1
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Ferree PM, Blagojević J, Houben A, Martins C, Trifonov VA, Vujošević M. What is a B chromosome? Early definitions revisited. G3 (BETHESDA, MD.) 2024; 14:jkae068. [PMID: 38626314 DOI: 10.1093/g3journal/jkae068] [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: 01/01/2024] [Accepted: 03/19/2024] [Indexed: 04/18/2024]
Abstract
Since the discovery of B chromosomes, multiple different definitions of these selfish genetic elements have been put forth. We reconsidered early definitions in light of recently published studies. While there are many characteristics that vary among different B chromosomes, such as their evolutionary origins, size, segregation behaviors, gene content, and function, there is one defining trait of all B chromosomes: they are nonessential for the organism. The points raised here may be useful for framing future B chromosome studies and help guide the categorization of new chromosomal elements that are uncovered in genomic studies.
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Affiliation(s)
- Patrick M Ferree
- Department of Natural Sciences, Pitzer College, Scripps College, Claremont, CA 91711, USA
| | - Jelena Blagojević
- Institute for Biological Research "Siniša Stanković" - National Institute for the Republic of Serbia, University of Belgrade, Belgrade 11060, Serbia
| | - Andreas Houben
- Department of Cytogenetics and Genome Analysis, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland 06466, Germany
| | - Cesar Martins
- Institute of Bioscience at Botucatu, São Paulo State University (UNESP), Botucatu, SP 18618-689, Brazil
| | - Vladimir A Trifonov
- Research Institute for Limnology, University of Innsbruck, Mondsee A-5310, Austria
| | - Mladen Vujošević
- Institute for Biological Research "Siniša Stanković" - National Institute for the Republic of Serbia, University of Belgrade, Belgrade 11060, Serbia
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2
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Liu S, Lin G, Ramachandran SR, Daza LC, Cruppe G, Tembo B, Singh PK, Cook D, Pedley KF, Valent B. Rapid mini-chromosome divergence among fungal isolates causing wheat blast outbreaks in Bangladesh and Zambia. THE NEW PHYTOLOGIST 2024; 241:1266-1276. [PMID: 37984076 DOI: 10.1111/nph.19402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 10/27/2023] [Indexed: 11/22/2023]
Abstract
The fungal pathogen, Magnaporthe oryzae Triticum pathotype, causing wheat blast disease was first identified in South America and recently spread across continents to South Asia and Africa. Here, we studied the genetic relationship among isolates found on the three continents. Magnaporthe oryzae strains closely related to a South American field isolate B71 were found to have caused the wheat blast outbreaks in South Asia and Africa. Genomic variation among isolates from the three continents was examined using an improved B71 reference genome and whole-genome sequences. We found strong evidence to support that the outbreaks in Bangladesh and Zambia were caused by the introductions of genetically separated isolates, although they were all close to B71 and, therefore, collectively referred to as the B71 branch. In addition, B71 branch strains carried at least one supernumerary mini-chromosome. Genome assembly of a Zambian strain revealed that its mini-chromosome was similar to the B71 mini-chromosome but with a high level of structural variation. Our findings show that while core genomes of the multiple introductions are highly similar, the mini-chromosomes have undergone marked diversification. The maintenance of the mini-chromosome and rapid genomic changes suggest the mini-chromosomes may serve important virulence or niche adaptation roles under diverse environmental conditions.
