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Gladieux P, van Oosterhout C, Fairhead S, Jouet A, Ortiz D, Ravel S, Shrestha RK, Frouin J, He X, Zhu Y, Morel JB, Huang H, Kroj T, Jones JDG. Extensive immune receptor repertoire diversity in disease-resistant rice landraces. Curr Biol 2024; 34:3983-3995.e6. [PMID: 39146939 DOI: 10.1016/j.cub.2024.07.061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 04/19/2024] [Accepted: 07/16/2024] [Indexed: 08/17/2024]
Abstract
Plants have powerful defense mechanisms and extensive immune receptor repertoires, yet crop monocultures are prone to epidemic diseases. Rice (Oryza sativa) is susceptible to many diseases, such as rice blast caused by Magnaporthe oryzae. Varietal resistance of rice to blast relies on intracellular nucleotide binding, leucine-rich repeat (NLR) receptors that recognize specific pathogen molecules and trigger immune responses. In the Yuanyang terraces in southwest China, rice landraces rarely show severe losses to disease whereas commercial inbred lines show pronounced field susceptibility. Here, we investigate within-landrace NLR sequence diversity of nine rice landraces and eleven modern varieties using complexity reduction techniques. We find that NLRs display high sequence diversity in landraces, consistent with balancing selection, and that balancing selection at NLRs is more pervasive in landraces than modern varieties. Notably, modern varieties lack many ancient NLR haplotypes that are retained in some landraces. Our study emphasizes the value of standing genetic variation that is maintained in farmer landraces as a resource to make modern crops and agroecosystems less prone to disease. The conservation of landraces is, therefore, crucial for ensuring food security in the face of dynamic biotic and abiotic threats.
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Affiliation(s)
- Pierre Gladieux
- Plant Health Institute Montpellier, University of Montpellier, INRAE, CIRAD, IRD, Institut Agro, 34398 Montpellier, France.
| | - Cock van Oosterhout
- School of Environmental Sciences, University of East Anglia, Norwich NR4 7TJ, UK
| | - Sebastian Fairhead
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
| | - Agathe Jouet
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
| | - Diana Ortiz
- Plant Health Institute Montpellier, University of Montpellier, INRAE, CIRAD, IRD, Institut Agro, 34398 Montpellier, France
| | - Sebastien Ravel
- Plant Health Institute Montpellier, University of Montpellier, INRAE, CIRAD, IRD, Institut Agro, 34398 Montpellier, France
| | - Ram-Krishna Shrestha
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
| | - Julien Frouin
- CIRAD, UMR AGAP Institut, 34398 Montpellier, France; UMR AGAP Institut, Université de Montpellier, CIRAD, INRAE, Institut Agro, 34398 Montpellier, France
| | - Xiahong He
- School of Landscape and Horticulture, Southwest Forestry University, Kunming 650233, China
| | - Youyong Zhu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China; Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming 650201, China
| | - Jean-Benoit Morel
- Plant Health Institute Montpellier, University of Montpellier, INRAE, CIRAD, IRD, Institut Agro, 34398 Montpellier, France
| | - Huichuan Huang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming 650201, China; Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming 650201, China.
| | - Thomas Kroj
- Plant Health Institute Montpellier, University of Montpellier, INRAE, CIRAD, IRD, Institut Agro, 34398 Montpellier, France.
| | - Jonathan D G Jones
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK.
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Kan W, Chen L, Wang B, Liu L, Yin F, Zhong Q, Li J, Zhang D, Xiao S, Zhang Y, Jiang C, Yu T, Wang Y, Cheng Z. Examination of the Expression Profile of Resistance Genes in Yuanjiang Common Wild Rice ( Oryza rufipogon). Genes (Basel) 2024; 15:924. [PMID: 39062703 PMCID: PMC11275508 DOI: 10.3390/genes15070924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2024] [Revised: 07/13/2024] [Accepted: 07/15/2024] [Indexed: 07/28/2024] Open
Abstract
The rice blight poses a significant threat to the rice industry, and the discovery of disease-resistant genes is a crucial strategy for its control. By exploring the rich genetic resources of Yuanjiang common wild rice (Oryza rufipogon) and analyzing their expression patterns, genetic resources can be provided for molecular rice breeding. The target genes' expression patterns, subcellular localization, and interaction networks were analyzed based on the annotated disease-resistant genes on the 9th and 10th chromosomes in the rice genome database using fluorescent quantitative PCR technology and bioinformatics tools. Thirty-three disease-resistant genes were identified from the database, including 20 on the 9th and 13 on the 10th. These genes were categorized into seven subfamilies of the NLR family, such as CNL and the G subfamily of the ABC family. Four genes were not expressed under the induction of the pathogen Y8, two genes were significantly down-regulated, and the majority were up-regulated. Notably, the expression levels of nine genes belonging to the ABCG, CN, and CNL classes were significantly up-regulated, yet the expression levels varied among roots, stems, and leaves; one was significantly expressed in the roots, one in the stems, and the remaining seven were primarily highly expressed in the leaves. Two interaction network diagrams were predicted based on the seven highly expressed genes in the leaves: complex networks regulated by CNL proteins and specific networks controlled by ABCG proteins. The disease-resistant genes on the 9th chromosome are actively expressed in response to the induction of rice blight, forming a critical gene pool for the resistance of Yuanjiang common wild rice (O. rufipogon) to rice blight. Meanwhile, the disease-resistant genes on the 10th chromosome not only participate in resisting the rice blight pathogen but may also be involved in the defense against other stem diseases.
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Affiliation(s)
- Wang Kan
- College of Plant Protection, Yunnan Agricultural University, Kunming 650224, China;
| | - Ling Chen
- Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences/Yunnan Provincial Key Lab of Agricultural Biotechnology/Key Lab of Southwestern Crop Gene Resources and Germplasm Innovation, Ministry of Agriculture, Kunming 650205, China; (L.C.); (B.W.); (L.L.); (F.Y.); (Q.Z.); (J.L.); (D.Z.); (S.X.); (Y.Z.); (C.J.); (T.Y.)
| | - Bo Wang
- Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences/Yunnan Provincial Key Lab of Agricultural Biotechnology/Key Lab of Southwestern Crop Gene Resources and Germplasm Innovation, Ministry of Agriculture, Kunming 650205, China; (L.C.); (B.W.); (L.L.); (F.Y.); (Q.Z.); (J.L.); (D.Z.); (S.X.); (Y.Z.); (C.J.); (T.Y.)
| | - Li Liu
- Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences/Yunnan Provincial Key Lab of Agricultural Biotechnology/Key Lab of Southwestern Crop Gene Resources and Germplasm Innovation, Ministry of Agriculture, Kunming 650205, China; (L.C.); (B.W.); (L.L.); (F.Y.); (Q.Z.); (J.L.); (D.Z.); (S.X.); (Y.Z.); (C.J.); (T.Y.)
| | - Fuyou Yin
- Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences/Yunnan Provincial Key Lab of Agricultural Biotechnology/Key Lab of Southwestern Crop Gene Resources and Germplasm Innovation, Ministry of Agriculture, Kunming 650205, China; (L.C.); (B.W.); (L.L.); (F.Y.); (Q.Z.); (J.L.); (D.Z.); (S.X.); (Y.Z.); (C.J.); (T.Y.)
| | - Qiaofang Zhong
- Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences/Yunnan Provincial Key Lab of Agricultural Biotechnology/Key Lab of Southwestern Crop Gene Resources and Germplasm Innovation, Ministry of Agriculture, Kunming 650205, China; (L.C.); (B.W.); (L.L.); (F.Y.); (Q.Z.); (J.L.); (D.Z.); (S.X.); (Y.Z.); (C.J.); (T.Y.)
| | - Jinlu Li
- Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences/Yunnan Provincial Key Lab of Agricultural Biotechnology/Key Lab of Southwestern Crop Gene Resources and Germplasm Innovation, Ministry of Agriculture, Kunming 650205, China; (L.C.); (B.W.); (L.L.); (F.Y.); (Q.Z.); (J.L.); (D.Z.); (S.X.); (Y.Z.); (C.J.); (T.Y.)
| | - Dunyu Zhang
- Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences/Yunnan Provincial Key Lab of Agricultural Biotechnology/Key Lab of Southwestern Crop Gene Resources and Germplasm Innovation, Ministry of Agriculture, Kunming 650205, China; (L.C.); (B.W.); (L.L.); (F.Y.); (Q.Z.); (J.L.); (D.Z.); (S.X.); (Y.Z.); (C.J.); (T.Y.)
| | - Suqin Xiao
- Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences/Yunnan Provincial Key Lab of Agricultural Biotechnology/Key Lab of Southwestern Crop Gene Resources and Germplasm Innovation, Ministry of Agriculture, Kunming 650205, China; (L.C.); (B.W.); (L.L.); (F.Y.); (Q.Z.); (J.L.); (D.Z.); (S.X.); (Y.Z.); (C.J.); (T.Y.)
| | - Yun Zhang
- Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences/Yunnan Provincial Key Lab of Agricultural Biotechnology/Key Lab of Southwestern Crop Gene Resources and Germplasm Innovation, Ministry of Agriculture, Kunming 650205, China; (L.C.); (B.W.); (L.L.); (F.Y.); (Q.Z.); (J.L.); (D.Z.); (S.X.); (Y.Z.); (C.J.); (T.Y.)
| | - Cong Jiang
- Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences/Yunnan Provincial Key Lab of Agricultural Biotechnology/Key Lab of Southwestern Crop Gene Resources and Germplasm Innovation, Ministry of Agriculture, Kunming 650205, China; (L.C.); (B.W.); (L.L.); (F.Y.); (Q.Z.); (J.L.); (D.Z.); (S.X.); (Y.Z.); (C.J.); (T.Y.)
| | - Tengqiong Yu
- Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences/Yunnan Provincial Key Lab of Agricultural Biotechnology/Key Lab of Southwestern Crop Gene Resources and Germplasm Innovation, Ministry of Agriculture, Kunming 650205, China; (L.C.); (B.W.); (L.L.); (F.Y.); (Q.Z.); (J.L.); (D.Z.); (S.X.); (Y.Z.); (C.J.); (T.Y.)
| | - Yunyue Wang
- College of Plant Protection, Yunnan Agricultural University, Kunming 650224, China;
| | - Zaiquan Cheng
- Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences/Yunnan Provincial Key Lab of Agricultural Biotechnology/Key Lab of Southwestern Crop Gene Resources and Germplasm Innovation, Ministry of Agriculture, Kunming 650205, China; (L.C.); (B.W.); (L.L.); (F.Y.); (Q.Z.); (J.L.); (D.Z.); (S.X.); (Y.Z.); (C.J.); (T.Y.)
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Li XY, Li ZF, Zhang XL, Yang MQ, Wu PQ, Huang MJ, Huang HQ. Adaptation mechanism of three Impatiens species to different habitats based on stem morphology, lignin and MYB4 gene. BMC PLANT BIOLOGY 2024; 24:453. [PMID: 38789944 PMCID: PMC11127381 DOI: 10.1186/s12870-024-05115-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Accepted: 05/07/2024] [Indexed: 05/26/2024]
Abstract
BACKGROUND Impatiens is an important genus with rich species of garden plants, and its distribution is extremely extensive, which is reflected in its diverse ecological environment. However, the specific mechanisms of Impatiens' adaptation to various environments and the mechanism related to lignin remain unclear. RESULTS Three representative Impatiens species,Impatiens chlorosepala (wet, low degree of lignification), Impatiens uliginosa (aquatic, moderate degree of lignification) and Impatiens rubrostriata (terrestrial, high degree of lignification), were selected and analyzed for their anatomical structures, lignin content and composition, and lignin-related gene expression. There are significant differences in anatomical parameters among the stems of three Impatiens species, and the anatomical structure is consistent with the determination results of lignin content. Furthermore, the thickness of the xylem and cell walls, as well as the ratio of cell wall thickness to stem diameter have a strong correlation with lignin content. The anatomical structure and degree of lignification in Impatiens can be attributed to the plant's growth environment, morphology, and growth rate. Our analysis of lignin-related genes revealed a negative correlation between the MYB4 gene and lignin content. The MYB4 gene may control the lignin synthesis in Impatiens by controlling the structural genes involved in the lignin synthesis pathway, such as HCT, C3H, and COMT. Nonetheless, the regulation pathway differs between species of Impatiens. CONCLUSIONS This study demonstrated consistency between the stem anatomy of Impatiens and the results obtained from lignin content and composition analyses. It is speculated that MYB4 negatively regulates the lignin synthesis in the stems of three Impatiens species by regulating the expression of structural genes, and its regulation mechanism appears to vary across different Impatiens species. This study analyses the variations among different Impatiens plants in diverse habitats, and can guide further molecular investigations of lignin biosynthesis in Impatiens.
