Global Verticillium dahliae Genomics Research
This project an extension of the cooperation initially between the Institute Plant Protection, Chinese Academy of Agricultural Sciences, P.R. China (IPP-CAAS) and the Department of Plant Pathology, University of California Davis (DPP-UCD), now include 16 organizations to participate in the ongoing research project. The overarching goal of this project is to uncover the evolutionary basis of V. dahliae lineages and the genomic basis of extensive host adaptations, to get a better understanding of evolution in V. dahliae and mechanisms of pandemics, and finally provide the theoretical support for the V. dahliae management and technology research.
Background
Verticillium dahliae is a soil-borne ascomycete that causes Verticillium wilt in over 200 plant species, including many important crops such as cotton, potato, lettuce, and tomato, and causes billions of dollars in agricultural losses annually (Klosterman et al., 2009). Since the first discovery of Verticillium wilt in 1879, researchers from different countries have made enormous progress in understanding the taxonomy of the genus Verticillium (Inderbitzin and Subbarao, 2014; Short et al., 2014), the host range and pathogenicity differentiation (Bhat and Subbarao, 1999), toxin components (Fradin and Thomma, 2006), pathogenicity-related gene mining and functional analysis (Klimes et al., 2015), and comparative genomics (Klosterman et al., 2011; de Jonge et al., 2013; Chen et al., 2017), etc. The above research has provided strategies for managing the disease and methods for biological characterization of the pathogen.
Verticillium dahliae is an asexually reproducing organism, with little or no evidence of recombination (Usami et al., 2009; Milgroom et al., 2014). Asexual organisms are often considered as evolutionary dead ends, due to the absence of meiotic recombination resulting in increased accumulation of deleterious mutations, an effect known as Muller’s ratchet (Felsenstein, 1974). However, V. dahliae has evolved abundant population variants (clonal lineages), and thus a contradiction exists between the evolution of the population in this fungus and its asexual reproduction. Currently, the divergence of clonal lineages of V. dahliae isolates from different hosts or geographical locations are well studied, including the six main vegetative compatibility groups (VCGs) identified by the compatibility of nitrate-nonutilizing (nit) mutants (Joaquim and Rowe, 1991; Milgroom et al., 2014), race 1 and 2 that respond to host differentials within tomato and lettuce (Amen and Shoemaker, 1985; Vallad et al., 2006), two mating type idiomorphs, MAT1-1 and MAT1-2 (Usami et al., 2009), two pathotypes, defoliating and non-defoliating, identified based on the disease phenotype caused the by Verticillium strains (Schnathorst and Mathre, 1966). Based on the analyses of genetic variation, researchers have also developed the PCR-based methods to detect races, pathotypes, and mating-types, although the detection results were negative in some cases (de Jonge et al., 2012; Inderbitzin et al., 2011; Pérez-Artés et al., 2000; Short et al., 2014). Few studies have also focused on the relationship of the different population structures and specific symptoms they cause, for instance, the VCG1A displayed high correlation with the defoliating pathotype, in contrast to those in other VCGs (Bell, 1994), and the pathotypes of non-defoliating and defoliating strains from cotton correlate with races 1 and 2 in V. dahliae (Hu et al., 2015). However, the relationships among races, pathotypes, VCGs, mating-types and population differentiation are still unclear, which seriously limit research in molecular epidemiology and developing prevention technologies.
Recently, variation in the genome structure and functional genomics were studied by whole genome sequencing of several V. dahliae strains. A consortium of researchers including Drs. Klosterman and Subbarao completed the whole genome sequence of V. dahliae strain VdLs.17 (isolated from lettuce, race 2) in 2011, and demonstrated niche adaptation of the pathogen to the xylem by V. dahliae using comparative genomics of 14 fungal genomes (Klosterman et al., 2011). The research group from Wageningen University has sequenced the genome of the V. dahliae strain JR2 (isolated from tomato, race 1) and found that extensive chromosomal reshuffling (rearrangement) among the genomes of JR2 and VdLs.17 (de Jonge et al., 2013) as the basis of genetic variation in V. dahliae. Furthermore, in collaboration with Prof. Krishna Subbarao from the Department of Plant Pathology, University of California Davis, our group sequenced the genome of V. dahliae strain Vd991 (isolated from cotton, race 2) and have also confirmed the frequent chromosomal reshuffling among three strains (VdLs.17, JR2 and Vd991) (Chen et al., 2018). The strain Vd991 belongs to the defoliating pathotype and strains VdLs.17 and JR2 belong to the non-defoliating pathotype, and all three strains belong to the MAT1-2 mating-type, which suggested that the chromosomal reshuffling occurred between the same races, pathotypes, and mating-types. Therefore, these results suggested that the chromosomal reshuffling was not the genetic basis for population divergence among races, pathotypes, and mating-types.
