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Moncada MM, Elvir MA, Lopez JR, Ortiz AS. Predicción bioinformática de proteínas NBS-LRR en el genoma de Coffea arabica. BIONATURA 2022. [DOI: 10.21931/rb/2022.07.03.19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Gracias al acceso al genoma completo de Coffea arabica y el Desarrollo de multiples herramientas de bioinformartica que permite la búsqueda de genes de resistencia de plantas (R-genes), ha sido posible implementar estas estrategias en programas de mejora genética. En las plantas, los R-genes codifican proteínas involucradas en mecanismos de defensa contra patógenos. Los genes con dominios tipo Nucleotide-Binding-Site Leucine-Rich-Repeat (NBS-LRR) forman la familia de R-genes de plantas más grande. El objetivo de este estudio fue identificar genes de proteínas NBS-LRR en el genoma de C. arabica utilizando un enfoque bioinformático. Identificamos motivos conservados de R-genes de C. arabica relacionados con genes similares encontrados en Coffea canephora y Coffea eugenoides, dos especies evolutivas relacionadas con C. arabica. Los resultados de estos análisis revelaron proteínas con origen evolutivo provenientes de dicotiledóneo ancestrales, así como proteínas de resistencia específicas del género Coffea. Además, todas las secuencias de los R-genes de C. arabica mostraron una gran similitud con proteína CNL de Arabidopsis thaliana. Finalmente, la presencia de motivos altamente conservados, la distribución cromosómica y las relaciones filogenéticas de los R-genes de C. arabica muestran procesos de coevolución con patógenos adaptados, demostrando de esta manera la importancia del estudio de estos genes en la inmunidad del café.
Palabras clave: Café, NBS-LRR, Proteínas de Resistencia, Bioinformática.
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Affiliation(s)
| | | | | | - Andrés S. Ortiz
- Universidad Nacional Autónoma de Honduras Instituto de Investigaciones en Microbiología
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2
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Aggarwal PR, Pramitha L, Choudhary P, Singh RK, Shukla P, Prasad M, Muthamilarasan M. Multi-omics intervention in Setaria to dissect climate-resilient traits: Progress and prospects. FRONTIERS IN PLANT SCIENCE 2022; 13:892736. [PMID: 36119586 PMCID: PMC9470963 DOI: 10.3389/fpls.2022.892736] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 08/05/2022] [Indexed: 06/15/2023]
Abstract
Millets constitute a significant proportion of underutilized grasses and are well known for their climate resilience as well as excellent nutritional profiles. Among millets, foxtail millet (Setaria italica) and its wild relative green foxtail (S. viridis) are collectively regarded as models for studying broad-spectrum traits, including abiotic stress tolerance, C4 photosynthesis, biofuel, and nutritional traits. Since the genome sequence release, the crop has seen an exponential increase in omics studies to dissect agronomic, nutritional, biofuel, and climate-resilience traits. These studies have provided first-hand information on the structure, organization, evolution, and expression of several genes; however, knowledge of the precise roles of such genes and their products remains elusive. Several open-access databases have also been instituted to enable advanced scientific research on these important crops. In this context, the current review enumerates the contemporary trend of research on understanding the climate resilience and other essential traits in Setaria, the knowledge gap, and how the information could be translated for the crop improvement of related millets, biofuel crops, and cereals. Also, the review provides a roadmap for studying other underutilized crop species using Setaria as a model.
