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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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Mei S, Song Y, Zhang Z, Cui H, Hou S, Miao W, Rong W. WRR4B contributes to a broad-spectrum disease resistance against powdery mildew in Arabidopsis. MOLECULAR PLANT PATHOLOGY 2024; 25:e13415. [PMID: 38279853 PMCID: PMC10777751 DOI: 10.1111/mpp.13415] [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: 09/06/2023] [Revised: 11/30/2023] [Accepted: 12/13/2023] [Indexed: 01/29/2024]
Abstract
Oidium heveae HN1106, a powdery mildew (PM) that infects rubber trees, has been found to trigger disease resistance in Arabidopsis thaliana through ENHANCED DISEASE SUSCEPTIBILITY 1 (EDS1)-, PHYTOALEXIN DEFICIENT 4 (PAD4)- and salicylic acid (SA)-mediated signalling pathways. In this study, a typical TOLL-INTERLEUKIN 1 RECEPTOR, NUCLEOTIDE-BINDING, LEUCINE-RICH REPEAT (TIR-NB-LRR)-encoding gene, WHITE RUST RESISTANCE 4 (WRR4B), was identified to be required for the resistance against O. heveae in Arabidopsis. The expression of WRR4B was upregulated by O. heveae inoculation, and WRR4B positively regulated the expression of genes involved in SA biosynthesis, such as EDS1, PAD4, ICS1 (ISOCHORISMATE SYNTHASE 1), SARD1 (SYSTEMIC-ACQUIRED RESISTANCE DEFICIENT 1) and CBP60g (CALMODULIN-BINDING PROTEIN 60 G). Furthermore, WRR4B triggered self-amplification, suggesting that WRR4B mediated plant resistance through taking part in the SA-based positive feedback loop. In addition, WRR4B induced an EDS1-dependent hypersensitive response in Nicotiana benthamiana and contributed to disease resistance against three other PM species: Podosphaera xanthii, Erysiphe quercicola and Erysiphe neolycopersici, indicating that WRR4B is a broad-spectrum disease resistance gene against PMs.
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Affiliation(s)
- Shuangshuang Mei
- College of Plant ProtectionHainan UniversityHaikouHainanChina
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and PestsHainan University, Ministry of EducationHaikouHainanChina
| | - Yuxin Song
- College of Plant ProtectionHainan UniversityHaikouHainanChina
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and PestsHainan University, Ministry of EducationHaikouHainanChina
| | - Zuer Zhang
- College of Plant ProtectionHainan UniversityHaikouHainanChina
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and PestsHainan University, Ministry of EducationHaikouHainanChina
| | - Haitao Cui
- Shandong Provincial Key Laboratory of Agricultural Microbiology, College of Plant ProtectionShandong Agricultural UniversityTai'anShandongChina
| | - Shuguo Hou
- Institute of Advanced Agricultural SciencesPeking UniversityWeifangShandongChina
| | - Weiguo Miao
- College of Plant ProtectionHainan UniversityHaikouHainanChina
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and PestsHainan University, Ministry of EducationHaikouHainanChina
| | - Wei Rong
- College of Plant ProtectionHainan UniversityHaikouHainanChina
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and PestsHainan University, Ministry of EducationHaikouHainanChina
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Tahir ul Qamar M, Sadaqat M, Zhu XT, Li H, Huang X, Fatima K, Almutairi MM, Chen LL. Comparative genomics profiling revealed multi-stress responsive roles of the CC-NBS-LRR genes in three mango cultivars. FRONTIERS IN PLANT SCIENCE 2023; 14:1285547. [PMID: 37965009 PMCID: PMC10642748 DOI: 10.3389/fpls.2023.1285547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 10/17/2023] [Indexed: 11/16/2023]
Abstract
The nucleotide-binding site-leucine-rich repeat (NBS-LRR) gene family is the largest group of disease resistance (R) genes in plants and is active in response to viruses, bacteria, and fungi usually involved in effector-triggered immunity (ETI). Pangenome-wide studies allow researchers to analyze the genetic diversity of multiple species or their members simultaneously, providing a comprehensive understanding of the evolutionary relationships and diversity present among them. The draft pan-genome of three Mangifera indica cultivars (Alphonso, Hong Xiang Ya, and Tommy atkins) was constructed and Presence/absence variants (PAVs) were filtered through the ppsPCP pipeline. As a result, 2823 genes and 5907 PAVs from H. Xiang Ya, and 1266 genes and 2098 PAVs from T. atkins were added to the reference genome. For the identification of CC-NBS-LRR (CNL) genes in these mango cultivars, this draft pan-genome study has successfully identified 47, 27, and 36 members in Alphonso, H. Xiang Ya, and T. atkins respectively. The phylogenetic analysis divided MiCNL proteins into four distinct subgroups. All MiCNL genes are unevenly distributed on chromosomes. Both tandem and segmental duplication events played a significant role in the expansion of the CNL gene family. These genes contain cis-elements related to light, stress, hormone, and development. The analysis of protein-protein interactions (PPI) revealed that MiCNL proteins interacted with other defense-responsive proteins. Gene Ontology (GO) analysis indicated that MiCNL genes play a role in defense mechanisms within the organism. The expression level of the identified genes in fruit peel was observed under disease and cold stress which showed that Mi_A_CNL13 and 14 were up-regulated while Mi_A_CNL15, 25, 30, 31, and 40 were down-regulated in disease stress. On the other hand, Mi_A_CNL2, 14, 41, and 45 were up-regulated and Mi_A_CNL47 is down-regulated in cold stress. Subsequently, the Random Forest (RF) classifier was used to assess the multi-stress response of MiCNLs. It was found that Mi_A_CNL14 is a gene that responds to multiple stress conditions. The CNLs have similar protein structures which show that they are involved in the same function. The above findings provide a foundation for a deeper understanding of the functional characteristics of the mango CNL gene family.
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Affiliation(s)
- Muhammad Tahir ul Qamar
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning, Guangxi, China
| | - Muhammad Sadaqat
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), Faisalabad, Pakistan
| | - Xi-Tong Zhu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning, Guangxi, China
| | - Huan Li
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Xing Huang
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Kinza Fatima
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), Faisalabad, Pakistan
| | - Mashal M. Almutairi
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Ling-Ling Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning, Guangxi, China
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Yu H, Wu X, Liang J, Han Z, Xiao Y, Du H, Liu Y, Guo J, Peng F. Genome-wide identification of nucleotide-binding domain leucine-rich repeat (NLR) genes and their association with green peach aphid (Myzus persicae) resistance in peach. BMC PLANT BIOLOGY 2023; 23:513. [PMID: 37880593 PMCID: PMC10598982 DOI: 10.1186/s12870-023-04474-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Accepted: 09/18/2023] [Indexed: 10/27/2023]
Abstract
Resistance genes (R genes) are a class of genes that are immune to a wide range of diseases and pests. In planta, NLR genes are essential components of the innate immune system. Currently, genes belonging to NLR family have been found in a number of plant species, but little is known in peach. Here, 286 NLR genes were identified on peach genome by using their homologous genes in Arabidopsis thaliana as queries. These 286 NLR genes contained at least one NBS domain and LRR domain. Phylogenetic and N-terminal domain analysis showed that these NLRs could be separated into four subfamilies (I-IV) and their promoters contained many cis-elements in response to defense and phytohormones. In addition, transcriptome analysis showed that 22 NLR genes were up-regulated after infected by Green Peach Aphid (GPA), and showed different expression patterns. This study clarified the NLR gene family and their potential functions in aphid resistance process. The candidate NLR genes might be useful in illustrating the mechanism of aphid resistance in peach.
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Affiliation(s)
- Haixiang Yu
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, Shandong, China
| | - Xuelian Wu
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, Shandong, China
| | - Jiahui Liang
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, Shandong, China
| | - Ziying Han
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, Shandong, China
| | - Yuansong Xiao
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, Shandong, China
| | - Hao Du
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, Shandong, China
| | - Yihua Liu
- College of Agriculture and Forestry Sciences, Linyi University, Linyi, Shandong, 276000, China
| | - Jian Guo
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, Shandong, China.
| | - Futian Peng
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, Shandong, China.
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Ijaz S, Ul Haq I, Razzaq HA, Nasir B, Ali HM, Kaur S. In silico structural-functional characterization of three differentially expressed resistance gene analogs identified in Dalbergia sissoo against dieback disease reveals their role in immune response regulation. FRONTIERS IN PLANT SCIENCE 2023; 14:1134806. [PMID: 37908834 PMCID: PMC10613980 DOI: 10.3389/fpls.2023.1134806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 09/19/2023] [Indexed: 11/02/2023]
Abstract
Plant immunity includes enemy recognition, signal transduction, and defensive response against pathogens. We experimented to identify the genes that contribute resistance against dieback disease to Dalbergia sissoo, an economically important timber tree. In this study, we investigated the role of three differentially expressed genes identified in the dieback-induced transcriptome in Dalbergia sissoo. The transcriptome was probed using DOP-rtPCR analysis. The identified RGAs were characterized in silico as the contributors of disease resistance that switch on under dieback stress. Their predicted fingerprints revealed involvement in stress response. Ds-DbRCaG-02-Rga.a, Ds-DbRCaG-04-Rga.b, and Ds-DbRCaG-06-Rga.c showed structural homology with the Transthyretin-52 domain, EAL associated YkuI_C domain, and Src homology-3 domain respectively, which are the attributes of signaling proteins possessing a role in regulating immune responses in plants. Based on in-silico structural and functional characterization, they were predicted to have a role in immune response regulation in D. sissoo.
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Affiliation(s)
- Siddra Ijaz
- Centre of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, Faisalabad, Pakistan
| | - Imran Ul Haq
- Department of Plant Pathology, University of Agriculture, Faisalabad, Pakistan
| | - Hafiza Arooj Razzaq
- Centre of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, Faisalabad, Pakistan
| | - Bukhtawer Nasir
- Centre of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, Faisalabad, Pakistan
| | - Hayssam M. Ali
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Sukhwinder Kaur
- Department of Plant Pathology, University of California Davis, Davis, CA, United States
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Joshi A, Song HG, Yang SY, Lee JH. Integrated Molecular and Bioinformatics Approaches for Disease-Related Genes in Plants. PLANTS (BASEL, SWITZERLAND) 2023; 12:2454. [PMID: 37447014 DOI: 10.3390/plants12132454] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 06/15/2023] [Accepted: 06/23/2023] [Indexed: 07/15/2023]
Abstract
Modern plant pathology relies on bioinformatics approaches to create novel plant disease diagnostic tools. In recent years, a significant amount of biological data has been generated due to rapid developments in genomics and molecular biology techniques. The progress in the sequencing of agriculturally important crops has made it possible to develop a better understanding of plant-pathogen interactions and plant resistance. The availability of host-pathogen genome data offers effective assistance in retrieving, annotating, analyzing, and identifying the functional aspects for characterization at the gene and genome levels. Physical mapping facilitates the identification and isolation of several candidate resistance (R) genes from diverse plant species. A large number of genetic variations, such as disease-causing mutations in the genome, have been identified and characterized using bioinformatics tools, and these desirable mutations were exploited to develop disease resistance. Moreover, crop genome editing tools, namely the CRISPR (clustered regulatory interspaced short palindromic repeats)/Cas9 (CRISPR-associated) system, offer novel and efficient strategies for developing durable resistance. This review paper describes some aspects concerning the databases, tools, and techniques used to characterize resistance (R) genes for plant disease management.
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Affiliation(s)
- Alpana Joshi
- Department of Bioenvironmental Chemistry, College of Agriculture & Life Sciences, Jeonbuk National University, Jeonju 54896, Republic of Korea
- Department of Agriculture Technology & Agri-Informatics, Shobhit Institute of Engineering & Technology, Meerut 250110, India
| | - Hyung-Geun Song
- Department of Bioenvironmental Chemistry, College of Agriculture & Life Sciences, Jeonbuk National University, Jeonju 54896, Republic of Korea
| | - Seo-Yeon Yang
- Department of Agricultural Chemistry, Jeonbuk National University, Jeonju 54896, Republic of Korea
| | - Ji-Hoon Lee
- Department of Bioenvironmental Chemistry, College of Agriculture & Life Sciences, Jeonbuk National University, Jeonju 54896, Republic of Korea
- Department of Agricultural Chemistry, Jeonbuk National University, Jeonju 54896, Republic of Korea
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Yin T, Han P, Xi D, Yu W, Zhu L, Du C, Yang N, Liu X, Zhang H. Genome-wide identification, characterization, and expression profile ofNBS-LRRgene family in sweet orange (Citrussinensis). Gene 2023; 854:147117. [PMID: 36526123 DOI: 10.1016/j.gene.2022.147117] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 12/05/2022] [Accepted: 12/09/2022] [Indexed: 12/15/2022]
Abstract
BACKGROUND The NBS-LRR (nucleotide-binding site-leucine-rich repeat gene) gene family, known as the plant R (resistance) gene family with the most members, plays a significant role in plant resistance to various external adversity stresses. The NBS-LRR gene family has been researched in many plant species. Citrus is one of the most vital global cash crops, the number one fruit group, and the third most traded agricultural product world wild. However, as one of the largest citrus species, a comprehensive study of the NBS-LRR gene family has not been reported on sweet oranges. METHODS In this study, NBS-LRR genes were identified from the Citrus sinensis genome (v3.0), with a comprehensive analysis of this gene family performed, including phylogenetic analysis, gene structure, cis-acting element of a promoter, and chromosomal localization, among others. The expression pattern of NBS-LRR genes was analyzed when sweet orange fruits were infected by Penicillium digitatum, employing experimental data from our research group. It first reported the expression patterns of NBS-LRR genes under abiotic stresses, using three transcript data from NCBI (National Center for Biotechnology Information). RESULTS In this study, 111 NBS-LRR genes were identified in the C. sinensis genome (v3.0) and classified into seven subfamilies according to their N-terminal and C-terminal domains. The phylogenetic tree results indicate that genes containing only the NBS structural domain are more ancient in the sweet orange NBS-LRR gene family. The chromosome localization results showed that 111 NBS-LRR genes were distributed unevenly on nine chromosomes, with the most genes distributed on chromosome 1. In addition, we identified a total of 18 tandem duplication gene pairs in the sweet orange NBS-LRR gene family, and based on the Ka/Ks ratio, all of the tandem duplication genes underwent purifying selection. Transcriptome data analysis showed a significant number of NBS-LRR genes expressed under biotic and abiotic stresses, and some reached significantly different levels of expression. It indicates that the NBS-LRR gene family is vital in resistance to biotic and abiotic stresses in sweet oranges. CONCLUSION Our study provides the first comprehensive framework on the NBS-LRR family of genes, which provides a basis for further in-depth studies on the biological functions of NBS-LRR in growth, development, and response to abiotic stresses in sweet orange.