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Affiliation(s)
- Xin-Yi Li
- Southwest Forestry University, College of Landscape Architecture and Horticulture Sciences, Southwest Research Center for Engineering Technology of Landscape Architecture (State Forestry and Grassland Administration), Yunnan Engineering Research Center for Functional Flower Resources and Industrialization, Research and Development Center of Landscape Plants and Horticulture Flowers, Kunming, Yunnan, 650224, China
| | - Ze-Feng Li
- Southwest Forestry University, College of Landscape Architecture and Horticulture Sciences, Southwest Research Center for Engineering Technology of Landscape Architecture (State Forestry and Grassland Administration), Yunnan Engineering Research Center for Functional Flower Resources and Industrialization, Research and Development Center of Landscape Plants and Horticulture Flowers, Kunming, Yunnan, 650224, China
| | - Xiao-Li Zhang
- Southwest Forestry University, College of Landscape Architecture and Horticulture Sciences, Southwest Research Center for Engineering Technology of Landscape Architecture (State Forestry and Grassland Administration), Yunnan Engineering Research Center for Functional Flower Resources and Industrialization, Research and Development Center of Landscape Plants and Horticulture Flowers, Kunming, Yunnan, 650224, China
| | - Meng-Qing Yang
- Southwest Forestry University, College of Landscape Architecture and Horticulture Sciences, Southwest Research Center for Engineering Technology of Landscape Architecture (State Forestry and Grassland Administration), Yunnan Engineering Research Center for Functional Flower Resources and Industrialization, Research and Development Center of Landscape Plants and Horticulture Flowers, Kunming, Yunnan, 650224, China
| | - Pei-Qing Wu
- Southwest Forestry University, College of Landscape Architecture and Horticulture Sciences, Southwest Research Center for Engineering Technology of Landscape Architecture (State Forestry and Grassland Administration), Yunnan Engineering Research Center for Functional Flower Resources and Industrialization, Research and Development Center of Landscape Plants and Horticulture Flowers, Kunming, Yunnan, 650224, China
| | - Mei-Juan Huang
- Southwest Forestry University, College of Landscape Architecture and Horticulture Sciences, Southwest Research Center for Engineering Technology of Landscape Architecture (State Forestry and Grassland Administration), Yunnan Engineering Research Center for Functional Flower Resources and Industrialization, Research and Development Center of Landscape Plants and Horticulture Flowers, Kunming, Yunnan, 650224, China.
| | - Hai-Quan Huang
- Southwest Forestry University, College of Landscape Architecture and Horticulture Sciences, Southwest Research Center for Engineering Technology of Landscape Architecture (State Forestry and Grassland Administration), Yunnan Engineering Research Center for Functional Flower Resources and Industrialization, Research and Development Center of Landscape Plants and Horticulture Flowers, Kunming, Yunnan, 650224, China.
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4
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Baruah AR, Bannai H, Meija Y, Kimura A, Ueno H, Koide Y, Kishima Y, Palta J, Kasuga J, Yamamoto MP, Onishi K. Genetics of chilling response at early growth stage in rice: a recessive gene for tolerance and importance of acclimation. AOB PLANTS 2023; 15:plad075. [PMID: 38028749 PMCID: PMC10676198 DOI: 10.1093/aobpla/plad075] [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: 08/03/2023] [Accepted: 11/06/2023] [Indexed: 12/01/2023]
Abstract
Low-temperature adaptation in rice is mediated by the ability of a genotype to tolerate chilling temperatures. A genetic locus on chromosome 11 was analysed for chilling tolerance at the plumule stage in rice. The tolerant allele of A58, a japonica landrace in Japan, was inherited as a recessive gene (ctp-1A58), whereas the susceptible alleles from wild rice (Ctp-1W107) and modern variety (Ctp-1HY) were the dominant genes. Another recessive tolerant allele (ctp-1Silewah) was found in a tropical japonica variety (Silewah). Fine-mapping revealed that a candidate gene for the ctp-1 locus encoded a protein similar to the nucleotide-binding domain and leucine-rich repeat (NLR) protein, in which frameshift mutation by a 73 bp-deletion might confer chilling tolerance in ctp-1A58. Analysis of near-isogenic lines demonstrated that ctp-1A58 imparted tolerance effects only at severe chilling temperatures of 0.5 °C and 2 °C, both at plumule and seedling stages. Chilling acclimation treatments at a wide range of temperatures (8 °C-16 °C) for 72 h concealed the susceptible phenotype of Ctp-1W107 and Ctp-1HY. Furthermore, short-term acclimation treatment of 12 h at 8 °C was enough to be fully acclimated. These results suggest that the NLR gene induces a susceptible response upon exposure to severe chilling stress, however, another interacting gene(s) for acclimation response could suppress the maladaptive phenotype caused by the Ctp-1 allele. This study provides new insights for the adaptation and breeding of rice in a low-temperature environment.
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Affiliation(s)
- Akhil Ranjan Baruah
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat-13, Assam, India
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido 060-8589, Japan
| | - Hiroaki Bannai
- Department of Agro-Environmental Science, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Hokkaido 080-8555, Japan
| | - Yan Meija
- Department of Agro-Environmental Science, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Hokkaido 080-8555, Japan
| | - Ayumi Kimura
- Department of Agro-Environmental Science, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Hokkaido 080-8555, Japan
| | - Haruka Ueno
- Department of Agro-Environmental Science, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Hokkaido 080-8555, Japan
| | - Yohei Koide
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido 060-8589, Japan
| | - Yuji Kishima
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido 060-8589, Japan
| | - Jiwan Palta
- Department of Horticulture, University of Wisconsin-Madison, 490 Moore Hall, 1575 Linden Drive, Madison, WI 53706, USA
| | - Jun Kasuga
- Department of Agro-Environmental Science, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Hokkaido 080-8555, Japan
| | - Masayuki P Yamamoto
- Faculty of Science, Academic Assembly, University of Toyama, 3190 Gofuku, Toyama 930-8555, Japan
| | - Kazumitsu Onishi
- Department of Agro-Environmental Science, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Hokkaido 080-8555, Japan
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Yadav S, Kalwan G, Meena S, Gill SS, Yadava YK, Gaikwad K, Jain PK. Unravelling the due importance of pseudogenes and their resurrection in plants. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 203:108062. [PMID: 37778114 DOI: 10.1016/j.plaphy.2023.108062] [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: 07/20/2023] [Revised: 09/22/2023] [Accepted: 09/26/2023] [Indexed: 10/03/2023]
Abstract
The complexities of a genome are underpinned to the vast expanses of the intergenic region, which constitutes ∼97-98% of the genome. This region is essentially composed of what is colloquially referred to as the "junk DNA" and is composed of various elements like transposons, repeats, pseudogenes, etc. The latter have long been considered as dead elements merely contributing to transcriptional noise in the genome. Many studies now describe the previously unknown regulatory functions of these genes. Recent advances in the Next-generation sequencing (NGS) technologies have allowed unprecedented access to these regions. With the availability of whole genome sequences of more than 788 different plant species in past 20 years, genome annotation has become feasible like never before. Different bioinformatic pipelines are available for the identification of pseudogenes. However, still little is known about their biological functions. The functional validation of these genes remains challenging and research in this area is still in infancy, particularly in plants. CRISPR/Cas-based genome editing could provide solutions to understand the biological roles of these genes by allowing creation of precise edits within these genes. The possibility of pseudogene reactivation or resurrection as has been demonstrated in a few studies might open new avenues of genetic manipulation to yield a desirable phenotype. This review aims at comprehensively summarizing the progress made with regards to the identification of pseudogenes and understanding their biological functions in plants.
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Affiliation(s)
- Sheel Yadav
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India; PG School, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India; Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, New Delhi, 110012, India
| | - Gopal Kalwan
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India; PG School, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Shashi Meena
- PG School, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India; Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Sarvajeet Singh Gill
- Stress Physiology & Molecular Biology Lab, Centre for Biotechnology, Maharshi Dayanand University, Rohtak, 124 001, Haryana, India
| | - Yashwant K Yadava
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India
| | - Kishor Gaikwad
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India
| | - P K Jain
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India.
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Cao Q, Wang S, Ma H, Luo S, He H, Zhang Y. Hyper non-CG methylation of expanded plant disease resistance NLR genes. PLANT CELL REPORTS 2023; 42:1251-1254. [PMID: 37052713 DOI: 10.1007/s00299-023-03018-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 04/06/2023] [Indexed: 06/16/2023]
Abstract
KEY MESSAGE We explored the phylogenomics and methylomics of NLR genes in 41 plant species and found that highly duplicated plant NLR genes are hyper methylated in non-CG context.
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Affiliation(s)
- Qianqian Cao
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
- Shenzhen Research Institute of Henan University, Shenzhen, 518000, China
| | - Shichao Wang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
| | - Huizhen Ma
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
- Shenzhen Research Institute of Henan University, Shenzhen, 518000, China
| | - Sha Luo
- Department of Horticulture, College of Agronomy, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Hai He
- School of Agriculture, Sun Yat-Sen University, Shenzhen, 518107, China.
| | - Yu Zhang
- School of Agriculture, Sun Yat-Sen University, Shenzhen, 518107, China.
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7
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Liang X, Dong J. Comparative-genomic analysis reveals dynamic NLR gene loss and gain across Apiaceae species. Front Genet 2023; 14:1141194. [PMID: 36936422 PMCID: PMC10017999 DOI: 10.3389/fgene.2023.1141194] [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: 01/10/2023] [Accepted: 02/21/2023] [Indexed: 03/06/2023] Open
Abstract
Introduction: Nucleotide-binding leucine-rich repeat (NLR) genes play a crucial role in green plants' responding to various pathogens. Genome-scale evolutionary studies of NLR genes are important for discovering and applying functional NLR genes. However, little is known about the evolution of NLR genes in the Apiaceae family including agricultural and medical plants. Methods: In this study, comparative genomic analysis was performed in four Apiaceae species to trace the dynamic evolutionary patterns of NLR genes during speciation in this family. Results: The results revealed different number of NLR genes in these four Apiaceae species, namely, Angelica sinensis (95), Coriandrum sativum (183), Apium graveolens (153) and Daucus carota (149). Phylogenetic analysis demonstrated that NLR genes in these four species were derived from 183 ancestral NLR lineages and experienced different levels of gene-loss and gain events. The contraction pattern of the ancestral NLR lineages was discovered during the evolution of D. carota, whereas a different pattern of contraction after first expansion of NLR genes was observed for A. sinensis, C. sativum and A. graveolens. Discussion: Taken together, rapid and dynamic gene content variation has shaped evolutionary history of NLR genes in Apiaceae species.
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8
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Evolution of resistance (R) gene specificity. Essays Biochem 2022; 66:551-560. [PMID: 35612398 DOI: 10.1042/ebc20210077] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 05/03/2022] [Accepted: 05/05/2022] [Indexed: 11/17/2022]
Abstract
Plant resistance (R) genes are members of large gene families with significant within and between species variation. It has been hypothesised that a variety of processes have shaped R gene evolution and the evolution of R gene specificity. In this review, we illustrate the main mechanisms that generate R gene diversity and provide examples of how they can change R gene specificity. Next, we explain which evolutionary mechanisms are at play and how they determine the fate of new R gene alleles and R genes. Finally, we place this in a larger context by comparing the diversity and evolution of R gene specificity within and between species scales.