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Affiliation(s)
- Pooja Rani Aggarwal
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India
| | - Lydia Pramitha
- School of Agriculture and Biosciences, Karunya Institute of Technology and Sciences, Coimbatore, Tamil Nadu, India
| | - Pooja Choudhary
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India
| | | | - Pooja Shukla
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India
| | - Manoj Prasad
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India
- National Institute of Plant Genome Research (NIPGR), New Delhi, India
| | - Mehanathan Muthamilarasan
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India
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Yu X, Zhong S, Yang H, Chen C, Chen W, Yang H, Guan J, Fu P, Tan F, Ren T, Shen J, Zhang M, Luo P. Identification and Characterization of NBS Resistance Genes in Akebia trifoliata. FRONTIERS IN PLANT SCIENCE 2021; 12:758559. [PMID: 34777439 PMCID: PMC8585750 DOI: 10.3389/fpls.2021.758559] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 10/08/2021] [Indexed: 05/26/2023]
Abstract
Akebia trifoliata is an important multiuse perennial plant that often suffers attacks from various pathogens due to its long growth cycle, seriously affecting its commercial value. The absence of research on the resistance (R) genes of A. trifoliata has greatly limited progress in the breeding of resistant varieties. Genes encoding proteins containing nucleotide binding sites (NBSs) and C-terminal leucine-rich repeats (LRRs), the largest family of plant resistance (R) genes, are vital for plant disease resistance. A comprehensive genome-wide analysis showed that there were only 73 NBS genes in the A. trifoliata genome, including three main subfamilies (50 coiled coil (CC)-NBS-LRR (CNL), 19 Toll/interleukin-1 receptor (TIR)-NBS-LRR (TNL) and four resistance to powdery mildew8 (RPW8)-NBS-LRR (RNL) genes). Additionally, 64 mapped NBS candidates were unevenly distributed on 14 chromosomes, most of which were assigned to the chromosome ends; 41 of these genes were located in clusters, and the remaining 23 genes were singletons. Both the CNLs and TNLs were further divided into four subgroups, and the CNLs had fewer exons than the TNLs. Structurally, all eight previously reported conserved motifs were identified in the NBS domains, and both their order and their amino acid sequences exhibited high conservation. Evolutionarily, tandem and dispersed duplications were shown to be the two main forces responsible for NBS expansion, producing 33 and 29 genes, respectively. A transcriptome analysis of three fruit tissues at four developmental stages showed that NBS genes were generally expressed at low levels, while a few of these genes showed relatively high expression during later development in rind tissues. Overall, this research is the first to identify and characterize A. trifoliata NBS genes and is valuable for both the development of new resistant cultivars and the study of molecular mechanisms of resistance.
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Affiliation(s)
- Xiaojiao Yu
- Provincial Key Laboratory for Plant Genetics and Breeding, Chengdu, China
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Shengfu Zhong
- Provincial Key Laboratory for Plant Genetics and Breeding, Chengdu, China
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Huai Yang
- Provincial Key Laboratory for Plant Genetics and Breeding, Chengdu, China
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Chen Chen
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Wei Chen
- Provincial Key Laboratory for Plant Genetics and Breeding, Chengdu, China
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
- Sichuan Akebia trifoliata Biotechnology Co., Ltd., Chengdu, China
| | - Hao Yang
- Provincial Key Laboratory for Plant Genetics and Breeding, Chengdu, China
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
- Sichuan Akebia trifoliata Biotechnology Co., Ltd., Chengdu, China
| | - Ju Guan
- Provincial Key Laboratory for Plant Genetics and Breeding, Chengdu, China
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Peng Fu
- Provincial Key Laboratory for Plant Genetics and Breeding, Chengdu, China
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Feiquan Tan
- Provincial Key Laboratory for Plant Genetics and Breeding, Chengdu, China
| | - Tianheng Ren
- Provincial Key Laboratory for Plant Genetics and Breeding, Chengdu, China
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Jinliang Shen
- College of Forestry, Sichuan Agricultural University, Chengdu, China
| | - Min Zhang
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Peigao Luo
- Provincial Key Laboratory for Plant Genetics and Breeding, Chengdu, China
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
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4
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Hunt HV, Przelomska NAS, Campana MG, Cockram J, Bligh HFJ, Kneale CJ, Romanova OI, Malinovskaya EV, Jones MK. Population genomic structure of Eurasian and African foxtail millet landrace accessions inferred from genotyping-by-sequencing. THE PLANT GENOME 2021; 14:e20081. [PMID: 33543599 PMCID: PMC8638668 DOI: 10.1002/tpg2.20081] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 10/15/2020] [Indexed: 05/11/2023]
Abstract