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Affiliation(s)
- Tuo Yin
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming 650224, China.
| | - Peichen Han
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming 650224, China.
| | - Dengxian Xi
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming 650224, China.
| | - Wencai Yu
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming 650224, China.
| | - Ling Zhu
- Key Laboratory of Biodiversity Conservation in Southwest China, National Forest and Grassland Administration, Southwest Forestry University, Kunming 650224, China.
| | - Chaojin Du
- Key Laboratory of Biodiversity Conservation in Southwest China, National Forest and Grassland Administration, Southwest Forestry University, Kunming 650224, China.
| | - Na Yang
- Key Laboratory of Biodiversity Conservation in Southwest China, National Forest and Grassland Administration, Southwest Forestry University, Kunming 650224, China.
| | - Xiaozhen Liu
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming 650224, China.
| | - Hanyao Zhang
- Key Laboratory of Biodiversity Conservation in Southwest China, National Forest and Grassland Administration, Southwest Forestry University, Kunming 650224, China.
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Tong C, Zhang Y, Shi F. Genome-wide identification and analysis of the NLR gene family in Medicago ruthenica. Front Genet 2023; 13:1088763. [PMID: 36704335 PMCID: PMC9871256 DOI: 10.3389/fgene.2022.1088763] [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: 11/03/2022] [Accepted: 12/22/2022] [Indexed: 01/11/2023] Open
Abstract
Medicago ruthenica, important forage in the legume family, possesses high nutritional value and carries abundant tolerance genes. This study used whole-genome data of M. ruthenica to perform a genome-wide analysis of the nucleotide-binding site-leucine-rich repeat receptor (NLR) gene family, which is the largest family of plant disease resistance genes (R genes). A total of 338 NLR genes were identified in the M. ruthenica genome, including 160 typical genes that contained 80 coiled-coil (CC)-NBS-LRR (CNL) genes, 76 toll/interleukin-1 receptor (TIR)-NBS-LRR (TNL) genes, four resistance to powdery mildew 8 (RPW8)-NBS-LRR (RNL) subclass genes, and 178 atypical NLR genes encoding proteins without at least one important domain. Among its eight chromosomes, M. ruthenica chromosomes 3 and 8 contained most of the NLR genes. More than 40% of all NLR genes were located on these two chromosomes, mainly in multigene clusters. The NLR proteins of M. ruthenica had six highly conserved motifs: P-loop, GLPL, RNBS-D, kinase-2, RNBS-C, and MHDV. Phylogenetic analysis revealed that the NLR genes of M. ruthenica formed three deeply separated clades according to the N-terminal domain of the proteins encoded by these genes. Gene duplication and syntenic analysis suggested four gene duplication types in the NLR genes of M. ruthenica, namely, tandem, proximal, dispersed, and segmental duplicates, which involved 189, 49, 59, and 41 genes, respectively. A total of 41 segmental duplication genes formed 23 NLR gene pairs located on syntenic chromosomal blocks mainly between chromosomes 6 and 7. In addition, syntenic analysis between M. truncatula and M. ruthenica revealed 193 gene pairs located on syntenic chromosomal blocks of the two species. The expression analysis of M. ruthenica NLR genes showed that 303 (89.6%) of the NLR genes were expressed in different varieties. Overall, this study described the full NLR profile of the M. ruthenica genome to provide an important resource for mining disease-resistant genes and disease-resistant breeding.
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Affiliation(s)
- Chunyan Tong
- College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Hohhot, China,Key Laboratory of Grassland Resources (IMAU), Ministry of Education, Hohhot, China
| | - Yutong Zhang
- College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Hohhot, China,Key Laboratory of Grassland Resources (IMAU), Ministry of Education, Hohhot, China
| | - Fengling Shi
- College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Hohhot, China,Key Laboratory of Grassland Resources (IMAU), Ministry of Education, Hohhot, China,*Correspondence: Fengling Shi,
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Zhang X, Wang F, Yang N, Chen N, Hu Y, Peng X, Shen S. Bioinformatics analysis and function prediction of NBS-LRR gene family in Broussonetia papyrifera. Biotechnol Lett 2023; 45:13-31. [PMID: 36357714 DOI: 10.1007/s10529-022-03318-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 06/15/2022] [Accepted: 10/17/2022] [Indexed: 11/12/2022]
Abstract
Most of the currently available disease resistance (R) genes have NBS (nucleotide-binding site) and LRR (leucine-rich-repeat) domain which belongs to the NBS-LRR gene family. The whole genome sequencing of Broussonetia papyrifera provides an important bioinformatics database for the study of the NBS-LRR gene family. In this study, 328 NBS-LRR family genes were identified and classified in B. papyrifera according to different classification schemes, where there are 92 N types, 47 CN type, 54 CNL type, 29 NL types, 55 TN type, and 51 TNL type. Subsequently, we conducted bioinformatics analysis of the NBS-LRR gene family. Classification, motif analysis of protein sequences, and phylogenetic tree studies of the NBS-LRR genes in B. papyrifera provide important basis for the functional study of NBS-LRR family genes. Additionally, we performed structural analysis of the chromosomal location, physicochemical properties, and sequences identified by genetic characterization. In addition, through the analysis of GO enrichment, it was found that NBS-LRR genes were involved in defense responses and were significantly enriched in biological stimulation, immune response, and abiotic stress. In addition, we found that Bp06g0955 was the most sensitive to low temperature and encoded the RPM1 protein by analyzing the low temperature transcriptome data of B. papyrifera. Quantitative results of gene expression after 48 h of Fusarium infection showed that Bp01g3293 increased 14 times after infection, which encodes RPM1 protein. The potential of NBS-LRR gene responsive to biotic and abiotic stresses can be exploited to improve the resistance of B. papyrifera.
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Affiliation(s)
- Xiaokang Zhang
- Key Laboratory of Plant Resources, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Fengfeng Wang
- Key Laboratory of Plant Resources, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China
| | - Nianhui Yang
- Key Laboratory of Plant Resources, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China
| | - Naizhi Chen
- Key Laboratory of Plant Resources, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China
| | - Yanmin Hu
- Key Laboratory of Plant Resources, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China
| | - Xianjun Peng
- Key Laboratory of Plant Resources, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China
| | - Shihua Shen
- Key Laboratory of Plant Resources, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China.
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Chelliah A, Arumugam C, Suthanthiram B, Raman T, Subbaraya U. Genome-wide identification, characterization, and evolutionary analysis of NBS genes and their association with disease resistance in Musa spp. Funct Integr Genomics 2022; 23:7. [PMID: 36538175 DOI: 10.1007/s10142-022-00925-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 11/01/2022] [Accepted: 11/15/2022] [Indexed: 12/24/2022]
Abstract
Banana is an important food crop that is susceptible to a wide range of pests and diseases that can reduce yield and quality. The primary objective of banana breeding programs is to increase disease resistance, which requires the identification of resistance (R) genes. Despite the fact that resistant sources have been identified in bananas, the genes, particularly the nucleotide-binding site (NBS) family, which play an important role in protecting plants against pathogens, have received little attention. As a result, this study included a thorough examination of the NBS disease resistance gene family's classification, phylogenetic analysis, genome organization, evolution, cis-elements, differential expression, regulation by microRNAs, and protein-protein interaction. A total of 116 and 43 putative NBS genes from M. acuminata and M. balbisiana, respectively, were identified and characterized, and were classified into seven sub-families. Structural analysis of NBS genes revealed the presence of signal peptides, their sub-cellular localization, molecular weight and pI. Eight commonly conserved motifs were found, and NBS genes were unevenly distributed across multiple chromosomes, with the majority of NBS genes being located in chr3 and chr1 of the A and B genomes, respectively. Tandem duplication occurrences have helped bananas' NBS genes spread throughout evolution. Transcriptome analysis of NBS genes revealed significant differences in expression between resistant and susceptible cultivars of fusarium wilt, eumusae leaf spot, root lesion nematode, and drought, implying that they can be used as candidate resistant genes. Ninety miRNAs were discovered to have targets in 104 NBS genes from the A genome, providing important insights into NBS gene expression regulation. Overall, this study offers a valuable genomic resource and understanding of the function and evolution of NBS genes in relation to rapidly evolving pathogens, as well as providing breeders with selection targets for fast-tracking breeding of banana varieties with more durable resistance to pathogens.
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Affiliation(s)
- Anuradha Chelliah
- ICAR-National Research Centre for Banana, Thogamalai Road, Thayanur Post, Tiruchirappalli - 620 102, Tamil Nadu, India.
| | - Chandrasekar Arumugam
- ICAR-National Research Centre for Banana, Thogamalai Road, Thayanur Post, Tiruchirappalli - 620 102, Tamil Nadu, India
| | - Backiyarani Suthanthiram
- ICAR-National Research Centre for Banana, Thogamalai Road, Thayanur Post, Tiruchirappalli - 620 102, Tamil Nadu, India
| | - Thangavelu Raman
- ICAR-National Research Centre for Banana, Thogamalai Road, Thayanur Post, Tiruchirappalli - 620 102, Tamil Nadu, India
| | - Uma Subbaraya
- ICAR-National Research Centre for Banana, Thogamalai Road, Thayanur Post, Tiruchirappalli - 620 102, Tamil Nadu, India
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11
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Huang Z, Qiao F, Yang B, Liu J, Liu Y, Wulff BBH, Hu P, Lv Z, Zhang R, Chen P, Xing L, Cao A. Genome-wide identification of the NLR gene family in Haynaldia villosa by SMRT-RenSeq. BMC Genomics 2022; 23:118. [PMID: 35144544 PMCID: PMC8832786 DOI: 10.1186/s12864-022-08334-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 01/24/2022] [Indexed: 01/19/2023] Open
Abstract
Background Nucleotide-binding and leucine-rich repeat (NLR) genes have attracted wide attention due to their crucial role in protecting plants from pathogens. SMRT-RenSeq, combining PacBio sequencing after resistance gene enrichment sequencing (RenSeq), is a powerful method for selectively capturing and sequencing full-length NLRs. Haynaldia villosa, a wild grass species with a proven potential for wheat improvement, confers resistance to multiple diseases. So, genome-wide identification of the NLR gene family in Haynaldia villosa by SMRT-RenSeq can facilitate disease resistance genes exploration. Results In this study, SMRT-RenSeq was performed to identify the genome-wide NLR complement of H. villosa. In total, 1320 NLRs were annotated in 1169 contigs, including 772 complete NLRs. All the complete NLRs were phylogenetically analyzed and 11 main clades with special characteristics were derived. NLRs could be captured with high efficiency when aligned with cloned R genes, and cluster expansion in some specific gene loci was observed. The physical location of NLRs to individual chromosomes in H. villosa showed a perfect homoeologous relationship with group 1, 2, 3, 5 and 6 of other Triticeae species, however, NLRs physically located on 4VL were largely in silico predicted to be located on the homoeologous group 7. Fifteen types of integrated domains (IDs) were integrated in 52 NLRs, and Kelch and B3 NLR-IDs were found to have expanded in H. villosa, while DUF948, NAM-associated and PRT_C were detected as unique integrated domains implying the new emergence of NLR-IDs after H. villosa diverged from other species. Conclusion SMRT-RenSeq is a powerful tool to identify NLR genes from wild species using the baits of the evolutionary related species with reference sequences. The availability of the NLRs from H. villosa provide a valuable library for R gene mining and transfer of disease resistance into wheat. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08334-w.
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Affiliation(s)
- Zhenpu Huang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/CIC-MCP, Nanjing, 210095, China
| | - Fangyuan Qiao
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/CIC-MCP, Nanjing, 210095, China
| | - Boming Yang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/CIC-MCP, Nanjing, 210095, China
| | - Jiaqian Liu
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/CIC-MCP, Nanjing, 210095, China
| | - Yangqi Liu
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/CIC-MCP, Nanjing, 210095, China
| | - Brande B H Wulff
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK.,Center for Desert Agriculture, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Ping Hu
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/CIC-MCP, Nanjing, 210095, China
| | - Zengshuai Lv
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/CIC-MCP, Nanjing, 210095, China
| | - Ruiqi Zhang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/CIC-MCP, Nanjing, 210095, China
| | - Peidu Chen
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/CIC-MCP, Nanjing, 210095, China
| | - Liping Xing
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/CIC-MCP, Nanjing, 210095, China.
| | - Aizhong Cao
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/CIC-MCP, Nanjing, 210095, China.
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12
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Zhong Y, Chen Z, Cheng ZM. Different scales of gene duplications occurring at different times have jointly shaped the NBS-LRR genes in Prunus species. Mol Genet Genomics 2022; 297:263-276. [PMID: 35031863 PMCID: PMC8803762 DOI: 10.1007/s00438-021-01849-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 12/16/2021] [Indexed: 11/25/2022]
Abstract
In this study, genome-wide identification, phylogenetic relationships, duplication time and selective pressure of the NBS-LRR genes, an important group of plant disease-resistance genes (R genes), were performed to uncover their genetic evolutionary patterns in the six Prunus species. A total of 1946 NBS-LRR genes were identified; specifically, 589, 361, 284, 281, 318, and 113 were identified in Prunus yedoensis, P. domestica, P. avium, P. dulcis, P. persica and P. yedoensis var. nudiflora, respectively. Two NBS-LRR gene subclasses, TIR-NBS-LRR (TNL) and non-TIR-NBS-LRR (non-TNL), were also discovered. In total, 435 TNL and 1511 non-TNL genes were identified and could be classified into 30/55/75 and 103/158/191 multi-gene families, respectively, according to three different criteria. Higher Ks and Ka/Ks values were detected in TNL gene families than in non-TNL gene families. These results indicated that the TNL genes had more members involved in relatively ancient duplications and were affected by stronger selection pressure than the non-TNL genes. In general, the NBS-LRR genes were shaped by species-specific duplications, and lineage-specific duplications occurred at recent and relatively ancient periods among the six Prunus species. Therefore, different duplicated copies of NBS-LRRs can resist specific pathogens and will provide an R-gene library for resistance breeding in Prunus species.
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Affiliation(s)
- Yan Zhong
- College of Horticulture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Zhao Chen
- College of Horticulture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zong-Ming Cheng
- College of Horticulture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China.