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Qian LH, Wu JY, Wang Y, Zou X, Zhou GC, Sun XQ. Genome-Wide Analysis of NBS-LRR Genes From an Early-Diverging Angiosperm Euryale ferox. Front Genet 2022; 13:880071. [PMID: 35646106 PMCID: PMC9140740 DOI: 10.3389/fgene.2022.880071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 04/11/2022] [Indexed: 11/13/2022] Open
Abstract
NBS-LRR genes are the largest gene family in plants conferring resistance to pathogens. At present, studies on the evolution of NBS-LRR genes in angiosperms mainly focused on monocots and eudicots, while studies on NBS-LRR genes in the basal angiosperms are limited. Euryale ferox represents an early-diverging angiosperm order, Nymphaeales, and confronts various pathogens during its lifetime, which can cause serious economic losses in terms of yield and quality. In this study, we performed a genome-wide identification and analysis of NBS-LRR genes in E. ferox. All 131 identified NBS-LRR genes could be divided into three subclasses according to different domain combinations, including 18 RNLs, 40 CNLs, and 73 TNLs. The E. ferox NBS-LRR genes are unevenly distributed on 29 chromosomes; 87 genes are clustered at 18 multigene loci, and 44 genes are singletons. Gene duplication analysis revealed that segmental duplications acted as a major mechanism for NBS-LRR gene expansions but not for RNL genes, because 18 RNL genes were scattered over 11 chromosomes without synteny loci, indicating that the expansion of RNL genes could have been caused by ectopic duplications. Ancestral gene reconciliation based on phylogenetic analysis revealed that there were at least 122 ancestral NBS-LRR lineages in the common ancestor of the three Nymphaeaceae species, suggesting that NBS-LRR genes expanded slightly during speciation in E. ferox. Transcriptome analysis showed that the majority of NBS-LRR genes were at a low level of expression without pathogen stimulation. Overall, this study characterized the profile of NBS-LRR genes in E. ferox and should serve as a valuable resource for disease resistance breeding in E. ferox.
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Affiliation(s)
- Lan-Hua Qian
- Suzhou Polytechnic Institute of Agriculture, Suzhou, China
| | - Jia-Yi Wu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Yue Wang
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Xin Zou
- Seed Administrative Station of Suzhou, Suzhou, China
| | - Guang-Can Zhou
- College of Agricultural and Biological Engineering (College of Tree Peony), Heze University, Heze, China
- *Correspondence: Guang-Can Zhou, ; Xiao-Qin Sun,
| | - Xiao-Qin Sun
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
- *Correspondence: Guang-Can Zhou, ; Xiao-Qin Sun,
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10
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Lee S, Fu F, Liao CJ, Mewa DB, Adeyanju A, Ejeta G, Lisch D, Mengiste T. Broad-spectrum fungal resistance in sorghum is conferred through the complex regulation of an immune receptor gene embedded in a natural antisense transcript. THE PLANT CELL 2022; 34:1641-1665. [PMID: 35018449 PMCID: PMC9048912 DOI: 10.1093/plcell/koab305] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 12/09/2021] [Indexed: 06/12/2023]
Abstract
Sorghum (Sorghum bicolor), the fifth most widely grown cereal crop globally, provides food security for millions of people. Anthracnose caused by the fungus Colletotrichum sublineola is a major disease of sorghum worldwide. We discovered a major fungal resistance locus in sorghum composed of the nucleotide-binding leucine-rich repeat receptor gene ANTHRACNOSE RESISTANCE GENE1 (ARG1) that is completely nested in an intron of a cis-natural antisense transcript (NAT) gene designated CARRIER OF ARG1 (CARG). Susceptible genotypes express CARG and two alternatively spliced ARG1 transcripts encoding truncated proteins lacking the leucine-rich repeat domains. In resistant genotypes, elevated expression of an intact allele of ARG1, attributed to the loss of CARG transcription and the presence of miniature inverted-repeat transposable element sequences, resulted in broad-spectrum resistance to fungal pathogens with distinct virulence strategies. Increased ARG1 expression in resistant genotypes is also associated with higher histone H3K4 and H3K36 methylation. In susceptible genotypes, lower ARG1 expression is associated with reduced H3K4 and H3K36 methylation and increased expression of NATs of CARG. The repressive chromatin state associated with H3K9me2 is low in CARG-expressing genotypes within the CARG exon and higher in genotypes with low CARG expression. Thus, ARG1 is regulated by multiple mechanisms and confers broad-spectrum, strong resistance to fungal pathogens.
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Affiliation(s)
| | | | - Chao-Jan Liao
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana 47907, USA
| | - Demeke B Mewa
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana 47907, USA
| | - Adedayo Adeyanju
- Department of Agronomy, Purdue University, West Lafayette, Indiana 47907, USA
| | - Gebisa Ejeta
- Department of Agronomy, Purdue University, West Lafayette, Indiana 47907, USA
| | - Damon Lisch
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana 47907, USA
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11
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Functional characterization of powdery mildew resistance gene MlIW172, a new Pm60 allele and its allelic variation in wild emmer wheat. J Genet Genomics 2022; 49:787-795. [DOI: 10.1016/j.jgg.2022.01.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Revised: 01/26/2022] [Accepted: 01/29/2022] [Indexed: 11/19/2022]
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12
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Lo KL, Chen YN, Chiang MY, Chen MC, Panibe JP, Chiu CC, Liu LW, Chen LJ, Chen CW, Li WH, Wang CS. Two genomic regions of a sodium azide induced rice mutant confer broad-spectrum and durable resistance to blast disease. RICE (NEW YORK, N.Y.) 2022; 15:2. [PMID: 35006368 PMCID: PMC8748607 DOI: 10.1186/s12284-021-00547-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 12/21/2021] [Indexed: 06/14/2023]
Abstract
Rice blast, one of the most destructive epidemic diseases, annually causes severe losses in grain yield worldwide. To manage blast disease, breeding resistant varieties is considered a more economic and environment-friendly strategy than chemical control. For breeding new resistant varieties, natural germplasms with broad-spectrum resistance are valuable resistant donors, but the number is limited. Therefore, artificially induced mutants are an important resource for identifying new broad-spectrum resistant (R) genes/loci. To pursue this approach, we focused on a broad-spectrum blast resistant rice mutant line SA0169, which was previously selected from a sodium azide induced mutation pool of TNG67, an elite japonica variety. We found that SA0169 was completely resistant against the 187 recently collected blast isolates and displayed durable resistance for almost 20 years. Linkage mapping and QTL-seq analysis indicated that a 1.16-Mb region on chromosome 6 (Pi169-6(t)) and a 2.37-Mb region on chromosome 11 (Pi169-11(t)) conferred the blast resistance in SA0169. Sequence analysis and genomic editing study revealed 2 and 7 candidate R genes in Pi169-6(t) and Pi169-11(t), respectively. With the assistance of mapping results, six blast and bacterial blight double resistant lines, which carried Pi169-6(t) and/or Pi169-11(t), were established. The complementation of Pi169-6(t) and Pi169-11(t), like SA0169, showed complete resistance to all tested isolates, suggesting that the combined effects of these two genomic regions largely confer the broad-spectrum resistance of SA0169. The sodium azide induced mutant SA0169 showed broad-spectrum and durable blast resistance. The broad resistance spectrum of SA0169 is contributed by the combined effects of two R regions, Pi169-6(t) and Pi169-11(t). Our study increases the understanding of the genetic basis of the broad-spectrum blast resistance induced by sodium azide mutagenesis, and lays a foundation for breeding new rice varieties with durable resistance against the blast pathogen.
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Affiliation(s)
- Kuan-Lin Lo
- Department of Agronomy, National Chung Hsing University, Taichung, Taiwan
| | - Yi-Nian Chen
- Division of Plant Pathology, Taiwan Agriculture Research Institute, Taichung, Taiwan
| | - Min-Yu Chiang
- Department of Agronomy, National Chung Hsing University, Taichung, Taiwan
| | - Mei-Chun Chen
- Division of Plant Pathology, Taiwan Agriculture Research Institute, Taichung, Taiwan
| | - Jerome P Panibe
- Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu, Taiwan
- Bioinformatics Program, Taiwan International Graduate Program, Institute of Information Science, Academia Sinica, Taipei, Taiwan
- Biodiversity Research Center, Academia Sinica, Taipei, 115, Taiwan
| | - Chung-Chun Chiu
- Department of Agronomy, National Chung Hsing University, Taichung, Taiwan
| | - Lu-Wei Liu
- Department of Agronomy, National Chung Hsing University, Taichung, Taiwan
| | - Liang-Jwu Chen
- Institute of Molecular Biology, National Chung Hsing University, Taichung, Taiwan
- Advanced Plant Biotechnology Center, National Chung Hsing University, Taichung, Taiwan
| | - Chun-Wei Chen
- Division of Plant Pathology, Taiwan Agriculture Research Institute, Taichung, Taiwan
| | - Wen-Hsiung Li
- Biodiversity Research Center, Academia Sinica, Taipei, 115, Taiwan
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, 60637, USA
| | - Chang-Sheng Wang
- Department of Agronomy, National Chung Hsing University, Taichung, Taiwan.
- Advanced Plant Biotechnology Center, National Chung Hsing University, Taichung, Taiwan.
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13
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Si Z, Wang L, Qiao Y, Roychowdhury R, Ji Z, Zhang K, Han J. Genome-wide comparative analysis of the nucleotide-binding site-encoding genes in four Ipomoea species. FRONTIERS IN PLANT SCIENCE 2022; 13:960723. [PMID: 36061812 PMCID: PMC9434374 DOI: 10.3389/fpls.2022.960723] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 07/27/2022] [Indexed: 05/14/2023]
Abstract
The nucleotide-binding site (NBS)-encoding gene is a major type of resistance (R) gene, and its diverse evolutionary patterns were analyzed in different angiosperm lineages. Until now, no comparative studies have been done on the NBS encoding genes in Ipomoea species. In this study, various numbers of NBS-encoding genes were identified across the whole genome of sweet potato (Ipomoea batatas) (#889), Ipomoea trifida (#554), Ipomoea triloba (#571), and Ipomoea nil (#757). Gene analysis showed that the CN-type and N-type were more common than the other types of NBS-encoding genes. The phylogenetic analysis revealed that the NBS-encoding genes formed three monophyletic clades: CNL, TNL, and RNL, which were distinguished by amino acid motifs. The distribution of the NBS-encoding genes among the chromosomes was non-random and uneven; 83.13, 76.71, 90.37, and 86.39% of the genes occurred in clusters in sweet potato, I. trifida, I. triloba, and I. nil, respectively. The duplication pattern analysis reveals the presence of higher segmentally duplicated genes in sweet potatoes than tandemly duplicated ones. The opposite trend was found for the other three species. A total of 201 NBS-encoding orthologous genes were found to form synteny gene pairs between any two of the four Ipomea species, suggesting that each of the synteny gene pairs was derived from a common ancestor. The gene expression patterns were acquired by analyzing using the published datasets. To explore the candidate resistant genes in sweet potato, transcriptome analysis has been carried out using two resistant (JK20 and JK274) and susceptible cultivars (Tengfei and Santiandao) of sweet potato for stem nematodes and Ceratocystis fimbriata pathogen, respectively. A total of 11 differentially expressed genes (DEGs) were found in Tengfei and JK20 for stem nematodes and 19 DEGs in Santiandao and JK274 for C. fimbriata. Moreover, six DEGs were further selected for quantitative reverse-transcription polymerase chain reaction (qRT-PCR) analysis, and the results were consistent with the transcriptome analysis. The results may provide new insights into the evolution of NBS-encoding genes in the Ipomoea genome and contribute to the future molecular breeding of sweet potatoes.
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Affiliation(s)
- Zengzhi Si
- Hebei Key Laboratory of Crop Stress Biology, Hebei Normal University of Science and Technology, Qinhuangdao, China
- *Correspondence: Zengzhi Si,
| | - Lianjun Wang
- Institute of Food Crops, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Yake Qiao
- Hebei Key Laboratory of Crop Stress Biology, Hebei Normal University of Science and Technology, Qinhuangdao, China
| | - Rajib Roychowdhury
- Department of Plant Pathology and Weed Research, Institute of Plant Protection, Agricultural Research Organization (ARO)–Volcani Center, Rishon LeZion, Israel
| | - Zhixin Ji
- 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
| | - Jinling Han
- Hebei Key Laboratory of Crop Stress Biology, Hebei Normal University of Science and Technology, Qinhuangdao, China
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14
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Chen R, Deng Y, Ding Y, Guo J, Qiu J, Wang B, Wang C, Xie Y, Zhang Z, Chen J, Chen L, Chu C, He G, He Z, Huang X, Xing Y, Yang S, Xie D, Liu Y, Li J. Rice functional genomics: decades' efforts and roads ahead. SCIENCE CHINA. LIFE SCIENCES 2022. [PMID: 34881420 DOI: 10.1007/s11427-021-2024-2020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 04/28/2023]
Abstract
Rice (Oryza sativa L.) is one of the most important crops in the world. Since the completion of rice reference genome sequences, tremendous progress has been achieved in understanding the molecular mechanisms on various rice traits and dissecting the underlying regulatory networks. In this review, we summarize the research progress of rice biology over past decades, including omics, genome-wide association study, phytohormone action, nutrient use, biotic and abiotic responses, photoperiodic flowering, and reproductive development (fertility and sterility). For the roads ahead, cutting-edge technologies such as new genomics methods, high-throughput phenotyping platforms, precise genome-editing tools, environmental microbiome optimization, and synthetic methods will further extend our understanding of unsolved molecular biology questions in rice, and facilitate integrations of the knowledge for agricultural applications.
