Mol Sci 2022; 23:ijms23010511. [PMID: 35008936 PMCID: PMC8745409 DOI: 10.3390/ijms23010511] [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: 11/08/2021] [Revised: 12/24/2021] [Accepted: 12/30/2021] [Indexed: 02/05/2023] Open
Abstract
K-homologous (KH) family is a type of nucleic acid-binding protein containing the KH domain and has been found to affect splicing and transcriptional regulation. However, KH family genes haven’t been investigated in plant species systematically. In this study, we identified 30 genes that belonged to the KH family based on HMM of the KH domain in Arabidopsis thaliana. Phylogenetic tree analysis showed that the KH family is grouped into three subgroups. Synteny analysis showed that AtKH9 and AtKH29 have the conserved synteny relationship between A. thaliana and the other five species. The AtKH9 and AtKH29 were located in the cytoplasm and nucleus. The seed germination rates of the mutants atkh9 and atkh29 were higher than wild-type after abscisic acid (ABA) and salicylic acid (SA) treatments. In addition, the expression of ABA-related genes, such as ABRE-binding factor 2 (ABF2), ABRE-binding factor 4 (ABF4), and delta 1-pyrroline-5-carboxylate synthase (P5CS), and an SA-related gene pathogenesis-related proteins b (PR1b) were downregulated after ABA and SA treatments, respectively. These results suggested that atkh9 and atkh29 mutants inhibit the effect of ABA and SA on seed germination. In conclusion, our results provide valuable information for further exploration of the function of KH family genes and propose directions and ideas for the identification and characterization of KH family genes in other plants.
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11
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Wen Y, Raza A, Chu W, Zou X, Cheng H, Hu Q, Liu J, Wei W. Comprehensive In Silico Characterization and Expression Profiling of TCP Gene Family in Rapeseed. Front Genet 2021; 12:794297. [PMID: 34868279 PMCID: PMC8635964 DOI: 10.3389/fgene.2021.794297] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 11/01/2021] [Indexed: 11/13/2022] Open
Abstract
TCP proteins are plant-specific transcription factors that have multipurpose roles in plant developmental procedures and stress responses. Therefore, a genome-wide analysis was performed to categorize the TCP genes in the rapeseed genome. In this study, a total of 80 BnTCP genes were identified in the rapeseed genome and grouped into two main classes (PCF and CYC/TB1) according to phylogenetic analysis. The universal evolutionary analysis uncovered that BnTCP genes had experienced segmental duplications and positive selection pressure. Gene structure and conserved motif examination presented that Class I and Class II have diverse intron-exon patterns and motifs numbers. Overall, nine conserved motifs were identified and varied from 2 to 7 in all TCP genes; and some of them were gene-specific. Mainly, Class II (PCF and CYC/TB1) possessed diverse structures compared to Class I. We identified four hormone- and four stress-related responsive cis-elements in the promoter regions. Moreover, 32 bna-miRNAs from 14 families were found to be targeting 21 BnTCPs genes. Gene ontology enrichment analysis presented that the BnTCP genes were primarily related to RNA/DNA binding, metabolic processes, transcriptional regulatory activities, etc. Transcriptome-based tissue-specific expression analysis showed that only a few genes (mainly BnTCP9, BnTCP22, BnTCP25, BnTCP48, BnTCP52, BnTCP60, BnTCP66, and BnTCP74) presented higher expression in root, stem, leaf, flower, seeds, and silique among all tested tissues. Likewise, qRT-PCR-based expression analysis exhibited that BnTCP36, BnTCP39, BnTCP53, BnTCP59, and BnTCP60 showed higher expression at certain time points under various hormones and abiotic stress conditions but not by drought and MeJA. Our results opened the new groundwork for future understanding of the intricate mechanisms of BnTCP in various developmental processes and abiotic stress signaling pathways in rapeseed.
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Affiliation(s)
- Yunfei Wen
- College of Agriculture, Yangtze University, Jingzhou, China.,Key Laboratory for Biological Sciences and Genetic Improvement of Oil Crops, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Ali Raza
- Key Laboratory for Biological Sciences and Genetic Improvement of Oil Crops, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Wuhan, China.,Fujian Provincial Key Laboratory of Crop Molecular and Cell Biology, Center of Legume Crop Genetics and Systems Biology/College of Agriculture, Oil Crops Research Institute, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
| | - Wen Chu
- Key Laboratory for Biological Sciences and Genetic Improvement of Oil Crops, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Xiling Zou
- Key Laboratory for Biological Sciences and Genetic Improvement of Oil Crops, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Hongtao Cheng
- Key Laboratory for Biological Sciences and Genetic Improvement of Oil Crops, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Qiong Hu
- Key Laboratory for Biological Sciences and Genetic Improvement of Oil Crops, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Jia Liu
- Key Laboratory for Biological Sciences and Genetic Improvement of Oil Crops, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Wenliang Wei
- College of Agriculture, Yangtze University, Jingzhou, China
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12
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El-Sappah AH, Elbaiomy RG, Elrys AS, Wang Y, Zhu Y, Huang Q, Yan K, Xianming Z, Abbas M, El-Tarabily KA, Li J. Genome-Wide Identification and Expression Analysis of Metal Tolerance Protein Gene Family in Medicago truncatula Under a Broad Range of Heavy Metal Stress. Front Genet 2021; 12:713224. [PMID: 34603378 PMCID: PMC8482800 DOI: 10.3389/fgene.2021.713224] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Accepted: 06/30/2021] [Indexed: 01/02/2023] Open
Abstract
Metal tolerance proteins (MTPs) encompass plant membrane divalent cation transporters to specifically participate in heavy metal stress resistance and mineral acquisition. However, the molecular behaviors and biological functions of this family in Medicago truncatula are scarcely known. A total of 12 potential MTP candidate genes in the M. truncatula genome were successfully identified and analyzed for a phylogenetic relationship, chromosomal distributions, gene structures, docking analysis, gene ontology, and previous gene expression. M. truncatula MTPs (MtMTPs) were further classified into three major cation diffusion facilitator (CDFs) groups: Mn-CDFs, Zn-CDFs, and Fe/Zn-CDFs. The structural analysis of MtMTPs displayed high gene similarity within the same group where all of them have cation_efflux domain or ZT_dimer. Cis-acting element analysis suggested that various abiotic stresses and phytohormones could induce the most MtMTP gene transcripts. Among all MTPs, PF16916 is the specific domain, whereas GLY, ILE, LEU, MET, ALA, SER, THR, VAL, ASN, and PHE amino acids were predicted to be the binding residues in the ligand-binding site of all these proteins. RNA-seq and gene ontology analysis revealed the significant role of MTP genes in the growth and development of M. truncatula. MtMTP genes displayed differential responses in plant leaves, stems, and roots under five divalent heavy metals (Cd2+, Co2+, Mn2+, Zn2+, and Fe2+). Ten, seven, and nine MtMTPs responded to at least one metal ion treatment in the leaves, stems, and roots, respectively. Additionally, MtMTP1.1, MtMTP1.2, and MtMTP4 exhibited the highest expression responses in most heavy metal treatments. Our results presented a standpoint on the evolution of MTPs in M. truncatula. Overall, our study provides a novel insight into the evolution of the MTP gene family in M. truncatula and paves the way for additional functional characterization of this gene family.
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Affiliation(s)
- Ahmed H El-Sappah
- School of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, China.,Genetics Department, Faculty of Agriculture, Zagazig University, Zagazig, Egypt
| | | | - Ahmed S Elrys
- Soil Science Department, Faculty of Agriculture, Zagazig University, Zagazig, Egypt
| | - Yu Wang
- School of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, China
| | - Yumin Zhu
- School of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, China
| | - Qiulan Huang
- College of Tea Science, Yibin University, Yibin, China
| | - Kuan Yan
- School of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, China
| | - Zhao Xianming
- School of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, China
| | - Manzar Abbas
- School of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, China
| | - Khaled A El-Tarabily
- Department of Biology, College of Science, United Arab Emirates University, Al Ain, United Arab Emirates.,Harry Butler Institute, Murdoch University, Murdoch, WA, Australia
| | - Jia Li
- School of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, China
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13
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Du Z, Su Q, Wu Z, Huang Z, Bao J, Li J, Tu H, Zeng C, Fu J, He H. Genome-wide characterization of MATE gene family and expression profiles in response to abiotic stresses in rice (Oryza sativa). BMC Ecol Evol 2021; 21:141. [PMID: 34243710 PMCID: PMC8268253 DOI: 10.1186/s12862-021-01873-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 06/29/2021] [Indexed: 01/09/2023] Open
Abstract
Multidrug and toxic compound extrusion (MATE) proteins are involved in many physiological functions of plant growth and development. Although an increasing number of MATE proteins have been identified, the understanding of MATE proteins is still very limited in rice. In this study, 46 MATE proteins were identified from the rice (Oryza sativa) genome by homology searches and domain prediction. The rice MATE family was divided into four subfamilies based on the phylogenetic tree. Tandem repeats and fragment replication contribute to the expansion of the rice MATE gene family. Gene structure and cis-regulatory elements reveal the potential functions of MATE genes. Analysis of gene expression showed that most of MATE genes were constitutively expressed and the expression patterns of genes in different tissues were analyzed using RNA-seq. Furthermore, qRT-PCR-based analysis showed differential expression patterns in response to salt and drought stress. The analysis results of this study provide comprehensive information on the MATE gene family in rice and will aid in understanding the functional divergence of MATE genes.