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Affiliation(s)
- Sanzhen Liu
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506-5502, USA
| | - Guifang Lin
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506-5502, USA
| | - Sowmya R Ramachandran
- United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Foreign Disease-Weed Science Research Unit, Ft. Detrick, MD, 21702-9253, USA
| | - Lidia Calderon Daza
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506-5502, USA
| | - Giovana Cruppe
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506-5502, USA
| | - Batiseba Tembo
- Zambia Agricultural Research Institute, Mt. Makulu Central Research Station, Lusaka, 10101, Zambia
| | - Pawan Kumar Singh
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, 56237, Mexico
| | - David Cook
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506-5502, USA
| | - Kerry F Pedley
- United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Foreign Disease-Weed Science Research Unit, Ft. Detrick, MD, 21702-9253, USA
| | - Barbara Valent
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506-5502, USA
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3
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Wei H, Zhong Z, Li Z, Zhang Y, Stukenbrock EH, Tang B, Yang N, Baroncelli R, Peng L, Liu Z, He X, Yang Y, Yuan Z. Loss of the accessory chromosome converts a pathogenic tree-root fungus into a mutualistic endophyte. PLANT COMMUNICATIONS 2024; 5:100672. [PMID: 37563834 PMCID: PMC10811371 DOI: 10.1016/j.xplc.2023.100672] [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: 02/17/2023] [Revised: 06/01/2023] [Accepted: 08/04/2023] [Indexed: 08/12/2023]
Abstract
Some fungal accessory chromosomes (ACs) may contribute to virulence in plants. However, the mechanisms by which ACs determine specific traits associated with lifestyle transitions along a symbiotic continuum are not clear. Here we delineated the genetic divergence in two sympatric but considerably variable isolates (16B and 16W) of the poplar-associated fungus Stagonosporopsis rhizophilae. We identified a ∼0.6-Mb horizontally acquired AC in 16W that resulted in a mildly parasitic lifestyle in plants. Complete deletion of the AC (Δ16W) significantly altered the fungal phenotype. Specifically, Δ16W was morphologically more similar to 16B, showed enhanced melanization, and established beneficial interactions with poplar plants, thereby acting as a dark septate endophyte. RNA sequencing (RNA-seq) analysis showed that AC loss induced the upregulation of genes related to root colonization and biosynthesis of indole acetic acid and melanin. We observed that the AC maintained a more open status of chromatin across the genome, indicating an impressive remodeling of cis-regulatory elements upon AC loss, which potentially enhanced symbiotic effectiveness. We demonstrated that the symbiotic capacities were non-host-specific through comparable experiments on Triticum- and Arabidopsis-fungus associations. Furthermore, the three isolates generated symbiotic interactions with a nonvascular liverwort. In summary, our study suggests that the AC is a suppressor of symbiosis and provides insights into the underlying mechanisms of mutualism with vascular plants in the absence of traits encoded by the AC. We speculate that AC-situated effectors and other potential secreted molecules may have evolved to specifically target vascular plants and promote mild virulence.
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Affiliation(s)
- Huanshen Wei
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100091, China; Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China
| | - Zhenhui Zhong
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zhongfeng Li
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100091, China; Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China
| | - Yuwei Zhang
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100091, China; Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China
| | - Eva H Stukenbrock
- Environmental Genomics, Christian-Albrechts University, 24118 Kiel, Germany; Max Planck Fellow Group Environmental Genomics, Max Planck Institute for Evolutionary Biology, 24306 Plön, Germany.
| | - Boping Tang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, School of Wetlands, Yancheng Teachers University, Yancheng 224002, China
| | - Ningning Yang
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100091, China; Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China
| | - Riccardo Baroncelli
- Department of Agricultural and Food Sciences (DISTAL), University of Bologna, 40127 Bologna, Italy
| | - Long Peng
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100091, China; Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China
| | - Zhuo Liu
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100091, China; Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China
| | - Xinghua He
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100091, China; Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China
| | - Yuzhan Yang
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100091, China; Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China
| | - Zhilin Yuan
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100091, China; Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China.