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Yu X, Zhong S, Yang H, Chen C, Chen W, Yang H, Guan J, Fu P, Tan F, Ren T, Shen J, Zhang M, Luo P. Identification and Characterization of NBS Resistance Genes in Akebia trifoliata. FRONTIERS IN PLANT SCIENCE 2021; 12:758559. [PMID: 34777439 PMCID: PMC8585750 DOI: 10.3389/fpls.2021.758559] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 10/08/2021] [Indexed: 05/26/2023]
Abstract
Akebia trifoliata is an important multiuse perennial plant that often suffers attacks from various pathogens due to its long growth cycle, seriously affecting its commercial value. The absence of research on the resistance (R) genes of A. trifoliata has greatly limited progress in the breeding of resistant varieties. Genes encoding proteins containing nucleotide binding sites (NBSs) and C-terminal leucine-rich repeats (LRRs), the largest family of plant resistance (R) genes, are vital for plant disease resistance. A comprehensive genome-wide analysis showed that there were only 73 NBS genes in the A. trifoliata genome, including three main subfamilies (50 coiled coil (CC)-NBS-LRR (CNL), 19 Toll/interleukin-1 receptor (TIR)-NBS-LRR (TNL) and four resistance to powdery mildew8 (RPW8)-NBS-LRR (RNL) genes). Additionally, 64 mapped NBS candidates were unevenly distributed on 14 chromosomes, most of which were assigned to the chromosome ends; 41 of these genes were located in clusters, and the remaining 23 genes were singletons. Both the CNLs and TNLs were further divided into four subgroups, and the CNLs had fewer exons than the TNLs. Structurally, all eight previously reported conserved motifs were identified in the NBS domains, and both their order and their amino acid sequences exhibited high conservation. Evolutionarily, tandem and dispersed duplications were shown to be the two main forces responsible for NBS expansion, producing 33 and 29 genes, respectively. A transcriptome analysis of three fruit tissues at four developmental stages showed that NBS genes were generally expressed at low levels, while a few of these genes showed relatively high expression during later development in rind tissues. Overall, this research is the first to identify and characterize A. trifoliata NBS genes and is valuable for both the development of new resistant cultivars and the study of molecular mechanisms of resistance.
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Affiliation(s)
- Xiaojiao Yu
- Provincial Key Laboratory for Plant Genetics and Breeding, Chengdu, China
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Shengfu Zhong
- Provincial Key Laboratory for Plant Genetics and Breeding, Chengdu, China
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Huai Yang
- Provincial Key Laboratory for Plant Genetics and Breeding, Chengdu, China
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Chen Chen
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Wei Chen
- Provincial Key Laboratory for Plant Genetics and Breeding, Chengdu, China
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
- Sichuan Akebia trifoliata Biotechnology Co., Ltd., Chengdu, China
| | - Hao Yang
- Provincial Key Laboratory for Plant Genetics and Breeding, Chengdu, China
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
- Sichuan Akebia trifoliata Biotechnology Co., Ltd., Chengdu, China
| | - Ju Guan
- Provincial Key Laboratory for Plant Genetics and Breeding, Chengdu, China
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Peng Fu
- Provincial Key Laboratory for Plant Genetics and Breeding, Chengdu, China
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Feiquan Tan
- Provincial Key Laboratory for Plant Genetics and Breeding, Chengdu, China
| | - Tianheng Ren
- Provincial Key Laboratory for Plant Genetics and Breeding, Chengdu, China
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Jinliang Shen
- College of Forestry, Sichuan Agricultural University, Chengdu, China
| | - Min Zhang
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Peigao Luo
- Provincial Key Laboratory for Plant Genetics and Breeding, Chengdu, China
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
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14
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Si Z, Qiao Y, Zhang K, Ji Z, Han J. Characterization of Nucleotide Binding -Site-Encoding Genes in Sweetpotato, Ipomoea batatas(L.) Lam., and Their Response to Biotic and Abiotic Stresses. Cytogenet Genome Res 2021; 161:257-271. [PMID: 34320507 DOI: 10.1159/000515834] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 03/12/2021] [Indexed: 11/19/2022] Open
Abstract
Sweetpotato, Ipomoea batatas (L.) Lam., is an important and widely grown crop, yet its production is affected severely by biotic and abiotic stresses. The nucleotide binding site (NBS)-encoding genes have been shown to improve stress tolerance in several plant species. However, the characterization of NBS-encoding genes in sweetpotato is not well-documented to date. In this study, a comprehensive analysis of NBS-encoding genes has been conducted on this species by using bioinformatics and molecular biology methods. A total of 315 NBS-encoding genes were identified, and 260 of them contained all essential conserved domains while 55 genes were truncated. Based on domain architectures, the 260 NBS-encoding genes were grouped into 6 distinct categories. Phylogenetic analysis grouped these genes into 3 classes: TIR, CC (I), and CC (II). Chromosome location analysis revealed that the distribution of NBS-encoding genes in chromosomes was uneven, with a number ranging from 1 to 34. Multiple stress-related regulatory elements were detected in the promoters, and the NBS-encoding genes' expression profiles under biotic and abiotic stresses were obtained. According to the bioinformatics analysis, 9 genes were selected for RT-qPCR analysis. The results revealed that IbNBS75, IbNBS219, and IbNBS256 respond to stem nematode infection; Ib-NBS240, IbNBS90, and IbNBS80 respond to cold stress, while IbNBS208, IbNBS71, and IbNBS159 respond to 30% PEG treatment. We hope these results will provide new insights into the evolution of NBS-encoding genes in the sweetpotato genome and contribute to the molecular breeding of sweetpotato in the future.
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Affiliation(s)
- Zengzhi Si
- Hebei Key Laboratory of Crop Stress Biology, Hebei Normal University of Science and Technology, Qinhuangdao, China
| | - Yake Qiao
- Hebei Key Laboratory of Crop Stress Biology, Hebei Normal University of Science and Technology, Qinhuangdao, China
| | - Kai Zhang
- Hebei Key Laboratory of Crop Stress Biology, Hebei Normal University of Science and Technology, Qinhuangdao, China
| | - Zhixin Ji
- Hebei Key Laboratory of Crop Stress Biology, Hebei Normal University of Science and Technology, Qinhuangdao, China
| | - Jinling Han
- Hebei Key Laboratory of Crop Stress Biology, Hebei Normal University of Science and Technology, Qinhuangdao, China
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Yang H, Bayer PE, Tirnaz S, Edwards D, Batley J. Genome-Wide Identification and Evolution of Receptor-Like Kinases (RLKs) and Receptor like Proteins (RLPs) in Brassica juncea. BIOLOGY 2020; 10:biology10010017. [PMID: 33396674 PMCID: PMC7823396 DOI: 10.3390/biology10010017] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 12/21/2020] [Accepted: 12/21/2020] [Indexed: 12/19/2022]
Abstract
Brassica juncea, an allotetraploid species, is an important germplasm resource for canola improvement, due to its many beneficial agronomic traits, such as heat and drought tolerance and blackleg resistance. Receptor-like kinase (RLK) and receptor-like protein (RLP) genes are two types of resistance gene analogues (RGA) that play important roles in plant innate immunity, stress response and various development processes. In this study, genome wide analysis of RLKs and RLPs is performed in B. juncea. In total, 493 RLKs (LysM-RLKs and LRR-RLKs) and 228 RLPs (LysM-RLPs and LRR-RLPs) are identified in the genome of B. juncea, using RGAugury. Only 13.54% RLKs and 11.79% RLPs are observed to be grouped within gene clusters. The majority of RLKs (90.17%) and RLPs (52.83%) are identified as duplicates, indicating that gene duplications significantly contribute to the expansion of RLK and RLP families. Comparative analysis between B. juncea and its progenitor species, B. rapa and B. nigra, indicate that 83.62% RLKs and 41.98% RLPs are conserved in B. juncea, and RLPs are likely to have a faster evolution than RLKs. This study provides a valuable resource for the identification and characterisation of candidate RLK and RLP genes.
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Affiliation(s)
- Hua Yang
- School of Biological Sciences, University of Western Australia, Crawley, WA 6009, Australia; (H.Y.); (P.E.B.); (S.T.); (D.E.)
- School of Agriculture and Food Sciences, University of Queensland, St Lucia, QLD 4067, Australia
| | - Philipp E. Bayer
- School of Biological Sciences, University of Western Australia, Crawley, WA 6009, Australia; (H.Y.); (P.E.B.); (S.T.); (D.E.)
| | - Soodeh Tirnaz
- School of Biological Sciences, University of Western Australia, Crawley, WA 6009, Australia; (H.Y.); (P.E.B.); (S.T.); (D.E.)
| | - David Edwards
- School of Biological Sciences, University of Western Australia, Crawley, WA 6009, Australia; (H.Y.); (P.E.B.); (S.T.); (D.E.)
| | - Jacqueline Batley
- School of Biological Sciences, University of Western Australia, Crawley, WA 6009, Australia; (H.Y.); (P.E.B.); (S.T.); (D.E.)
- Correspondence: ; Tel.: +61-8-6488-5929
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16
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Yang M, Zhou C, Yang H, Kuang R, Huang B, Wei Y. Genome-wide analysis of basic helix-loop-helix transcription factors in papaya ( Carica papaya L.). PeerJ 2020; 8:e9319. [PMID: 32704439 PMCID: PMC7341539 DOI: 10.7717/peerj.9319] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 05/17/2020] [Indexed: 11/20/2022] Open
Abstract
The basic helix-loop-helix (bHLH) transcription factors (TFs) have been identified and functionally characterized in many plants. However, no comprehensive analysis of the bHLH family in papaya (Carica papaya L.) has been reported previously. Here, a total of 73 CpbHLHs were identified in papaya, and these genes were classified into 18 subfamilies based on phylogenetic analysis. Almost all of the CpbHLHs in the same subfamily shared similar gene structures and protein motifs according to analysis of exon/intron organizations and motif compositions. The number of exons in CpbHLHs varied from one to 10 with an average of five. The amino acid sequences of the bHLH domains were quite conservative, especially Leu-27 and Leu-63. Promoter cis-element analysis revealed that most of the CpbHLHs contained cis-elements that can respond to various biotic/abiotic stress-related events. Gene ontology (GO) analysis revealed that CpbHLHs mainly functions in protein dimerization activity and DNA-binding, and most CpbHLHs were predicted to localize in the nucleus. Abiotic stress treatment and quantitative real-time PCR (qRT-PCR) revealed some important candidate CpbHLHs that might be responsible for abiotic stress responses in papaya. These findings would lay a foundation for further investigate of the molecular functions of CpbHLHs.
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Affiliation(s)
- Min Yang
- Guangdong Academy of Agricultural Sciences, Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization (MOA), Guangdong Province Key Laboratory of Tropical and Subtropical Fruit Tree Research, Institute of Fruit Tree Research, Guangzhou, China
| | - Chenping Zhou
- Guangdong Academy of Agricultural Sciences, Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization (MOA), Guangdong Province Key Laboratory of Tropical and Subtropical Fruit Tree Research, Institute of Fruit Tree Research, Guangzhou, China
| | - Hu Yang
- Guangdong Academy of Agricultural Sciences, Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization (MOA), Guangdong Province Key Laboratory of Tropical and Subtropical Fruit Tree Research, Institute of Fruit Tree Research, Guangzhou, China
| | - Ruibin Kuang
- Guangdong Academy of Agricultural Sciences, Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization (MOA), Guangdong Province Key Laboratory of Tropical and Subtropical Fruit Tree Research, Institute of Fruit Tree Research, Guangzhou, China
| | - Bingxiong Huang
- Guangdong Academy of Agricultural Sciences, Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization (MOA), Guangdong Province Key Laboratory of Tropical and Subtropical Fruit Tree Research, Institute of Fruit Tree Research, Guangzhou, China
| | - Yuerong Wei
- Guangdong Academy of Agricultural Sciences, Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization (MOA), Guangdong Province Key Laboratory of Tropical and Subtropical Fruit Tree Research, Institute of Fruit Tree Research, Guangzhou, China
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Dolatabadian A, Bayer PE, Tirnaz S, Hurgobin B, Edwards D, Batley J. Characterization of disease resistance genes in the Brassica napus pangenome reveals significant structural variation. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:969-982. [PMID: 31553100 PMCID: PMC7061875 DOI: 10.1111/pbi.13262] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 08/30/2019] [Accepted: 09/13/2019] [Indexed: 05/18/2023]
Abstract
Methods based on single nucleotide polymorphism (SNP), copy number variation (CNV) and presence/absence variation (PAV) discovery provide a valuable resource to study gene structure and evolution. However, as a result of these structural variations, a single reference genome is unable to cover the entire gene content of a species. Therefore, pangenomics analysis is needed to ensure that the genomic diversity within a species is fully represented. Brassica napus is one of the most important oilseed crops in the world and exhibits variability in its resistance genes across different cultivars. Here, we characterized resistance gene distribution across 50 B. napus lines. We identified a total of 1749 resistance gene analogs (RGAs), of which 996 are core and 753 are variable, 368 of which are not present in the reference genome (cv. Darmor-bzh). In addition, a total of 15 318 SNPs were predicted within 1030 of the RGAs. The results showed that core R-genes harbour more SNPs than variable genes. More nucleotide binding site-leucine-rich repeat (NBS-LRR) genes were located in clusters than as singletons, with variable genes more likely to be found in clusters. We identified 106 RGA candidates linked to blackleg resistance quantitative trait locus (QTL). This study provides a better understanding of resistance genes to target for genomics-based improvement and improved disease resistance.
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Affiliation(s)
- Aria Dolatabadian
- UWA School of Biological Sciences and the UWA Institute of AgricultureFaculty of ScienceThe University of Western AustraliaCrawleyWAAustralia
| | - Philipp E. Bayer
- UWA School of Biological Sciences and the UWA Institute of AgricultureFaculty of ScienceThe University of Western AustraliaCrawleyWAAustralia
| | - Soodeh Tirnaz
- UWA School of Biological Sciences and the UWA Institute of AgricultureFaculty of ScienceThe University of Western AustraliaCrawleyWAAustralia
| | - Bhavna Hurgobin
- UWA School of Biological Sciences and the UWA Institute of AgricultureFaculty of ScienceThe University of Western AustraliaCrawleyWAAustralia
| | - David Edwards
- UWA School of Biological Sciences and the UWA Institute of AgricultureFaculty of ScienceThe University of Western AustraliaCrawleyWAAustralia
| | - Jacqueline Batley
- UWA School of Biological Sciences and the UWA Institute of AgricultureFaculty of ScienceThe University of Western AustraliaCrawleyWAAustralia
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Roles of transcription factor SQUAMOSA promoter binding protein-like gene family in papaya (Carica papaya) development and ripening. Genomics 2020; 112:2734-2747. [PMID: 32194147 DOI: 10.1016/j.ygeno.2020.03.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 03/12/2020] [Accepted: 03/14/2020] [Indexed: 02/05/2023]
Abstract
SQUAMOSA promoter binding protein-like (SPL) family plays vital regulatory roles in plant growth and development. The SPL family in climacteric fruit Carica papaya has not been reported. This study identified 14 papaya SPLs (CpSPL) from papaya genome and analyzed their sequence features, phylogeny, intron/exon structure, conserved motif, miR156-mediated posttranscriptional regulation, and expression patterns. 14 CpSPLs were clustered into 8 groups, and two distinct expression patterns were revealed for miR156-targeted and nontargeted CpSPLs in different tissues and fruit development stages. The expression changes of CpSPLs in ethephon and 1-MCP treated fruit during ripening suggested that the CpSPLs guided by CpmiR156 play crucial roles in ethylene signaling pathway. This study sheds light on the new function of SPL family in fruit development and ripening, providing insights on understanding evolutionary divergence of the members of SPL family among plant species.