Foxtail millet [Setaria italica (L.) P. Beauv.] is the second most important millet species globally and is adapted to cultivation in diverse environments. Like its wild progenitor, green foxtail [S. viridis (L.) P. Beauv.], it is a model species for C4 photosynthetic pathways and stress tolerance genes in related bioenergy crops. We addressed questions regarding the evolution and spread of foxtail millet through a population genomic study of landraces from across its cultivated range in Europe, Asia, and Africa. We sought to determine population genomic structure and the relationship of domesticated lineages relative to green foxtail. Further, we aimed to identify genes involved in environmental stress tolerance that have undergone differential selection between geographical and genetic groups. Foxtail millet landrace accessions (n = 328) and green foxtail accessions (n = 12) were sequenced by genotyping-by-sequencing (GBS). After filtering, 5,677 single nucleotide polymorphisms (SNPs) were retained for the combined foxtail millet-green foxtail dataset and 5,020 for the foxtail millet dataset. We extended geographic coverage of green foxtail by including previously published GBS sequence tags, yielding a 4,515-SNP dataset for phylogenetic reconstruction. All foxtail millet samples were monophyletic relative to green foxtail, suggesting a single origin of foxtail millet, although no group of foxtail millet was clearly the most ancestral. Four genetic clusters were found within foxtail millet, each with a distinctive geographical distribution. These results, together with archaeobotanical evidence, suggest plausible routes of spread of foxtail millet. Selection scans identified nine candidate genes potentially involved in environmental adaptations, particularly to novel climates encountered, as domesticated foxtail millet spread to new altitudes and latitudes.
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Affiliation(s)
- Harriet V. Hunt
- McDonald Institute for Archaeological ResearchUniversity of CambridgeDowning StreetCambridgeCB2 3ERUK
| | - Natalia A. S. Przelomska
- Comparative Plant and Fungal BiologyRoyal Botanic GardensKewRichmondTW9 3AEUK
- Department of AnthropologyNational Museum of Natural HistorySmithsonian InstitutionWashingtonDC20560USA
- Center for Conservation GenomicsSmithsonian's National Zoo and Conservation Biology InstituteSmithsonian InstitutionWashingtonDC20008USA
- Department of ArchaeologyUniversity of CambridgeDowning StreetCambridgeCB2 3DZUK
| | - Michael G. Campana
- Center for Conservation GenomicsSmithsonian's National Zoo and Conservation Biology InstituteSmithsonian InstitutionWashingtonDC20008USA
| | - James Cockram
- The John Bingham LaboratoryNIAB93 Lawrence Weaver RoadCambridgeCB3 0LEUK
| | | | - Catherine J. Kneale
- McDonald Institute for Archaeological ResearchUniversity of CambridgeDowning StreetCambridgeCB2 3ERUK
| | - Olga I. Romanova
- N.I. Vavilov Institute of Plant Genetic Resources (VIR)St. Petersburg190000Russia
| | | | - Martin K. Jones
- Department of ArchaeologyUniversity of CambridgeDowning StreetCambridgeCB2 3DZUK
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5
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Xu M, Liu CL, Fu Y, Liao ZW, Guo PY, Xiong R, Cheng Y, Wei SS, Huang JQ, Tang H. Molecular characterization and expression analysis of pitaya (Hylocereus polyrhizus) HpLRR genes in response to Neoscytalidium dimidiatum infection. BMC PLANT BIOLOGY 2020; 20:160. [PMID: 32293269 PMCID: PMC7161156 DOI: 10.1186/s12870-020-02368-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 03/27/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND Canker disease caused by Neoscytalidium dimidiatum is a devastating disease resulting in a major loss to the pitaya industry. However, resistance proteins in plants play crucial roles to against pathogen infection. Among resistance proteins, the leucine-rich repeat (LRR) protein is a major family that plays crucial roles in plant growth, development, and biotic and abiotic stress responses, especially in disease defense. RESULTS In the present study, a transcriptomics analysis identified a total of 272 LRR genes, 233 of which had coding sequences (CDSs), in the plant pitaya (Hylocereus polyrhizus) in response to fungal Neoscytalidium dimidiatum infection. These genes were divided into various subgroups based on specific domains and phylogenetic analysis. Molecular characterization, functional annotation of proteins, and an expression analysis of the LRR genes were conducted. Additionally, four LRR genes (CL445.Contig4_All, Unigene28_All, CL28.Contig2_All, and Unigene2712_All, which were selected because they had the four longest CDSs were further assessed using quantitative reverse transcription PCR (qRT-PCR) at different fungal infection stages in different pitaya species (Hylocereus polyrhizus and Hylocereus undatus), in different pitaya tissues, and after treatment with salicylic acid (SA), methyl jasmonate (MeJA), and abscisic acid (ABA) hormones. The associated protein functions and roles in signaling pathways were identified. CONCLUSIONS This study provides a comprehensive overview of the HpLRR family genes at transcriptional level in pitaya in response to N. dimidiatum infection, it will be helpful to understand the molecular mechanism of pitaya canker disease, and lay a strong foundation for further research.
