1
|
Matson MEH, Liang Q, Lonardi S, Judelson HS. Karyotype variation, spontaneous genome rearrangements affecting chemical insensitivity, and expression level polymorphisms in the plant pathogen Phytophthora infestans revealed using its first chromosome-scale assembly. PLoS Pathog 2022; 18:e1010869. [PMID: 36215336 PMCID: PMC9584435 DOI: 10.1371/journal.ppat.1010869] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 10/20/2022] [Accepted: 09/09/2022] [Indexed: 11/18/2022] Open
Abstract
Natural isolates of the potato and tomato pathogen Phytophthora infestans exhibit substantial variation in virulence, chemical sensitivity, ploidy, and other traits. A chromosome-scale assembly was developed to expand genomic resources for this oomyceteous microbe, and used to explore the basis of variation. Using PacBio and Illumina data, a long-range linking library, and an optical map, an assembly was created and coalesced into 15 pseudochromosomes spanning 219 Mb using SNP-based genetic linkage data. De novo gene prediction combined with transcript evidence identified 19,981 protein-coding genes, plus about eight thousand tRNA genes. The chromosomes were comprised of a mosaic of gene-rich and gene-sparse regions plus very long centromeres. Genes exhibited a biased distribution across chromosomes, especially members of families encoding RXLR and CRN effectors which clustered on certain chromosomes. Strikingly, half of F1 progeny of diploid parents were polyploid or aneuploid. Substantial expression level polymorphisms between strains were identified, much of which could be attributed to differences in chromosome dosage, transposable element insertions, and adjacency to repetitive DNA. QTL analysis identified a locus on the right arm of chromosome 3 governing sensitivity to the crop protection chemical metalaxyl. Strains heterozygous for resistance often experienced megabase-sized deletions of that part of the chromosome when cultured on metalaxyl, increasing resistance due to loss of the sensitive allele. This study sheds light on diverse phenomena affecting variation in P. infestans and relatives, helps explain the prevalence of polyploidy in natural populations, and provides a new foundation for biologic and genetic investigations.
Collapse
Affiliation(s)
- Michael E. H. Matson
- Department of Microbiology and Plant Pathology, University of California, Riverside, California, United States of America
| | - Qihua Liang
- Department of Computer Science and Engineering, University of California, Riverside, California, United States of America
| | - Stefano Lonardi
- Department of Computer Science and Engineering, University of California, Riverside, California, United States of America
| | - Howard S. Judelson
- Department of Microbiology and Plant Pathology, University of California, Riverside, California, United States of America
- * E-mail:
| |
Collapse
|
2
|
Engelbrecht J, Duong TA, Prabhu SA, Seedat M, van den Berg N. Genome of the destructive oomycete Phytophthora cinnamomi provides insights into its pathogenicity and adaptive potential. BMC Genomics 2021; 22:302. [PMID: 33902447 PMCID: PMC8074420 DOI: 10.1186/s12864-021-07552-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 03/24/2021] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Phytophthora cinnamomi is an oomycete pathogen of global relevance. It is considered as one of the most invasive species, which has caused irreversible damage to natural ecosystems and horticultural crops. There is currently a lack of a high-quality reference genome for this species despite several attempts that have been made towards sequencing its genome. The lack of a good quality genome sequence has been a setback for various genetic and genomic research to be done on this species. As a consequence, little is known regarding its genome characteristics and how these contribute to its pathogenicity and invasiveness. RESULTS In this work we generated a high-quality genome sequence and annotation for P. cinnamomi using a combination of Oxford Nanopore and Illumina sequencing technologies. The annotation was done using RNA-Seq data as supporting gene evidence. The final assembly consisted of 133 scaffolds, with an estimated genome size of 109.7 Mb, N50 of 1.18 Mb, and BUSCO completeness score of 97.5%. Genome partitioning analysis revealed that P. cinnamomi has a two-speed genome characteristic, similar to that of other oomycetes and fungal plant pathogens. In planta gene expression analysis revealed up-regulation of pathogenicity-related genes, suggesting their important roles during infection and host degradation. CONCLUSION This study has provided a high-quality reference genome and annotation for P. cinnamomi. This is among the best assembled genomes for any Phytophthora species assembled to date and thus resulted in improved identification and characterization of pathogenicity-related genes, some of which were undetected in previous versions of genome assemblies. Phytophthora cinnamomi harbours a large number of effector genes which are located in the gene-poor regions of the genome. This unique genomic partitioning provides P. cinnamomi with a high level of adaptability and could contribute to its success as a highly invasive species. Finally, the genome sequence, its annotation and the pathogenicity effectors identified in this study will serve as an important resource that will enable future studies to better understand and mitigate the impact of this important pathogen.