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Affiliation(s)
- Zhixuan Du
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Research Center of Super Rice Engineering and Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Qitao Su
- School of Life Sciences, Jinggangshan University, Ji'an, 343009, China
| | - Zheng Wu
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Research Center of Super Rice Engineering and Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Zhou Huang
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Research Center of Super Rice Engineering and Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Jianzhong Bao
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Research Center of Super Rice Engineering and Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Jianbin Li
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Research Center of Super Rice Engineering and Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Hang Tu
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Research Center of Super Rice Engineering and Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Chuihai Zeng
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Research Center of Super Rice Engineering and Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Junru Fu
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Research Center of Super Rice Engineering and Technology, Jiangxi Agricultural University, Nanchang, 330045, China.
| | - Haohua He
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Research Center of Super Rice Engineering and Technology, Jiangxi Agricultural University, Nanchang, 330045, China.
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14
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Hossain MM, Pérez-López E, Todd CD, Wei Y, Bonham-Smith PC. Endomembrane-Targeting Plasmodiophora brassicae Effectors Modulate PAMP Triggered Immune Responses in Plants. Front Microbiol 2021; 12:651279. [PMID: 34276588 PMCID: PMC8282356 DOI: 10.3389/fmicb.2021.651279] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Accepted: 05/31/2021] [Indexed: 11/13/2022] Open
Abstract
Plasmodiophora brassicae is a devastating obligate, intracellular, biotrophic pathogen that causes clubroot disease in crucifer plants. Disease progression is regulated by effector proteins secreted by P. brassicae. Twelve P. brassicae putative effectors (PbPEs), expressed at various stages of disease development [0, 2, 5, 7, 14, 21, and 28 days post inoculation (DPI)] in Arabidopsis and localizing to the plant endomembrane system, were studied for their roles in pathogenesis. Of the 12 PbPEs, seven showed an inhibitory effect on programmed cell death (PCD) as triggered by the PCD inducers, PiINF1 (Phytophthora infestans Infestin 1) and PiNPP1 (P. infestans necrosis causing protein). Showing the strongest level of PCD suppression, PbPE15, a member of the 2-oxoglutarate (2OG) and Fe (II)-dependent oxygenase superfamily and with gene expression during later stages of infection, appears to have a role in tumorigenesis as well as defense signaling in plants. PbPE13 produced an enhanced PiINF1-induced PCD response. Transient expression, in Nicotiana benthamiana leaves of these PbPEs minus the signal peptide (SP) (Δsp PbPEGFPs), showed localization to the endomembrane system, targeting the endoplasmic reticulum (ER), Golgi bodies and nucleo-cytoplasm, suggesting roles in manipulating plant cell secretion and vesicle trafficking. Δsp PbPE13GFP localized to plasma membrane (PM) lipid rafts with an association to plasmodesmata, suggesting a role at the cell-to-cell communication junction. Membrane relocalization of Δsp PbPE13GFP, triggered by flagellin N-terminus of Pseudomonas aeruginosa (flg22 - known to elicit a PAMP triggered immune response in plants), supports its involvement in raft-mediated immune signaling. This study is an important step in deciphering P. brassicae effector roles in the disruption of plant immunity to clubroot disease.
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Affiliation(s)
| | - Edel Pérez-López
- Department of Plant Sciences, Laval University, CRIV, Quebec City, QC, Canada
| | - Christopher D Todd
- Department of Biology, University of Saskatchewan, Saskatoon, SK, Canada
| | - Yangdou Wei
- Department of Biology, University of Saskatchewan, Saskatoon, SK, Canada
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15
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Ali E, Saand MA, Khan AR, Shah JM, Feng S, Ming C, Sun P. Genome-wide identification and expression analysis of detoxification efflux carriers (DTX) genes family under abiotic stresses in flax. PHYSIOLOGIA PLANTARUM 2021; 171:483-501. [PMID: 32270877 DOI: 10.1111/ppl.13105] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 03/31/2020] [Accepted: 04/04/2020] [Indexed: 05/19/2023]
Abstract
The detoxification efflux carriers (DTX)/multidrug and toxic compound extrusion (MATE) transporters encompass an ancient gene family of secondary transporters involved in the process of plant detoxification. A genome-wide analysis of these transporters was carried out in order to better understand the transport of secondary metabolites in flaxseed genome (Linum usitassimum). A total of 73 genes coding for DTX/MATE transporters were identified. Gene structure, protein domain and motif organization were found to be notably conserved over the distinct phylogenetic groups, showing the evolutionary significant role of each class. Gene ontology (GO) annotation revealed a link to transporter activities, response to stimulus and localizations. The presence of various hormone and stress-responsive cis-regulatory elements in promoter regions could be directly correlated with the alteration of their transcripts. Tertiary structure showed conservation for pore size and constrains in the pore, which indicate their involvement in the exclusion of toxic substances from the cell. MicroRNA target analysis revealed that LuDTXs genes were targeted by different classes of miRNA families. Twelve LuDTX genes were chosen for further quantitative real-time polymerase chain reaction analysis in response to cold, salinity and cadmium stress at 0, 6, 12 and 24 hours after treatment. Altogether, the identified members of the DTX gene family, their expression profile, phylogenetic and miRNAs analysis might provide opportunities for future functional validation of this important gene family in flax.
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Affiliation(s)
- Essa Ali
- Department of Food Science and Technology, Zhejiang University of Technology, Zhejiang, 310014, China
| | - Mumtaz Ali Saand
- Department of Botany, Shah Abdul Latif University, Sindh, 66020, Pakistan
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, 571339, China
| | - Ali Raza Khan
- Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | | | - Simin Feng
- Department of Food Science and Technology, Zhejiang University of Technology, Zhejiang, 310014, China
| | - Cai Ming
- Department of Food Science and Technology, Zhejiang University of Technology, Zhejiang, 310014, China
| | - Peilong Sun
- Department of Food Science and Technology, Zhejiang University of Technology, Zhejiang, 310014, China
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16
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Ding C, Chen C, Su N, Lyu W, Yang J, Hu Z, Zhang M. Identification and characterization of a natural SNP variant in ALTERNATIVE OXIDASE gene associated with cold stress tolerance in watermelon. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2021; 304:110735. [PMID: 33568287 DOI: 10.1016/j.plantsci.2020.110735] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 10/23/2020] [Accepted: 10/24/2020] [Indexed: 06/12/2023]
Abstract
Alternative oxidase (AOX) is a mitochondrial enzyme encoded by a small nuclear gene family, which contains the two subfamilies, AOX1 and AOX2. In the present study on watermelon (Citrullus lanatus), only one ClAOX gene, belonging to AOX2 subfamily but having a similar gene structure to AtAOX1a, was found in the watermelon genome. The expression analysis suggested that ClAOX had the constitutive expression feature of AOX2 subfamily, but was cold inducible, which is normally considered an AOX1 subfamily feature. Moreover, one single nucleotide polymorphism (SNP) in ClAOX sequence, which led to the change from Lys (N) to Asn (K) in the 96th amino acids, was found among watermelon subspecies. Ectopic expression of two ClAOX alleles in the Arabidopsis aox1a knock-out mutant indicated that ClAOXK-expressing plants had stronger cold tolerance than aox1a mutant and ClAOXN-expressing plants. Our findings suggested watermelon genome contained a single ClAOX that possessed the expression features of both AOX1 and AOX2 subfamilies. A naturally existing SNP in ClAOX differentiated the cold tolerance of transgenic Arabidopsis plants, impling a possibility this gene might be a functional marker for stress-tolerance breeding.