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Affiliation(s)
- Min Xu
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, No.58 Renmin Avenue, Haikou, 570228 Hainan People’s Republic of China
| | - Cheng-Li Liu
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, No.58 Renmin Avenue, Haikou, 570228 Hainan People’s Republic of China
| | - Yu Fu
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, No.58 Renmin Avenue, Haikou, 570228 Hainan People’s Republic of China
| | - Zhi-Wen Liao
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, No.58 Renmin Avenue, Haikou, 570228 Hainan People’s Republic of China
| | - Pan-Yang Guo
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, No.58 Renmin Avenue, Haikou, 570228 Hainan People’s Republic of China
| | - Rui Xiong
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, No.58 Renmin Avenue, Haikou, 570228 Hainan People’s Republic of China
| | - Yu Cheng
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, No.58 Renmin Avenue, Haikou, 570228 Hainan People’s Republic of China
| | - Shuang-Shuang Wei
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, No.58 Renmin Avenue, Haikou, 570228 Hainan People’s Republic of China
| | - Jia-Quan Huang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, No.58 Renmin Avenue, Haikou, 570228 Hainan People’s Republic of China
| | - Hua Tang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, No.58 Renmin Avenue, Haikou, 570228 Hainan People’s Republic of China
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6
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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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7
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Jiang N, Cui J, Shi Y, Yang G, Zhou X, Hou X, Meng J, Luan Y. Tomato lncRNA23468 functions as a competing endogenous RNA to modulate NBS-LRR genes by decoying miR482b in the tomato -Phytophthora infestans interaction. HORTICULTURE RESEARCH 2019; 6:28. [PMID: 30729018 PMCID: PMC6355781 DOI: 10.1038/s41438-018-0096-0] [Citation(s) in RCA: 90] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 09/07/2018] [Accepted: 09/19/2018] [Indexed: 05/05/2023]
Abstract
Our previous studies indicated that tomato miR482b could negatively regulate the resistance of tomato to Phytophthora infestans and the expression of miR482b was decreased after inoculation with P. infestans. However, the mechanism by which the accumulation of miR482b is suppressed remains unclear. In this study, we wrote a program to identify 89 long noncoding RNA (lncRNA)-originated endogenous target mimics (eTMs) for 46 miRNAs from our RNA-Seq data. Three tomato lncRNAs, lncRNA23468, lncRNA01308 and lncRNA13262, contained conserved eTM sites for miR482b. When lncRNA23468 was overexpressed in tomato, miR482b expression was significantly decreased, and the expression of the target genes, NBS-LRRs, was significantly increased, resulting in enhanced resistance to P. infestans. Silencing lncRNA23468 in tomato led to the increased accumulation of miR482b and decreased accumulation of NBS-LRRs, as well as reduced resistance to P. infestans. In addition, the accumulation of both miR482b and NBS-LRRs was not significantly changed in tomato plants that overexpressed lncRNA23468 with a mutated eTM site. Based on the VIGS system, a target gene of miR482b, Solyc02g036270.2, was silenced. The disease symptoms of the VIGS-Solyc02g036270.2 tomato plants were in accordance with those of tomato plants in which lncRNA23468 was silenced after inoculation with P. infestans. More severe disease symptoms were found in the modified plants than in the control plants. Our results demonstrate that lncRNAs functioning as eTMs may modulate the effects of miRNAs in tomato and provide insight into how the lncRNA23468-miR482b-NBS-LRR module regulates tomato resistance to P. infestans.