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Affiliation(s)
- Rongzhi Chen
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Yiwen Deng
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology & Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Yanglin Ding
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Jingxin Guo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Jie Qiu
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Bing Wang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Changsheng Wang
- National Center for Gene Research, Center of Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200233, China
| | - Yongyao Xie
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Zhihua Zhang
- College of Plant Science, Jilin University, Changchun, 130062, China
| | - Jiaxin Chen
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Letian Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Chengcai Chu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Guangcun He
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Zuhua He
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology & Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Xuehui Huang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Yongzhong Xing
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan, 430070, China
| | - Shuhua Yang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Daoxin Xie
- MOE Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
| | - Yaoguang Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China.
| | - Jiayang Li
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.
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15
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Rice functional genomics: decades' efforts and roads ahead. SCIENCE CHINA. LIFE SCIENCES 2021; 65:33-92. [PMID: 34881420 DOI: 10.1007/s11427-021-2024-0] [Citation(s) in RCA: 100] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 11/01/2021] [Indexed: 12/16/2022]
Abstract
Rice (Oryza sativa L.) is one of the most important crops in the world. Since the completion of rice reference genome sequences, tremendous progress has been achieved in understanding the molecular mechanisms on various rice traits and dissecting the underlying regulatory networks. In this review, we summarize the research progress of rice biology over past decades, including omics, genome-wide association study, phytohormone action, nutrient use, biotic and abiotic responses, photoperiodic flowering, and reproductive development (fertility and sterility). For the roads ahead, cutting-edge technologies such as new genomics methods, high-throughput phenotyping platforms, precise genome-editing tools, environmental microbiome optimization, and synthetic methods will further extend our understanding of unsolved molecular biology questions in rice, and facilitate integrations of the knowledge for agricultural applications.
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16
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Liu Y, Zeng Z, Zhang YM, Li Q, Jiang XM, Jiang Z, Tang JH, Chen D, Wang Q, Chen JQ, Shao ZQ. An angiosperm NLR Atlas reveals that NLR gene reduction is associated with ecological specialization and signal transduction component deletion. MOLECULAR PLANT 2021; 14:2015-2031. [PMID: 34364002 DOI: 10.1016/j.molp.2021.08.001] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 07/16/2021] [Accepted: 08/02/2021] [Indexed: 05/06/2023]
Abstract
Nucleotide-binding leucine-rich-repeat (NLR) genes comprise the largest family of plant disease-resistance genes. Angiosperm NLR genes are phylogenetically divided into the TNL, CNL, and RNL subclasses. NLR copy numbers and subclass composition vary tremendously across angiosperm genomes. However, the evolutionary associations between genomic NLR content and ecological adaptation, or between NLR content and signal transduction components, are poorly characterized because of limited genome availability. In this study, we established an angiosperm NLR atlas (ANNA, https://biobigdata.nju.edu.cn/ANNA/) that includes NLR genes from over 300 angiosperm genomes. Using ANNA, we revealed that NLR copy numbers differ up to 66-fold among closely related species owing to rapid gene loss and gain. Interestingly, NLR contraction was associated with adaptations to aquatic, parasitic, and carnivorous lifestyles. The convergent NLR reduction in aquatic plants resembles the lack of NLR expansion during the long-term evolution of green algae before the colonization of land. A co-evolutionary pattern between NLR subclasses and plant immune pathway components was also identified, suggesting that immune pathway deficiencies may drive TNL loss. Finally, we identified a conserved TNL lineage that may function independently of the EDS1-SAG101-NRG1 module. Collectively, these findings provide new insights into the evolution of NLR genes in the context of ecological adaptation and genome content variation.
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Affiliation(s)
- Yang Liu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Zhen Zeng
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Yan-Mei Zhang
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China
| | - Qian Li
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Xing-Mei Jiang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Zhen Jiang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Ji-Hong Tang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Dijun Chen
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Qiang Wang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Jian-Qun Chen
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China.
| | - Zhu-Qing Shao
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China.
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17
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Frequent Gene Duplication/Loss Shapes Distinct Evolutionary Patterns of NLR Genes in Arecaceae Species. HORTICULTURAE 2021. [DOI: 10.3390/horticulturae7120539] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Nucleotide-binding leucine-rich repeat (NLR) genes play a key role in plant immune responses and have co-evolved with pathogens since the origin of green plants. Comparative genomic studies on the evolution of NLR genes have been carried out in several angiosperm lineages. However, most of these lineages come from the dicot clade. In this study, comparative analysis was performed on NLR genes from five Arecaceae species to trace the dynamic evolutionary pattern of the gene family during species speciation in this monocot lineage. The results showed that NLR genes from the genomes of Elaeis guineensis (262), Phoenix dactylifera (85), Daemonorops jenkinsiana (536), Cocos nucifera (135) and Calamus simplicifolius (399) are highly variable. Frequent domain loss and alien domain integration have occurred to shape the NLR protein structures. Phylogenetic analysis revealed that NLR genes from the five genomes were derived from dozens of ancestral genes. D. jenkinsiana and E. guineensis genomes have experienced “consistent expansion” of the ancestral NLR lineages, whereas a pattern of “first expansion and then contraction” of NLR genes was observed for P. dactylifera, C. nucifera and C. simplicifolius. The results suggest that rapid and dynamic gene content and structure variation have shaped the NLR profiles of Arecaceae species.
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18
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An G, Simko I, Chen J, Yu C, Lavelle D, Zhang W, Michelmore RW, Kuang H. Hypersensitivity to triforine in lettuce is triggered by a TNL gene through the disease-resistance pathway. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:2144-2146. [PMID: 34363733 PMCID: PMC8541772 DOI: 10.1111/pbi.13679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 07/22/2021] [Accepted: 08/05/2021] [Indexed: 06/13/2023]
Affiliation(s)
- Guanghui An
- Key Laboratory of Horticultural Plant BiologyHuazhong Agricultural UniversityWuhanChina
| | - Ivan Simko
- U.S. Department of AgricultureAgricultural Research ServiceU.S. Agricultural Research Station, Crop Improvement and Protection Research UnitSalinasCAUSA
| | - Jiongjiong Chen
- Key Laboratory of Horticultural Plant BiologyHuazhong Agricultural UniversityWuhanChina
| | - Changchun Yu
- Key Laboratory of Horticultural Plant BiologyHuazhong Agricultural UniversityWuhanChina
| | - Dean Lavelle
- Genome Center and Department of Plant SciencesUniversity of CaliforniaDavisCAUSA
| | - Weiyi Zhang
- Key Laboratory of Horticultural Plant BiologyHuazhong Agricultural UniversityWuhanChina
| | | | - Hanhui Kuang
- Key Laboratory of Horticultural Plant BiologyHuazhong Agricultural UniversityWuhanChina
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19
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Diao P, Sun H, Bao Z, Li W, Niu N, Li W, Wuriyanghan H. Expression of an Antiviral Gene GmRUN1 from Soybean Is Regulated via Intron-Mediated Enhancement (IME). Viruses 2021; 13:2032. [PMID: 34696462 PMCID: PMC8539222 DOI: 10.3390/v13102032] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 09/28/2021] [Accepted: 09/29/2021] [Indexed: 12/18/2022] Open
Abstract
Most of R (resistance) genes encode the protein containing NBS-LRR (nucleotide binding site and leucine-rich repeat) domains. Here, N. benthamiana plants were used for transient expression assays at 3-4 weeks of age. We identified a TNL (TIR-NBS-LRR) encoding gene GmRUN1 that was resistant to both soybean mosaic virus (SMV) and tobacco mosaic virus (TMV). Truncation analysis indicated the importance of all three canonical domains for GmRUN1-mediated antiviral activity. Promoter-GUS analysis showed that GmRUN1 expression is inducible by both salicylic acid (SA) and a transcription factor GmDREB3 via the cis-elements as-1 and ERE (ethylene response element), which are present in its promoter region. Interestingly, GmRUN1 gDNA (genomic DNA) shows higher viral resistance than its cDNA (complementary DNA), indicating the existence of intron-mediated enhancement (IME) for GmRUN1 regulation. We provided evidence that intron2 of GmRUN1 increased the mRNA level of native gene GmRUN1, a soybean antiviral gene SRC7 and also a reporter gene Luciferase, indicating the general transcriptional enhancement of intron2 in different genes. In summary, we identified an antiviral TNL type soybean gene GmRUN1, expression of which was regulated at different layers. The investigation of GmRUN1 gene regulatory network would help to explore the mechanism underlying soybean-SMV interactions.
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Affiliation(s)
- Pengfei Diao
- Key Laboratory of Forage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot 010070, China; (P.D.); (H.S.); (Z.B.); (W.L.); (N.N.)
| | - Hongyu Sun
- Key Laboratory of Forage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot 010070, China; (P.D.); (H.S.); (Z.B.); (W.L.); (N.N.)
| | - Zhuo Bao
- Key Laboratory of Forage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot 010070, China; (P.D.); (H.S.); (Z.B.); (W.L.); (N.N.)
| | - Wenxia Li
- Key Laboratory of Forage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot 010070, China; (P.D.); (H.S.); (Z.B.); (W.L.); (N.N.)
| | - Niu Niu
- Key Laboratory of Forage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot 010070, China; (P.D.); (H.S.); (Z.B.); (W.L.); (N.N.)
| | - Weimin Li
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China;
| | - Hada Wuriyanghan
- Key Laboratory of Forage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot 010070, China; (P.D.); (H.S.); (Z.B.); (W.L.); (N.N.)
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20
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Odongo PJ, Onaga G, Ricardo O, Natsuaki KT, Alicai T, Geuten K. Insights Into Natural Genetic Resistance to Rice Yellow Mottle Virus and Implications on Breeding for Durable Resistance. FRONTIERS IN PLANT SCIENCE 2021; 12:671355. [PMID: 34267770 PMCID: PMC8276079 DOI: 10.3389/fpls.2021.671355] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 05/14/2021] [Indexed: 06/13/2023]
Abstract
Rice is the main food crop for people in low- and lower-middle-income countries in Asia and sub-Saharan Africa (SSA). Since 1982, there has been a significant increase in the demand for rice in SSA, and its growing importance is reflected in the national strategic food security plans of several countries in the region. However, several abiotic and biotic factors undermine efforts to meet this demand. Rice yellow mottle virus (RYMV) caused by Solemoviridae is a major biotic factor affecting rice production and continues to be an important pathogen in SSA. To date, six pathogenic strains have been reported. RYMV infects rice plants through wounds and rice feeding vectors. Once inside the plant cells, viral genome-linked protein is required to bind to the rice translation initiation factor [eIF(iso)4G1] for a compatible interaction. The development of resistant cultivars that can interrupt this interaction is the most effective method to manage this disease. Three resistance genes are recognized to limit RYMV virulence in rice, some of which have nonsynonymous single mutations or short deletions in the core domain of eIF(iso)4G1 that impair viral host interaction. However, deployment of these resistance genes using conventional methods has proved slow and tedious. Molecular approaches are expected to be an alternative to facilitate gene introgression and/or pyramiding and rapid deployment of these resistance genes into elite cultivars. In this review, we summarize the knowledge on molecular genetics of RYMV-rice interaction, with emphasis on host plant resistance. In addition, we provide strategies for sustainable utilization of the novel resistant sources. This knowledge is expected to guide breeding programs in the development and deployment of RYMV resistant rice varieties.