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Affiliation(s)
- Changqing Ding
- Laboratory of Germplasm Innovation and Molecular Breeding, Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, PR China
| | - Cuiting Chen
- Laboratory of Germplasm Innovation and Molecular Breeding, Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, PR China
| | - Nan Su
- Laboratory of Germplasm Innovation and Molecular Breeding, Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, PR China
| | - Wenhui Lyu
- Laboratory of Germplasm Innovation and Molecular Breeding, Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, PR China
| | - Jinghua Yang
- Laboratory of Germplasm Innovation and Molecular Breeding, Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, PR China; Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture, Hangzhou 310058, PR China
| | - Zhongyuan Hu
- Laboratory of Germplasm Innovation and Molecular Breeding, Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, PR China; Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture, Hangzhou 310058, PR China.
| | - Mingfang Zhang
- Laboratory of Germplasm Innovation and Molecular Breeding, Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, PR China; Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture, Hangzhou 310058, PR China
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17
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Liu Z, Shi L, Yang S, Qiu S, Ma X, Cai J, Guan D, Wang Z, He S. A conserved double-W box in the promoter of CaWRKY40 mediates autoregulation during response to pathogen attack and heat stress in pepper. MOLECULAR PLANT PATHOLOGY 2021; 22:3-18. [PMID: 33151622 PMCID: PMC7749755 DOI: 10.1111/mpp.13004] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 09/01/2020] [Accepted: 09/07/2020] [Indexed: 05/11/2023]
Abstract
CaWRKY40 was previously found to be transcriptionally up-regulated by Ralstonia solanacearum inoculation (RSI) or heat stress (HS), but the underlying mechanism remains unknown. Herein, we report that a double-W box-element (DWE) in the promoter of CaWRKY40 is critical for these responses. The upstream W box unit WI of this composite element is crucial for preferential binding by CaWRKY40 and responsiveness to RSI or HS. DWE-driven CaWRKY40 can be transcriptionally and nonspecifically regulated by itself and by CaWRKY58 and CaWRKY27. The DWE was also found in the promoters of CaWRKY40 orthologs, including AtWRKY40, VvWRKY40, GmWRKY40, CplWRKY40, SaWRKY40, SpWRKY40, NtWRKY40, and NaWRKY40. DWEAtWRKY40 was analogous to DWECaWRKY40 by responding to RSI or HS and AtWRKY40 expression. These data suggest that a conserved response of plants to pathogen infection or HS is probably mediated by binding of the DWE by WRKY40.
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Affiliation(s)
- Zhi‐Qin Liu
- National Education Minster Key Laboratory of Plant Genetic Improvement and Comprehensive UtilizationFujian Agriculture and Forestry UniversityFuzhouChina
- College of AgricultureFujian Agriculture and Forestry UniversityFuzhouChina
| | - Lan‐Ping Shi
- National Education Minster Key Laboratory of Plant Genetic Improvement and Comprehensive UtilizationFujian Agriculture and Forestry UniversityFuzhouChina
- College of AgricultureFujian Agriculture and Forestry UniversityFuzhouChina
| | - Sheng Yang
- National Education Minster Key Laboratory of Plant Genetic Improvement and Comprehensive UtilizationFujian Agriculture and Forestry UniversityFuzhouChina
- College of AgricultureFujian Agriculture and Forestry UniversityFuzhouChina
| | - Shan‐Shan Qiu
- National Education Minster Key Laboratory of Plant Genetic Improvement and Comprehensive UtilizationFujian Agriculture and Forestry UniversityFuzhouChina
- College of AgricultureFujian Agriculture and Forestry UniversityFuzhouChina
| | - Xiao‐Ling Ma
- National Education Minster Key Laboratory of Plant Genetic Improvement and Comprehensive UtilizationFujian Agriculture and Forestry UniversityFuzhouChina
- College of AgricultureFujian Agriculture and Forestry UniversityFuzhouChina
| | - Jin‐Sen Cai
- National Education Minster Key Laboratory of Plant Genetic Improvement and Comprehensive UtilizationFujian Agriculture and Forestry UniversityFuzhouChina
- College of AgricultureFujian Agriculture and Forestry UniversityFuzhouChina
| | - De‐Yi Guan
- National Education Minster Key Laboratory of Plant Genetic Improvement and Comprehensive UtilizationFujian Agriculture and Forestry UniversityFuzhouChina
- College of AgricultureFujian Agriculture and Forestry UniversityFuzhouChina
| | - Zong‐Hua Wang
- Fujian University Key Laboratory for Plant‐Microbe InteractionCollege of Plant ProtectionFujian Agriculture and Forestry UniversityFuzhouChina
- Institute of OceanographyMinjiang UniversityFuzhouChina
| | - Shui‐Lin He
- National Education Minster Key Laboratory of Plant Genetic Improvement and Comprehensive UtilizationFujian Agriculture and Forestry UniversityFuzhouChina
- College of AgricultureFujian Agriculture and Forestry UniversityFuzhouChina
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18
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Wen Y, Raza A, Chu W, Zou X, Cheng H, Hu Q, Liu J, Wei W. Comprehensive In Silico Characterization and Expression Profiling of TCP Gene Family in Rapeseed. Front Genet 2021. [PMID: 34868279 DOI: 10.3389/fgene2021.794297] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/20/2023] Open
Abstract
TCP proteins are plant-specific transcription factors that have multipurpose roles in plant developmental procedures and stress responses. Therefore, a genome-wide analysis was performed to categorize the TCP genes in the rapeseed genome. In this study, a total of 80 BnTCP genes were identified in the rapeseed genome and grouped into two main classes (PCF and CYC/TB1) according to phylogenetic analysis. The universal evolutionary analysis uncovered that BnTCP genes had experienced segmental duplications and positive selection pressure. Gene structure and conserved motif examination presented that Class I and Class II have diverse intron-exon patterns and motifs numbers. Overall, nine conserved motifs were identified and varied from 2 to 7 in all TCP genes; and some of them were gene-specific. Mainly, Class II (PCF and CYC/TB1) possessed diverse structures compared to Class I. We identified four hormone- and four stress-related responsive cis-elements in the promoter regions. Moreover, 32 bna-miRNAs from 14 families were found to be targeting 21 BnTCPs genes. Gene ontology enrichment analysis presented that the BnTCP genes were primarily related to RNA/DNA binding, metabolic processes, transcriptional regulatory activities, etc. Transcriptome-based tissue-specific expression analysis showed that only a few genes (mainly BnTCP9, BnTCP22, BnTCP25, BnTCP48, BnTCP52, BnTCP60, BnTCP66, and BnTCP74) presented higher expression in root, stem, leaf, flower, seeds, and silique among all tested tissues. Likewise, qRT-PCR-based expression analysis exhibited that BnTCP36, BnTCP39, BnTCP53, BnTCP59, and BnTCP60 showed higher expression at certain time points under various hormones and abiotic stress conditions but not by drought and MeJA. Our results opened the new groundwork for future understanding of the intricate mechanisms of BnTCP in various developmental processes and abiotic stress signaling pathways in rapeseed.
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Affiliation(s)
- Yunfei Wen
- College of Agriculture, Yangtze University, Jingzhou, China
- Key Laboratory for Biological Sciences and Genetic Improvement of Oil Crops, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Ali Raza
- Key Laboratory for Biological Sciences and Genetic Improvement of Oil Crops, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Wuhan, China
- Fujian Provincial Key Laboratory of Crop Molecular and Cell Biology, Center of Legume Crop Genetics and Systems Biology/College of Agriculture, Oil Crops Research Institute, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
| | - Wen Chu
- Key Laboratory for Biological Sciences and Genetic Improvement of Oil Crops, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Xiling Zou
- Key Laboratory for Biological Sciences and Genetic Improvement of Oil Crops, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Hongtao Cheng
- Key Laboratory for Biological Sciences and Genetic Improvement of Oil Crops, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Qiong Hu
- Key Laboratory for Biological Sciences and Genetic Improvement of Oil Crops, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Jia Liu
- Key Laboratory for Biological Sciences and Genetic Improvement of Oil Crops, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Wenliang Wei
- College of Agriculture, Yangtze University, Jingzhou, China
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19
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Li R, Zhu F, Duan D. Function analysis and stress-mediated cis-element identification in the promoter region of VqMYB15. PLANT SIGNALING & BEHAVIOR 2020; 15:1773664. [PMID: 32475217 PMCID: PMC8570707 DOI: 10.1080/15592324.2020.1773664] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 05/17/2020] [Accepted: 05/19/2020] [Indexed: 05/21/2023]
Abstract
The transcription factor MYB15 plays an important role in grape basal immunity, and its promoter can be used as a potential target in resistance breeding. However, the regulatory mechanisms of cis-elements in its promoter region under a variety of stresses remain unclear. In this study, we identified some putative cis-regulatory elements present upstream of MYB15 in Vitis quinquangularis Shanyang (pVqMYB15_SY) and subsequently characterized the function of these elements using reporter assays. Our results showed that TCA-elements 1 and 2, ABRE, MYC and 3-AF1 binding site 1 are key cis-regulatory elements in pVqMYB15_SY and play important roles in plant bio/abiotic stress resistance.