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Affiliation(s)
- Ning Jiang
- School of Life Science and Biotechnology, Dalian University of Technology, 116024 Dalian, China
| | - Jun Cui
- School of Life Science and Biotechnology, Dalian University of Technology, 116024 Dalian, China
| | - Yunsheng Shi
- School of Computer Science and Technology, Dalian University of Technology, 116024 Dalian, China
| | - Guanglei Yang
- School of Life Science and Biotechnology, Dalian University of Technology, 116024 Dalian, China
| | - Xiaoxu Zhou
- School of Life Science and Biotechnology, Dalian University of Technology, 116024 Dalian, China
| | - Xinxin Hou
- School of Life Science and Biotechnology, Dalian University of Technology, 116024 Dalian, China
| | - Jun Meng
- School of Computer Science and Technology, Dalian University of Technology, 116024 Dalian, China
| | - Yushi Luan
- School of Life Science and Biotechnology, Dalian University of Technology, 116024 Dalian, China
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Wang Z, Zhao K, Pan Y, Wang J, Song X, Ge W, Yuan M, Lei T, Wang L, Zhang L, Li Y, Liu T, Chen W, Meng W, Sun C, Cui X, Bai Y, Wang X. Genomic, expressional, protein-protein interactional analysis of Trihelix transcription factor genes in Setaria italia and inference of their evolutionary trajectory. BMC Genomics 2018; 19:665. [PMID: 30208846 PMCID: PMC6134603 DOI: 10.1186/s12864-018-5051-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 08/31/2018] [Indexed: 02/07/2023] Open
Abstract
Background Trihelix transcription factors (TTF) play important roles in plant growth and response to adversity stress. Until now, genome-wide identification and analysis of this gene family in foxtail millet has not been available. Here, we identified TTF genes in the foxtail millet and its grass relatives, and characterized their functional domains. Results As to sequence divergence, TTF genes were previously divided into five subfamilies, I-V. We found that Trihelix family members in foxtail millet and other grasses mostly preserved their ancestral chromosomal locations during millions of years’ evolution. Six amino acid sites of the SIP1 subfamily possibly were likely subjected to significant positive selection. Highest expression level was observed in the spica, with the SIP1 subfamily having highest expression level. As to the origination and expansion of the gene family, notably we showed that a subgroup of subfamily IV was the oldest, and therefore was separated to define a new subfamily O. Overtime, starting from the subfamily O, certain genes evolved to form subfamilies III and I, and later from subfamily I to develop subfamilies II and V. The oldest gene, Si1g016284, has the most structural changes, and a high expression in different tissues. What’s more interesting is that it may have bridge the interaction with different proteins. Conclusions By performing phylogenetic analysis using non-plant species, notably we showed that a subgroup of subfamily IV was the oldest, and therefore was separated to define a new subfamily O. Starting from the subfamily O, certain genes evolved to form other subfamilies. Our work will contribute to understanding the structural and functional innovation of Trihelix transcription factor, and the evolutionary trajectory. Electronic supplementary material The online version of this article (10.1186/s12864-018-5051-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Zhenyi Wang
- College of Life Sciences, North China University of Science and Technology, Caofeidian Dist, Tangshan, 063210, Hebei, China. .,Center for Genomics and Computational Biology, North China University of Science and Technology, Caofeidian Dist, Tangshan, 063210, Hebei, China.