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4
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Sokolova GD, Budynkov NI, Tselipanova EE, Glinushkin AP. Species Diversity in the Fusarium solani (Neocosmospora) Complex and Their Pathogenicity for Plants and Humans. DOKLADY BIOLOGICAL SCIENCES : PROCEEDINGS OF THE ACADEMY OF SCIENCES OF THE USSR, BIOLOGICAL SCIENCES SECTIONS 2022; 507:416-427. [PMID: 36781537 DOI: 10.1134/s0012496622060217] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 08/15/2022] [Accepted: 08/22/2022] [Indexed: 02/15/2023]
Abstract
The Fusarium solani species complex is a large group of soil saprotrophs with a broad adaptive potential, which allows the fungi to exist under various conditions and to parasitize on different hosts. The review analyzes the modern data concerning the genetic peculiarities of species from this complex by the example of F. solani f. sp. pisi and generalizes the data on the most widespread species pathogenic for both plants and humans. The enhanced resistance of the F. solani species complex to the most of modern antifungal agents and the need for novel therapeutic agents against fusariosis has been considered.
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Affiliation(s)
- G D Sokolova
- All-Russian Research Institute of Phytopathology, Bolshiye Vyazemy, Russia.
| | - N I Budynkov
- All-Russian Research Institute of Phytopathology, Bolshiye Vyazemy, Russia
| | - E E Tselipanova
- Moscow Regional Vladimirsky Research Clinical Institute, Moscow, Russia.
| | - A P Glinushkin
- All-Russian Research Institute of Phytopathology, Bolshiye Vyazemy, Russia
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5
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Huang J, Cook DE. The contribution of DNA repair pathways to genome editing and evolution in filamentous pathogens. FEMS Microbiol Rev 2022; 46:fuac035. [PMID: 35810003 PMCID: PMC9779921 DOI: 10.1093/femsre/fuac035] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 06/29/2022] [Accepted: 07/06/2022] [Indexed: 01/09/2023] Open
Abstract
DNA double-strand breaks require repair or risk corrupting the language of life. To ensure genome integrity and viability, multiple DNA double-strand break repair pathways function in eukaryotes. Two such repair pathways, canonical non-homologous end joining and homologous recombination, have been extensively studied, while other pathways such as microhomology-mediated end joint and single-strand annealing, once thought to serve as back-ups, now appear to play a fundamental role in DNA repair. Here, we review the molecular details and hierarchy of these four DNA repair pathways, and where possible, a comparison for what is known between animal and fungal models. We address the factors contributing to break repair pathway choice, and aim to explore our understanding and knowledge gaps regarding mechanisms and regulation in filamentous pathogens. We additionally discuss how DNA double-strand break repair pathways influence genome engineering results, including unexpected mutation outcomes. Finally, we review the concept of biased genome evolution in filamentous pathogens, and provide a model, termed Biased Variation, that links DNA double-strand break repair pathways with properties of genome evolution. Despite our extensive knowledge for this universal process, there remain many unanswered questions, for which the answers may improve genome engineering and our understanding of genome evolution.
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Affiliation(s)
- Jun Huang
- Department of Plant Pathology, Kansas State University, 1712 Claflin Road, Throckmorton Hall, Manhattan, KS 66506, United States
| | - David E Cook
- Department of Plant Pathology, Kansas State University, 1712 Claflin Road, Throckmorton Hall, Manhattan, KS 66506, United States
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6
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Komluski J, Stukenbrock EH, Habig M. Non-Mendelian transmission of accessory chromosomes in fungi. Chromosome Res 2022; 30:241-253. [PMID: 35881207 PMCID: PMC9508043 DOI: 10.1007/s10577-022-09691-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 03/15/2022] [Accepted: 04/11/2022] [Indexed: 11/27/2022]
Abstract
Non-Mendelian transmission has been reported for various genetic elements, ranging from small transposons to entire chromosomes. One prime example of such a transmission pattern are B chromosomes in plants and animals. Accessory chromosomes in fungi are similar to B chromosomes in showing presence/absence polymorphism and being non-essential. How these chromosomes are transmitted during meiosis is however poorly understood—despite their often high impact on the fitness of the host. For several fungal organisms, a non-Mendelian transmission or a mechanistically unique meiotic drive of accessory chromosomes have been reported. In this review, we provide an overview of the possible mechanisms that can cause the non-Mendelian transmission or meiotic drives of fungal accessory chromosomes. We compare processes responsible for the non-Mendelian transmission of accessory chromosomes for different fungal eukaryotes and discuss the structural traits of fungal accessory chromosomes affecting their meiotic transmission. We conclude that research on fungal accessory chromosomes, due to their small size, ease of sequencing, and epigenetic profiling, can complement the study of B chromosomes in deciphering factors that influence and regulate the non-Mendelian transmission of entire chromosomes.