Collapse
Affiliation(s)
- Juanita Engelbrecht
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa.
| | - Tuan A Duong
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa
| | - S Ashok Prabhu
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa
| | - Mohamed Seedat
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa
| | - Noëlani van den Berg
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa
| |
Collapse
|
3
|
Elliott M, Yuzon J, C MM, Tripathy S, Bui M, Chastagner GA, Coats K, Rizzo DM, Garbelotto M, Kasuga T. Characterization of phenotypic variation and genome aberrations observed among Phytophthora ramorum isolates from diverse hosts. BMC Genomics 2018; 19:320. [PMID: 29720102 PMCID: PMC5932867 DOI: 10.1186/s12864-018-4709-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 04/22/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Accumulating evidence suggests that genome plasticity allows filamentous plant pathogens to adapt to changing environments. Recently, the generalist plant pathogen Phytophthora ramorum has been documented to undergo irreversible phenotypic alterations accompanied by chromosomal aberrations when infecting trunks of mature oak trees (genus Quercus). In contrast, genomes and phenotypes of the pathogen derived from the foliage of California bay (Umbellularia californica) are usually stable. We define this phenomenon as host-induced phenotypic diversification (HIPD). P. ramorum also causes a severe foliar blight in some ornamental plants such as Rhododendron spp. and Viburnum spp., and isolates from these hosts occasionally show phenotypes resembling those from oak trunks that carry chromosomal aberrations. The aim of this study was to investigate variations in phenotypes and genomes of P. ramorum isolates from non-oak hosts and substrates to determine whether HIPD changes may be equivalent to those among isolates from oaks. RESULTS We analyzed genomes of diverse non-oak isolates including those taken from foliage of Rhododendron and other ornamental plants, as well as from natural host species, soil, and water. Isolates recovered from artificially inoculated oak logs were also examined. We identified diverse chromosomal aberrations including copy neutral loss of heterozygosity (cnLOH) and aneuploidy in isolates from non-oak hosts. Most identified aberrations in non-oak hosts were also common among oak isolates; however, trisomy, a frequent type of chromosomal aberration in oak isolates was not observed in isolates from Rhododendron. CONCLUSION This work cross-examined phenotypic variation and chromosomal aberrations in P. ramorum isolates from oak and non-oak hosts and substrates. The results suggest that HIPD comparable to that occurring in oak hosts occurs in non-oak environments such as in Rhododendron leaves. Rhododendron leaves are more easily available than mature oak stems and thus can potentially serve as a model host for the investigation of HIPD, the newly described plant-pathogen interaction.