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Affiliation(s)
- Ruixiang Li
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an, China
| | - Fanding Zhu
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an, China
| | - Dong Duan
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an, China
- CONTACT Dong Duan Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an710069, China
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Gordon A, McCartney C, Knox RE, Ereful N, Hiebert CW, Konkin DJ, Hsueh YC, Bhadauria V, Sgroi M, O'Sullivan DM, Hadley C, Boyd LA, Menzies JG. Genetic and transcriptional dissection of resistance to Claviceps purpurea in the durum wheat cultivar Greenshank. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:1873-1886. [PMID: 32060572 PMCID: PMC7237535 DOI: 10.1007/s00122-020-03561-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 01/29/2020] [Indexed: 06/02/2023]
Abstract
Four QTL for ergot resistance (causal pathogen Claviceps purpurea) have been identified in the durum wheat cultivar Greenshank. Claviceps purpurea is a pathogen of grasses that infects flowers, replacing the seed with an ergot sclerotium. Ergot presents a significant problem to rye, barley and wheat, in particular hybrid seed production systems. In addition, there is evidence that the highly toxic alkaloids that accumulate within sclerotia can cross-contaminate otherwise healthy grain. Host resistance to C. purpurea is rare, few resistance loci having been identified. In this study, four ergot resistance loci are located on chromosomes 1B, 2A, 5A and 5B in the durum wheat cv. Greenshank. Ergot resistance was assessed through analysis of phenotypes associated with C. purpurea infection, namely the number of inoculated flowers that produced sclerotia, or resulted in ovary death but no sclerotia, the levels of honeydew produced, total sclerotia weight and average sclerotia weight and size per spike. Ergot testing was undertaken in Canada and the UK. A major effect QTL, QCp.aafc.DH-2A, was detected in both the Canadian and UK experiments and had a significant effect on honeydew production levels. QCp.aafc.DH-5B had the biggest influence on total sclerotia weight per spike. QCp.aafc.DH-1B was only detected in the Canadian experiments and QCp.aafc.DH-5A in the UK experiment. An RNASeq analysis, undertaken to identify wheat differentially expressed genes associated with different combinations of the four ergot resistance QTL, revealed a disproportionate number of DEGs locating to the QCp.aafc.DH-1B, QCp.aafc.DH-2A and QCp.aafc.DH-5B QTL intervals.
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Affiliation(s)
- Anna Gordon
- NIAB, 93 Lawrence Weaver Road, Cambridge, CB3 0LE, UK.
| | - Curt McCartney
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB, R6M 1Y5, Canada
| | - Ron E Knox
- Swift Current Research and Development Centre, Agriculture and Agri-Food Canada, Swift Current, SK, Canada
| | - Nelzo Ereful
- NIAB, 93 Lawrence Weaver Road, Cambridge, CB3 0LE, UK
| | - Colin W Hiebert
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB, R6M 1Y5, Canada
| | - David J Konkin
- Aquatic and Crop Resource Development, National Research Council Canada, Saskatoon, SK, Canada
| | - Ya-Chih Hsueh
- Aquatic and Crop Resource Development, National Research Council Canada, Saskatoon, SK, Canada
| | - Vijai Bhadauria
- Swift Current Research and Development Centre, Agriculture and Agri-Food Canada, Swift Current, SK, Canada
| | - Mara Sgroi
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, UK
| | - Donal M O'Sullivan
- School of Agriculture, Policy and Development, University of Reading, Whiteknights, Reading, RG6 6AR, UK
| | - Caroline Hadley
- School of Agriculture, Policy and Development, University of Reading, Whiteknights, Reading, RG6 6AR, UK
| | - Lesley A Boyd
- NIAB, 93 Lawrence Weaver Road, Cambridge, CB3 0LE, UK
| | - Jim G Menzies
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB, R6M 1Y5, Canada.
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21
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Genomic Dissection of Anthracnose ( Colletotrichum sublineolum) Resistance Response in Sorghum Differential Line SC112-14. G3-GENES GENOMES GENETICS 2020; 10:1403-1412. [PMID: 32102832 PMCID: PMC7144069 DOI: 10.1534/g3.120.401121] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Sorghum production is expanding to warmer and more humid regions where its production is being limited by multiple fungal pathogens. Anthracnose, caused by Colletotrichum sublineolum, is one of the major diseases in these regions, where it can cause yield losses of both grain and biomass. In this study, 114 recombinant inbred lines (RILs) derived from resistant sorghum line SC112-14 were evaluated at four distinct geographic locations in the United States for response to anthracnose. A genome scan using a high-density linkage map of 3,838 single nucleotide polymorphisms (SNPs) detected two loci at 5.25 and 1.18 Mb on chromosomes 5 and 6, respectively, that explain up to 59% and 44% of the observed phenotypic variation. A bin-mapping approach using a subset of 31 highly informative RILs was employed to determine the disease response to inoculation with ten anthracnose pathotypes in the greenhouse. A genome scan showed that the 5.25 Mb region on chromosome 5 is associated with a resistance response to nine pathotypes. Five SNP markers were developed and used to fine map the locus on chromosome 5 by evaluating 1,500 segregating F2:3 progenies. Based on the genotypic and phenotypic analyses of 11 recombinants, the locus was narrowed down to a 470-kb genomic region. Following a genome-wide association study based on 574 accessions previously phenotyped and genotyped, the resistance locus was delimited to a 34-kb genomic interval with five candidate genes. All five candidate genes encode proteins associated with plant immune systems, suggesting they may act in synergy in the resistance response.
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22
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Lopez-Ortiz C, Peña-Garcia Y, Natarajan P, Bhandari M, Abburi V, Dutta SK, Yadav L, Stommel J, Nimmakayala P, Reddy UK. The ankyrin repeat gene family in Capsicum spp: Genome-wide survey, characterization and gene expression profile. Sci Rep 2020; 10:4044. [PMID: 32132613 PMCID: PMC7055287 DOI: 10.1038/s41598-020-61057-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2019] [Accepted: 02/20/2020] [Indexed: 11/09/2022] Open
Abstract
The ankyrin (ANK) repeat protein family is largely distributed across plants and has been found to participate in multiple processes such as plant growth and development, hormone response, response to biotic and abiotic stresses. It is considered as one of the major markers of capsaicin content in pepper fruits. In this study, we performed a genome-wide identification and expression analysis of genes encoding ANK proteins in three Capsicum species: Capsicum baccatum, Capsicum annuum and Capsicum chinense. We identified a total of 87, 85 and 96 ANK genes in C. baccatum, C. annuum and C. chinense genomes, respectively. Next, we performed a comprehensive bioinformatics analysis of the Capsicum ANK gene family including gene chromosomal localization, Cis-elements, conserved motif identification, intron/exon structural patterns and gene ontology classification as well as profile expression. Phylogenetic and domain organization analysis grouped the Capsicum ANK gene family into ten subfamilies distributed across all 12 pepper chromosomes at different densities. Analysis of the expression of ANK genes in leaf and pepper fruits suggested that the ANKs have specific expression patterns at various developmental stages in placenta tissue. Our results provide valuable information for further studies of the evolution, classification and putative functions of ANK genes in pepper.
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Affiliation(s)
- Carlos Lopez-Ortiz
- Department of Biology, Gus R. Douglass Institute, West Virginia State University, Institute, West Virginia, United States of America
| | - Yadira Peña-Garcia
- Department of Biology, Gus R. Douglass Institute, West Virginia State University, Institute, West Virginia, United States of America
| | - Purushothaman Natarajan
- Department of Biology, Gus R. Douglass Institute, West Virginia State University, Institute, West Virginia, United States of America.,Department of Genetic Engineering, School of Bioengineering, SRM Institute of Science and Technology, Kattankulathur, 603203, India
| | - Menuka Bhandari
- Department of Biology, Gus R. Douglass Institute, West Virginia State University, Institute, West Virginia, United States of America
| | - Venkata Abburi
- Department of Biology, Gus R. Douglass Institute, West Virginia State University, Institute, West Virginia, United States of America
| | - Sudip Kumar Dutta
- Department of Biology, Gus R. Douglass Institute, West Virginia State University, Institute, West Virginia, United States of America.,ICAR RC NEH Region, Mizoram Centre, Kolasib, Mizoram, India
| | - Lav Yadav
- Department of Biology, Gus R. Douglass Institute, West Virginia State University, Institute, West Virginia, United States of America
| | - John Stommel
- Genetic Improvement of Fruits and Vegetables Laboratory (USDA, ARS), Beltsville, MD, 20705, USA
| | - Padma Nimmakayala
- Department of Biology, Gus R. Douglass Institute, West Virginia State University, Institute, West Virginia, United States of America.
| | - Umesh K Reddy
- Department of Biology, Gus R. Douglass Institute, West Virginia State University, Institute, West Virginia, United States of America.