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Affiliation(s)
- Jovan Komluski
- Environmental Genomics, Christian-Albrechts University of Kiel, Kiel, Germany
- Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Eva H Stukenbrock
- Environmental Genomics, Christian-Albrechts University of Kiel, Kiel, Germany.
- Max Planck Institute for Evolutionary Biology, Plön, Germany.
| | - Michael Habig
- Environmental Genomics, Christian-Albrechts University of Kiel, Kiel, Germany.
- Max Planck Institute for Evolutionary Biology, Plön, Germany.
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7
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Ayukawa Y, Asai S, Gan P, Tsushima A, Ichihashi Y, Shibata A, Komatsu K, Houterman PM, Rep M, Shirasu K, Arie T. A pair of effectors encoded on a conditionally dispensable chromosome of Fusarium oxysporum suppress host-specific immunity. Commun Biol 2021; 4:707. [PMID: 34108627 PMCID: PMC8190069 DOI: 10.1038/s42003-021-02245-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 05/18/2021] [Indexed: 11/29/2022] Open
Abstract
Many plant pathogenic fungi contain conditionally dispensable (CD) chromosomes that are associated with virulence, but not growth in vitro. Virulence-associated CD chromosomes carry genes encoding effectors and/or host-specific toxin biosynthesis enzymes that may contribute to determining host specificity. Fusarium oxysporum causes devastating diseases of more than 100 plant species. Among a large number of host-specific forms, F. oxysporum f. sp. conglutinans (Focn) can infect Brassicaceae plants including Arabidopsis (Arabidopsis thaliana) and cabbage. Here we show that Focn has multiple CD chromosomes. We identified specific CD chromosomes that are required for virulence on Arabidopsis, cabbage, or both, and describe a pair of effectors encoded on one of the CD chromosomes that is required for suppression of Arabidopsis-specific phytoalexin-based immunity. The effector pair is highly conserved in F. oxysporum isolates capable of infecting Arabidopsis, but not of other plants. This study provides insight into how host specificity of F. oxysporum may be determined by a pair of effector genes on a transmissible CD chromosome. Yu Ayukawa, Shuta Asai, et al. report the genome sequence of a Fusarium oxysporum isolate and demonstrate that it contains different conditionally dispensable chromosomes which are important to confer virulence on specific hosts, like Arabidopsis thaliana or cabbage. Altogether, these results provide further insight into the mechanisms underlying F. oxysporum pathogenicity.
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Affiliation(s)
- Yu Ayukawa
- Center for Sustainable Resource Science, RIKEN, Yokohama, Kanagawa, Japan.,Laboratory of Plant Pathology, Graduate School of Agriculture, Tokyo University of Agriculture and Technology (TUAT), Fuchu, Tokyo, Japan
| | - Shuta Asai
- Center for Sustainable Resource Science, RIKEN, Yokohama, Kanagawa, Japan. .,PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan.