| | - Kanglu Zhao
- College of Life Sciences, North China University of Science and Technology, Caofeidian Dist, Tangshan, 063210, Hebei, China
| | - Yuxin Pan
- College of Life Sciences, North China University of Science and Technology, Caofeidian Dist, Tangshan, 063210, Hebei, China.,Center for Genomics and Computational Biology, North China University of Science and Technology, Caofeidian Dist, Tangshan, 063210, Hebei, China
| | - Jinpeng Wang
- College of Life Sciences, North China University of Science and Technology, Caofeidian Dist, Tangshan, 063210, Hebei, China.,Center for Genomics and Computational Biology, North China University of Science and Technology, Caofeidian Dist, Tangshan, 063210, Hebei, China
| | - Xiaoming Song
- College of Life Sciences, North China University of Science and Technology, Caofeidian Dist, Tangshan, 063210, Hebei, China.,Center for Genomics and Computational Biology, North China University of Science and Technology, Caofeidian Dist, Tangshan, 063210, Hebei, China
| | - Weina Ge
- College of Life Sciences, North China University of Science and Technology, Caofeidian Dist, Tangshan, 063210, Hebei, China.,Center for Genomics and Computational Biology, North China University of Science and Technology, Caofeidian Dist, Tangshan, 063210, Hebei, China
| | - Min Yuan
- College of Life Sciences, North China University of Science and Technology, Caofeidian Dist, Tangshan, 063210, Hebei, China.,Center for Genomics and Computational Biology, North China University of Science and Technology, Caofeidian Dist, Tangshan, 063210, Hebei, China
| | - Tianyu Lei
- College of Life Sciences, North China University of Science and Technology, Caofeidian Dist, Tangshan, 063210, Hebei, China.,Center for Genomics and Computational Biology, North China University of Science and Technology, Caofeidian Dist, Tangshan, 063210, Hebei, China
| | - Li Wang
- College of Life Sciences, North China University of Science and Technology, Caofeidian Dist, Tangshan, 063210, Hebei, China.,Center for Genomics and Computational Biology, North China University of Science and Technology, Caofeidian Dist, Tangshan, 063210, Hebei, China
| | - Lan Zhang
- College of Life Sciences, North China University of Science and Technology, Caofeidian Dist, Tangshan, 063210, Hebei, China.,Center for Genomics and Computational Biology, North China University of Science and Technology, Caofeidian Dist, Tangshan, 063210, Hebei, China
| | - Yuxian Li
- College of Life Sciences, North China University of Science and Technology, Caofeidian Dist, Tangshan, 063210, Hebei, China.,Center for Genomics and Computational Biology, North China University of Science and Technology, Caofeidian Dist, Tangshan, 063210, Hebei, China
| | - Tao Liu
- Center for Genomics and Computational Biology, North China University of Science and Technology, Caofeidian Dist, Tangshan, 063210, Hebei, China.,College of Science, North China University of Science and Technology, Caofeidian Dist, Tangshan, 063210, Hebei, China
| | - Wei Chen
- Center for Genomics and Computational Biology, North China University of Science and Technology, Caofeidian Dist, Tangshan, 063210, Hebei, China.,College of Science, North China University of Science and Technology, Caofeidian Dist, Tangshan, 063210, Hebei, China
| | - Wenjing Meng
- College of Life Sciences, North China University of Science and Technology, Caofeidian Dist, Tangshan, 063210, Hebei, China
| | - Changkai Sun
- College of Life Sciences, North China University of Science and Technology, Caofeidian Dist, Tangshan, 063210, Hebei, China
| | - Xiaobo Cui
- College of Life Sciences, North China University of Science and Technology, Caofeidian Dist, Tangshan, 063210, Hebei, China
| | - Yun Bai
- College of Life Sciences, North China University of Science and Technology, Caofeidian Dist, Tangshan, 063210, Hebei, China
| | - Xiyin Wang
- College of Life Sciences, North China University of Science and Technology, Caofeidian Dist, Tangshan, 063210, Hebei, China. .,Center for Genomics and Computational Biology, North China University of Science and Technology, Caofeidian Dist, Tangshan, 063210, Hebei, China.