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Affiliation(s)
- Patrick J. Odongo
- Molecular Biotechnology of Plants and Micro-Organisms, Institute of Botany and Microbiology, KU Leuven, Leuven, Belgium
- National Crops Resources Research Institute, National Agriculture Research Organization, Kampala, Uganda
| | - Geoffrey Onaga
- National Crops Resources Research Institute, National Agriculture Research Organization, Kampala, Uganda
- M’bé Research Station, Africa Rice Center (AfricaRice), Bouaké, Côte d’Ivoire
| | - Oliver Ricardo
- Breeding Innovations Platform, International Rice Research Institute, Metro Manila, Philippines
| | - Keiko T. Natsuaki
- Graduate School of Agriculture, Tokyo University of Agriculture, Tokyo, Japan
| | - Titus Alicai
- National Crops Resources Research Institute, National Agriculture Research Organization, Kampala, Uganda
| | - Koen Geuten
- Molecular Biotechnology of Plants and Micro-Organisms, Institute of Botany and Microbiology, KU Leuven, Leuven, Belgium
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21
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Zhang Y, Edwards D, Batley J. Comparison and evolutionary analysis of Brassica nucleotide binding site leucine rich repeat (NLR) genes and importance for disease resistance breeding. THE PLANT GENOME 2021; 14:e20060. [PMID: 33179454 DOI: 10.1002/tpg2.20060] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 08/11/2020] [Indexed: 06/11/2023]
Abstract
The Brassica genus contains many agriculturally significant oilseed and vegetable crops, however the crop yield is threatened by a range of fungal and bacterial pathogens. Nucleotide Binding Site Leucine Rich Repeat (NLR) genes play important roles in plant innate immunity. The evolution of NLR genes is influenced by genomic processes and pathogen selection. At the whole genome level, whole genome duplications (WGDs) generate abundant gene copies, most of which are lost during genome fractionation. At sub-genomic levels, some retained copies undergo duplication forming clusters which facilitate rapid evolution through recombination. The number, distribution and genetic variations of the NLR genes vary among Brassica species and within populations suggesting differential selection pressure exerted by pathogen populations throughout the evolutionary history. A study of the evolution of disease resistance genes in agriculturally important plants such as Brassicas helps gain insights into their function and inform the identification of resistance genes for breeding of resistant lines.
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Affiliation(s)
- Yueqi Zhang
- School of Biological Sciences, University of Western Australia, Perth, WA, Australia
| | - David Edwards
- School of Biological Sciences, University of Western Australia, Perth, WA, Australia
| | - Jacqueline Batley
- School of Biological Sciences, University of Western Australia, Perth, WA, Australia
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22
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Tian P, Zhang X, Xia R, Liu Y, Wang M, Li B, Liu T, Shi J, Wing RA, Meyers BC, Chen M. Evolution and diversification of reproductive phased small interfering RNAs in Oryza species. THE NEW PHYTOLOGIST 2021; 229:2970-2983. [PMID: 33111313 DOI: 10.1111/nph.17035] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 10/12/2020] [Indexed: 05/20/2023]
Abstract
In grasses, two types of phased, small interfering RNAs (phasiRNAs) are expressed largely in young, developing anthers. They are 21 or 24 nucleotides (nt) in length and are triggered by miR2118 or miR2275, respectively. However, most of their functions and activities are not fully understood. We performed comparative genomic analysis of their source loci (PHAS) in five Oryza genomes and combined this with analysis of high-throughput sRNA and degradome datasets. In total, we identified 8216 21-PHAS and 626 24-PHAS loci. Local tandem and segmental duplications mainly contributed to the expansion and supercluster distribution of the 21-PHAS loci. Despite their relatively conserved genomic positions, PHAS sequences diverged rapidly, except for the miR2118/2275 target sites, which were under strong selection for conservation. We found that 21-nt phasiRNAs with a 5'-terminal uridine (U) demonstrated cis-cleavage at PHAS precursors, and these cis-acting sites were also variable among close species. miR2118 could trigger phasiRNA production from its own antisense transcript and the derived phasiRNAs might reversibly regulate miR2118 precursors. We hypothesised that successful initiation of phasiRNA biogenesis is conservatively maintained, while phasiRNA products diverged quickly and are not individually conserved. In particular, phasiRNA production is under the control of multiple reciprocal regulation mechanisms.
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Affiliation(s)
- Peng Tian
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Xuemei Zhang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Rui Xia
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
| | - Yang Liu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Meijiao Wang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Bo Li
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Tieyan Liu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jinfeng Shi
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Rod A Wing
- Arizona Genomics Institute, BIO5 Institute and School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, USA
| | - Blake C Meyers
- Division of Plant Sciences, 52 Agriculture Laboratory, University of Missouri, Columbia, Missouri, 65211, USA
- Donald Danforth Plant Science Center, 975 North Warson Road, St Louis, MO, 63132, USA
| | - Mingsheng Chen
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100039, China
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23
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Wu JY, Xue JY, Van de Peer Y. Evolution of NLR Resistance Genes in Magnoliids: Dramatic Expansions of CNLs and Multiple Losses of TNLs. FRONTIERS IN PLANT SCIENCE 2021; 12:777157. [PMID: 34992620 PMCID: PMC8724549 DOI: 10.3389/fpls.2021.777157] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 11/24/2021] [Indexed: 05/05/2023]
Abstract
Magnoliids are the third-largest group of angiosperms and occupy a critical position in angiosperm evolution. In the past years, due to the lack of sequenced genomes, the disease resistance gene (R gene) profile of magnoliids remains poorly understood. By the genome-wide identification of 1,832 NLR genes from seven magnoliid genomes, we built a framework for the evolution of magnoliid R genes. TNL genes were completely absent from five magnoliids, presumably due to immune pathway deficiencies. A total of 74 ancestral R genes (70 CNLs, 3 TNLs, and 1 RNL) were recovered in a common ancestor of magnoliids, from which all current NLR gene repertoires were derived. Tandem duplication served as the major drive for NLR genes expansion in seven magnoliid genomes, as most surveyed angiosperms. Due to recent rapid expansions, most magnoliids exhibited "a first expansion followed by a slight contraction and a further stronger expansion" evolutionary pattern, while both Litsea cubeba and Persea americana showed a two-times-repeated pattern of "expansion followed by contraction." The transcriptome analysis of seven different tissues of Saururus chinensis revealed a low expression of most NLR genes, with some R genes displaying a relatively higher expression in roots and fruits. Overall, our study sheds light on the evolution of NLR genes in magnoliids, compensates for insufficiency in major angiosperm lineages, and provides an important reference for a better understanding of angiosperm NLR genes.
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Affiliation(s)
- Jia-Yi Wu
- College of Horticulture, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, China
| | - Jia-Yu Xue
- College of Horticulture, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, China
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology (CAS), Nanjing, China
- *Correspondence: Jia-Yu Xue, ;
| | - Yves Van de Peer
- College of Horticulture, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, China
- Department of Plant Biotechnology and Bioinformatics, VIB-UGent Center for Plant Systems Biology, Ghent University, Ghent, Belgium
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
- Yves Van de Peer, ;
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24
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Zhou GC, Li W, Zhang YM, Liu Y, Zhang M, Meng GQ, Li M, Wang YL. Distinct Evolutionary Patterns of NBS-Encoding Genes in Three Soapberry Family (Sapindaceae) Species. Front Genet 2020; 11:737. [PMID: 32754204 PMCID: PMC7365912 DOI: 10.3389/fgene.2020.00737] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 06/19/2020] [Indexed: 12/22/2022] Open
Abstract
Nucleotide-binding site (NBS)-type disease resistance genes (R genes) play key roles in plant immune responses and have co-evolved with pathogens over the course of plant lifecycles. Comparative genomic studies tracing the dynamic evolution of NBS-encoding genes have been conducted using many important plant lineages. However, studies on Sapindaceae species have not been performed. In this study, a discrepant number of NBS-encoding genes were identified in the genomes of Xanthoceras sorbifolium (180), Dinnocarpus longan (568), and Acer yangbiense (252). These genes were unevenly distributed and usually clustered as tandem arrays on chromosomes, with few existed as singletons. The phylogenetic analysis revealed that NBS-encoding genes formed three monophyletic clades, RPW8-NBS-LRR (RNL), TIR-NBS-LRR (TNL), and CC-NBS-LRR (CNL), which were distinguished by amino acid motifs. The NBS-encoding genes of the X. sorbifolium, D. longan, and A. yangbiense genomes were derived from 181 ancestral genes (three RNL, 23 TNL, and 155 CNL), which exhibited dynamic and distinct evolutionary patterns due to independent gene duplication/loss events. Specifically, X. sorbifolium exhibited a “first expansion and then contraction” evolutionary pattern, while A. yangbiense and D. longan exhibited a “first expansion followed by contraction and further expansion” evolutionary pattern. However, further expansion in D. longan was stronger than in A. yangbiense after divergence, suggesting that D. longan gained more genes in response to various pathogens. Additionally, the ancient and recent expansion of CNL genes generated the dominance of this subclass in terms of gene numbers, while the low copy number status of RNL genes was attributed to their conserved functions.
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Affiliation(s)
- Guang-Can Zhou
- College of Agricultural and Biological Engineering (College of Tree Peony), Heze University, Heze, China
| | - Wen Li
- College of Agricultural and Biological Engineering (College of Tree Peony), Heze University, Heze, China
| | - Yan-Mei Zhang
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Yang Liu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Ming Zhang
- College of Agricultural and Biological Engineering (College of Tree Peony), Heze University, Heze, China
| | - Guo-Qing Meng
- College of Agricultural and Biological Engineering (College of Tree Peony), Heze University, Heze, China
| | - Min Li
- College of Agricultural and Biological Engineering (College of Tree Peony), Heze University, Heze, China
| | - Yi-Lei Wang
- College of Agricultural and Biological Engineering (College of Tree Peony), Heze University, Heze, China
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25
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Tamborski J, Krasileva KV. Evolution of Plant NLRs: From Natural History to Precise Modifications. ANNUAL REVIEW OF PLANT BIOLOGY 2020; 71:355-378. [PMID: 32092278 DOI: 10.1146/annurev-arplant-081519-035901] [Citation(s) in RCA: 90] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Nucleotide-binding leucine-rich repeat receptors (NLRs) monitor the plant intracellular environment for signs of pathogen infection. Several mechanisms of NLR-mediated immunity arose independently across multiple species. These include the functional specialization of NLRs into sensors and helpers, the independent emergence of direct and indirect recognition within NLR subfamilies, the regulation of NLRs by small RNAs, and the formation of NLR networks. Understanding the evolutionary history of NLRs can shed light on both the origin of pathogen recognition and the common constraints on the plant immune system. Attempts to engineer disease resistance have been sparse and rarely informed by evolutionary knowledge. In this review, we discuss the evolution of NLRs, give an overview of previous engineering attempts, and propose how to use evolutionary knowledge to advance future research in the generation of novel disease-recognition capabilities.
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Affiliation(s)
- Janina Tamborski
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA;
| | - Ksenia V Krasileva
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA;
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26
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Lunardon A, Johnson NR, Hagerott E, Phifer T, Polydore S, Coruh C, Axtell MJ. Integrated annotations and analyses of small RNA-producing loci from 47 diverse plants. Genome Res 2020; 30:497-513. [PMID: 32179590 PMCID: PMC7111516 DOI: 10.1101/gr.256750.119] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 01/27/2020] [Indexed: 01/25/2023]
Abstract
Plant endogenous small RNAs (sRNAs) are important regulators of gene expression. There are two broad categories of plant sRNAs: microRNAs (miRNAs) and endogenous short interfering RNAs (siRNAs). MicroRNA loci are relatively well-annotated but compose only a small minority of the total sRNA pool; siRNA locus annotations have lagged far behind. Here, we used a large data set of published and newly generated sRNA sequencing data (1333 sRNA-seq libraries containing more than 20 billion reads) and a uniform bioinformatic pipeline to produce comprehensive sRNA locus annotations of 47 diverse plants, yielding more than 2.7 million sRNA loci. The two most numerous classes of siRNA loci produced mainly 24- and 21-nucleotide (nt) siRNAs, respectively. Most often, 24-nt-dominated siRNA loci occurred in intergenic regions, especially at the 5′-flanking regions of protein-coding genes. In contrast, 21-nt-dominated siRNA loci were most often derived from double-stranded RNA precursors copied from spliced mRNAs. Genic 21-nt-dominated loci were especially common from disease resistance genes, including from a large number of monocots. Individual siRNA sequences of all types showed very little conservation across species, whereas mature miRNAs were more likely to be conserved. We developed a web server where our data and several search and analysis tools are freely accessible.