In 2014, the Cornell University, Pennsylvania State University and the University of Córdoba performed the genetic variation analysis of 141 V. dahliae isolates from diverse geographic and host origins by genotyping-by-sequencing (GBS) method, and found that the population of V. dahliae can be classified into eight clonal lineages, which displayed high association with the VCGs (Milgroom et al., 2014). These results indicated V. dahliae populations have diverged during the long evolutionary process. The partner of this project, professor Krishna Subbarao found that the V. dahliae have developed into seven divergent genetic clusters (genetic lineages), by genetic variation analysis of 1104 strains, collected from 12 countries and 25 host plants from an analysis of the microsatellite loci (Short et al., 2015).
The above results, while providing potentially important basis for divergence of V. dahliae population structures, also raise important questions regarding the relationship between the emergence of lineages and chromosomal reshuffling, the relationship between emergence of lineages and population structure involving races, pathotypes, etc., the genetic basis of V. dahliae asexual reproduction, and the genomic basis of the extensive host adaptation and worldwide distribution.
Reference
Amen J, Shoemaker PB. (1985). Phytopathol. 75:1361–1362.
Bell AA. (1994). Pages 225-235 in: Proc. World Cotton Res. Conf.
Bhat RG, Subbarao KV. (1999). Phytopathol. 89:1218–1225.
Chen JY, Liu C, Gui YJ, Si KW, Zhang DD, Wang J, et al. (2018). New Phytol. 217:756-770.
de Jonge R, Bolton MD, Kombrink A, van den Berg GC, Yadeta KA, Thomma BP. (2013). Genome Res. 23:1271–1282.
de Jonge R, van Esse HP, Maruthachalam K, Bolton MD, Santhanam P, Saber MK, et al. (2012). Proc Natl Acad Sci U S A. 109:5110-5115.
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Fradin EF, Thomma BP. (2006). Mol Plant Pathol. 7:71–86.
Hu XP, Gurung S, Short DPG, Sandoya GV, Shang W, Hayes RJ, et al. (2015). Plant Dis. 99:1713-1720.
Inderbitzin P, Bostock RM, Davis RM, Usami T, Platt HW, Subbarao KV. (2011). PLoS One. 6:e28341.
Inderbitzin P, Subbarao KV. (2014). Phytopathol. 104:564-574.
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Klimes A, Dobinson KF, Thomma BP, Klosterman SJ. (2015). Annu Rev Phytopathol. 53:181-198.
Klosterman SJ, Atallah ZK, Vallad GE, Subbarao KV. (2009). Annu Rev Phytopathol. 47:39-62.
Klosterman SJ, Subbarao KV, Kang S, Veronese P, Gold SE, Thomma BP, et al. (2011). PLoS Pathog. 7:e1002137.
Milgroom MG, Jiménez-Gasco Mdel M, Olivares García C, Drott MT, Jiménez-Díaz RM. (2014). PLoS One 9:e106740.
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Short DP, Gurung S, Hu X, Inderbitzin P, Subbarao KV. (2014). PLoS One 9:e112145.
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Objectives
The overarching goal of this project is to uncover the evolutionary basis of V. dahliae lineages and the genomic basis of extensive host adaptations, to get a better understanding of evolution in V. dahliae and mechanisms of pandemics, and finally provide the theoretical support for the V. dahliae management and technology research. The specific objectives are as follows:
Uncover the basis of the emergence of lineages and evolution in Verticillium dahliae, and define the relationship between lineages and races, pathotypes, VCGs, etc.;
Analyze the relationship between the lineage divergence and the life cycle (sexual-asexual) evolution by the genetic variation of sex-related genes;
Illuminate the genomic basis of the extensive host adaptations by a combination of functional comparative genomics and identification of crucial functional genes.