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Jiang N, Cui J, Meng J, Luan Y. A Tomato Nucleotide Binding Sites-Leucine-Rich Repeat Gene Is Positively Involved in Plant Resistance to Phytophthora infestans. PHYTOPATHOLOGY 2018; 108:980-987. [PMID: 29595084 DOI: 10.1094/phyto-12-17-0389-r] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The nucleotide binding sites-leucine-rich repeat (NBS-LRR) genes are key regulatory components of plant to pathogens. Phytophthora infestans-inducible coding sequence encoding an NBS-LRR (SpNBS-LRR) protein in tomato (Solanum pimpinellifolium L3708) was cloned and characterized based on our RNA-Seq data and tomato genome. After sequence analysis, SpNBS-LRR was identified as a hydrophilic protein with no transmembrane topological structure and no signal peptide. SpNBS-LRR had a close genetic relationship to RPS2 of Arabidopsis thaliana by phylogenetic analysis. In addition, SpNBS-LRR gene was mainly expressed in root, with low expression observed in leaf and stem. To further investigate the role of SpNBS-LRR in tomato-P. infestans interaction, SpNBS-LRR was introduced in susceptible tomatoes and three transgenic lines with higher expression level of SpNBS-LRR were selected. These transgenic tomato plants that overexpressed SpNBS-LRR displayed greater resistance than wild-type tomato plants after infection with P. infestans, as shown by decreased disease index, lesion diameters, number of necrotic cells, P. infestans abundance, and higher expression levels of the defense-related genes. This information provides insight into SpNBS-LRR involved in the resistance of tomato to P. infestans infection and candidate for breeding to enhance biotic stress-resistance in tomato.
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Affiliation(s)
- Ning Jiang
- First, second, and fourth authors: School of Life Science and Biotechnology, Dalian University of Technology, Dalian, 116024, China; and third author: School of Computer Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Jun Cui
- First, second, and fourth authors: School of Life Science and Biotechnology, Dalian University of Technology, Dalian, 116024, China; and third author: School of Computer Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Jun Meng
- First, second, and fourth authors: School of Life Science and Biotechnology, Dalian University of Technology, Dalian, 116024, China; and third author: School of Computer Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Yushi Luan
- First, second, and fourth authors: School of Life Science and Biotechnology, Dalian University of Technology, Dalian, 116024, China; and third author: School of Computer Science and Technology, Dalian University of Technology, Dalian 116024, China
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Borrelli GM, Mazzucotelli E, Marone D, Crosatti C, Michelotti V, Valè G, Mastrangelo AM. Regulation and Evolution of NLR Genes: A Close Interconnection for Plant Immunity. Int J Mol Sci 2018; 19:E1662. [PMID: 29867062 PMCID: PMC6032283 DOI: 10.3390/ijms19061662] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 06/01/2018] [Accepted: 06/02/2018] [Indexed: 12/12/2022] Open
Abstract
NLR (NOD-like receptor) genes belong to one of the largest gene families in plants. Their role in plants' resistance to pathogens has been clearly described for many members of this gene family, and dysregulation or overexpression of some of these genes has been shown to induce an autoimmunity state that strongly affects plant growth and yield. For this reason, these genes have to be tightly regulated in their expression and activity, and several regulatory mechanisms are described here that tune their gene expression and protein levels. This gene family is subjected to rapid evolution, and to maintain diversity at NLRs, a plethora of genetic mechanisms have been identified as sources of variation. Interestingly, regulation of gene expression and evolution of this gene family are two strictly interconnected aspects. Indeed, some examples have been reported in which mechanisms of gene expression regulation have roles in promotion of the evolution of this gene family. Moreover, co-evolution of the NLR gene family and other gene families devoted to their control has been recently demonstrated, as in the case of miRNAs.
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Affiliation(s)
- Grazia M Borrelli
- Council for Agricultural Research and Economics-Research Centre for Cereal and Industrial Crops, s.s. 673, km 25.2, 71122 Foggia, Italy.
| | - Elisabetta Mazzucotelli
- Council for Agricultural Research and Economics-Research Centre for Genomics and Bioinformatics, via San Protaso 302, 29017 Fiorenzuola d'Arda (PC), Italy.
| | - Daniela Marone
- Council for Agricultural Research and Economics-Research Centre for Cereal and Industrial Crops, s.s. 673, km 25.2, 71122 Foggia, Italy.
| | - Cristina Crosatti
- Council for Agricultural Research and Economics-Research Centre for Genomics and Bioinformatics, via San Protaso 302, 29017 Fiorenzuola d'Arda (PC), Italy.