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Chen L, Wu Q, He W, He T, Wu Q, Miao Y. Combined De Novo Transcriptome and Metabolome Analysis of Common Bean Response to Fusarium oxysporum f. sp. phaseoli Infection. Int J Mol Sci 2019; 20:ijms20246278. [PMID: 31842411 PMCID: PMC6941151 DOI: 10.3390/ijms20246278] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2019] [Revised: 12/09/2019] [Accepted: 12/11/2019] [Indexed: 12/17/2022] Open
Abstract
Molecular changes elicited by common bean (Phaseolus vulgaris L.) in response to Fusarium oxysproum f. sp. Phaseoli (FOP) remain elusive. We studied the changes in root metabolism during common bean–FOP interactions using a combined de novo transcriptome and metabolome approach. Our results demonstrated alterations of transcript levels and metabolite concentrations in common bean roots 24 h post infection as compared to control. The transcriptome and metabolome responses in common bean roots revealed significant changes in structural defense i.e., cell-wall loosening and weakening characterized by hyper accumulation of cell-wall loosening and degradation related transcripts. The levels of pathogenesis related genes were significantly higher upon FOP inoculation. Interestingly, we found the involvement of glycosylphosphatidylinositol- anchored proteins (GPI-APs) in signal transduction in response to FOP infection. Our results confirmed that hormones have strong role in signaling pathways i.e., salicylic acid, jasmonate, and ethylene pathways. FOP induced energy metabolism and nitrogen mobilization in infected common bean roots as compared to control. Importantly, the flavonoid biosynthesis pathway was the most significantly enriched pathway in response to FOP infection as revealed by the combined transcriptome and metabolome analysis. Overall, the observed modulations in the transcriptome and metabolome flux as outcome of several orchestrated molecular events are determinant of host’s role in common bean–FOP interactions.
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Affiliation(s)
- Limin Chen
- Integrated Plant Protection Center, Lishui Institute of Agricultural and Forestry Sciences, 827 Liyang Stress, Lishui 323000, China
| | - Quancong Wu
- Integrated Plant Protection Center, Lishui Institute of Agricultural and Forestry Sciences, 827 Liyang Stress, Lishui 323000, China
- Correspondence: ; Tel.: +86-578-2028375; Fax: +86-578-2173070
| | - Weimin He
- Integrated Plant Protection Center, Lishui Institute of Agricultural and Forestry Sciences, 827 Liyang Stress, Lishui 323000, China
| | - Tianjun He
- Integrated Plant Protection Center, Lishui Institute of Agricultural and Forestry Sciences, 827 Liyang Stress, Lishui 323000, China
| | - Qianqian Wu
- School of Agricultural and Food Science, Zhejiang A&F University, Hangzhou 311300, China
| | - Yeminzi Miao
- Integrated Plant Protection Center, Lishui Institute of Agricultural and Forestry Sciences, 827 Liyang Stress, Lishui 323000, China
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Liu Z, Shi L, Weng Y, Zou H, Li X, Yang S, Qiu S, Huang X, Huang J, Hussain A, Zhang K, Guan D, He S. ChiIV3 Acts as a Novel Target of WRKY40 to Mediate Pepper Immunity Against Ralstonia solanacearum Infection. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2019; 32:1121-1133. [PMID: 31039081 DOI: 10.1094/mpmi-11-18-0313-r] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
ChiIV3, a chitinase of pepper (Capsicum annuum), stimulates cell death in pepper plants. However, there are only scarce reports on its role in resistance against bacterial wilt disease such as that caused by Ralstonia solanacearum and their transcriptional regulation. In this study, the silencing of ChiIV3 in pepper plants significantly reduced the resistance to R. solanacearum. The transcript of ChiIV3 was induced by R. solanacearum inoculation (RSI) as well as exogenous application of methyl jasmonate and abscisic acid. The bioinformatics analysis revealed that the ChiIV3 promoter consists of multiple stress-related cis elements, including six W-boxes and one MYB1AT. With the 5' deletion assay in the ChiIV3 promoter, the W4-box located from -640 to -635 bp was identified as the cis element that is required for the response to RSI. In addition, the W4-box element was shown to be essential for the binding of the ChiIV3 promoter by the WRKY40 transcription factor, which is known to positively regulate the defense response to R. solanacearum. Site-directed mutagenesis in the W4-box sequence impaired the binding of WRKY40 to the ChiIV3 promoter. Subsequently, the transcription of ChiIV3 decreased in WRKY40-silenced pepper plants. These results demonstrated that the expression of the defense gene ChiIV3 is controlled through multiple modes of regulation, and WRKY40 directly binds to the W4-box element of the ChiIV3 promoter region for its transcriptional regulation.
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Affiliation(s)
- Zhiqin Liu
- Ministry of Education Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- College of Crop Science, Fujian Agriculture and Forestry University
| | - Lanping Shi
- Ministry of Education Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- College of Crop Science, Fujian Agriculture and Forestry University
| | - Yahong Weng
- Ministry of Education Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- College of Crop Science, Fujian Agriculture and Forestry University
| | - Huasong Zou
- College of Plant Protection, Fujian Agriculture and Forestry University
| | - Xia Li
- Ministry of Education Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- College of Crop Science, Fujian Agriculture and Forestry University
| | - Sheng Yang
- Ministry of Education Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- College of Crop Science, Fujian Agriculture and Forestry University
| | - Shanshan Qiu
- Ministry of Education Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- College of Crop Science, Fujian Agriculture and Forestry University
| | - Xueying Huang
- Ministry of Education Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- College of Crop Science, Fujian Agriculture and Forestry University
| | - Jinfeng Huang
- Ministry of Education Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- College of Crop Science, Fujian Agriculture and Forestry University
| | - Ansar Hussain
- Ministry of Education Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- College of Crop Science, Fujian Agriculture and Forestry University
| | - Kan Zhang
- Ministry of Education Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- College of Crop Science, Fujian Agriculture and Forestry University
| | - Deyi Guan
- Ministry of Education Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- College of Crop Science, Fujian Agriculture and Forestry University
| | - Shuilin He
- Ministry of Education Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- College of Crop Science, Fujian Agriculture and Forestry University
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25
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Liu S, Ge F, Huang W, Lightfoot DA, Peng D. Effective identification of soybean candidate genes involved in resistance to soybean cyst nematode via direct whole genome re-sequencing of two segregating mutants. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:2677-2687. [PMID: 31250041 DOI: 10.1007/s00122-019-03381-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 06/14/2019] [Indexed: 06/09/2023]
Abstract
KEY MESSAGE Three soybean candidate genes involved in resistance to soybean cyst nematode race 4 were identified via direct whole genome re-sequencing of two segregating mutants. The genes conferring resistance to soybean cyst nematode (SCN) race 4 (Hg type 1.2.3.5.7) in soybean (Glycine max L. Merr.) remains unknown. Next generation sequencing-based methods identify a wide range of targets, it is difficult to identify genes underlying traits. Use of the MutMap and QTL-seq methods to identify trait candidate genes needs backcrossing and is very time-consuming. Here we report a simple method to effectively identify candidate genes involved in resistance to SCN race 4. Two ethane methylsulfonate mutagenized mutants of soybean 'PI 437654', whose SCN race 4-infection phenotype altered, were selected. Six relevant whole genomes were re-sequenced, and then calling of genomic variants (SNPs and InDels) was conducted and compared to 'Williams 82'. The comparison eliminated many genomic variants from the mutant lines that overlapped two non-phenotypic but mutant progeny plants, wild-type PI 437654 and 'Zhonghuang 13'. Finally, only 27 mutations were found among 10 genes. Of these 10 genes, 3 genes, Glyma.09g054000, Glyma.16g065700 and Glyma.18g192200 were overlapped between two phenotypic mutant progeny plants. Therefore, the three genes may be the candidate genes involved in resistance of PI 437654 to soybean cyst nematode race 4. This method simplifies the effective identification of candidate genes.
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Affiliation(s)
- Shiming Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, People's Republic of China.
- College of Plant Protection, Hunan Agricultural University, Changsha, 410128, People's Republic of China.
| | - Fengyong Ge
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, People's Republic of China
| | - Wenkun Huang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, People's Republic of China
| | - David A Lightfoot
- College of Agricultural Sciences, Southern Illinois University, Carbondale, IL, 62901, USA
| | - Deliang Peng
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, People's Republic of China
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26
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Mapping Gene Markers for Apple Fruit Ring Rot Disease Resistance Using a Multi-omics Approach. G3-GENES GENOMES GENETICS 2019; 9:1663-1678. [PMID: 30910819 PMCID: PMC6505150 DOI: 10.1534/g3.119.400167] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Apple fruit ring rot (FRR), caused by Botryosphaeria dothidea, is a worldwide disease that impacts Asian apple production regions. However, no substantial progress has thus far been made toward the mapping of candidate genes or the development of effective genetic makers. In this five-year study, the resistance of 1,733 F1 hybrids from the cross ‘Jonathan’ × ‘Golden Delicious’ was phenotyped by non-wounding inoculation with four B. dothidea isolates. We first conducted systematic comparison of different analytic strategies for bulk segregant analysis by re-sequencing (BSA-Seq) and obtained suitable one for outbreeding species such as Malus. Forty-six quantitative trait loci (QTL) for resistance/susceptibility to the four isolates, including one QTL ‘hotspot’ on chromosome 14, were identified via BSA-Seq. Using integrated multi-omics strategies including RNA-sequencing, parental re-sequencing, BSA-Seq and meta-analysis of RNA-sequencing, fifty-seven candidate genes and corresponding functional mutations from the QTL were predicted. Functional mutations located on the candidate genes were validated using kompetitive allele-specific PCR in hybrids and Malus germplasm accessions with extremely resistant/susceptible phenotypes. Ten effective markers for apple ring rot were developed. The results provide an example of rapid candidate gene mapping for complex traits in outbreeding species.