| | - Pamela Gan
- Center for Sustainable Resource Science, RIKEN, Yokohama, Kanagawa, Japan
| | - Ayako Tsushima
- Center for Sustainable Resource Science, RIKEN, Yokohama, Kanagawa, Japan.,John Innes Centre, Norwich, UK
| | - Yasunori Ichihashi
- Center for Sustainable Resource Science, RIKEN, Yokohama, Kanagawa, Japan.,RIKEN BioResource Research Center, Tsukuba, Ibaraki, Japan
| | - Arisa Shibata
- Center for Sustainable Resource Science, RIKEN, Yokohama, Kanagawa, Japan
| | - Ken Komatsu
- Laboratory of Plant Pathology, Graduate School of Agriculture, Tokyo University of Agriculture and Technology (TUAT), Fuchu, Tokyo, Japan
| | - Petra M Houterman
- Molecular Plant Pathology, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Martijn Rep
- Molecular Plant Pathology, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Ken Shirasu
- Center for Sustainable Resource Science, RIKEN, Yokohama, Kanagawa, Japan
| | - Tsutomu Arie
- Laboratory of Plant Pathology, Graduate School of Agriculture, Tokyo University of Agriculture and Technology (TUAT), Fuchu, Tokyo, Japan.
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8
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Abstract
Plant pathogens can adapt to quantitative resistance, eroding its effectiveness. The aim of this work was to reveal the genomic basis of adaptation to such a resistance in populations of the fungus Pseudocercospora fijiensis, a major devastating pathogen of banana, by studying convergent adaptation on different cultivars. Samples from P. fijiensis populations showing a local adaptation pattern on new banana hybrids with quantitative resistance were compared, based on a genome scan approach, with samples from traditional and more susceptible cultivars in Cuba and the Dominican Republic. Whole-genome sequencing of pools of P. fijiensis isolates (pool-seq) sampled from three locations per country was conducted according to a paired population design. The findings of different combined analyses highly supported the existence of convergent adaptation on the study cultivars between locations within but not between countries. Five to six genomic regions involved in this adaptation were detected in each country. An annotation analysis and available biological data supported the hypothesis that some genes within the detected genomic regions may play a role in quantitative pathogenicity, including gene regulation. The results suggested that the genetic basis of fungal adaptation to quantitative plant resistance is at least oligogenic, while highlighting the existence of specific host-pathogen interactions for this kind of resistance.IMPORTANCE Understanding the genetic basis of pathogen adaptation to quantitative resistance in plants has a key role to play in establishing durable strategies for resistance deployment. In this context, a population genomic approach was developed for a major plant pathogen (the fungus Pseudocercospora fijiensis causing black leaf streak disease of banana) whereby samples from new resistant banana hybrids were compared with samples from more susceptible conventional cultivars in two countries. A total of 11 genomic regions for which there was strong evidence of selection by quantitative resistance were detected. An annotation analysis and available biological data supported the hypothesis that some of the genes within these regions may play a role in quantitative pathogenicity. These results suggested a polygenic basis of quantitative pathogenicity in this fungal pathogen and complex molecular plant-pathogen interactions in quantitative disease development involving several genes on both sides.
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9
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Ridenour JB, Möller M, Freitag M. Polycomb Repression without Bristles: Facultative Heterochromatin and Genome Stability in Fungi. Genes (Basel) 2020; 11:E638. [PMID: 32527036 PMCID: PMC7348808 DOI: 10.3390/genes11060638] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 05/27/2020] [Accepted: 06/04/2020] [Indexed: 02/06/2023] Open
Abstract
Genome integrity is essential to maintain cellular function and viability. Consequently, genome instability is frequently associated with dysfunction in cells and associated with plant, animal, and human diseases. One consequence of relaxed genome maintenance that may be less appreciated is an increased potential for rapid adaptation to changing environments in all organisms. Here, we discuss evidence for the control and function of facultative heterochromatin, which is delineated by methylation of histone H3 lysine 27 (H3K27me) in many fungi. Aside from its relatively well understood role in transcriptional repression, accumulating evidence suggests that H3K27 methylation has an important role in controlling the balance between maintenance and generation of novelty in fungal genomes. We present a working model for a minimal repressive network mediated by H3K27 methylation in fungi and outline challenges for future research.