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Affiliation(s)
- Alice Lunardon
- Department of Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Nathan R Johnson
- Department of Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.,Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Emily Hagerott
- Department of Biology, Knox College, Galesburg, Illinois 61401, USA
| | - Tamia Phifer
- Department of Biology, Knox College, Galesburg, Illinois 61401, USA
| | - Seth Polydore
- Department of Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.,Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Ceyda Coruh
- Department of Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.,Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Michael J Axtell
- Department of Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.,Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
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27
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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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28
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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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29
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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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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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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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Cai Q, Liang C, Wang S, Hou Y, Gao L, Liu L, He W, Ma W, Mo B, Chen X. The disease resistance protein SNC1 represses the biogenesis of microRNAs and phased siRNAs. Nat Commun 2018; 9:5080. [PMID: 30498229 PMCID: PMC6265325 DOI: 10.1038/s41467-018-07516-z] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 10/29/2018] [Indexed: 11/21/2022] Open
Abstract
Plants evolved an array of disease resistance genes (R genes) to fight pathogens. In the absence of pathogen infection, NBS-LRR genes, which comprise a major subfamily of R genes, are suppressed by a small RNA cascade involving microRNAs (miRNAs) that trigger the biogenesis of phased siRNAs (phasiRNAs) from R gene transcripts. However, whether or how R genes influence small RNA biogenesis is unknown. In this study, we isolate a mutant with global defects in the biogenesis of miRNAs and phasiRNAs in Arabidopsis thaliana and trace the defects to the over accumulation and nuclear localization of an R protein SNC1. We show that nuclear SNC1 represses the transcription of miRNA and phasiRNA loci, probably through the transcriptional corepressor TPR1. Intriguingly, nuclear SNC1 reduces the accumulation of phasiRNAs from three source R genes and concomitantly, the expression of a majority of the ~170R genes is up-regulated. Taken together, this study suggests an R gene-miRNA-phasiRNA regulatory module that amplifies plant immune responses. A small RNA-based signaling cascade prevents the induction of plant resistance genes (R-genes) in the absence of pathogen challenge. Here Cai et al. show that nuclear accumulation of the R protein SNC1 can activate immunity by suppressing small RNA production and releasing R-gene repression.
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Affiliation(s)
- Qiang Cai
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China.,Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, 518060, China
| | - Chao Liang
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China.,Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, 518060, China
| | - Suikang Wang
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China.,Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA, 92521, USA
| | - Yingnan Hou
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA, 92521, USA
| | - Lei Gao
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China
| | - Li Liu
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA, 92521, USA
| | - Wenrong He
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA, 92521, USA
| | - Wenbo Ma
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA, 92521, USA
| | - Beixin Mo
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China.
| | - Xuemei Chen
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA, 92521, USA.
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Van Ghelder C, Esmenjaud D, Callot C, Dubois E, Mazier M, Duval H. Ma Orthologous Genes in Prunus spp. Shed Light on a Noteworthy NBS-LRR Cluster Conferring Differential Resistance to Root-Knot Nematodes. FRONTIERS IN PLANT SCIENCE 2018; 9:1269. [PMID: 30254651 PMCID: PMC6141779 DOI: 10.3389/fpls.2018.01269] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 08/10/2018] [Indexed: 06/01/2023]
Abstract
Root-knot nematodes (RKNs) are considerable polyphagous pests that severely challenge plants worldwide and especially perennials. The specific genetic resistance of plants mainly relies on the NBS-LRR genes that are pivotal factors for pathogens control. In Prunus spp., the Ma plum and RMja almond genes possess different spectra for resistance to RKNs. While previous works based on the Ma gene allowed to clone it and to decipher its peculiar TIR-NBS-LRR (TNL) structure, we only knew that the RMja gene mapped on the same chromosome as Ma. We carried out a high-resolution mapping using an almond segregating F2 progeny of 1448 seedlings from resistant (R) and susceptible (S) parental accessions, to locate precisely RMja on the peach genome, the reference sequence for Prunus species. We showed that the RMja gene maps in the Ma resistance cluster and that the Ma ortholog is the best candidate for RMja. This co-localization is a crucial step that opens the way to unravel the molecular determinants involved in the resistance to RKNs. Then we sequenced both almond parental NGS genomes and aligned them onto the RKN susceptible reference peach genome. We produced a BAC library of the R parental accession and, from two overlapping BAC clones, we obtained a 336-kb sequence encompassing the RMja candidate region. Thus, we could benefit from three Ma orthologous regions to investigate their sequence polymorphism, respectively, within plum (complete R spectrum), almond (incomplete R spectrum) and peach (null R spectrum). We showed that the Ma TNL cluster has evolved orthologs with a unique conserved structure comprised of five repeated post-LRR (PL) domains, which contain most polymorphism. In addition to support the Ma and RMja orthologous relationship, our results suggest that the polymorphism contained in the PL sequences might underlie differential resistance interactions with RKNs and an original immune mechanism in woody perennials. Besides, our study illustrates how PL exon duplications and losses shape TNL structure and give rise to atypical PL domain repeats of yet unknown role.
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Affiliation(s)
- Cyril Van Ghelder
- Institut Sophia Agrobiotech, INRA, CNRS, Université Côte d’Azur, Sophia Antipolis, France
| | - Daniel Esmenjaud
- Institut Sophia Agrobiotech, INRA, CNRS, Université Côte d’Azur, Sophia Antipolis, France
| | - Caroline Callot
- Centre National de Ressources Génomiques Végétales, INRA, CNRS, Université de Toulouse, Castanet-Tolosan, France
| | | | - Marianne Mazier
- Unité de Génétique et Amélioration des Fruits et Légumes (GAFL), INRA, Montfavet, France
| | - Henri Duval
- Unité de Génétique et Amélioration des Fruits et Légumes (GAFL), INRA, Montfavet, France
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Neupane S, Ma Q, Mathew FM, Varenhorst AJ, Andersen EJ, Nepal MP. Evolutionary Divergence of TNL Disease-Resistant Proteins in Soybean (Glycine max) and Common Bean (Phaseolus vulgaris). Biochem Genet 2018; 56:397-422. [PMID: 29500532 DOI: 10.1007/s10528-018-9851-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 02/21/2018] [Indexed: 10/17/2022]
Abstract
Disease-resistant genes (R genes) encode proteins that are involved in protecting plants from their pathogens and pests. Availability of complete genome sequences from soybean and common bean allowed us to perform a genome-wide identification and analysis of the Toll interleukin-1 receptor-like nucleotide-binding site leucine-rich repeat (TNL) proteins. Hidden Markov model (HMM) profiling of all protein sequences resulted in the identification of 117 and 77 regular TNL genes in soybean and common bean, respectively. We also identified TNL gene homologs with unique domains, and signal peptides as well as nuclear localization signals. The TNL genes in soybean formed 28 clusters located on 10 of the 20 chromosomes, with the majority found on chromosome 3, 6 and 16. Similarly, the TNL genes in common bean formed 14 clusters located on five of the 11 chromosomes, with the majority found on chromosome 10. Phylogenetic analyses of the TNL genes from Arabidopsis, soybean and common bean revealed less divergence within legumes relative to the divergence between legumes and Arabidopsis. Syntenic blocks were found between chromosomes Pv10 and Gm03, Pv07 and Gm10, as well as Pv01 and Gm14. The gene expression data revealed basal level expression and tissue specificity, while analysis of available microRNA data showed 37 predicted microRNA families involved in targeting the identified TNL genes in soybean and common bean.
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Affiliation(s)
- Surendra Neupane
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD, USA
| | - Qin Ma
- Department of Agronomy, Horticulture and Plant Science, South Dakota State University, Brookings, SD, USA
| | - Febina M Mathew
- Department of Agronomy, Horticulture and Plant Science, South Dakota State University, Brookings, SD, USA
| | - Adam J Varenhorst
- Department of Agronomy, Horticulture and Plant Science, South Dakota State University, Brookings, SD, USA
| | - Ethan J Andersen
- 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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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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Chen NWG, Thareau V, Ribeiro T, Magdelenat G, Ashfield T, Innes RW, Pedrosa-Harand A, Geffroy V. Common Bean Subtelomeres Are Hot Spots of Recombination and Favor Resistance Gene Evolution. FRONTIERS IN PLANT SCIENCE 2018; 9:1185. [PMID: 30154814 PMCID: PMC6102362 DOI: 10.3389/fpls.2018.01185] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 07/24/2018] [Indexed: 05/10/2023]
Abstract
Subtelomeres of most eukaryotes contain fast-evolving genes usually involved in adaptive processes. In common bean (Phaseolus vulgaris), the Co-2 anthracnose resistance (R) locus corresponds to a cluster of nucleotide-binding-site leucine-rich-repeat (NL) encoding sequences, the prevalent class of plant R genes. To study the recent evolution of this R gene cluster, we used a combination of sequence, genetic and cytogenetic comparative analyses between common bean genotypes from two distinct gene pools (Andean and Mesoamerican) that diverged 0.165 million years ago. Co-2 is a large subtelomeric cluster on chromosome 11 comprising from 32 (Mesoamerican) to 52 (Andean) NL sequences embedded within khipu satellite repeats. Since the recent split between Andean and Mesoamerican gene pools, the Co-2 cluster has experienced numerous gene-pool specific NL losses, leading to distinct NL repertoires. The high proportion of solo-LTR retrotransposons indicates that the Co-2 cluster is located in a hot spot of unequal intra-strand homologous recombination. Furthermore, we observe large segmental duplications involving both Non-Homologous End Joining and Homologous Recombination double-strand break repair pathways. Finally, the identification of a Mesoamerican-specific subtelomeric sequence reveals frequent interchromosomal recombinations between common bean subtelomeres. Altogether, our results highlight that common bean subtelomeres are hot spots of recombination and favor the rapid evolution of R genes. We propose that chromosome ends could act as R gene incubators in many plant genomes.
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Affiliation(s)
- Nicolas W. G. Chen
- Institute of Plant Sciences Paris-Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d’Evry, Université Paris-Diderot Sorbonne Paris Cité, Orsay, France
- IRHS, INRA, AGROCAMPUS OUEST, Université d’Angers, SFR 4207 QUASAV, Beaucouzé, France
| | - Vincent Thareau
- Institute of Plant Sciences Paris-Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d’Evry, Université Paris-Diderot Sorbonne Paris Cité, Orsay, France
| | - Tiago Ribeiro
- Laboratory of Plant Cytogenetics, Federal University of Pernambuco, Recife, Brazil
| | - Ghislaine Magdelenat
- Genoscope/Commissariat à l’Energie Atomique-Centre National de Séquençage, Evry, France
| | - Tom Ashfield
- Department of Biology, Indiana University, Bloomington, IN, United States
| | - Roger W. Innes
- Department of Biology, Indiana University, Bloomington, IN, United States
| | | | - Valérie Geffroy
- Institute of Plant Sciences Paris-Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d’Evry, Université Paris-Diderot Sorbonne Paris Cité, Orsay, France
- *Correspondence: Valérie Geffroy,
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Xiao G, Borja FN, Mauleon R, Padilla J, Telebanco-Yanoria MJ, Yang J, Lu G, Dionisio-Sese M, Zhou B. Identification of resistant germplasm containing novel resistance genes at or tightly linked to the Pi2/9 locus conferring broad-spectrum resistance against rice blast. RICE (NEW YORK, N.Y.) 2017; 10:37. [PMID: 28779340 PMCID: PMC5544663 DOI: 10.1186/s12284-017-0176-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 07/31/2017] [Indexed: 05/04/2023]
Abstract
BACKGROUND The rice Pi2/9 locus harbors multiple resistance (R) genes each controlling broad-spectrum resistance against diverse isolates of Magnaporthe oryzae, a fungal pathogen causing devastating blast disease to rice. Identification of more resistance germplasm containing novel R genes at or tightly linked to the Pi2/9 locus would promote breeding of resistance rice cultivars. RESULTS In this study, we aim to identify resistant germplasm containing novel R genes at or tightly linked to the Pi2/9 locus using a molecular marker, designated as Pi2/9-RH (Pi2/9 resistant haplotype), developed from the 5' portion of the Pi2 sequence which was conserved only in the rice lines containing functional Pi2/9 alleles. DNA analysis using Pi2/9-RH identified 24 positive lines in 55 shortlisted landraces which showed resistance to 4 rice blast isolates. Analysis of partial sequences of the full-length cDNAs of Pi2/9 homologues resulted in the clustering of these 24 lines into 5 haplotypes each containing different Pi2/9 homologues which were designated as Pi2/9-A5, -A15, -A42, -A53, and -A54. Interestingly, Pi2/9-A5 and Pi2/9-A54 are identical to Piz-t and Pi2, respectively. To validate the association of other three novel Pi2/9 homologues with the blast resistance, monogenic lines at BC3F3 generation were generated by marker assisted backcrossing (MABC). Resistance assessment of the derived monogenic lines in both the greenhouse and the field hotspot indicated that they all controlled broad-spectrum resistance against rice blast. Moreover, genetic analysis revealed that the blast resistance of these three monogenic lines was co-segregated with Pi2/9-RH, suggesting that the Pi2/9 locus or tightly linked loci could be responsible for the resistance. CONCLUSION The newly developed marker Pi2/9-RH could be used as a potentially diagnostic marker for the quick identification of resistant donors containing functional Pi2/9 alleles or unknown linked R genes. The three new monogenic lines containing the Pi2/9 introgression segment could be used as valuable materials for disease assessment and resistance donors in breeding program.