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Wei H, Liu J, Guo Q, Pan L, Chai S, Cheng Y, Ruan M, Ye Q, Wang R, Yao Z, Zhou G, Wan H. Genomic Organization and Comparative Phylogenic Analysis of NBS-LRR Resistance Gene Family in Solanum pimpinellifolium and Arabidopsis thaliana. Evol Bioinform Online 2020; 16:1176934320911055. [PMID: 32214791 PMCID: PMC7065440 DOI: 10.1177/1176934320911055] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 02/13/2020] [Indexed: 12/23/2022] Open
Abstract
NBS-LRR (nucleotide-binding site and leucine-rich repeat) is one of the largest resistance gene families in plants. The completion of the genome sequencing of wild tomato Solanum pimpinellifolium provided an opportunity to conduct a comprehensive analysis of the NBS-LRR gene superfamily at the genome-wide level. In this study, gene identification, chromosome mapping, and phylogenetic analysis of the NBS-LRR gene family were analyzed using the bioinformatics methods. The results revealed 245 NBS-LRRs in total, similar to that in the cultivated tomato. These genes are unevenly distributed on 12 chromosomes, and ~59.6% of them form gene clusters, most of which are tandem duplications. Phylogenetic analysis divided the NBS-LRRs into 2 subfamilies (CNL-coiled-coil NBS-LRR and TNL-TIR NBS-LRR), and the expansion of the CNL subfamily was more extensive than the TNL subfamily. Novel conserved structures were identified through conserved motif analysis between the CNL and TNL subfamilies. Compared with the NBS-LRR sequences from the model plant Arabidopsis thaliana, wide genetic variation occurred after the divergence of S. pimpinellifolium and A thaliana. Species-specific expansion was also found in the CNL subfamily in S. pimpinellifolium. The results of this study provide the basis for the deeper analysis of NBS-LRR resistance genes and contribute to mapping and isolation of candidate resistance genes in S. pimpinellifolium.
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Affiliation(s)
- Huawei Wei
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- College of Horticulture, Anhui Agricultural University, Hefei, China
| | - Jia Liu
- Wulanchabu Academy of Agricultural and Husbandry Sciences, Wulanchabu, China
| | - Qinwei Guo
- Quzhou Academy of Agricultural Sciences, Quzhou, China
| | - Luzhao Pan
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Songlin Chai
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Yuan Cheng
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Meiying Ruan
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Qingjing Ye
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Rongqing Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Zhuping Yao
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Guozhi Zhou
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Hongjian Wan
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- China-Australia Research Centre for Crop Improvement, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
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20
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van Wersch S, Tian L, Hoy R, Li X. Plant NLRs: The Whistleblowers of Plant Immunity. PLANT COMMUNICATIONS 2020; 1:100016. [PMID: 33404540 PMCID: PMC7747998 DOI: 10.1016/j.xplc.2019.100016] [Citation(s) in RCA: 95] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 12/10/2019] [Accepted: 12/13/2019] [Indexed: 05/19/2023]
Abstract
The study of plant diseases is almost as old as agriculture itself. Advancements in molecular biology have given us much more insight into the plant immune system and how it detects the many pathogens plants may encounter. Members of the primary family of plant resistance (R) proteins, NLRs, contain three distinct domains, and appear to use several different mechanisms to recognize pathogen effectors and trigger immunity. Understanding the molecular process of NLR recognition and activation has been greatly aided by advancements in structural studies, with ZAR1 recently becoming the first full-length NLR to be visualized. Genetic and biochemical analysis identified many critical components for NLR activation and homeostasis control. The increased study of helper NLRs has also provided insights into the downstream signaling pathways of NLRs. This review summarizes the progress in the last decades on plant NLR research, focusing on the mechanistic understanding that has been achieved.
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Affiliation(s)
- Solveig van Wersch
- Department of Botany, University of British Columbia, Vancouver, BC, Canada
- Michael Smith Labs, University of British Columbia, Vancouver, BC, Canada
| | - Lei Tian
- Department of Botany, University of British Columbia, Vancouver, BC, Canada
- Michael Smith Labs, University of British Columbia, Vancouver, BC, Canada
| | - Ryan Hoy
- Department of Botany, University of British Columbia, Vancouver, BC, Canada
| | - Xin Li
- Department of Botany, University of British Columbia, Vancouver, BC, Canada
- Michael Smith Labs, University of British Columbia, Vancouver, BC, Canada
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21
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Xue JY, Zhao T, Liu Y, Liu Y, Zhang YX, Zhang GQ, Chen H, Zhou GC, Zhang SZ, Shao ZQ. Genome- Wide Analysis of the Nucleotide Binding Site Leucine-Rich Repeat Genes of Four Orchids Revealed Extremely Low Numbers of Disease Resistance Genes. Front Genet 2020; 10:1286. [PMID: 31998358 PMCID: PMC6960632 DOI: 10.3389/fgene.2019.01286] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 11/22/2019] [Indexed: 11/16/2022] Open
Abstract
Orchids are one of the most diverse flowering plant families, yet possibly maintain the smallest number of the nucleotide-binding site-leucine-rich repeat (NBS-LRR) type plant resistance (R) genes among the angiosperms. In this study, a genome-wide search in four orchid taxa identified 186 NBS-LRR genes. Furthermore, 214 NBS-LRR genes were identified from seven orchid transcriptomes. A phylogenetic analysis recovered 30 ancestral lineages (29 CNL and one RNL), far fewer than other angiosperm families. From the genetics aspect, the relatively low number of ancestral R genes is unlikely to explain the low number of R genes in orchids alone, as historical gene loss and scarce gene duplication has continuously occurred, which also contributes to the low number of R genes. Due to recent sharp expansions, Phalaenopsis equestris and Dendrobium catenatum having 52 and 115 genes, respectively, and exhibited an “early shrinking to recent expanding” evolutionary pattern, while Gastrodia elata and Apostasia shenzhenica both exhibit a “consistently shrinking” evolutionary pattern and have retained only five and 14 NBS-LRR genes, respectively. RNL genes remain in extremely low numbers with only one or two copies per genome. Notably, all of the orchid RNL genes belong to the ADR1 lineage. A separate lineage, NRG1, was entirely absent and was likely lost in the common ancestor of all monocots. All of the TNL genes were absent as well, coincident with the RNL NRG1 lineage, which supports the previously proposed notion that a potential functional association between the TNL and RNL NRG1 genes.
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Affiliation(s)
- Jia-Yu Xue
- Shenzhen Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen and Chinese Academy of Sciences, Shenzhen, China.,Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China.,VIB-UGent Center for Plant Systems Biology and Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Tao Zhao
- VIB-UGent Center for Plant Systems Biology and Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Yang Liu
- Shenzhen Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen and Chinese Academy of Sciences, Shenzhen, China
| | - Yang Liu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Yong-Xia Zhang
- College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Guo-Qiang Zhang
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Hongfeng Chen
- South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Guang-Can Zhou
- College of Agricultural and Biological Engineering (College of Tree Peony), Heze University, Heze, China
| | - Shou-Zhou Zhang
- Shenzhen Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen and Chinese Academy of Sciences, Shenzhen, China
| | - Zhu-Qing Shao
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
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22
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Kumar A, Kumar R, Sengupta D, Das SN, Pandey MK, Bohra A, Sharma NK, Sinha P, Sk H, Ghazi IA, Laha GS, Sundaram RM. Deployment of Genetic and Genomic Tools Toward Gaining a Better Understanding of Rice- Xanthomonas oryzae pv. oryzae Interactions for Development of Durable Bacterial Blight Resistant Rice. FRONTIERS IN PLANT SCIENCE 2020; 11:1152. [PMID: 32849710 PMCID: PMC7417518 DOI: 10.3389/fpls.2020.01152] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 07/15/2020] [Indexed: 05/05/2023]
Abstract
Rice is the most important food crop worldwide and sustainable rice production is important for ensuring global food security. Biotic stresses limit rice production significantly and among them, bacterial blight (BB) disease caused by Xanthomonas oryzae pv. oryzae (Xoo) is very important. BB reduces rice yields severely in the highly productive irrigated and rainfed lowland ecosystems and in recent years; the disease is spreading fast to other rice growing ecosystems as well. Being a vascular pathogen, Xoo interferes with a range of physiological and biochemical exchange processes in rice. The response of rice to Xoo involves specific interactions between resistance (R) genes of rice and avirulence (Avr) genes of Xoo, covering most of the resistance genes except the recessive ones. The genetic basis of resistance to BB in rice has been studied intensively, and at least 44 genes conferring resistance to BB have been identified, and many resistant rice cultivars and hybrids have been developed and released worldwide. However, the existence and emergence of new virulent isolates of Xoo in the realm of a rapidly changing climate necessitates identification of novel broad-spectrum resistance genes and intensification of gene-deployment strategies. This review discusses about the origin and occurrence of BB in rice, interactions between Xoo and rice, the important roles of resistance genes in plant's defense response, the contribution of rice resistance genes toward development of disease resistance varieties, identification and characterization of novel, and broad-spectrum BB resistance genes from wild species of Oryza and also presents a perspective on potential strategies to achieve the goal of sustainable disease management.
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Affiliation(s)
- Anirudh Kumar
- Department of Botany, Indira Gandhi National Tribal University (IGNTU), Amarkantak, India
- *Correspondence: Raman Meenakshi Sundaram, ; Anirudh Kumar,
| | - Rakesh Kumar
- Department of Life Science, Central University of Karnataka, Kalaburagi, India
| | - Debashree Sengupta
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad (UoH), Hyderabad, India
| | - Subha Narayan Das
- Department of Botany, Indira Gandhi National Tribal University (IGNTU), Amarkantak, India
| | - Manish K. Pandey
- Department of Biotechnology, ICAR-Indian Institute of Rice Research (IIRR), Hyderabad, India
| | - Abhishek Bohra
- ICAR-Crop Improvement Division, Indian Institute of Pulses Research (IIPR), Kanpur, India
| | - Naveen K. Sharma
- Department of Botany, Indira Gandhi National Tribal University (IGNTU), Amarkantak, India
| | - Pragya Sinha
- Department of Biotechnology, ICAR-Indian Institute of Rice Research (IIRR), Hyderabad, India
| | - Hajira Sk
- Department of Biotechnology, ICAR-Indian Institute of Rice Research (IIRR), Hyderabad, India
| | - Irfan Ahmad Ghazi
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad (UoH), Hyderabad, India
| | - Gouri Sankar Laha
- Department of Biotechnology, ICAR-Indian Institute of Rice Research (IIRR), Hyderabad, India
| | - Raman Meenakshi Sundaram
- Department of Biotechnology, ICAR-Indian Institute of Rice Research (IIRR), Hyderabad, India
- *Correspondence: Raman Meenakshi Sundaram, ; Anirudh Kumar,
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23
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Van Ghelder C, Parent GJ, Rigault P, Prunier J, Giguère I, Caron S, Stival Sena J, Deslauriers A, Bousquet J, Esmenjaud D, MacKay J. The large repertoire of conifer NLR resistance genes includes drought responsive and highly diversified RNLs. Sci Rep 2019; 9:11614. [PMID: 31406137 PMCID: PMC6691002 DOI: 10.1038/s41598-019-47950-7] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 07/26/2019] [Indexed: 12/25/2022] Open
Abstract
The NLRs or NBS-LRRs (nucleotide-binding, leucine-rich-repeat) form the largest resistance gene family in plants, with lineage-specific contingents of TNL, CNL and RNL subfamilies and a central role in resilience to stress. The origin, evolution and distribution of NLR sequences has been unclear owing in part to the variable size and diversity of the RNL subfamily and a lack of data in Gymnosperms. We developed, searched and annotated transcriptomes assemblies of seven conifers and identified a resource of 3816 expressed NLR sequences. Our analyses encompassed sequences data spanning the major groups of land plants and determinations of NLR transcripts levels in response to drought in white spruce. We showed that conifers have among the most diverse and numerous RNLs in tested land plants. We report an evolutionary swap in the formation of RNLs, which emerged from the fusion of an RPW8 domain to a NB-ARC domain of CNL. We uncovered a quantitative relationship between RNLs and TNLs across all land plants investigated, with an average ratio of 1:10. The conifer RNL repertoire harbours four distinct groups, with two that differ from Angiosperms, one of which contained several upregulated sequences in response to drought while the majority of responsive NLRs are downregulated.
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Affiliation(s)
- Cyril Van Ghelder
- INRA, Université Côte d'Azur, CNRS, ISA, 400 route des Chappes, BP167, 06903, Sophia Antipolis, France. .,Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK.
| | - Geneviève J Parent
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK.,Forest Research Centre and Institute for Systems and Integrative Biology, Université Laval, 1030 rue de la Médecine, Québec, QC, G1V 0A6, Canada
| | - Philippe Rigault
- Gydle Inc., 1135 Grande Allée Ouest Suite 220, Québec, QC, G1S 1E7, Canada.,Center for Organismal Studies (COS), University of Heidelberg, Im Neuenheimer Feld 345, 69120, Heidelberg, Germany
| | - Julien Prunier
- Forest Research Centre and Institute for Systems and Integrative Biology, Université Laval, 1030 rue de la Médecine, Québec, QC, G1V 0A6, Canada
| | - Isabelle Giguère
- Forest Research Centre and Institute for Systems and Integrative Biology, Université Laval, 1030 rue de la Médecine, Québec, QC, G1V 0A6, Canada
| | - Sébastien Caron
- Gydle Inc., 1135 Grande Allée Ouest Suite 220, Québec, QC, G1S 1E7, Canada
| | - Juliana Stival Sena
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Québec, G1V 4C7, Canada
| | - Annie Deslauriers
- Département des Sciences Fondamentales, Université du Québec à Chicoutimi, 555 Boulevard de l'Université, Chicoutimi, QC, G7H2B1, Canada
| | - Jean Bousquet
- Forest Research Centre and Institute for Systems and Integrative Biology, Université Laval, 1030 rue de la Médecine, Québec, QC, G1V 0A6, Canada.,Canada Research Chair in Forest Genomics, Université Laval, 1030 rue de la Médecine, Québec, QC, G1V 0A6, Canada
| | - Daniel Esmenjaud
- INRA, Université Côte d'Azur, CNRS, ISA, 400 route des Chappes, BP167, 06903, Sophia Antipolis, France
| | - John MacKay
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK.,Forest Research Centre and Institute for Systems and Integrative Biology, Université Laval, 1030 rue de la Médecine, Québec, QC, G1V 0A6, Canada
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24
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van Wersch S, Li X. Stronger When Together: Clustering of Plant NLR Disease resistance Genes. TRENDS IN PLANT SCIENCE 2019; 24:688-699. [PMID: 31266697 DOI: 10.1016/j.tplants.2019.05.005] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2019] [Revised: 05/05/2019] [Accepted: 05/16/2019] [Indexed: 05/14/2023]
Abstract
Gene clustering is rare in eukaryotes. However, nucleotide-binding leucine-rich repeat (NLR)-encoding disease resistance (R) genes show consistent clustering in plant genomes. These arrangements are likely to provide coregulatory benefits, as suggested by growing evidence that the gene products of both paired and larger clusters of NLRs act together in triggering immunity. Head-to-head gene pairs where one of the encoded NLRs includes an integrated decoy domain appear to behave differently than clusters evolved from closely related typical NLRs. These patterns may help to explain the broad resistance that most plants have despite their finite number of R genes. By taking into consideration the relationship between genomic arrangement and function, we can improve our understanding of and ability to predict plant immune detection.