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Affiliation(s)
| | | | - Michael Freitag
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis OR 97331, USA; (J.B.R.); (M.M.)
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10
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Peng Z, Oliveira-Garcia E, Lin G, Hu Y, Dalby M, Migeon P, Tang H, Farman M, Cook D, White FF, Valent B, Liu S. Effector gene reshuffling involves dispensable mini-chromosomes in the wheat blast fungus. PLoS Genet 2019; 15:e1008272. [PMID: 31513573 PMCID: PMC6741851 DOI: 10.1371/journal.pgen.1008272] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 06/24/2019] [Indexed: 11/28/2022] Open
Abstract
Newly emerged wheat blast disease is a serious threat to global wheat production. Wheat blast is caused by a distinct, exceptionally diverse lineage of the fungus causing rice blast disease. Through sequencing a recent field isolate, we report a reference genome that includes seven core chromosomes and mini-chromosome sequences that harbor effector genes normally found on ends of core chromosomes in other strains. No mini-chromosomes were observed in an early field strain, and at least two from another isolate each contain different effector genes and core chromosome end sequences. The mini-chromosome is enriched in transposons occurring most frequently at core chromosome ends. Additionally, transposons in mini-chromosomes lack the characteristic signature for inactivation by repeat-induced point (RIP) mutation genome defenses. Our results, collectively, indicate that dispensable mini-chromosomes and core chromosomes undergo divergent evolutionary trajectories, and mini-chromosomes and core chromosome ends are coupled as a mobile, fast-evolving effector compartment in the wheat pathogen genome.
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Affiliation(s)
- Zhao Peng
- Department of Plant Pathology, Kansas State University, Manhattan, KS, United States of America
- Department of Plant Pathology, University of Florida, Gainesville, FL, United States of America
| | - Ely Oliveira-Garcia
- Department of Plant Pathology, Kansas State University, Manhattan, KS, United States of America
| | - Guifang Lin
- Department of Plant Pathology, Kansas State University, Manhattan, KS, United States of America
| | - Ying Hu
- Department of Plant Pathology, Kansas State University, Manhattan, KS, United States of America
| | - Melinda Dalby
- Department of Plant Pathology, Kansas State University, Manhattan, KS, United States of America
| | - Pierre Migeon
- Department of Plant Pathology, Kansas State University, Manhattan, KS, United States of America
| | - Haibao Tang
- Center for Genomics and Biotechnology and Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fujian, China
| | - Mark Farman
- Department of Plant Pathology, University of Kentucky, Lexington, KY, United States of America
| | - David Cook
- Department of Plant Pathology, Kansas State University, Manhattan, KS, United States of America
| | - Frank F. White
- Department of Plant Pathology, University of Florida, Gainesville, FL, United States of America
| | - Barbara Valent
- Department of Plant Pathology, Kansas State University, Manhattan, KS, United States of America
| | - Sanzhen Liu
- Department of Plant Pathology, Kansas State University, Manhattan, KS, United States of America
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11
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Peng Z, Oliveira-Garcia E, Lin G, Hu Y, Dalby M, Migeon P, Tang H, Farman M, Cook D, White FF, Valent B, Liu S. Effector gene reshuffling involves dispensable mini-chromosomes in the wheat blast fungus. PLoS Genet 2019; 15:e1008272. [PMID: 31513573 DOI: 10.1101/359455] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 06/24/2019] [Indexed: 05/26/2023] Open
Abstract
Newly emerged wheat blast disease is a serious threat to global wheat production. Wheat blast is caused by a distinct, exceptionally diverse lineage of the fungus causing rice blast disease. Through sequencing a recent field isolate, we report a reference genome that includes seven core chromosomes and mini-chromosome sequences that harbor effector genes normally found on ends of core chromosomes in other strains. No mini-chromosomes were observed in an early field strain, and at least two from another isolate each contain different effector genes and core chromosome end sequences. The mini-chromosome is enriched in transposons occurring most frequently at core chromosome ends. Additionally, transposons in mini-chromosomes lack the characteristic signature for inactivation by repeat-induced point (RIP) mutation genome defenses. Our results, collectively, indicate that dispensable mini-chromosomes and core chromosomes undergo divergent evolutionary trajectories, and mini-chromosomes and core chromosome ends are coupled as a mobile, fast-evolving effector compartment in the wheat pathogen genome.