Provide the theoretical basis and technology for studying the lineage evolution, distribution, and prevention of Verticillium wilt in China and the world.
Merits and importance of the project
Verticillium dahliae is a soil-borne ascomycete that causes Verticillium wilt in over 200 plant species, including many important crops and causes billions of dollars in agricultural losses annually. V. dahliae is known as an asexually reproducing organism but also has abundant population (clonal lineages) divergence. Few studies have investigated adequate number of strains representing extensive population divergence. In this project, we integrated strains from collaborating laboratories to select 159 strains from 10 counties (Australia, Chile, China, Denmark, Israel, Italy, Japan, Netherlands, Turkey, and USA) and 26 host plants (almond, amaranthus, aralia, artichoke, bell pepper, cabbage, cantaloupe, cotton, eggplant, guar, horseradish, lettuce, maple, mint, napa cabbage, olive, papaver, pepper, potato, purselane, spinach seed, strawberry, tomato, watermelon, smoke tree, and sunflower) that represents the genetic diversity of all seven lineages, races, pathotypes, mating-types, and obtained the whole genome sequences of these strains. Moreover, more than 3000 strains from these countries and host plants were collected for the whole genome re-resequencing. The project will confirm whether the evolution of lineages is mediated by chromosomal rearrangements or other mechanisms, uncover the relationship between lineage divergence and population structure involving races, pathotypes, and mating-types, and demonstrate the genetic variation of sex-related genes and the evolution of life cycle (sexual-asexual), illustrate the genomic basis of host adaptation and worldwide distribution of different V. dahliae lineages, develop the molecular markers for detecting and monitoring the distribution/prevalence. The project also envisages to decipher a number of questions associated with the biology of the pathogen and the disease it causes. Together, this project will promote us to understand the genetic basis and extensive prevalence of V. dahliae in worldwide, and to monitor/control of Verticillium wilt in field.
Committee Members of Verticilli-Omics Project
The Committee Members of Verticilli-Omics Project including 42 people before 30th, November, 2019, included two Project Principal Investigators of Prof. Xiaofeng Dai and Prof. Krishna Subbarao that are responsible for the Verticilli-Omics Project. There are 20 Project Investigators that are responsible for different issues from the Verticilli-Omics Project, and 22 participants. Prof. Jieyin Chen also serves as the Executor of the Verticilli-Omics Project. Main investigators are shown below:
BGI-SHENZHEN, Guangdong, Guangzhou, China
Dr. Gengyun Zhang (Project Investigator)
Mr. Jinqun Huang (Project Investigator)
Mr. Lin Yang (Participant)
Mr. Bangzhuo Tong (Participant)
Mr. Peiwen Zhang (Participant)
College of Forestry, Beijing Forestry University, Beijing, China
Prof. Yonglin Wang (Project Investigator)
College of Forestry, Nanjing Forestry University, Nanjing, Jiangsu, China
Prof. Fengmao Chen (Project Investigator)
Dr. Huan Li (Participant)
Ms. Qi Geng (Participant)
College of Horticulture and Plant Protection, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
Prof. Jun Zhao (Project Investigator)
Prof. Hongyou Zhou (Project Investigator)
Dr. Yuanyuan Zhang (Participant)
Ms. Lin Liu (Participant)
College of Life Sciences, Qufu Normal University, Qufu, Shandong, China
Dr. Li Tian (Project Investigator)
College of Plant Protection, Northwest A&F University, Yanngling, Shannxi, China
Dr. Xiaoping Hu (Project Investigator)
Dr. Wenjing Shang (Participant)
Dr. Jun Qin (Participant)
Dr. Haiyuan Li (Participant)
Department of Microbiology and Plant Pathology, University of California, Riverside, California, USA
Dr. Alexander Putman (Project Investigator)
Department Plant Pathology, University of California, Davis, California, USA
Prof. Krishna V. Subbarao (Project Principal Investigator)
Dr. Krishna Puri (Participant)
Mrs. Rosa Marchebout (Participant)
Department of Soil, Plant, and Food Sciences, University of Bari 'Aldo Moro', Bari, Italy
Dr. Franco Nigro (Project Investigator)
Graduate School of Horticulture, Chiba University, Matsudo City, Chiba Prefecture, Japan
Dr. Toshiyuki Usami (Project Investigator)
Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
Prof. Xiaofeng Dai (Project Principal Investigator)
Prof. Jieyin Chen (Project Investigator and Executor)
Prof. Kejian Lin (Project Investigator)
Dr. Dandan Zhang (Participant)