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Affiliation(s)
- Solveig van Wersch
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada; Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Xin Li
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada; Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada.
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25
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Zhang Y, Guo M, Shen J, Song X, Dong S, Wen Y, Yuan X, Guo P. Comparative Genomics Analysis in Grass Species Reveals Two Distinct Evolutionary Strategies Adopted by R Genes. Sci Rep 2019; 9:10735. [PMID: 31341223 PMCID: PMC6656885 DOI: 10.1038/s41598-019-47121-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 07/05/2019] [Indexed: 12/04/2022] Open
Abstract
Resistance genes play an important role in the defense of plants against the invasion of pathogens. In Setaria italica and closely related grass species, R genes have been identified through genetic mapping and genome-wide homologous/domain searching. However, there has been to date no systematic analysis of the evolutionary features of R genes across all sequenced grass genomes. Here, we determined and comprehensively compared R genes in all 12 assembled grass genomes and an outgroup species (Arabidopsis thaliana) through synteny and selection analyses of multiple genomes. We found that the two groups of nucleotide binding site (NBS) domains containing R genes—R tandem duplications (TD) and R singletons—adopted different strategies and showed different features in their evolution. Based on Ka/Ks analysis between syntenic R loci pairs of TDs or singletons, we conclude that R singletons are under stronger purifying selection to be conserved among different grass species than R TDs, while R genes located at TD arrays have evolved much faster through diversifying selection. Furthermore, using the variome datasets of S. italica populations, we scanned for selection signals on genes and observed that a part of R singleton genes have been under purifying selection in populations of S. italica, which is consistent with the pattern observed in syntenic R singletons among different grass species. Additionally, we checked the synteny relationships of reported R genes in grass species and found that the functionally mapped R genes for novel resistance traits are prone to appear in TDs and are heavily divergent from their syntenic orthologs in other grass species, such the black streak R gene Rxo1 in Z. mays and the blast R gene Pi37 in O. sativa. These findings indicate that the R genes from TDs adopted tandem duplications to evolve faster and accumulate more mutations to facilitate functional innovation to cope with variable threats from a fluctuating environment, while R singletons provide a way for R genes to maintain sequence stability and retain conservation of function.
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Affiliation(s)
- Yinan Zhang
- Agronomy College, Shanxi Agricultural University, Taigu, 030801, China
| | - Meijun Guo
- Agronomy College, Shanxi Agricultural University, Taigu, 030801, China
| | - Jie Shen
- Agronomy College, Shanxi Agricultural University, Taigu, 030801, China
| | - Xie Song
- Agronomy College, Shanxi Agricultural University, Taigu, 030801, China
| | - Shuqi Dong
- Agronomy College, Shanxi Agricultural University, Taigu, 030801, China
| | - Yinyuan Wen
- Agronomy College, Shanxi Agricultural University, Taigu, 030801, China
| | - Xiangyang Yuan
- Agronomy College, Shanxi Agricultural University, Taigu, 030801, China
| | - Pingyi Guo
- Agronomy College, Shanxi Agricultural University, Taigu, 030801, China.
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26
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Genome-wide characterization revealed role of NBS-LRR genes during powdery mildew infection in Vitis vinifera. Genomics 2019; 112:312-322. [PMID: 30802599 DOI: 10.1016/j.ygeno.2019.02.011] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 01/11/2019] [Accepted: 02/14/2019] [Indexed: 11/23/2022]
Abstract
NBS-LRR comprises a large class of disease resistance (R) proteins that play a widespread role in plant protection against pathogens. In grapevine, powdery mildew cause significant losses in its productivity and efforts are being directed towards finding of resistance loci or genes imparting resistance/tolerance against such fungal diseases. In the present study, we performed genome-wide analysis of NBS-LRR genes during PM infection in grapevine. We identified 18, 23, 12, 16, 10, 10, 9, 20 and 14 differentially expressed NBS-LRR genes in response to PM infection in seven partially PM-resistant (DVIT3351.27, Husseine, Karadzhandal, Khalchili, Late vavilov, O34-16, Sochal) and 2 PM-susceptible (Carignan and Thompson seedless) V. vinifera accessions. Further, the identified sequences were characterized based on chromosomal locations, physicochemical properties, gene structure and motif analysis, and functional annotation by Gene Ontology (GO) mapping. The NBS-LRR genes responsive to powdery mildew could potentially be exploited to improve resistance in grapes.
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27
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Evolution of Disease Defense Genes and Their Regulators in Plants. Int J Mol Sci 2019; 20:ijms20020335. [PMID: 30650550 PMCID: PMC6358896 DOI: 10.3390/ijms20020335] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 12/28/2018] [Accepted: 01/10/2019] [Indexed: 02/06/2023] Open
Abstract
Biotic stresses do damage to the growth and development of plants, and yield losses for some crops. Confronted with microbial infections, plants have evolved multiple defense mechanisms, which play important roles in the never-ending molecular arms race of plant–pathogen interactions. The complicated defense systems include pathogen-associated molecular patterns (PAMP) triggered immunity (PTI), effector triggered immunity (ETI), and the exosome-mediated cross-kingdom RNA interference (CKRI) system. Furthermore, plants have evolved a classical regulation system mediated by miRNAs to regulate these defense genes. Most of the genes/small RNAs or their regulators that involve in the defense pathways can have very rapid evolutionary rates in the longitudinal and horizontal co-evolution with pathogens. According to these internal defense mechanisms, some strategies such as molecular switch for the disease resistance genes, host-induced gene silencing (HIGS), and the new generation of RNA-based fungicides, have been developed to control multiple plant diseases. These broadly applicable new strategies by transgene or spraying ds/sRNA may lead to reduced application of pesticides and improved crop yield.
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28
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Araújo ACD, Fonseca FCDA, Cotta MG, Alves GSC, Miller RNG. Plant NLR receptor proteins and their potential in the development of durable genetic resistance to biotic stresses. ACTA ACUST UNITED AC 2019. [DOI: 10.1016/j.biori.2020.01.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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29
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Fu Y, Zhang Y, Mason AS, Lin B, Zhang D, Yu H, Fu D. NBS-Encoding Genes in Brassica napus Evolved Rapidly After Allopolyploidization and Co-localize With Known Disease Resistance Loci. FRONTIERS IN PLANT SCIENCE 2019; 10:26. [PMID: 30761170 PMCID: PMC6363714 DOI: 10.3389/fpls.2019.00026] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 01/09/2019] [Indexed: 05/19/2023]
Abstract
Genes containing nucleotide-binding sites (NBS) play an important role in pathogen resistance in plants. However, the evolutionary fate of NBS-encoding genes after formation of allotetraploid Brassica napus (AnAnCnCn, 2n = 38) is still unknown. We performed a genome-wide comparison of putatively functional NBS-encoding genes in B. napus and its progenitor species Brassica rapa (ArAr, 2n = 20) and Brassica oleracea (CoCo, 2n = 18), identifying 464, 202, and 146 putatively functional NBS-encoding genes respectively, with genes unevenly distributed in several clusters. The An-subgenome of B. napus possessed similar numbers of NBS-encoding genes (191 genes) to the Ar genome of B. rapa (202 genes) and similar clustering patterns. However, the Cn genome of B. napus had many more genes (273) than the B. oleracea Co genome (146), with different clustering trends. Only 97 NBS-encoding genes (66.4%) in B. oleracea were homologous with NBS-encoding genes in B. napus, while 176 NBS-encoding genes (87.1%) were homologous between B. rapa and B. napus. These results suggest a greater diversification of NBS-encoding genes in the C genome may have occurred after formation of B. napus. Although most NBS-encoding genes in B. napus appeared to derive from the progenitors, the birth and death of several NBS-encoding genes was also putatively mediated by non-homologous recombination. The Ka/Ks values of most homologous pairs between B. napus and the progenitor species were less than 1, suggesting purifying selection during B. napus evolution. The majority of NBS-encoding genes (60% in all species) showed higher expression levels in root tissue (out of root, leaf, stem, seed and flower tissue types). Comparative analysis of NBS-encoding genes with mapped resistance QTL against three major diseases of B. napus (blackleg, clubroot and Sclerotinia stem rot) found 204 NBS-encoding genes in B. napus located within 71 resistance QTL intervals. The majority of NBS-encoding genes were co-located with resistance QTLs against a single disease, while 47 genes were co-located with QTLs against two diseases and 3 genes were co-located with QTLs against all three. Our results revealed significant variation as well as interesting evolutionary trajectories of NBS-encoding genes in the different Brassica subgenomes, while co-localization of NBS-encoding genes and resistance QTL may facilitate resistance breeding in oilseed rape.
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Affiliation(s)
- Ying Fu
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Yaofeng Zhang
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Annaliese S. Mason
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University Giessen, Giessen, Germany
| | - Baogang Lin
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Dongqing Zhang
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Huasheng Yu
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- *Correspondence: Huasheng Yu, Donghui Fu,
| | - Donghui Fu
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Agronomy College, Jiangxi Agricultural University, Nanchang, China
- *Correspondence: Huasheng Yu, Donghui Fu,
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Die JV, Castro P, Millán T, Gil J. Segmental and Tandem Duplications Driving the Recent NBS-LRR Gene Expansion in the Asparagus Genome. Genes (Basel) 2018; 9:E568. [PMID: 30477134 PMCID: PMC6316259 DOI: 10.3390/genes9120568] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2018] [Revised: 11/07/2018] [Accepted: 11/19/2018] [Indexed: 11/21/2022] Open
Abstract
Garden asparagus is an important horticultural plant worldwide. It is, however, susceptible to a variety of diseases, which can affect the potential yield, spear quality, and lifespan of production fields. Screening studies have identified resistant germplasm. The genetic resistance is usually complex, and the genes underlying that resistance are still unknown. Most often, disease resistance is determined by resistance genes (R). The most predominant R-genes contain nucleotide binding site and leucine-rich repeat (NBS-LRR) domains. Using bioinformatics and data mining approaches, we identified and characterized 68 NBS predicted proteins encoded by 49 different loci in the asparagus genome. The NBS-encoding genes were grouped into seven distinct classes based on their domain architecture. The NBS genes are unevenly distributed through the genome and nearly 50% of the genes are present in clusters. Chromosome 6 is significantly NBS-enriched and one single cluster hosts 10% of the genes. Phylogenetic analysis points to their diversification into three families during their evolution. Recent duplications are likely to have dominated the NBS expansion with both tandem genes and duplication events across multiple chromosomes. Transcriptome sequencing data provided evidence for their transcription and tissue-specific expression. The total number of cis-regulatory elements as well as their relative positions within the NBS promoters suggests a complex transcriptional network regulating defense responses. Our study provides a strong groundwork for the isolation of candidate R-genes in garden asparagus.
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Affiliation(s)
- Jose V Die
- Department of Genetics, ETSIAM, University of Córdoba, 14071 Córdoba, Spain.
| | - Patricia Castro
- Department of Genetics, ETSIAM, University of Córdoba, 14071 Córdoba, Spain.
| | - Teresa Millán
- Department of Genetics, ETSIAM, University of Córdoba, 14071 Córdoba, Spain.
| | - Juan Gil
- Department of Genetics, ETSIAM, University of Córdoba, 14071 Córdoba, Spain.
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Habachi-Houimli Y, Khalfallah Y, Mezghani-Khemakhem M, Makni H, Makni M, Bouktila D. Genome-wide identification, characterization, and evolutionary analysis of NBS-encoding resistance genes in barley. 3 Biotech 2018; 8:453. [PMID: 30370194 DOI: 10.1007/s13205-018-1478-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 10/11/2018] [Indexed: 12/29/2022] Open
Abstract
In this study, a systematic analysis of Nucleotide-Binding Site (NBS) disease resistance (R) gene family in the barley, Hordeum vulgare L. cv. Bowman, genome was performed. Using multiple computational analyses, we could identify 96 regular NBS-encoding genes and characterize them on the bases of structural diversity, conserved protein signatures, genomic distribution, gene duplications, differential expression, selection pressure, codon usage, regulation by microRNAs and phylogenetic relationships. Depending on the presence or absence of CC and LRR domains; the identified NBS genes were assigned to four distinct groups; NBS-LRR (53.1%), CC-NBS-LRR (14.6%), NBS (26%), and CC-NBS (6.3%). NBS-associated domain analysis revealed the presence of signal peptides, zinc fingers, diverse kinases, and other structural features. Eighty-five of the identified NBS-encoding genes were mapped onto the seven barley chromosomes, revealing that 50% of them were located on chromosomes 7H, 2H, and 3H, with a tendency of NBS genes to be clustered in the distal telomeric regions of the barley chromosomes. Nine gene clusters, representing 22.35% of total mapped barley NBS-encoding genes, were found, suggesting that tandem duplication stands for an important mechanism in the expansion of this gene family in barley. Phylogenetic analysis determined 31 HvNBS orthologs from rice and Brachypodium. 87 out of 96 HvNBSs were supported by expression evidence, exhibiting various and quantitatively uneven expression patterns across distinct tissues, organs, and development stages. Fourteen potential miRNA-R gene target pairs were further identified, providing insight into the regulation of NBS genes expression. These findings offer candidate target genes to engineer disease-resistant barley genotypes, and promote our understanding of the evolution of NBS-encoding genes in Poaceae crops.