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Affiliation(s)
- Zhao Peng
- Department of Plant Pathology, Kansas State University, Manhattan, KS, United States of America
- Department of Plant Pathology, University of Florida, Gainesville, FL, United States of America
| | - Ely Oliveira-Garcia
- Department of Plant Pathology, Kansas State University, Manhattan, KS, United States of America
| | - Guifang Lin
- Department of Plant Pathology, Kansas State University, Manhattan, KS, United States of America
| | - Ying Hu
- Department of Plant Pathology, Kansas State University, Manhattan, KS, United States of America
| | - Melinda Dalby
- Department of Plant Pathology, Kansas State University, Manhattan, KS, United States of America
| | - Pierre Migeon
- Department of Plant Pathology, Kansas State University, Manhattan, KS, United States of America
| | - Haibao Tang
- Center for Genomics and Biotechnology and Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fujian, China
| | - Mark Farman
- Department of Plant Pathology, University of Kentucky, Lexington, KY, United States of America
| | - David Cook
- Department of Plant Pathology, Kansas State University, Manhattan, KS, United States of America
| | - Frank F White
- Department of Plant Pathology, University of Florida, Gainesville, FL, United States of America
| | - Barbara Valent
- Department of Plant Pathology, Kansas State University, Manhattan, KS, United States of America
| | - Sanzhen Liu
- Department of Plant Pathology, Kansas State University, Manhattan, KS, United States of America
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12
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Ahmad SF, Martins C. The Modern View of B Chromosomes Under the Impact of High Scale Omics Analyses. Cells 2019; 8:E156. [PMID: 30781835 PMCID: PMC6406668 DOI: 10.3390/cells8020156] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 02/10/2019] [Accepted: 02/12/2019] [Indexed: 12/11/2022] Open
Abstract
Supernumerary B chromosomes (Bs) are extra karyotype units in addition to A chromosomes, and are found in some fungi and thousands of animals and plant species. Bs are uniquely characterized due to their non-Mendelian inheritance, and represent one of the best examples of genomic conflict. Over the last decades, their genetic composition, function and evolution have remained an unresolved query, although a few successful attempts have been made to address these phenomena. A classical concept based on cytogenetics and genetics is that Bs are selfish and abundant with DNA repeats and transposons, and in most cases, they do not carry any function. However, recently, the modern quantum development of high scale multi-omics techniques has shifted B research towards a new-born field that we call "B-omics". We review the recent literature and add novel perspectives to the B research, discussing the role of new technologies to understand the mechanistic perspectives of the molecular evolution and function of Bs. The modern view states that B chromosomes are enriched with genes for many significant biological functions, including but not limited to the interesting set of genes related to cell cycle and chromosome structure. Furthermore, the presence of B chromosomes could favor genomic rearrangements and influence the nuclear environment affecting the function of other chromatin regions. We hypothesize that B chromosomes might play a key function in driving their transmission and maintenance inside the cell, as well as offer an extra genomic compartment for evolution.
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Affiliation(s)
- Syed Farhan Ahmad
- Department of Morphology, Institute of Biosciences at Botucatu, Sao Paulo State University (UNESP), CEP 18618689, Botucatu, SP, Brazil.
| | - Cesar Martins
- Department of Morphology, Institute of Biosciences at Botucatu, Sao Paulo State University (UNESP), CEP 18618689, Botucatu, SP, Brazil.
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