Dr. Zhiqiang Kong (Participant)
Dr. Yaduo Zhang (Participant)
Dr. Dan Wang (Participant)
Dr. Ran Li (Participant)
Dr. Jian Song (Participant)
Ms. Shijun Hao (Participant)
Ms. Xiaobing Ji (Participant)
Institute of Plant Protection, Xinjiang Academy of Agriculture and Reclamation Science, Shihezi, Xinjiang, China
Dr. Zheng Liu (Project Investigator)
Institute of Plant Protection, Xinjiang Academy of Agricultural Science, Urumchi, Xinjiang, China
Dr. Haiyang Liu (Project Investigator)
Liaoning Research Institute of Cash Crops, Liaoning Academy of Agricultural Sciences, Shenyang, Liaoning, China
Dr. Zisheng Wang (Project Investigator)
Mr. He Zhu (Participant)
School of Life Sciences,Chongqing Normal University, Chongqing, China
Prof. Xingyong Yang (Project Investigator)
United States Department of Agriculture, Agricultural Research Service, Salinas, California, USA
Dr. Steve Klosterman (Project Investigator)
Note: Sorted alphabetically by organizations
Verticilli-Omics Data Utilization Policy
The Data Usage Policy for data generated under proposals accepted before 2025 is:
By accessing these data, you agree not to publish any articles containing analyses of genes or genomic data prior to publication by the principal investigators of its comprehensive analysis without the consent of project's principal investigators. These restrictions will be lifted once the publication of the whole genome or comparable description occurs. Scientists must contact the principal investigators about their intentions to include any data from this project in a publication prior to publication of principal investigator’s primary report in order to ensure that their publication does not compete directly with planned publications (e.g. reserved analyses) of the Verticilli-Omics Project.
The principal investigators are the point of contact and arbiter regarding publication plans. Reserved analyses include but are not limited to the identification and analysis of complete (whole genome) sets of genomic features, such as genes and gene expression levels, gene families, gene clusters, regulatory elements, repeat structures, GC content, etc., and whole-genome comparisons of regions of evolutionary conservation or change. Manually annotated genes within the Genome Portal are also reserved. Studies of any type on the reserved data sets that are not in direct competition with those planned by the Verticilli-Omics Project may also be undertaken after an agreement with principal investigators. Interested parties must contact the principal investigators to discuss such possibilities.
If these data are used for publication, the following acknowledgment should be included: "These sequence data were produced by the Verticilli-Omics Project in collaboration with the user community." We request that you notify us upon publication so that this information can be included in the final annotation.
The Data Usage Policy for data generated under proposals accepted after 2025 is:
By accessing Verticilli-Omics Project data, you agree not to publish any articles containing analyses of genes or genomic data prior to publication by the principal investigators of its comprehensive analysis without the consent of the project's principal investigator(s). These restrictions will be lifted upon publication(s) of the dataset or five years after the public release of this data, whichever is first. Scientists are expected to contact the principal investigators about their intentions to include any data from this project in a publication prior to publication of the primary report in order to ensure that their publication does not compete directly with planned publications (e.g. reserved analyses) of the principal investigators.
The principal investigators are the point of contact regarding publication plans. Reserved analyses include but are not limited to the identification and analysis of complete (whole genome) sets of genomic features such as genes and gene expression levels, gene families, gene clusters, regulatory elements, repeat structures, etc., and whole-genome comparisons of regions of evolutionary conservation or change. Studies of any type on the reserved data sets that are not in direct competition with those planned by the principal investigators may also be undertaken after agreement with the principal investigators. Interested parties must contact the principal investigators to discuss such possibilities.
If these data are used for publication, the following acknowledgment should be included: "These sequence data were produced by the Verticilli-Omics Project in collaboration with the user community."