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27
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Sircar S, Parekh N. Meta-analysis of drought-tolerant genotypes in Oryza sativa: A network-based approach. PLoS One 2019; 14:e0216068. [PMID: 31059518 PMCID: PMC6502313 DOI: 10.1371/journal.pone.0216068] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Accepted: 04/12/2019] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Drought is a severe environmental stress. It is estimated that about 50% of the world rice production is affected mainly by drought. Apart from conventional breeding strategies to develop drought-tolerant crops, innovative computational approaches may provide insights into the underlying molecular mechanisms of stress response and identify drought-responsive markers. Here we propose a network-based computational approach involving a meta-analytic study of seven drought-tolerant rice genotypes under drought stress. RESULTS Co-expression networks enable large-scale analysis of gene-pair associations and tightly coupled clusters that may represent coordinated biological processes. Considering differentially expressed genes in the co-expressed modules and supplementing external information such as resistance/tolerance QTLs, transcription factors, network-based topological measures, we identify and prioritize drought-adaptive co-expressed gene modules and potential candidate genes. Using the candidate genes that are well-represented across the datasets as 'seed' genes, two drought-specific protein-protein interaction networks (PPINs) are constructed with up- and down-regulated genes. Cluster analysis of the up-regulated PPIN revealed ABA signalling pathway as a central process in drought response with a probable crosstalk with energy metabolic processes. Tightly coupled gene clusters representing up-regulation of core cellular respiratory processes and enhanced degradation of branched chain amino acids and cell wall metabolism are identified. Cluster analysis of down-regulated PPIN provides a snapshot of major processes associated with photosynthesis, growth, development and protein synthesis, most of which are shut down during drought. Differential regulation of phytohormones, e.g., jasmonic acid, cell wall metabolism, signalling and posttranslational modifications associated with biotic stress are elucidated. Functional characterization of topologically important, drought-responsive uncharacterized genes that may play a role in important processes such as ABA signalling, calcium signalling, photosynthesis and cell wall metabolism is discussed. Further transgenic studies on these genes may help in elucidating their biological role under stress conditions. CONCLUSION Currently, a large number of resources for rice functional genomics exist which are mostly underutilized by the scientific community. In this study, a computational approach integrating information from various resources such as gene co-expression networks, protein-protein interactions and pathway-level information is proposed to provide a systems-level view of complex drought-responsive processes across the drought-tolerant genotypes.
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Affiliation(s)
- Sanchari Sircar
- Centre for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad, India
| | - Nita Parekh
- Centre for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad, India
- * E-mail:
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28
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Hu Z, Olatoye MO, Marla S, Morris GP. An Integrated Genotyping-by-Sequencing Polymorphism Map for Over 10,000 Sorghum Genotypes. THE PLANT GENOME 2019; 12:180044. [PMID: 30951089 DOI: 10.3835/plantgenome2018.06.0044] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Mining crop genomic variation can facilitate the genetic research of complex traits and molecular breeding. In sorghum [ L. (Moench)], several large-scale single nucleotide polymorphism (SNP) datasets have been generated using genotyping-by-sequencing of KI reduced representation libraries. However, data reuse has been impeded by differences in reference genome coordinates among datasets. To facilitate reuse of these data, we constructed and characterized an integrated 459,304-SNP dataset for 10,323 sorghum genotypes on the version 3.1 reference genome. The SNP distribution showed high enrichment in subtelomeric chromosome arms and in genic regions (48% of SNPs) and was highly correlated ( = 0.82) to the distribution of KI restriction sites. The genetic structure reflected population differences by botanical race, as well as familial structure among recombinant inbred lines (RILs). Faster linkage disequilibrium decay was observed in the diversity panel than in the RILs, as expected, given the greater opportunity for recombination in diverse populations. To validate the quality and utility of the integrated SNP dataset, we used genome-wide association studies (GWAS) of genebank phenotype data, precisely mapping several known genes (e.g and ) and identifying novel associations for other traits. We further validated the dataset with GWAS of new and published plant height and flowering time data in a nested association mapping population, precisely mapping known genes and identifying epistatic interactions underlying both traits. These findings validate this integrated SNP dataset as a useful genomics resource for sorghum genetics and breeding.
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29
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Kavas M, Kurt Kızıldoğan A, Balık Hİ. Gene expression analysis of bud burst process in European hazelnut ( Corylus avellana L.) using RNA-Seq. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2019; 25:13-29. [PMID: 30804627 PMCID: PMC6352538 DOI: 10.1007/s12298-018-0588-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 07/11/2018] [Accepted: 07/24/2018] [Indexed: 05/27/2023]
Abstract
The control of bud burst process depending on temperature is crucial factor in woody perennial plants to survive in unfavorable ecological conditions. Although it has important economic and agronomic values, little information is available on the molecular mechanism of the bud burst process in Corylus avellana. Here for the first time, we conducted a de novo transcriptome-based experiment using eco-dormant leaf bud tissues. Four transcriptome libraries were constructed from the leaf bud tissues and sequenced via Illumina platform. Transcriptome analysis revealed 86,394 unigenes with a mean length of 1189 nt and an N50 of 1916 nt. Among these unigenes, 63,854 (73.78%) of them were annotated by at least one database. De novo assembled transcripts were enriched in phenylpropanoid metabolism, phytohormone biosynthesis and signal transduction pathways. Analyses of phytohormone-associated genes revealed important changes during bud burst, in response to gibberellic acid, auxin, and brassinosteroids. Approximately 2163 putative transcription factors were predicted, of which the largest number of unique transcripts belonged to the MYB transcription factor family. These results contribute to a better understanding of the regulation of bud burst genes in perennial plants.
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Affiliation(s)
- Musa Kavas
- Department of Agricultural Biotechnology, Faculty of Agriculture, Ondokuz Mayıs University, Samsun, Turkey
| | - Aslıhan Kurt Kızıldoğan
- Department of Agricultural Biotechnology, Faculty of Agriculture, Ondokuz Mayıs University, Samsun, Turkey
| | - Hüseyin İrfan Balık
- Giresun Hazelnut Research Station, Ministry of Food, Agriculture and Livestock, Giresun, Turkey
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30
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Genome-Wide Analysis of Multidrug and Toxic Compound Extrusion ( MATE) Family in Gossypium raimondii and Gossypium arboreum and Its Expression Analysis Under Salt, Cadmium, and Drought Stress. G3-GENES GENOMES GENETICS 2018; 8:2483-2500. [PMID: 29794162 PMCID: PMC6027885 DOI: 10.1534/g3.118.200232] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The extrusion of toxins and substances at a cellular level is a vital life process in plants under abiotic stress. The multidrug and toxic compound extrusion (MATE) gene family plays a large role in the exportation of toxins and other substrates. We carried out a genome-wide analysis of MATE gene families in Gossypium raimondii and Gossypium arboreum and assessed their expression levels under salt, cadmium and drought stresses. We identified 70 and 68 MATE genes in G. raimondii and G. arboreum, respectively. The majority of the genes were predicted to be localized within the plasma membrane, with some distributed in other cell parts. Based on phylogenetic analysis, the genes were subdivided into three subfamilies, designated as M1, M2 and M3. Closely related members shared similar gene structures, and thus were highly conserved in nature and have mainly evolved through purifying selection. The genes were distributed in all chromosomes. Twenty-nine gene duplication events were detected, with segmental being the dominant type. GO annotation revealed a link to salt, drought and cadmium stresses. The genes exhibited differential expression, with GrMATE18, GrMATE34, GaMATE41 and GaMATE51 significantly upregulated under drought, salt and cadmium stress, and these could possibly be the candidate genes. Our results provide the first data on the genome-wide and functional characterization of MATE genes in diploid cotton, and are important for breeders of more stress-tolerant cotton genotypes.