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Affiliation(s)
- Yosra Habachi-Houimli
- 1Université de Tunis El Manar, Faculté des Sciences de Tunis, Unité de Recherche Génomique des Insectes Ravageurs des Cultures d'intérêt agronomique (GIRC, UR11ES10), El Manar, 2092 Tunis, Tunisia
| | - Yosra Khalfallah
- 1Université de Tunis El Manar, Faculté des Sciences de Tunis, Unité de Recherche Génomique des Insectes Ravageurs des Cultures d'intérêt agronomique (GIRC, UR11ES10), El Manar, 2092 Tunis, Tunisia
| | - Maha Mezghani-Khemakhem
- 1Université de Tunis El Manar, Faculté des Sciences de Tunis, Unité de Recherche Génomique des Insectes Ravageurs des Cultures d'intérêt agronomique (GIRC, UR11ES10), El Manar, 2092 Tunis, Tunisia
| | - Hanem Makni
- 1Université de Tunis El Manar, Faculté des Sciences de Tunis, Unité de Recherche Génomique des Insectes Ravageurs des Cultures d'intérêt agronomique (GIRC, UR11ES10), El Manar, 2092 Tunis, Tunisia
- 2Université de Tunis, Institut Supérieur de l'Animation pour la Jeunesse et la Culture (ISAJC), Bir El Bey, Tunisia
| | - Mohamed Makni
- 1Université de Tunis El Manar, Faculté des Sciences de Tunis, Unité de Recherche Génomique des Insectes Ravageurs des Cultures d'intérêt agronomique (GIRC, UR11ES10), El Manar, 2092 Tunis, Tunisia
| | - Dhia Bouktila
- 1Université de Tunis El Manar, Faculté des Sciences de Tunis, Unité de Recherche Génomique des Insectes Ravageurs des Cultures d'intérêt agronomique (GIRC, UR11ES10), El Manar, 2092 Tunis, Tunisia
- 3Université de Jendouba, Institut Supérieur de Biotechnologie de Béja (ISBB), 9000 Béja, Tunisia
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Madroñero J, Rodrigues SP, Antunes TFS, Abreu PMV, Ventura JA, Fernandes AAR, Fernandes PMB. Transcriptome analysis provides insights into the delayed sticky disease symptoms in Carica papaya. PLANT CELL REPORTS 2018; 37:967-980. [PMID: 29564545 DOI: 10.1007/s00299-018-2281-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 03/16/2018] [Indexed: 05/25/2023]
Abstract
Global gene expression analysis indicates host stress responses, mainly those mediated by SA, associated to the tolerance to sticky disease symptoms at pre-flowering stage in Carica papaya. Carica papaya plants develop the papaya sticky disease (PSD) as a result of the combined infection of papaya meleira virus (PMeV) and papaya meleira virus 2 (PMeV2), or PMeV complex. PSD symptoms appear only after C. papaya flowers. To understand the mechanisms involved in this phenomenon, the global gene expression patterns of PMeV complex-infected C. papaya at pre-and post-flowering stages were assessed by RNA-Seq. The result was 633 and 88 differentially expressed genes at pre- and post-flowering stages, respectively. At pre-flowering stage, genes related to stress and transport were up-regulated while metabolism-related genes were down-regulated. It was observed that induction of several salicylic acid (SA)-activated genes, including PR1, PR2, PR5, WRKY transcription factors, ROS and callose genes, suggesting SA signaling involvement in the delayed symptoms. In fact, pre-flowering C. papaya treated with exogenous SA showed a tendency to decrease the PMeV and PMeV2 loads when compared to control plants. However, pre-flowering C. papaya also accumulated transcripts encoding a NPR1-inhibitor (NPR1-I/NIM1-I) candidate, genes coding for UDP-glucosyltransferases (UGTs) and several genes involved with ethylene pathway, known to be negative regulators of SA signaling. At post-flowering, when PSD symptoms appeared, the down-regulation of PR-1 encoding gene and the induction of BSMT1 and JA metabolism-related genes were observed. Hence, SA signaling likely operates at the pre-flowering stage of PMeV complex-infected C. papaya inhibiting the development of PSD symptoms, but the induction of its negative regulators prevents the full-scale and long-lasting tolerance.
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Affiliation(s)
- Johana Madroñero
- Núcleo de Biotecnologia, Universidade Federal do Espírito Santo, Av. Marechal Campos, 1468, Vitória, ES, 29040-090, Brazil
| | - Silas P Rodrigues
- Núcleo de Biotecnologia, Universidade Federal do Espírito Santo, Av. Marechal Campos, 1468, Vitória, ES, 29040-090, Brazil
- Núcleo Multidisciplinar de Pesquisa-Polo de Xerém, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Tathiana F S Antunes
- Núcleo de Biotecnologia, Universidade Federal do Espírito Santo, Av. Marechal Campos, 1468, Vitória, ES, 29040-090, Brazil
| | - Paolla M V Abreu
- Núcleo de Biotecnologia, Universidade Federal do Espírito Santo, Av. Marechal Campos, 1468, Vitória, ES, 29040-090, Brazil
| | - José A Ventura
- Núcleo de Biotecnologia, Universidade Federal do Espírito Santo, Av. Marechal Campos, 1468, Vitória, ES, 29040-090, Brazil
- Instituto Capixaba de Pesquisa, Assistência Técnica e Extensão Rural, Vitória, ES, Brazil
| | - A Alberto R Fernandes
- Núcleo de Biotecnologia, Universidade Federal do Espírito Santo, Av. Marechal Campos, 1468, Vitória, ES, 29040-090, Brazil
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Identification of NBS-encoding genes linked to black rot resistance in cabbage (Brassica oleracea var. capitata). Mol Biol Rep 2018; 45:773-785. [PMID: 29931534 DOI: 10.1007/s11033-018-4217-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 06/14/2018] [Indexed: 12/14/2022]
Abstract
Heading cabbage is a nutritionally rich and economically important cruciferous vegetable. Black rot disease, caused by the bacterium Xanthomonas campestris pv. campestris, reduces both the yield and quality of the cabbage head. Nucleotide binding site (NBS)-encoding resistance (R) genes play a vital role in the plant immune response to various pathogens. In this study, we analyzed the expression and DNA sequence variation of 31 NBS-encoding genes in cabbage (Brassica oleracea var. capitata). These genes encoded TIR, NBS, LRR and RPW8 protein domains, all of which are known to be involved in disease resistance. RNA-seq revealed that these 31 genes were differentially expressed in leaf, root, silique, and stem tissues. Furthermore, qPCR analyses revealed that several of these genes were more highly expressed in resistant compared to susceptible cabbage lines, including Bol003711, Bol010135, Bol010559, Bol022784, Bol029866, Bol042121, Bol031422, Bol040045 and Bol042095. Further analysis of these genes promises to yield both practical benefits, such as molecular markers for marker-assisted breeding, and fundamental insights to the mechanisms of resistance to black rot in cabbage.
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Borrelli GM, Mazzucotelli E, Marone D, Crosatti C, Michelotti V, Valè G, Mastrangelo AM. Regulation and Evolution of NLR Genes: A Close Interconnection for Plant Immunity. Int J Mol Sci 2018; 19:E1662. [PMID: 29867062 PMCID: PMC6032283 DOI: 10.3390/ijms19061662] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 06/01/2018] [Accepted: 06/02/2018] [Indexed: 12/12/2022] Open
Abstract
NLR (NOD-like receptor) genes belong to one of the largest gene families in plants. Their role in plants' resistance to pathogens has been clearly described for many members of this gene family, and dysregulation or overexpression of some of these genes has been shown to induce an autoimmunity state that strongly affects plant growth and yield. For this reason, these genes have to be tightly regulated in their expression and activity, and several regulatory mechanisms are described here that tune their gene expression and protein levels. This gene family is subjected to rapid evolution, and to maintain diversity at NLRs, a plethora of genetic mechanisms have been identified as sources of variation. Interestingly, regulation of gene expression and evolution of this gene family are two strictly interconnected aspects. Indeed, some examples have been reported in which mechanisms of gene expression regulation have roles in promotion of the evolution of this gene family. Moreover, co-evolution of the NLR gene family and other gene families devoted to their control has been recently demonstrated, as in the case of miRNAs.
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Affiliation(s)
- Grazia M Borrelli
- Council for Agricultural Research and Economics-Research Centre for Cereal and Industrial Crops, s.s. 673, km 25.2, 71122 Foggia, Italy.
| | - Elisabetta Mazzucotelli
- Council for Agricultural Research and Economics-Research Centre for Genomics and Bioinformatics, via San Protaso 302, 29017 Fiorenzuola d'Arda (PC), Italy.
| | - Daniela Marone
- Council for Agricultural Research and Economics-Research Centre for Cereal and Industrial Crops, s.s. 673, km 25.2, 71122 Foggia, Italy.
| | - Cristina Crosatti
- Council for Agricultural Research and Economics-Research Centre for Genomics and Bioinformatics, via San Protaso 302, 29017 Fiorenzuola d'Arda (PC), Italy.
| | - Vania Michelotti
- Council for Agricultural Research and Economics-Research Centre for Genomics and Bioinformatics, via San Protaso 302, 29017 Fiorenzuola d'Arda (PC), Italy.
| | - Giampiero Valè
- Council for Agricultural Research and Economics-Research Centre for Cereal and Industrial Crops, s.s. 11 to Torino, km 2.5, 13100 Vercelli, Italy.
| | - Anna M Mastrangelo
- Council for Agricultural Research and Economics-Research Centre for Cereal and Industrial Crops, via Stezzano 24, 24126 Bergamo, Italy.
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Richard MMS, Gratias A, Thareau V, Kim KD, Balzergue S, Joets J, Jackson SA, Geffroy V. Genomic and epigenomic immunity in common bean: the unusual features of NB-LRR gene family. DNA Res 2018; 25:161-172. [PMID: 29149287 PMCID: PMC5909424 DOI: 10.1093/dnares/dsx046] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Accepted: 10/26/2017] [Indexed: 12/20/2022] Open
Abstract
In plants, a key class of genes comprising most of disease resistance (R) genes encodes Nucleotide-binding leucine-rich repeat (NL) proteins. Access to common bean (Phaseolus vulgaris) genome sequence provides unparalleled insight into the organization and evolution of this large gene family (∼400 NL) in this important crop. As observed in other plant species, most common bean NL are organized in cluster of genes. However, a particularity of common bean is that these clusters are often located in subtelomeric regions close to terminal knobs containing the satellite DNA khipu. Phylogenetically related NL are spread between different chromosome ends, suggesting frequent exchanges between non-homologous chromosomes. NL peculiar location, in proximity to heterochromatic regions, led us to study their DNA methylation status using a whole-genome cytosine methylation map. In common bean, NL genes displayed an unusual body methylation pattern since half of them are methylated in the three contexts, reminiscent of the DNA methylation pattern of repeated sequences. Moreover, 90 NL were also abundantly targeted by 24 nt siRNA, with 90% corresponding to methylated NL genes. This suggests the existence of a transcriptional gene silencing mechanism of NL through the RdDM (RNA-directed DNA methylation) pathway in common bean that has not been described in other plant species.
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Affiliation(s)
- Manon M S Richard
- Institute of Plant Sciences Paris-Saclay IPS2, CNRS, INRA, Univ Paris-Saclay, Univ Paris-Sud, Univ Evry, Univ Paris-Diderot, Sorbone Paris-Cité, 91405 Orsay, France
| | - Ariane Gratias
- Institute of Plant Sciences Paris-Saclay IPS2, CNRS, INRA, Univ Paris-Saclay, Univ Paris-Sud, Univ Evry, Univ Paris-Diderot, Sorbone Paris-Cité, 91405 Orsay, France
| | - Vincent Thareau
- Institute of Plant Sciences Paris-Saclay IPS2, CNRS, INRA, Univ Paris-Saclay, Univ Paris-Sud, Univ Evry, Univ Paris-Diderot, Sorbone Paris-Cité, 91405 Orsay, France
| | - Kyung Do Kim
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA 30602, USA
| | - Sandrine Balzergue
- Institute of Plant Sciences Paris-Saclay IPS2, CNRS, INRA, Univ Paris-Saclay, Univ Paris-Sud, Univ Evry, Univ Paris-Diderot, Sorbone Paris-Cité, 91405 Orsay, France
- IRHS, INRA, AGROCAMPUS-Ouest, Université d’Angers, SFR 4207 QUASAV, 49071 Beaucouzé cedex, France
| | - Johann Joets
- GQE – Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, 91190 Gif-sur-Yvette, France
| | - Scott A Jackson
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA 30602, USA
| | - Valérie Geffroy
- Institute of Plant Sciences Paris-Saclay IPS2, CNRS, INRA, Univ Paris-Saclay, Univ Paris-Sud, Univ Evry, Univ Paris-Diderot, Sorbone Paris-Cité, 91405 Orsay, France
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Chávez-Pesqueira M, Núñez-Farfán J. Domestication and Genetics of Papaya: A Review. Front Ecol Evol 2017. [DOI: 10.3389/fevo.2017.00155] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Jia R, Zhao H, Huang J, Kong H, Zhang Y, Guo J, Huang Q, Guo Y, Wei Q, Zuo J, Zhu YJ, Peng M, Guo A. Use of RNAi technology to develop a PRSV-resistant transgenic papaya. Sci Rep 2017; 7:12636. [PMID: 28974762 PMCID: PMC5626737 DOI: 10.1038/s41598-017-13049-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 09/14/2017] [Indexed: 12/13/2022] Open
Abstract
Papaya ringspot virus (PRSV) seriously limits papaya (Carica papaya L.) production in tropical and subtropical areas throughout the world. Coat protein (CP)- transgenic papaya lines resistant to PRSV isolates in the sequence-homology-dependent manner have been developed in the U.S.A. and Taiwan. A previous investigation revealed that genetic divergence among Hainan isolates of PRSV has allowed the virus to overcome the CP-mediated transgenic resistance. In this study, we designed a comprehensive RNAi strategy targeting the conserved domain of the PRSV CP gene to develop a broader-spectrum transgenic resistance to the Hainan PRSV isolates. We used an optimized particle-bombardment transformation system to produce RNAi-CP-transgenic papaya lines. Southern blot analysis and Droplet Digital PCR revealed that line 474 contained a single transgene insert. Challenging this line with different viruses (PRSV I, II and III subgroup) under greenhouse conditions validated the transgenic resistance of line 474 to the Hainan isolates. Northern blot analysis detected the siRNAs products in virus-free transgenic papaya tissue culture seedlings. The siRNAs also accumulated in PRSV infected transgenic papaya lines. Our results indicated that this transgenic papaya line has a useful application against PRSV in the major growing area of Hainan, China.