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Affiliation(s)
- Gui Xiao
- Genetics and Biotechnology Division, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
- Institute of Biological Sciences, University of the Philippines Los Baños, 4031 Laguna, Philippines
| | - Frances Nikki Borja
- Genetics and Biotechnology Division, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - Ramil Mauleon
- Genetics and Biotechnology Division, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - Jonas Padilla
- Genetics and Biotechnology Division, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - Mary Jeanie Telebanco-Yanoria
- Genetics and Biotechnology Division, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - Jianxia Yang
- Fujian Agriculture and Forest University, Fuzhou, 350002 China
| | - Guodong Lu
- Fujian Agriculture and Forest University, Fuzhou, 350002 China
| | - Maribel Dionisio-Sese
- Institute of Biological Sciences, University of the Philippines Los Baños, 4031 Laguna, Philippines
| | - Bo Zhou
- Genetics and Biotechnology Division, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
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Nepal MP, Andersen EJ, Neupane S, Benson BV. Comparative Genomics of Non-TNL Disease Resistance Genes from Six Plant Species. Genes (Basel) 2017; 8:E249. [PMID: 28973974 PMCID: PMC5664099 DOI: 10.3390/genes8100249] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Revised: 09/14/2017] [Accepted: 09/20/2017] [Indexed: 12/19/2022] Open
Abstract
Disease resistance genes (R genes), as part of the plant defense system, have coevolved with corresponding pathogen molecules. The main objectives of this project were to identify non-Toll interleukin receptor, nucleotide-binding site, leucine-rich repeat (nTNL) genes and elucidate their evolutionary divergence across six plant genomes. Using reference sequences from Arabidopsis, we investigated nTNL orthologs in the genomes of common bean, Medicago, soybean, poplar, and rice. We used Hidden Markov Models for sequence identification, performed model-based phylogenetic analyses, visualized chromosomal positioning, inferred gene clustering, and assessed gene expression profiles. We analyzed 908 nTNL R genes in the genomes of the six plant species, and classified them into 12 subgroups based on the presence of coiled-coil (CC), nucleotide binding site (NBS), leucine rich repeat (LRR), resistance to Powdery mildew 8 (RPW8), and BED type zinc finger domains. Traditionally classified CC-NBS-LRR (CNL) genes were nested into four clades (CNL A-D) often with abundant, well-supported homogeneous subclades of Type-II R genes. CNL-D members were absent in rice, indicating a unique R gene retention pattern in the rice genome. Genomes from Arabidopsis, common bean, poplar and soybean had one chromosome without any CNL R genes. Medicago and Arabidopsis had the highest and lowest number of gene clusters, respectively. Gene expression analyses suggested unique patterns of expression for each of the CNL clades. Differential gene expression patterns of the nTNL genes were often found to correlate with number of introns and GC content, suggesting structural and functional divergence.
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Affiliation(s)
- Madhav P Nepal
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57007, USA.
| | - Ethan J Andersen
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57007, USA.
| | - Surendra Neupane
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57007, USA.
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A Class II small heat shock protein OsHsp18.0 plays positive roles in both biotic and abiotic defense responses in rice. Sci Rep 2017; 7:11333. [PMID: 28900229 PMCID: PMC5595972 DOI: 10.1038/s41598-017-11882-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Accepted: 08/31/2017] [Indexed: 11/08/2022] Open
Abstract
Bacterial blight caused by Xanthomonas oryzae pv. oryzae (Xoo) is one of the most devastating diseases of rice. However, the molecular mechanism underpinning the Xoo resistance of rice is still not fully understood. Here, we report that a class II small heat shock protein gene, OsHsp18.0, whose expression was differentially induced between a resistant and a susceptible variety in response to Xoo infection, plays positive roles in both biotic and abiotic resistance. The molecular chaperone activity of OsHsp18.0 was confirmed by a bacterium-expressed glutathione S-transferase fusion protein. Overexpression of OsHsp18.0 in a susceptible rice variety significantly enhanced its resistance to multiple Xoo strains, whereas silencing of OsHsp18.0 in a resistant variety drastically increased its susceptibility. The enhanced Xoo resistance in OsHsp18.0-overexpressing lines was positively correlated with the sensitized salicylic acid-dependent defense responses. In addition to disease resistance, the OsHsp18.0 overexpressing and silencing lines exhibited enhanced and reduced tolerance, respectively, to heat and salt treatments. The subcellular localization study revealed that the green fluorescent protein-OsHsp18.0 was enriched on the nuclear envelope, suggesting a potential role of OsHsp18.0 in the nucleo-cytoplasmic trafficking. Together, our results reveal that the rice OsHsp18.0 is a positive regulator in both biotic and abiotic defense responses.
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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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Di Donato A, Andolfo G, Ferrarini A, Delledonne M, Ercolano MR. Investigation of orthologous pathogen recognition gene-rich regions in solanaceous species. Genome 2017; 60:850-859. [PMID: 28742982 DOI: 10.1139/gen-2016-0217] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Pathogen receptor proteins such as receptor-like protein (RLP), receptor-like kinase (RLK), and nucleotide-binding leucine-rich repeat (NLR) play a leading role in plant immunity activation. The genome architecture of such genes has been extensively investigated in several plant species. However, we still know little about their elaborate reorganization that arose during the plant speciation process. Using recently released pepper and eggplant genome sequences, we were able to identify 1097 pathogen recognition genes (PRGs) in the cultivated pepper Zunla-1 and 775 in the eggplant line Nakate-Shinkuro. The retrieved genes were analysed for their tendency to cluster, using different methods to infer the means of grouping. Orthologous relationships among clustering loci were found, and interesting reshuffling within given loci was observed for each analysed species. The information obtained was integrated into a comparative map to highlight the evolutionary dynamics in which the PRG loci were involved. Diversification of 14 selected PRG-rich regions was also explored using a DNA target-enrichment approach. A large number of gene variants were found as well as rearrangements of sequences encoding single protein domain and changes in chromosome gene order among species. Gene duplication and transposition activity have clearly influenced plant genome R-gene architecture and diversification. Our findings contribute to addressing several biological questions concerning the parallel evolution that occurred between genomes of the family Solanaceae. Moreover, the integration of different methods proved a powerful approach to reconstruct the evolutionary history in plant families and to transfer important biology findings among plant genomes.
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Affiliation(s)
- A Di Donato
- a Dipartimento di Agraria, Università di Napoli 'Federico II', Via Università 100, 80055 Portici, Italy
| | - G Andolfo
- a Dipartimento di Agraria, Università di Napoli 'Federico II', Via Università 100, 80055 Portici, Italy
| | - A Ferrarini
- b Dipartimento di Biotecnologie, Università degli Studi di Verona, Strada le Grazie, 15, 37134 Verona, Italy
| | - M Delledonne
- b Dipartimento di Biotecnologie, Università degli Studi di Verona, Strada le Grazie, 15, 37134 Verona, Italy
| | - M R Ercolano
- a Dipartimento di Agraria, Università di Napoli 'Federico II', Via Università 100, 80055 Portici, Italy
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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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Xiao J, Sekhwal MK, Li P, Ragupathy R, Cloutier S, Wang X, You FM. Pseudogenes and Their Genome-Wide Prediction in Plants. Int J Mol Sci 2016; 17:E1991. [PMID: 27916797 PMCID: PMC5187791 DOI: 10.3390/ijms17121991] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2016] [Revised: 11/20/2016] [Accepted: 11/22/2016] [Indexed: 11/17/2022] Open
Abstract
Pseudogenes are paralogs generated from ancestral functional genes (parents) during genome evolution, which contain critical defects in their sequences, such as lacking a promoter, having a premature stop codon or frameshift mutations. Generally, pseudogenes are functionless, but recent evidence demonstrates that some of them have potential roles in regulation. The majority of pseudogenes are generated from functional progenitor genes either by gene duplication (duplicated pseudogenes) or retro-transposition (processed pseudogenes). Pseudogenes are primarily identified by comparison to their parent genes. Bioinformatics tools for pseudogene prediction have been developed, among which PseudoPipe, PSF and Shiu's pipeline are publicly available. We compared these three tools using the well-annotated Arabidopsis thaliana genome and its known 924 pseudogenes as a test data set. PseudoPipe and Shiu's pipeline identified ~80% of A. thaliana pseudogenes, of which 94% were shared, while PSF failed to generate adequate results. A need for improvement of the bioinformatics tools for pseudogene prediction accuracy in plant genomes was thus identified, with the ultimate goal of improving the quality of genome annotation in plants.
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Affiliation(s)
- Jin Xiao
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB R6M 1Y5, Canada.
- Department of Agronomy, Nanjing Agricultural University, Nanjing 210095, China.
| | - Manoj Kumar Sekhwal
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB R6M 1Y5, Canada.
- Department of Soil Science, University of Saskatchewan, Saskatoon, SK S7N 5A8, Canada.
| | - Pingchuan Li
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB R6M 1Y5, Canada.
| | - Raja Ragupathy
- Department of Plant Science, University of Saskatchewan, Saskatoon, SK S7N 5A2, Canada.
| | - Sylvie Cloutier
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada.
| | - Xiue Wang
- Department of Agronomy, Nanjing Agricultural University, Nanjing 210095, China.
| | - Frank M You
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB R6M 1Y5, Canada.
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Dong L, Huo N, Wang Y, Deal K, Wang D, Hu T, Dvorak J, Anderson OD, Luo MC, Gu YQ. Rapid evolutionary dynamics in a 2.8-Mb chromosomal region containing multiple prolamin and resistance gene families in Aegilops tauschii. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 87:495-506. [PMID: 27228577 DOI: 10.1111/tpj.13214] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Revised: 05/03/2016] [Accepted: 05/09/2016] [Indexed: 06/05/2023]
Abstract
Prolamin and resistance gene families are important in wheat food use and in defense against pathogen attacks, respectively. To better understand the evolution of these multi-gene families, the DNA sequence of a 2.8-Mb genomic region, representing an 8.8 cM genetic interval and harboring multiple prolamin and resistance-like gene families, was analyzed in the diploid grass Aegilops tauschii, the D-genome donor of bread wheat. Comparison with orthologous regions from rice, Brachypodium, and sorghum showed that the Ae. tauschii region has undergone dramatic changes; it has acquired more than 80 non-syntenic genes and only 13 ancestral genes are shared among these grass species. These non-syntenic genes, including prolamin and resistance-like genes, originated from various genomic regions and likely moved to their present locations via sequence evolution processes involving gene duplication and translocation. Local duplication of non-syntenic genes contributed significantly to the expansion of gene families. Our analysis indicates that the insertion of prolamin-related genes occurred prior to the separation of the Brachypodieae and Triticeae lineages. Unlike in Brachypodium, inserted prolamin genes have rapidly evolved and expanded to encode different classes of major seed storage proteins in Triticeae species. Phylogenetic analyses also showed that the multiple insertions of resistance-like genes and subsequent differential expansion of each R gene family. The high frequency of non-syntenic genes and rapid local gene evolution correlate with the high recombination rate in the 2.8-Mb region with nine-fold higher than the genome-wide average. Our results demonstrate complex evolutionary dynamics in this agronomically important region of Triticeae species.