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Ning X, Sun Y, Wang C, Zhang W, Sun M, Hu H, Liu J, Yang L. A Rice CPYC-Type Glutaredoxin OsGRX20 in Protection against Bacterial Blight, Methyl Viologen and Salt Stresses. FRONTIERS IN PLANT SCIENCE 2018; 9:111. [PMID: 29479359 PMCID: PMC5811478 DOI: 10.3389/fpls.2018.00111] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 01/22/2018] [Indexed: 05/23/2023]
Abstract
Glutaredoxins (GRXs) belong to the antioxidants involved in the cellular stress responses. In spite of the identification 48 GRX genes in rice genomes, the biological functions of most of them remain unknown. Especially, the biological roles of members of GRX family in disease resistance are still lacking. Our proteomic analysis found that OsGRX20 increased by 2.7-fold after infection by bacterial blight. In this study, we isolated and characterized the full-length nucleotide sequences of the rice OsGRX20 gene, which encodes a GRX family protein with CPFC active site of CPYC-type class. OsGRX20 protein was localized in nucleus and cytosol, and its transcripts were expressed predominantly in leaves. Several stress- and hormone-related motifs putatively acting as regulatory elements were found in the OsGRX20 promoter. Real-time quantitative PCR analysis indicated that OsGRX20 was expressed at a significantly higher level in leaves of a resistant or tolerant rice genotype, Yongjing 50A, than in a sensitive genotype, Xiushui 11, exposed to bacterial blight, methyl viologen, heat, and cold. Its expression could be induced by salt, PEG-6000, 2,4-D, salicylic acid, jasmonic acid, and abscisic acid treatments in Yongjing 50A. Overexpression of OsGRX20 in rice Xiushui 11 significantly enhanced its resistance to bacterial blight attack, and tolerance to methyl viologen and salt stresses. In contrast, interference of OsGRX20 in Yongjing 50A led to increased susceptibility to bacterial blight, methyl viologen and salt stresses. OsGRX20 restrained accumulation of superoxide radicals in aerial tissue during methyl viologen treatment. Consistently, alterations in OsGRX20 expression affect the ascorbate/dehydroascorbate ratio and the abundance of transcripts encoding four reactive oxygen species scavenging enzymes after methyl viologen-induced stress. Our results demonstrate that OsGRX20 functioned as a positive regulator in rice tolerance to multiple stresses, which may be of significant use in the genetic improvement of rice resistance.
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Le Provost G, Lesur I, Lalanne C, Da Silva C, Labadie K, Aury JM, Leple JC, Plomion C. Implication of the suberin pathway in adaptation to waterlogging and hypertrophied lenticels formation in pedunculate oak (Quercus robur L.). TREE PHYSIOLOGY 2016; 36:1330-1342. [PMID: 27358207 DOI: 10.1093/treephys/tpw056] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Accepted: 05/29/2016] [Indexed: 05/12/2023]
Abstract
Waterlogging causes stressful conditions for perennial species. The temporary overabundance of water in waterlogged soil can induce hypoxia in the rhizosphere, leading to root death, tree decline and even dieback. Two closely related members of the European white oak complex, pedunculate (Quercus robur L.) and sessile (Quercus petraea Matt. Liebl.) oaks, have different ecological characteristics, especially regarding their adaptation to soil waterlogging. The tolerance of waterlogging observed in pedunculate oak is driven principally by its ability to produce adaptive structures, hypertrophied lenticels and adventitious roots, and to switch rapidly its metabolism to the fermentative pathway. This study had two objectives: (i) to identify genes important for adaptation to waterlogging and (ii) to gain insight into the molecular mechanisms involved in hypertrophied lenticel formation in pedunculate oak. We subjected seedlings of the two species to hypoxia by maintaining the water level 2 cm above the collar. The immersed part of the stem (i.e., containing hypertrophied lenticels in pedunculate oak) was sampled after 9 days of waterlogging stress and its gene expression was investigated by RNA-seq. Genes displaying differential expression between the two species were identified with the DESeq R package and a false discovery rate of 0.001. We found that 3705 contigs were differentially regulated between the two species. Twenty-two differentially expressed genes were validated by real-time quantitative polymerase chain reaction. The suberin biosynthesis pathway was found to be upregulated in pedunculate oak, consistent with molecular mechanisms analogous to those operating in the radial oxygen loss barrier in waterlogging-tolerant species.
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Affiliation(s)
| | - Isabelle Lesur
- BIOGECO, INRA, Univ. Bordeaux, F-33610 Cestas, France
- HelixVenture, F-33700 Mérignac, France
| | | | - Corinne Da Silva
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, F-91057 Evry, France
| | - Karine Labadie
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, F-91057 Evry, France
| | - Jean Marc Aury
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, F-91057 Evry, France
| | - Jean Charles Leple
- INRA, UR0588 Amélioration Génétique et Physiologie Forestières, F-45075 Orlèans, France
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Ngaki MN, Wang B, Sahu BB, Srivastava SK, Farooqi MS, Kambakam S, Swaminathan S, Bhattacharyya MK. Tanscriptomic Study of the Soybean-Fusarium virguliforme Interaction Revealed a Novel Ankyrin-Repeat Containing Defense Gene, Expression of Whose during Infection Led to Enhanced Resistance to the Fungal Pathogen in Transgenic Soybean Plants. PLoS One 2016; 11:e0163106. [PMID: 27760122 PMCID: PMC5070833 DOI: 10.1371/journal.pone.0163106] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 09/04/2016] [Indexed: 12/13/2022] Open
Abstract
Fusarium virguliforme causes the serious disease sudden death syndrome (SDS) in soybean. Host resistance to this pathogen is partial and is encoded by a large number of quantitative trait loci, each conditioning small effects. Breeding SDS resistance is therefore challenging and identification of single-gene encoded novel resistance mechanisms is becoming a priority to fight this devastating this fungal pathogen. In this transcriptomic study we identified a few putative soybean defense genes, expression of which is suppressed during F. virguliforme infection. The F. virguliforme infection-suppressed genes were broadly classified into four major classes. The steady state transcript levels of many of these genes were suppressed to undetectable levels immediately following F. virguliforme infection. One of these classes contains two novel genes encoding ankyrin repeat-containing proteins. Expression of one of these genes, GmARP1, during F. virguliforme infection enhances SDS resistance among the transgenic soybean plants. Our data suggest that GmARP1 is a novel defense gene and the pathogen presumably suppress its expression to establish compatible interaction.
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Affiliation(s)
- Micheline N. Ngaki
- Department of Agronomy, Iowa State University, Ames, IA, United States of America
| | - Bing Wang
- Department of Agronomy, Iowa State University, Ames, IA, United States of America
| | - Binod B. Sahu
- Department of Agronomy, Iowa State University, Ames, IA, United States of America
| | - Subodh K. Srivastava
- Department of Agronomy, Iowa State University, Ames, IA, United States of America
| | - Mohammad S. Farooqi
- Department of Agronomy, Iowa State University, Ames, IA, United States of America
| | - Sekhar Kambakam
- Department of Agronomy, Iowa State University, Ames, IA, United States of America
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Liu J, Li Y, Wang W, Gai J, Li Y. Genome-wide analysis of MATE transporters and expression patterns of a subgroup of MATE genes in response to aluminum toxicity in soybean. BMC Genomics 2016; 17:223. [PMID: 26968518 PMCID: PMC4788864 DOI: 10.1186/s12864-016-2559-8] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2016] [Accepted: 02/29/2016] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND Multidrug and toxic compound extrusion (MATE) family is an important group of the multidrug efflux transporters that extrude organic compounds, transporting a broad range of substrates such as organic acids, plant hormones and secondary metabolites. However, genome-wide analysis of MATE family in plant species is limited and no such studies have been reported in soybean. RESULTS A total of 117 genes encoding MATE transporters were identified from the whole genome sequence of soybean (Glycine max), which were denominated as GmMATE1 - GmMATE117. These 117 GmMATE genes were unevenly localized on soybean chromosomes 1 to 20, with both tandem and segmental duplication events detected, and most genes showed tissue-specific expression patterns. Soybean MATE family could be classified into four subfamilies comprising ten smaller subgroups, with diverse potential functions such as transport and accumulation of flavonoids or alkaloids, extrusion of plant-derived or xenobiotic compounds, regulation of disease resistance, and response to abiotic stresses. Eight soybean MATE transporters clustered together with the previously reported MATE proteins related to aluminum (Al) detoxification and iron translocation were further analyzed. Seven stress-responsive cis-elements such as ABRE, ARE, HSE, LTR, MBS, as well as a cis-element of ART1 (Al resistance transcription factor 1), GGNVS, were identified in the upstream region of these eight GmMATE genes. Differential gene expression analysis of these eight GmMATE genes in response to Al stress helps us identify GmMATE75 as the candidate gene for Al tolerance in soybean, whose relative transcript abundance increased at 6, 12 and 24 h after Al treatment, with more fold changes in Al-tolerant than Al-sensitive cultivar, which is consistent with previously reported Al-tolerance related MATE genes. CONCLUSIONS A total of 117 MATE transporters were identified in soybean and their potential functions were proposed by phylogenetic analysis with known plant MATE transporters. The cis-elements and expression patterns of eight soybean MATE genes related to Al detoxification/iron translocation were analyzed, and GmMATE75 was identified as a candidate gene for Al tolerance in soybean. This study provides a first insight on soybean MATE family and their potential roles in soybean response to abiotic stresses especially Al toxicity.