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Affiliation(s)
- Ruizong Jia
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agriculture Sciences, 571101, Haikou, Hainan, China
- Hawaii Agriculture Research Center, 96797, Waipahu, HI, USA
| | - Hui Zhao
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agriculture Sciences, 571101, Haikou, Hainan, China
| | - Jing Huang
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agriculture Sciences, 571101, Haikou, Hainan, China
- School of Basic and Life Science, Hainan Medical University, Haikou, 571199, Hainan, China
| | - Hua Kong
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agriculture Sciences, 571101, Haikou, Hainan, China
| | - Yuliang Zhang
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agriculture Sciences, 571101, Haikou, Hainan, China
| | - Jingyuan Guo
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agriculture Sciences, 571101, Haikou, Hainan, China
| | - Qixing Huang
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agriculture Sciences, 571101, Haikou, Hainan, China
| | - Yunling Guo
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agriculture Sciences, 571101, Haikou, Hainan, China
| | - Qing Wei
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agriculture Sciences, 571101, Haikou, Hainan, China
- Institute of Banana and Plantain, Haikou Substation, Chinese Academy of Tropical Agriculture Sciences, 570102, Haikou, Hainan, China
| | - Jiao Zuo
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agriculture Sciences, 571101, Haikou, Hainan, China
| | - Yun J Zhu
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agriculture Sciences, 571101, Haikou, Hainan, China.
- Hawaii Agriculture Research Center, 96797, Waipahu, HI, USA.
| | - Ming Peng
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agriculture Sciences, 571101, Haikou, Hainan, China.
| | - Anping Guo
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agriculture Sciences, 571101, Haikou, Hainan, China.
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Arya P, Acharya V. Plant STAND P-loop NTPases: a current perspective of genome distribution, evolution, and function : Plant STAND P-loop NTPases: genomic organization, evolution, and molecular mechanism models contribute broadly to plant pathogen defense. Mol Genet Genomics 2017; 293:17-31. [PMID: 28900732 DOI: 10.1007/s00438-017-1368-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 09/07/2017] [Indexed: 01/18/2023]
Abstract
STAND P-loop NTPase is the common weapon used by plant and other organisms from all three kingdoms of life to defend themselves against pathogen invasion. The purpose of this study is to review comprehensively the latest finding of plant STAND P-loop NTPase related to their genomic distribution, evolution, and their mechanism of action. Earlier, the plant STAND P-loop NTPase known to be comprised of only NBS-LRRs/AP-ATPase/NB-ARC ATPase. However, recent finding suggests that genome of early green plants comprised of two types of STAND P-loop NTPases: (1) mammalian NACHT NTPases and (2) NBS-LRRs. Moreover, YchF (unconventional G protein and members of P-loop NTPase) subfamily has been reported to be exceptionally involved in biotic stress (in case of Oryza sativa), thereby a novel member of STAND P-loop NTPase in green plants. The lineage-specific expansion and genome duplication events are responsible for abundance of plant STAND P-loop NTPases; where "moderate tandem and low segmental duplication" trajectory followed in majority of plant species with few exception (equal contribution of tandem and segmental duplication). Since the past decades, systematic research is being investigated into NBS-LRR function supported the direct recognition of pathogen or pathogen effectors by the latest models proposed via 'integrated decoy' or 'sensor domains' model. Here, we integrate the recently published findings together with the previous literature on the genomic distribution, evolution, and distinct models proposed for functional molecular mechanism of plant STAND P-loop NTPases.
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Affiliation(s)
- Preeti Arya
- Functional Genomics and Complex System Lab, Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Council of Scientific and Industrial Research, Palampur, Himachal Pradesh, 176061, India.,Academy of Scientific and Innovative Research (AcSIR), CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT) Campus, Palampur, Himachal Pradesh, India.,National Agri-Food Biotechnology Institute, Sector-81 (Knowledge City), SAS Nagar, Punjab, 140306, India
| | - Vishal Acharya
- Functional Genomics and Complex System Lab, Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Council of Scientific and Industrial Research, Palampur, Himachal Pradesh, 176061, India. .,Academy of Scientific and Innovative Research (AcSIR), CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT) Campus, Palampur, Himachal Pradesh, India.
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Genome-wide identification and tissue-specific expression analysis of nucleotide binding site-leucine rich repeat gene family in Cicer arietinum (kabuli chickpea). GENOMICS DATA 2017; 14:24-31. [PMID: 28840100 PMCID: PMC5558467 DOI: 10.1016/j.gdata.2017.08.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Revised: 08/05/2017] [Accepted: 08/09/2017] [Indexed: 12/30/2022]
Abstract
The nucleotide binding site-leucine rich repeat (NBS-LRR) proteins play an important role in the defense mechanisms against pathogens. Using bioinformatics approach, we identified and annotated 104 NBS-LRR genes in chickpea. Phylogenetic analysis points to their diversification into two families namely TIR-NBS-LRR and non-TIR-NBS-LRR. Gene architecture revealed intron gain/loss events in this resistance gene family during their independent evolution into two families. Comparative genomics analysis elucidated its evolutionary relationship with other fabaceae species. Around 50% NBS-LRRs reside in macro-syntenic blocks underlining positional conservation along with sequence conservation of NBS-LRR genes in chickpea. Transcriptome sequencing data provided evidence for their transcription and tissue-specific expression. Four cis-regulatory elements namely WBOX, DRE, CBF, and GCC boxes, that commonly occur in resistance genes, were present in the promoter regions of these genes. Further, the findings will provide a strong background to use candidate disease resistance NBS-encoding genes and identify their specific roles in chickpea.
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40
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Yin R, Zhao M, Wang K, Lin Y, Wang Y, Sun C, Wang Y, Zhang M. Functional differentiation and spatial-temporal co-expression networks of the NBS-encoding gene family in Jilin ginseng, Panax ginseng C.A. Meyer. PLoS One 2017; 12:e0181596. [PMID: 28727829 PMCID: PMC5519184 DOI: 10.1371/journal.pone.0181596] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2017] [Accepted: 07/03/2017] [Indexed: 11/30/2022] Open
Abstract
Ginseng, Panax ginseng C.A. Meyer, is one of the most important medicinal plants for human health and medicine. It has been documented that over 80% of genes conferring resistance to bacteria, viruses, fungi and nematodes are contributed by the nucleotide binding site (NBS)-encoding gene family. Therefore, identification and characterization of NBS genes expressed in ginseng are paramount to its genetic improvement and breeding. However, little is known about the NBS-encoding genes in ginseng. Here we report genome-wide identification and systems analysis of the NBS genes actively expressed in ginseng (PgNBS genes). Four hundred twelve PgNBS gene transcripts, derived from 284 gene models, were identified from the transcriptomes of 14 ginseng tissues. These genes were classified into eight types, including TNL, TN, CNL, CN, NL, N, RPW8-NL and RPW8-N. Seven conserved motifs were identified in both the Toll/interleukine-1 receptor (TIR) and coiled-coil (CC) typed genes whereas six were identified in the RPW8 typed genes. Phylogenetic analysis showed that the PgNBS gene family is an ancient family, with a vast majority of its genes originated before ginseng originated. In spite of their belonging to a family, the PgNBS genes have functionally dramatically differentiated and been categorized into numerous functional categories. The expressions of the across tissues, different aged roots and the roots of different genotypes. However, they are coordinating in expression, forming a single co-expression network. These results provide a deeper understanding of the origin, evolution and functional differentiation and expression dynamics of the NBS-encoding gene family in plants in general and in ginseng particularly, and a NBS gene toolkit useful for isolation and characterization of disease resistance genes and for enhanced disease resistance breeding in ginseng and related species.
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Affiliation(s)
- Rui Yin
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, China
| | - Mingzhu Zhao
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, China
| | - Kangyu Wang
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, China
- The Center of Ginseng Germplasm Research, Development and Utilization, Changchun, Jilin, China
| | - Yanping Lin
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, China
| | - Yanfang Wang
- College of Chinese Medicinal Materials, Jilin Agricultural University, Changchun, Jilin, China
| | - Chunyu Sun
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, China
- The Center of Ginseng Germplasm Research, Development and Utilization, Changchun, Jilin, China
| | - Yi Wang
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, China
- The Center of Ginseng Germplasm Research, Development and Utilization, Changchun, Jilin, China
- * E-mail: (MPZ); (YW)
| | - Meiping Zhang
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, China
- The Center of Ginseng Germplasm Research, Development and Utilization, Changchun, Jilin, China
- * E-mail: (MPZ); (YW)
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Distinct Patterns of Gene Gain and Loss: Diverse Evolutionary Modes of NBS-Encoding Genes in Three Solanaceae Crop Species. G3-GENES GENOMES GENETICS 2017; 7:1577-1585. [PMID: 28364035 PMCID: PMC5427506 DOI: 10.1534/g3.117.040485] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Plant resistance conferred by nucleotide binding site (NBS)-encoding resistance genes plays a key role in the defense against various pathogens throughout the entire plant life cycle. However, comparative analyses for the systematic evaluation and determination of the evolutionary modes of NBS-encoding genes among Solanaceae species are rare. In this study, 447, 255, and 306 NBS-encoding genes were identified from the genomes of potato, tomato, and pepper, respectively. These genes usually clustered as tandem arrays on chromosomes; few existed as singletons. Phylogenetic analysis indicated that three subclasses [TNLs (TIR-NBS-LRR), CNLs (CC-NBS-LRR), and RNLs (RPW8-NBS-LRR)] each formed a monophyletic clade and were distinguished by unique exon/intron structures and amino acid motif sequences. By comparing phylogenetic and systematic relationships, we inferred that the NBS-encoding genes in the present genomes of potato, tomato, and pepper were derived from 150 CNL, 22 TNL, and 4 RNL ancestral genes, and underwent independent gene loss and duplication events after speciation. The NBS-encoding genes therefore exhibit diverse and dynamic evolutionary patterns in the three Solanaceae species, giving rise to the discrepant gene numbers observed today. Potato shows a “consistent expansion” pattern, tomato exhibits a pattern of “first expansion and then contraction,” and pepper presents a “shrinking” pattern. The earlier expansion of CNLs in the common ancestor led to the dominance of this subclass in gene numbers. However, RNLs remained at low copy numbers due to their specific functions. Along the evolutionary process of NBS-encoding genes in Solanaceae, species-specific tandem duplications contributed the most to gene expansions.
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Genome-wide identification and resistance expression analysis of the NBS gene family in Triticum urartu. Genes Genomics 2017. [DOI: 10.1007/s13258-017-0526-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Sagi MS, Deokar AA, Tar’an B. Genetic Analysis of NBS-LRR Gene Family in Chickpea and Their Expression Profiles in Response to Ascochyta Blight Infection. FRONTIERS IN PLANT SCIENCE 2017; 8:838. [PMID: 28580004 PMCID: PMC5437156 DOI: 10.3389/fpls.2017.00838] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 05/04/2017] [Indexed: 05/21/2023]
Abstract
Ascochyta blight is one of the major diseases of chickpea worldwide. The genetic resistance to ascochyta blight in chickpea is complex and governed by multiple QTLs. However, the molecular mechanism of quantitative disease resistance to ascochyta blight and the genes underlying these QTLs are still unknown. Most often disease resistance is determined by resistance (R) genes. The most predominant R-genes contain nucleotide binding site and leucine rich repeat (NBS-LRR) domains. A total of 121 NBS-LRR genes were identified in the chickpea genome. Ninety-eight of these genes contained all essential conserved domains while 23 genes were truncated. The NBS-LRR genes were grouped into eight distinct classes based on their domain architecture. Phylogenetic analysis grouped these genes into two major clusters based on their structural variation, the first cluster with toll or interleukin-1 like receptor (TIR) domain and the second cluster either with or without a coiled-coil domain. The NBS-LRR genes are distributed unevenly across the eight chickpea chromosomes and nearly 50% of the genes are present in clusters. Thirty of the NBS-LRR genes were co-localized with nine of the previously reported ascochyta blight QTLs and were tested as potential candidate genes for ascochyta blight resistance. Expression pattern of these genes was studied in two resistant (CDC Corinne and CDC Luna) and one susceptible (ICCV 96029) genotypes at different time points after ascochyta blight infection using real-time quantitative PCR. Twenty-seven NBS-LRR genes showed differential expression in response to ascochyta blight infection in at least one genotype at one time point. Among these 27 genes, the majority of the NBS-LRR genes showed differential expression after inoculation in both resistant and susceptible genotypes which indicates the involvement of these genes in response to ascochyta blight infection. Five NBS-LRR genes showed genotype specific expression. Our study provides a new insight of NBS-LRR gene family in chickpea and the potential involvement of NBS-LRR genes in response to ascochyta blight infection.
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Frazier TP, Palmer NA, Xie F, Tobias CM, Donze-Reiner TJ, Bombarely A, Childs KL, Shu S, Jenkins JW, Schmutz J, Zhang B, Sarath G, Zhao B. Identification, characterization, and gene expression analysis of nucleotide binding site (NB)-type resistance gene homologues in switchgrass. BMC Genomics 2016; 17:892. [PMID: 27821048 PMCID: PMC5100175 DOI: 10.1186/s12864-016-3201-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Accepted: 10/25/2016] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Switchgrass (Panicum virgatum L.) is a warm-season perennial grass that can be used as a second generation bioenergy crop. However, foliar fungal pathogens, like switchgrass rust, have the potential to significantly reduce switchgrass biomass yield. Despite its importance as a prominent bioenergy crop, a genome-wide comprehensive analysis of NB-LRR disease resistance genes has yet to be performed in switchgrass. RESULTS In this study, we used a homology-based computational approach to identify 1011 potential NB-LRR resistance gene homologs (RGHs) in the switchgrass genome (v 1.1). In addition, we identified 40 RGHs that potentially contain unique domains including major sperm protein domain, jacalin-like binding domain, calmodulin-like binding, and thioredoxin. RNA-sequencing analysis of leaf tissue from 'Alamo', a rust-resistant switchgrass cultivar, and 'Dacotah', a rust-susceptible switchgrass cultivar, identified 2634 high quality variants in the RGHs between the two cultivars. RNA-sequencing data from field-grown cultivar 'Summer' plants indicated that the expression of some of these RGHs was developmentally regulated. CONCLUSIONS Our results provide useful insight into the molecular structure, distribution, and expression patterns of members of the NB-LRR gene family in switchgrass. These results also provide a foundation for future work aimed at elucidating the molecular mechanisms underlying disease resistance in this important bioenergy crop.