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Affiliation(s)
- Lingli Dong
- United States Department of Agriculture-Agricultural Research Service, Western Regional Research Center, Albany, CA, 94710, USA
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
- State Key Laboratory of Plant Cell and Chromosome Engineering, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Naxin Huo
- United States Department of Agriculture-Agricultural Research Service, Western Regional Research Center, Albany, CA, 94710, USA
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Yi Wang
- United States Department of Agriculture-Agricultural Research Service, Western Regional Research Center, Albany, CA, 94710, USA
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Karin Deal
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Daowen Wang
- State Key Laboratory of Plant Cell and Chromosome Engineering, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Tiezhu Hu
- United States Department of Agriculture-Agricultural Research Service, Western Regional Research Center, Albany, CA, 94710, USA
| | - Jan Dvorak
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Olin D Anderson
- United States Department of Agriculture-Agricultural Research Service, Western Regional Research Center, Albany, CA, 94710, USA
| | - Ming-Cheng Luo
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA.
| | - Yong Q Gu
- United States Department of Agriculture-Agricultural Research Service, Western Regional Research Center, Albany, CA, 94710, 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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Zhang Y, Xia R, Kuang H, Meyers BC. The Diversification of Plant NBS-LRR Defense Genes Directs the Evolution of MicroRNAs That Target Them. Mol Biol Evol 2016; 33:2692-705. [PMID: 27512116 PMCID: PMC5026261 DOI: 10.1093/molbev/msw154] [Citation(s) in RCA: 129] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
High expression of plant nucleotide binding site leucine-rich repeat (NBS-LRR) defense genes is often lethal to plant cells, a phenotype perhaps associated with fitness costs. Plants implement several mechanisms to control the transcript level of NBS-LRR defense genes. As negative transcriptional regulators, diverse miRNAs target NBS-LRRs in eudicots and gymnosperms. To understand the evolutionary benefits of this miRNA-NBS-LRR regulatory system, we investigated the NBS-LRRs of 70 land plants, coupling this analysis with extensive small RNA data. A tight association between the diversity of NBS-LRRs and miRNAs was found. The miRNAs typically target highly duplicated NBS-LRRs In comparison, families of heterogeneous NBS-LRRs were rarely targeted by miRNAs in Poaceae and Brassicaceae genomes. We observed that duplicated NBS-LRRs from different gene families periodically gave birth to new miRNAs. Most of these newly emerged miRNAs target the same conserved, encoded protein motif of NBS-LRRs, consistent with a model of convergent evolution for these miRNAs. By assessing the interactions between miRNAs and NBS-LRRs, we found nucleotide diversity in the wobble position of the codons in the target site drives the diversification of miRNAs. Taken together, we propose a co-evolutionary model of plant NBS-LRRs and miRNAs hypothesizing how plants balance the benefits and costs of NBS-LRR defense genes.
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Affiliation(s)
- Yu Zhang
- Key Laboratory of Horticulture Biology, Ministry of Education, and Department of Vegetable Crops, College of Horticulture and Forestry, Huazhong Agricultural University, Wuhan, People's Republic of China Donald Danforth Plant Science Center, St. Louis
| | - Rui Xia
- Donald Danforth Plant Science Center, St. Louis
| | - Hanhui Kuang
- Key Laboratory of Horticulture Biology, Ministry of Education, and Department of Vegetable Crops, College of Horticulture and Forestry, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Blake C Meyers
- Donald Danforth Plant Science Center, St. Louis Division of Plant Sciences, University of Missouri - Columbia
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Liang J, Fu B, Tang W, Khan NU, Li N, Ma Z. Fine Mapping of Two Wheat Powdery Mildew Resistance Genes Located at the Cluster. THE PLANT GENOME 2016; 9. [PMID: 27898804 DOI: 10.3835/plantgenome2015.09.0084] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Powdery mildew caused by (DC.) f. sp. () is a globally devastating foliar disease of wheat ( L.). More than a dozen genes against this disease, identified from wheat germplasms of different ploidy levels, have been mapped to the region surrounding the locus on the long arm of chromosome 7A, which forms a resistance ()-gene cluster. and from einkorn wheat ( L.) were two of the genes belonging to this cluster. This study was initiated to fine map these two genes toward map-based cloning. Comparative genomics study showed that macrocolinearity exists between L. chromosome 1 (Bd1) and the - region, which allowed us to develop markers based on the wheat sequences orthologous to genes contained in the Bd1 region. With these and other newly developed and published markers, high-resolution maps were constructed for both and using large F populations. Moreover, a physical map of was constructed through chromosome walking with bacterial artificial chromosome (BAC) clones and comparative mapping. Eventually, and were restricted to a 0.12- and 0.86-cM interval, respectively. Based on the closely linked common markers, , , and (another powdery mildew resistance gene in the cluster) were not allelic to one another. Severe recombination suppression and disruption of synteny were noted in the region encompassing . These results provided useful information for map-based cloning of the genes in the cluster and interpretation of their evolution.
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Ogawa T, Mori A, Igari K, Morita MT, Tasaka M, Uchida N. Efficient In Planta Detection and Dissection of De Novo Mutation Events in the Arabidopsis thaliana Disease Resistance Gene UNI. PLANT & CELL PHYSIOLOGY 2016; 57:1123-1132. [PMID: 27016096 DOI: 10.1093/pcp/pcw060] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Accepted: 03/16/2016] [Indexed: 06/05/2023]
Abstract
Plants possess disease resistance (R) proteins encoded by R genes, and each R protein recognizes a specific pathogen factor(s) for immunity. Interestingly, a remarkably high degree of polymorphisms in R genes, which are traces of past mutation events during evolution, suggest the rapid diversification of R genes. However, little is known about molecular aspects that facilitate the rapid change of R genes because of the lack of tools that enable us to monitor de novo R gene mutations efficiently in an experimentally feasible time scale, especially in living plants. Here we introduce a model assay system that enables efficient in planta detection of de novo mutation events in the Arabidopsis thaliana R gene UNI in one generation. The uni-1D mutant harbors a gain-of-function allele of the UNI gene. uni-1D heterozygous individuals originally exhibit dwarfism with abnormally short stems. However, interestingly, morphologically normal stems sometimes emerge spontaneously from the uni-1D plants, and the morphologically reverted tissues carry additional de novo mutations in the UNI gene. Strikingly, under an extreme condition, almost half of the examined population shows the reversion phenomenon. By taking advantage of this phenomenon, we demonstrate that the reversion frequency is remarkably sensitive to a variety of fluctuations in DNA stability, underlying a mutable tendency of the UNI gene. We also reveal that activities of the salicylic acid pathway and DNA damage sensor pathway are involved in the reversion phenomenon. Thus, we provide an experimentally feasible model tool to explore factors and conditions that significantly affect the R gene mutation phenomenon.
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Affiliation(s)
- Tomohiko Ogawa
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, 630-0192 Japan
| | - Akiko Mori
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8602 Japan
| | - Kadunari Igari
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, 630-0192 Japan
| | - Miyo Terao Morita
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8602 Japan
| | - Masao Tasaka
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, 630-0192 Japan
| | - Naoyuki Uchida
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601 Japan
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49
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Zheng F, Wu H, Zhang R, Li S, He W, Wong FL, Li G, Zhao S, Lam HM. Molecular phylogeny and dynamic evolution of disease resistance genes in the legume family. BMC Genomics 2016; 17:402. [PMID: 27229309 PMCID: PMC4881053 DOI: 10.1186/s12864-016-2736-9] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2015] [Accepted: 05/12/2016] [Indexed: 02/06/2023] Open
Abstract
Background Legumes are the second-most important crop family in agriculture for its economic and nutritional values. Disease resistance (R-) genes play an important role in responding to pathogen infections in plants. To further increase the yield of legume crops, we need a comprehensive understanding of the evolution of R-genes in the legume family. Results In this study, we developed a robust pipeline and identified a total of 4,217 R-genes in the genomes of seven sequenced legume species. A dramatic diversity of R-genes with structural variances indicated a rapid birth-and-death rate during the R-gene evolution in legumes. The number of R-genes transiently expanded and then quickly contracted after whole-genome duplications, which meant that R-genes were sensitive to subsequent diploidization. R proteins with the Coiled-coil (CC) domain are more conserved than others in legumes. Meanwhile, other types of legume R proteins with only one or two typical domains were subjected to higher rates of loss during evolution. Although R-genes evolved quickly in legumes, they tended to undergo purifying selection instead of positive selection during evolution. In addition, domestication events in some legume species preferentially selected for the genes directly involved in the plant-pathogen interaction pathway while suppressing those R-genes with low occurrence rates. Conclusions Our results provide insights into the dynamic evolution of R-genes in the legume family, which will be valuable for facilitating genetic improvements in the disease resistance of legume cultivars. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2736-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Fengya Zheng
- Centre for Soybean Research, Partner State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, New Territories, Hong Kong
| | - Haiyang Wu
- BGI-Shenzhen, Shenzhen, 518083, China.,HKU-BGI Bioinformatics Laboratory and Department of Computer Science, University of Hong Kong, Pofulam, Hong Kong
| | - Rongzhi Zhang
- Crop research institution, Shandong Academy of Agricultural Sciences, Jinan, 250100, China
| | | | | | - Fuk-Ling Wong
- Centre for Soybean Research, Partner State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, New Territories, Hong Kong
| | - Genying Li
- Crop research institution, Shandong Academy of Agricultural Sciences, Jinan, 250100, China
| | - Shancen Zhao
- Centre for Soybean Research, Partner State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, New Territories, Hong Kong. .,BGI-Shenzhen, Shenzhen, 518083, China.
| | - Hon-Ming Lam
- Centre for Soybean Research, Partner State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, New Territories, Hong Kong.
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50
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Kroj T, Chanclud E, Michel‐Romiti C, Grand X, Morel J. Integration of decoy domains derived from protein targets of pathogen effectors into plant immune receptors is widespread. THE NEW PHYTOLOGIST 2016; 210:618-26. [PMID: 26848538 PMCID: PMC5067614 DOI: 10.1111/nph.13869] [Citation(s) in RCA: 157] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Accepted: 12/16/2015] [Indexed: 05/18/2023]
Abstract
Plant immune receptors of the class of nucleotide-binding and leucine-rich repeat domain (NLR) proteins can contain additional domains besides canonical NB-ARC (nucleotide-binding adaptor shared by APAF-1, R proteins, and CED-4 (NB-ARC)) and leucine-rich repeat (LRR) domains. Recent research suggests that these additional domains act as integrated decoys recognizing effectors from pathogens. Proteins homologous to integrated decoys are suspected to be effector targets and involved in disease or resistance. Here, we scrutinized 31 entire plant genomes to identify putative integrated decoy domains in NLR proteins using the Interpro search. The involvement of the Zinc Finger-BED type (ZBED) protein containing a putative decoy domain, called BED, in rice (Oryza sativa) resistance was investigated by evaluating susceptibility to the blast fungus Magnaporthe oryzae in rice over-expression and knock-out mutants. This analysis showed that all plants tested had integrated various atypical protein domains into their NLR proteins (on average 3.5% of all NLR proteins). We also demonstrated that modifying the expression of the ZBED gene modified disease susceptibility. This study suggests that integration of decoy domains in NLR immune receptors is widespread and frequent in plants. The integrated decoy model is therefore a powerful concept to identify new proteins involved in disease resistance. Further in-depth examination of additional domains in NLR proteins promises to unravel many new proteins of the plant immune system.
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Affiliation(s)
- Thomas Kroj
- INRACIRADSupAgroUMR BGPI INRA/CIRAD/SupAgroCampus International de BaillarguetTA A 54/K34398MontpellierFrance
| | - Emilie Chanclud
- Université Montpellier2 Place Eugène Bataillon34095Montpellier Cedex 5France
| | - Corinne Michel‐Romiti
- INRACIRADSupAgroUMR BGPI INRA/CIRAD/SupAgroCampus International de BaillarguetTA A 54/K34398MontpellierFrance
| | - Xavier Grand
- INRACIRADSupAgroUMR BGPI INRA/CIRAD/SupAgroCampus International de BaillarguetTA A 54/K34398MontpellierFrance
| | - Jean‐Benoit Morel
- INRACIRADSupAgroUMR BGPI INRA/CIRAD/SupAgroCampus International de BaillarguetTA A 54/K34398MontpellierFrance
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