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Affiliation(s)
- Juge Liu
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095 China
| | - Yang Li
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095 China
| | - Wei Wang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095 China
| | - Junyi Gai
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095 China
| | - Yan Li
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095 China
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Deng S, Wang CY, Zhang X, Wang Q, Lin L. VdNUC-2, the Key Regulator of Phosphate Responsive Signaling Pathway, Is Required for Verticillium dahliae Infection. PLoS One 2015; 10:e0145190. [PMID: 26670613 PMCID: PMC4682923 DOI: 10.1371/journal.pone.0145190] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Accepted: 12/01/2015] [Indexed: 02/07/2023] Open
Abstract
In fungal cells, a phosphate (Pi) responsive signaling and metabolism (PHO) pathway regulates Pi-homeostasis. NUC-2/PHO81 and its homologs are one of the most important components in the regulation pathway. In soil-borne phytopathogenic fungus Verticillium dahliae, we identified a Neurospora crassa nuc-2 homolog gene VdNUC-2. VdNUC-2 is composed of 1,018 amino acids, and is highly conserved in tested filamentous fungi. Under conditions of Pi-starvation, compared with the wild-type strain and ectopic complementation strains, the VdNUC-2 knocked out mutants exhibited reduced radial growth, decreased production of conidia and microsclerotia, and were more sensitive to hydrogen peroxide stress. The virulence of VdNUC-2 defective mutants was significantly compromised, and that was unable to be restored by exogenous application of extra Pi. Additionally, the deletion mutants of VdNUC-1, a key transcription factor gene positively controlled by VdNUC-2 in the PHO pathway, showed the similar cultural phenotypes as VdNUC-2 mutants when both of them grew in Pi-limited conditions. However, the virulence of VdNUC-1 mutants was comparable to the wild-type strain. These evidences indicated that the virulence reduction in VdNUC-2 mutants is not due to the interruptions in the PHO pathway or the disturbance of Pi-homeostasis in V. dahliae cytoplasm. VdNUC-2 is not only a crucial gene in the PHO pathway in V. dahliae, but also is required for the full virulence during host-infection.
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Affiliation(s)
- Sheng Deng
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Cai-yue Wang
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Xin Zhang
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Qing Wang
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Ling Lin
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, China
- * E-mail:
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Mou S, Shi L, Lin W, Liu Y, Shen L, Guan D, He S. Over-Expression of Rice CBS Domain Containing Protein, OsCBSX3, Confers Rice Resistance to Magnaporthe oryzae Inoculation. Int J Mol Sci 2015; 16:15903-17. [PMID: 26184180 PMCID: PMC4519930 DOI: 10.3390/ijms160715903] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2015] [Revised: 07/03/2015] [Accepted: 07/09/2015] [Indexed: 11/27/2022] Open
Abstract
Cystathionine β-synthase (CBS) domain containing proteins (CDCPs) constitute a big family in plants and some members in this family have been implicated in a variety of biological processes, but the precise functions and the underlying mechanism of the majority of this family in plant immunity remain to be elucidated. In the present study, a CBS domain containing protein gene, OsCBSX3, is functionally characterized in rice resistance against Magnaporthe oryzae (M. oryzae). By quantitative real-time PCR, transcripts of OsCBSX3 are up-regulated significantly by inoculation of M. oryzae and the exogenously applied salicylic acid (SA) and methyl jasmonate (MeJA). OsCBSX3 is exclusively localized to the plasma membrane by transient expression of OsCBSX3 fused to green fluorescent protein (GFP) through approach of Agrobacterium infiltration in Nicotiana benthamiana leaves. The plants of homozygous T3 transgenic rice lines of over-expressing OsCBSX3 exhibit significant enhanced resistance to M. oryzae inoculation, manifested by decreased disease symptoms, and inhibition of pathogen growth detected in DNA. Consistently, the over-expression of OsCBSX3 enhances the transcript levels of immunity associated marker genes including PR1a, PR1b, PR5, AOS2, PAL, NH1, and OsWRKY13 in plants inoculated with M. oryzae. These results suggest that OsCBSX3 acts as a positive regulator in resistance of rice to M. oryzae regulated by SA and JA-mediated signaling pathways synergistically.
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Affiliation(s)
- Shaoliang Mou
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
- National Education Minster Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Lanping Shi
- National Education Minster Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
- College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Wei Lin
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Yanyan Liu
- National Education Minster Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
- College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Lei Shen
- National Education Minster Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
- College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Deyi Guan
- National Education Minster Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
- College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Shuilin He
- National Education Minster Key Laboratory of Plant Genetic Improvement and Comprehensive Utilization, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
- College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
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Sharma M, Pandey GK. Expansion and Function of Repeat Domain Proteins During Stress and Development in Plants. FRONTIERS IN PLANT SCIENCE 2015; 6:1218. [PMID: 26793205 PMCID: PMC4707873 DOI: 10.3389/fpls.2015.01218] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 12/17/2015] [Indexed: 05/18/2023]
Abstract
The recurrent repeats having conserved stretches of amino acids exists across all domains of life. Subsequent repetition of single sequence motif and the number and length of the minimal repeating motifs are essential characteristics innate to these proteins. The proteins with tandem peptide repeats are essential for providing surface to mediate protein-protein interactions for fundamental biological functions. Plants are enriched in tandem repeat containing proteins typically distributed into various families. This has been assumed that the occurrence of multigene repeats families in plants enable them to cope up with adverse environmental conditions and allow them to rapidly acclimatize to these conditions. The evolution, structure, and function of repeat proteins have been studied in all kingdoms of life. The presence of repeat proteins is particularly profuse in multicellular organisms in comparison to prokaryotes. The precipitous expansion of repeat proteins in plants is presumed to be through internal tandem duplications. Several repeat protein gene families have been identified in plants. Such as Armadillo (ARM), Ankyrin (ANK), HEAT, Kelch-like repeats, Tetratricopeptide (TPR), Leucine rich repeats (LRR), WD40, and Pentatricopeptide repeats (PPR). The structure and functions of these repeat proteins have been extensively studied in plants suggesting a critical role of these repeating peptides in plant cell physiology, stress and development. In this review, we illustrate the structural, functional, and evolutionary prospects of prolific repeat proteins in plants.
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Liu T, Tang S, Zhu S, Tang Q, Zheng X. Transcriptome comparison reveals the patterns of selection in domesticated and wild ramie (Boehmeria nivea L. Gaud). PLANT MOLECULAR BIOLOGY 2014; 86:85-92. [PMID: 24934879 DOI: 10.1007/s11103-014-0214-9] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Accepted: 06/10/2014] [Indexed: 06/03/2023]
Abstract
Ramie is an old fiber crop, cultivated for thousands of years in China. The cultivar ramie evolved from the wild species Qingyezhuma (QYZM, Boehmeria nivea var. tenacissima). However, the mechanism of domestication of this old fiber crop is poorly understood. In order to characterize the selective pattern in ramie domestication, orthologous genes between the transcriptomes of domesticated ramie variety Zhongzhu 1 (ZZ1) and wild QYZM were assessed using bidirectional best-hit method and ratio of non-synonymous (Ka) to synonymous (Ks) nucleotide substitutions was estimated. Sequence comparison of 56,932 and 59,246 unigenes from the wild QYZM and domesticated ZZ1, respectively, helped identify 10,745 orthologous unigene pairs with a total orthologous length of 10.18 Mb. Among these unigenes, 85 and 13 genes were found to undergo significant purifying and positive selection, respectively. Most of the selected genes were homologs of those involved in abiotic stress tolerance or disease resistance in other plants, suggesting that abiotic and biotic stresses were important selective pressures in ramie domestication. Two genes probably related to the fiber yield of ramie were subjected to positive selection, which may be caused by human manipulation. Thus, our results show the pervasive effects of artificial and natural selections on the accelerated domestication of ramie from its wild relative.
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Affiliation(s)
- Touming Liu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China,
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Schaper E, Gascuel O, Anisimova M. Deep conservation of human protein tandem repeats within the eukaryotes. Mol Biol Evol 2014; 31:1132-48. [PMID: 24497029 PMCID: PMC3995336 DOI: 10.1093/molbev/msu062] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Tandem repeats (TRs) are a major element of protein sequences in all domains of life. They are particularly abundant in mammals, where by conservative estimates one in three proteins contain a TR. High generation-scale duplication and deletion rates were reported for nucleic TR units. However, it is not known whether protein TR units can also be frequently lost or gained providing a source of variation for rapid adaptation of protein function, or alternatively, tend to have conserved TR unit configurations over long evolutionary times. To obtain a systematic picture, we performed a proteome-wide analysis of the mode of evolution for human protein TRs. For this purpose, we propose a novel method for the detection of orthologous TRs based on circular profile hidden Markov models. For all detected TRs, we reconstructed bispecies TR unit phylogenies across 61 eukaryotes ranging from human to yeast. Moreover, we performed additional analyses to correlate functional and structural annotations of human TRs with their mode of evolution. Surprisingly, we find that the vast majority of human TRs are ancient, with TR unit number and order preserved intact since distant speciation events. For example, ≥61% of all human TRs have been strongly conserved at least since the root of all mammals, approximately 300 Ma. Further, we find no human protein TR that shows evidence for strong recent duplications and deletions. The results are in contrast to the high generation-scale mutability of nucleic TRs. Presumably, most protein TRs fold into stable and conserved structures that are indispensable for the function of the TR-containing protein. All of our data and results are available for download from http://www.atgc-montpellier.fr/TRE.
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Affiliation(s)
- Elke Schaper
- Department of Computer Science, ETH Zürich, Zürich, Switzerland
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