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Affiliation(s)
| | - Nathan A. Palmer
- Grain, Forage and Bioenergy Research Unit, USDA-ARS, Lincoln, NE 68583-0937 USA
| | - Fuliang Xie
- Department of Biology, East Carolina University, Greenville, NC 27858 USA
| | | | - Teresa J. Donze-Reiner
- Department of Biology, West Chester University of Pennsylvania, Wester Chester, PA 19382 USA
| | | | - Kevin L. Childs
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824 USA
| | - Shengqiang Shu
- Department of Energy Joint Genome Institute, Walnut Creek, CA 94595 USA
| | - Jerry W. Jenkins
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806 USA
| | - Jeremy Schmutz
- Department of Energy Joint Genome Institute, Walnut Creek, CA 94595 USA
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806 USA
| | - Baohong Zhang
- Department of Biology, East Carolina University, Greenville, NC 27858 USA
| | - Gautam Sarath
- Grain, Forage and Bioenergy Research Unit, USDA-ARS, Lincoln, NE 68583-0937 USA
| | - Bingyu Zhao
- Department of Horticulture, Virginia Tech, Blacksburg, VA 24061 USA
- 407 Latham Hall, 220 Ag Quad Lane, Blacksburg, VA 24061 USA
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Puch-Hau C, Oropeza C, Góngora-Paredes M, Córdova I, Tun-Suárez J, Sáenz L. New insights into the evolutionary history of resistance gene candidates in coconut palms and their expression profiles in palms affected by lethal yellowing disease. Genes Genomics 2016. [DOI: 10.1007/s13258-016-0422-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Seo E, Kim S, Yeom SI, Choi D. Genome-Wide Comparative Analyses Reveal the Dynamic Evolution of Nucleotide-Binding Leucine-Rich Repeat Gene Family among Solanaceae Plants. FRONTIERS IN PLANT SCIENCE 2016; 7:1205. [PMID: 27559340 PMCID: PMC4978739 DOI: 10.3389/fpls.2016.01205] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Accepted: 07/29/2016] [Indexed: 05/18/2023]
Abstract
Plants have evolved an elaborate innate immune system against invading pathogens. Within this system, intracellular nucleotide-binding leucine-rich repeat (NLR) immune receptors are known play critical roles in effector-triggered immunity (ETI) plant defense. We performed genome-wide identification and classification of NLR-coding sequences from the genomes of pepper, tomato, and potato using fixed criteria. We then compared genomic duplication and evolution features. We identified intact 267, 443, and 755 NLR-encoding genes in tomato, potato, and pepper genomes, respectively. Phylogenetic analysis and classification of Solanaceae NLRs revealed that the majority of NLR super family members fell into 14 subgroups, including a TIR-NLR (TNL) subgroup and 13 non-TNL subgroups. Specific subgroups have expanded in each genome, with the expansion in pepper showing subgroup-specific physical clusters. Comparative analysis of duplications showed distinct duplication patterns within pepper and among Solanaceae plants suggesting subgroup- or species-specific gene duplication events after speciation, resulting in divergent evolution. Taken together, genome-wide analysis of NLR family members provide insights into their evolutionary history in Solanaceae. These findings also provide important foundational knowledge for understanding NLR evolution and will empower broader characterization of disease resistance genes to be used for crop breeding.
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Affiliation(s)
- Eunyoung Seo
- Department of Plant Science, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National UniversitySeoul, South Korea
| | - Seungill Kim
- Department of Plant Science, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National UniversitySeoul, South Korea
| | - Seon-In Yeom
- Department of Horticulture, Institute of Agriculture and Life Science, Gyeongsang National UniversityJinju, South Korea
| | - Doil Choi
- Department of Plant Science, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National UniversitySeoul, South Korea
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Habachi-Houimli Y, Khalfallah Y, Makni H, Makni M, Bouktila D. Large-scale bioinformatic analysis of the regulation of the disease resistance NBS gene family by microRNAs in Poaceae. C R Biol 2016; 339:347-56. [PMID: 27349470 DOI: 10.1016/j.crvi.2016.05.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Revised: 05/23/2016] [Accepted: 05/24/2016] [Indexed: 01/06/2023]
Abstract
In the present study, we have screened 71, 713, 525, 119 and 241 mature miRNA variants from Hordeum vulgare, Oryza sativa, Brachypodium distachyon, Triticum aestivum, and Sorghum bicolor, respectively, and classified them with respect to their conservation status and expression levels. These Poaceae non-redundant miRNA species (1,669) were distributed over a total of 625 MIR families, among which only 54 were conserved across two or more plant species, confirming the relatively recent evolutionary differentiation of miRNAs in grasses. On the other hand, we have used 257 H. vulgare, 286T. aestivum, 119 B. distachyon, 269 O. sativa, and 139 S. bicolor NBS domains, which were either mined directly from the annotated proteomes, or predicted from whole genome sequence assemblies. The hybridization potential between miRNAs and their putative NBS genes targets was analyzed, revealing that at least 454 NBS genes from all five Poaceae were potentially regulated by 265 distinct miRNA species, most of them expressed in leaves and predominantly co-expressed in additional tissues. Based on gene ontology, we could assign these probable miRNA target genes to 16 functional groups, among which three conferring resistance to bacteria (Rpm1, Xa1 and Rps2), and 13 groups of resistance to fungi (Rpp8,13, Rp3, Tsn1, Lr10, Rps1-k-1, Pm3, Rpg5, and MLA1,6,10,12,13). The results of the present analysis provide a large-scale platform for a better understanding of biological control strategies of disease resistance genes in Poaceae, and will serve as an important starting point for enhancing crop disease resistance improvement by means of transgenic lines with artificial miRNAs.
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Affiliation(s)
- Yosra Habachi-Houimli
- Unité de recherche UR11ES10, Génomique des insectes ravageurs des cultures d'intérêt agronomique (GIRC), faculté des sciences de Tunis, université de Tunis El Manar, 2092 El Manar, Tunis, Tunisia
| | - Yosra Khalfallah
- Unité de recherche UR11ES10, Génomique des insectes ravageurs des cultures d'intérêt agronomique (GIRC), faculté des sciences de Tunis, université de Tunis El Manar, 2092 El Manar, Tunis, Tunisia
| | - Hanem Makni
- Unité de recherche UR11ES10, Génomique des insectes ravageurs des cultures d'intérêt agronomique (GIRC), faculté des sciences de Tunis, université de Tunis El Manar, 2092 El Manar, Tunis, Tunisia; Institut supérieur de l'animation pour la jeunesse et la culture (ISAJC), université de Tunis, 2055 Bir El Bey, Tunisia
| | - Mohamed Makni
- Unité de recherche UR11ES10, Génomique des insectes ravageurs des cultures d'intérêt agronomique (GIRC), faculté des sciences de Tunis, université de Tunis El Manar, 2092 El Manar, Tunis, Tunisia
| | - Dhia Bouktila
- Unité de recherche UR11ES10, Génomique des insectes ravageurs des cultures d'intérêt agronomique (GIRC), faculté des sciences de Tunis, université de Tunis El Manar, 2092 El Manar, Tunis, Tunisia; Institut supérieur de biotechnologie de Béja (ISBB), université de Jendouba, 9000 Béja, Tunisia.
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Wei L, Jian H, Lu K, Filardo F, Yin N, Liu L, Qu C, Li W, Du H, Li J. Genome-wide association analysis and differential expression analysis of resistance to Sclerotinia stem rot in Brassica napus. PLANT BIOTECHNOLOGY JOURNAL 2016; 14:1368-80. [PMID: 26563848 DOI: 10.1111/pbi.12501] [Citation(s) in RCA: 105] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2015] [Revised: 10/08/2015] [Accepted: 10/13/2015] [Indexed: 05/20/2023]
Abstract
Brassica napus is one of the most important oil crops in the world, and stem rot caused by the fungus Sclerotinia sclerotiorum results in major losses in yield and quality. To elucidate resistance genes and pathogenesis-related genes, genome-wide association analysis of 347 accessions was performed using the Illumina 60K Brassica SNP (single nucleotide polymorphism) array. In addition, the detached stem inoculation assay was used to select five highly resistant (R) and susceptible (S) B. napus lines, 48 h postinoculation with S. sclerotiorum for transcriptome sequencing. We identified 17 significant associations for stem resistance on chromosomes A8 and C6, five of which were on A8 and 12 on C6. The SNPs identified on A8 were located in a 409-kb haplotype block, and those on C6 were consistent with previous QTL mapping efforts. Transcriptome analysis suggested that S. sclerotiorum infection activates the immune system, sulphur metabolism, especially glutathione (GSH) and glucosinolates in both R and S genotypes. Genes found to be specific to the R genotype related to the jasmonic acid pathway, lignin biosynthesis, defence response, signal transduction and encoding transcription factors. Twenty-four genes were identified in both the SNP-trait association and transcriptome sequencing analyses, including a tau class glutathione S-transferase (GSTU) gene cluster. This study provides useful insight into the molecular mechanisms underlying the plant's response to S. sclerotiorum.
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Affiliation(s)
- Lijuan Wei
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Hongju Jian
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Kun Lu
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Fiona Filardo
- Queensland Department of Agriculture and Fisheries (QDAF), Ecosciences Precinct, Brisbane, Old, Australia
| | - Nengwen Yin
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Liezhao Liu
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Cunmin Qu
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Wei Li
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Hai Du
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Jiana Li
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
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Andersen EJ, Ali S, Reese RN, Yen Y, Neupane S, Nepal MP. Diversity and Evolution of Disease Resistance Genes in Barley (Hordeum vulgare L.). Evol Bioinform Online 2016; 12:99-108. [PMID: 27168720 PMCID: PMC4857794 DOI: 10.4137/ebo.s38085] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Revised: 02/15/2016] [Accepted: 02/21/2016] [Indexed: 11/05/2022] Open
Abstract
Plant disease resistance genes (R-genes) play a critical role in the defense response to pathogens. Barley is one of the most important cereal crops, having a genome recently made available, for which the diversity and evolution of R-genes are not well understood. The main objectives of this research were to conduct a genome-wide identification of barley Coiled-coil, Nucleotide-binding site, Leucine-rich repeat (CNL) genes and elucidate their evolutionary history. We employed a Hidden Markov Model using 52 Arabidopsis thaliana CNL reference sequences and analyzed for phylogenetic relationships, structural variation, and gene clustering. We identified 175 barley CNL genes nested into three clades, showing (a) evidence of an expansion of the CNL-C clade, primarily due to tandem duplications; (b) very few members of clade CNL-A and CNL-B; and (c) a complete absence of clade CNL-D. Our results also showed that several of the previously identified mildew locus A (MLA) genes may be allelic variants of two barley CNL genes, MLOC_66581 and MLOC_10425, which respond to powdery mildew. Approximately 23% of the barley CNL genes formed 15 gene clusters located in the extra-pericentromeric regions on six of the seven chromosomes; more than half of the clustered genes were located on chromosomes 1H and 7H. Higher average numbers of exons and multiple splice variants in barley relative to those in Arabidopsis and rice may have contributed to a diversification of the CNL-C members. These results will help us understand the evolution of R-genes with potential implications for developing durable resistance in barley cultivars.
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Affiliation(s)
- Ethan J. Andersen
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD, USA
| | - Shaukat Ali
- Department of Plant Science, South Dakota State University, Brookings, SD, USA
| | - R. Neil Reese
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD, USA
| | - Yang Yen
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD, USA
| | - Surendra Neupane
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD, USA
| | - Madhav P. Nepal
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD, USA
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50
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Shao ZQ, Xue JY, Wu P, Zhang YM, Wu Y, Hang YY, Wang B, Chen JQ. Large-Scale Analyses of Angiosperm Nucleotide-Binding Site-Leucine-Rich Repeat Genes Reveal Three Anciently Diverged Classes with Distinct Evolutionary Patterns. PLANT PHYSIOLOGY 2016; 170:2095-109. [PMID: 26839128 PMCID: PMC4825152 DOI: 10.1104/pp.15.01487] [Citation(s) in RCA: 186] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Accepted: 02/01/2016] [Indexed: 05/18/2023]
Abstract
Nucleotide-binding site-leucine-rich repeat (NBS-LRR) genes make up the largest plant disease resistance gene family (R genes), with hundreds of copies occurring in individual angiosperm genomes. However, the expansion history of NBS-LRR genes during angiosperm evolution is largely unknown. By identifying more than 6,000 NBS-LRR genes in 22 representative angiosperms and reconstructing their phylogenies, we present a potential framework of NBS-LRR gene evolution in the angiosperm. Three anciently diverged NBS-LRR classes (TNLs, CNLs, and RNLs) were distinguished with unique exon-intron structures and DNA motif sequences. A total of seven ancient TNL, 14 CNL, and two RNL lineages were discovered in the ancestral angiosperm, from which all current NBS-LRR gene repertoires were evolved. A pattern of gradual expansion during the first 100 million years of evolution of the angiosperm clade was observed for CNLs. TNL numbers remained stable during this period but were eventually deleted in three divergent angiosperm lineages. We inferred that an intense expansion of both TNL and CNL genes started from the Cretaceous-Paleogene boundary. Because dramatic environmental changes and an explosion in fungal diversity occurred during this period, the observed expansions of R genes probably reflect convergent adaptive responses of various angiosperm families. An ancient whole-genome duplication event that occurred in an angiosperm ancestor resulted in two RNL lineages, which were conservatively evolved and acted as scaffold proteins for defense signal transduction. Overall, the reconstructed framework of angiosperm NBS-LRR gene evolution in this study may serve as a fundamental reference for better understanding angiosperm NBS-LRR genes.
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Affiliation(s)
- Zhu-Qing Shao
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China (Z.-Q.S., P.W., Y.-M.Z., Y.W., B.W., J.-Q.C.); andInstitute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China (J.-Y.X., Y.-M.Z., Y.-Y.H.)
| | - Jia-Yu Xue
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China (Z.-Q.S., P.W., Y.-M.Z., Y.W., B.W., J.-Q.C.); andInstitute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China (J.-Y.X., Y.-M.Z., Y.-Y.H.)
| | - Ping Wu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China (Z.-Q.S., P.W., Y.-M.Z., Y.W., B.W., J.-Q.C.); andInstitute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China (J.-Y.X., Y.-M.Z., Y.-Y.H.)
| | - Yan-Mei Zhang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China (Z.-Q.S., P.W., Y.-M.Z., Y.W., B.W., J.-Q.C.); andInstitute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China (J.-Y.X., Y.-M.Z., Y.-Y.H.)
| | - Yue Wu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China (Z.-Q.S., P.W., Y.-M.Z., Y.W., B.W., J.-Q.C.); andInstitute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China (J.-Y.X., Y.-M.Z., Y.-Y.H.)
| | - Yue-Yu Hang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China (Z.-Q.S., P.W., Y.-M.Z., Y.W., B.W., J.-Q.C.); andInstitute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China (J.-Y.X., Y.-M.Z., Y.-Y.H.)
| | - Bin Wang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China (Z.-Q.S., P.W., Y.-M.Z., Y.W., B.W., J.-Q.C.); andInstitute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China (J.-Y.X., Y.-M.Z., Y.-Y.H.)
| | - Jian-Qun Chen
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China (Z.-Q.S., P.W., Y.-M.Z., Y.W., B.W., J.-Q.C.); andInstitute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China (J.-Y.X., Y.-M.Z., Y.-Y.H.)
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