| | - Vania Michelotti
- Council for Agricultural Research and Economics-Research Centre for Genomics and Bioinformatics, via San Protaso 302, 29017 Fiorenzuola d'Arda (PC), Italy.
| | - Giampiero Valè
- Council for Agricultural Research and Economics-Research Centre for Cereal and Industrial Crops, s.s. 11 to Torino, km 2.5, 13100 Vercelli, Italy.
| | - Anna M Mastrangelo
- Council for Agricultural Research and Economics-Research Centre for Cereal and Industrial Crops, via Stezzano 24, 24126 Bergamo, Italy.
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Kochetov AV, Glagoleva AY, Strygina KV, Khlestkina EK, Gerasimova SV, Ibragimova SM, Shatskaya NV, Vasilyev GV, Afonnikov DA, Shmakov NA, Antonova OY, Gavrilenko TA, Alpatyeva NV, Khiutti A, Afanasenko OS. Differential expression of NBS-LRR-encoding genes in the root transcriptomes of two Solanum phureja genotypes with contrasting resistance to Globodera rostochiensis. BMC PLANT BIOLOGY 2017; 17:251. [PMID: 29297325 PMCID: PMC5751396 DOI: 10.1186/s12870-017-1193-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
BACKGROUND The characterization of major resistance genes (R genes) in the potato remains an important task for molecular breeding. However, R genes are rapidly evolving and frequently occur in genomes as clusters with complex structures, and their precise mapping and identification are complicated and time consuming. RESULTS Comparative analysis of root transcriptomes of Solanum phureja genotypes with contrasting resistance to Globodera rostochiensis revealed a number of differentially expressed genes. However, compiling a list of candidate R genes for further segregation analysis was hampered by their scarce annotation. Nevertheless, combination of transcriptomic analysis with data on predicted potato NBS-LRR-encoding genes considerably improved the quality of the results and provided a reasonable number of candidate genes that provide S. phureja with strong resistance to the potato golden cyst nematode. CONCLUSION Combination of comparative analyses of tissue-specific transcriptomes in resistant and susceptible genotypes may be used as an approach for the rapid identification of candidate potato R genes for co-segregation analysis and may be used in parallel with more sophisticated studies based on genome resequencing.
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Affiliation(s)
- Alex V Kochetov
- Institute of Cytology and Genetics, SB RAS, Novosibirsk, 630090, Russia.
- Novosibirsk State University, Novosibirsk, 630090, Russia.
- Novosibirsk State Agrarian University, Novosibirsk, 630039, Russia.
| | - Anastasiya Y Glagoleva
- Institute of Cytology and Genetics, SB RAS, Novosibirsk, 630090, Russia
- Novosibirsk State University, Novosibirsk, 630090, Russia
| | | | - Elena K Khlestkina
- Institute of Cytology and Genetics, SB RAS, Novosibirsk, 630090, Russia
- Novosibirsk State University, Novosibirsk, 630090, Russia
| | | | | | | | | | | | - Nikolay A Shmakov
- Institute of Cytology and Genetics, SB RAS, Novosibirsk, 630090, Russia
| | - Olga Y Antonova
- Vavilov Institute of Plant Genetic Resources (VIR), Saint Petersburg, 190000, Russia
| | - Tatyana A Gavrilenko
- Vavilov Institute of Plant Genetic Resources (VIR), Saint Petersburg, 190000, Russia
- St. Petersburg State University, St. Petersburg, 199034, Russia
| | - Natalia V Alpatyeva
- Vavilov Institute of Plant Genetic Resources (VIR), Saint Petersburg, 190000, Russia
| | - Alexander Khiutti
- All Russian Research Institute for Plant Protection, Saint Petersburg, 196608, Russia
| | - Olga S Afanasenko
- All Russian Research Institute for Plant Protection, Saint Petersburg, 196608, Russia
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Genome-wide identification and resistance expression analysis of the NBS gene family in Triticum urartu. Genes Genomics 2017. [DOI: 10.1007/s13258-017-0526-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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