Collapse
Affiliation(s)
- Marianne Elliott
- Washington State University Puyallup Research and Extension Center, Puyallup, Washington, 98371, USA
| | - Jennifer Yuzon
- Department of Plant Pathology, University of California, Davis, California, 95616, USA
| | - Mathu Malar C
- Computational Genomics Lab, Structural Biology and Bioinformatics Division, CSIR Indian Institute of Chemical Biology, Kolkata, 700032, India
| | - Sucheta Tripathy
- Computational Genomics Lab, Structural Biology and Bioinformatics Division, CSIR Indian Institute of Chemical Biology, Kolkata, 700032, India
| | - Mai Bui
- Crops Pathology and Genetics Research Unit, USDA Agricultural Research Service, Davis, California, 95616, USA
| | - Gary A Chastagner
- Washington State University Puyallup Research and Extension Center, Puyallup, Washington, 98371, USA
| | - Katie Coats
- Washington State University Puyallup Research and Extension Center, Puyallup, Washington, 98371, USA
| | - David M Rizzo
- Department of Plant Pathology, University of California, Davis, California, 95616, USA
| | - Matteo Garbelotto
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, California, 94720, USA
| | - Takao Kasuga
- Crops Pathology and Genetics Research Unit, USDA Agricultural Research Service, Davis, California, 95616, USA.
| |
Collapse
|
4
|
Li Y, Shen H, Zhou Q, Qian K, van der Lee T, Huang S. Changing Ploidy as a Strategy: The Irish Potato Famine Pathogen Shifts Ploidy in Relation to Its Sexuality. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2017; 30:45-52. [PMID: 27957885 DOI: 10.1094/mpmi-08-16-0156-r] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The oomycete Phytophthora infestans was the causal agent of the Irish Great Famine and is a recurring threat to global food security. The pathogen can reproduce both sexually and asexually, with high potential to adapt to various environments and great risk to break disease resistance genes in potato. As are other oomycetes, P. infestans is regarded to be diploid during the vegetative phase of its life cycle, although some studies reported trisomy and polyploidy. Using microsatellite fingerprinting, genome-wide assessment of single nucleotide polymorphisms, nuclear DNA quantification, and microscopic counting of chromosome numbers, we assessed the ploidy level of a comprehensive selection of isolates. All progenies from sexual populations of P. infestans in nature were found to be diploid, in contrast nearly all dominant asexual lineages, including the most important pandemic clonal lineages US-1 and 13_A2 were triploid. Such triploids possess significantly more allelic variation than diploids. We observed that triploid genotype can change to a diploid genome constitution when exposed to artificial stress conditions. This study reveals that fluctuations in the ploidy level may be a key factor in the adaptation process of this notorious plant destroyer and imposes an extra challenge to control this disease.
Collapse
Affiliation(s)
- Ying Li
- 1 Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - He Shen
- 1 Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Qian Zhou
- 1 Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- 2 Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China; and
| | - Kun Qian
- 1 Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Theo van der Lee
- 3 Biointeractions & Plant Health, Wageningen University & Research Center, Plant Research International, Wageningen 6700AA, The Netherlands
| | - Sanwen Huang
- 1 Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- 2 Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China; and
| |
Collapse
|
5
|
Kasuga T, Bui M, Bernhardt E, Swiecki T, Aram K, Cano LM, Webber J, Brasier C, Press C, Grünwald NJ, Rizzo DM, Garbelotto M. Host-induced aneuploidy and phenotypic diversification in the Sudden Oak Death pathogen Phytophthora ramorum. BMC Genomics 2016; 17:385. [PMID: 27206972 PMCID: PMC4875591 DOI: 10.1186/s12864-016-2717-z] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Accepted: 04/28/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Aneuploidy can result in significant phenotypic changes, which can sometimes be selectively advantageous. For example, aneuploidy confers resistance to antifungal drugs in human pathogenic fungi. Aneuploidy has also been observed in invasive fungal and oomycete plant pathogens in the field. Environments conducive to the generation of aneuploids, the underlying genetic mechanisms, and the contribution of aneuploidy to invasiveness are underexplored. We studied phenotypic diversification and associated genome changes in Phytophthora ramorum, a highly destructive oomycete pathogen with a wide host-range that causes Sudden Oak Death in western North America and Sudden Larch Death in the UK. Introduced populations of the pathogen are exclusively clonal. In California, oak (Quercus spp.) isolates obtained from trunk cankers frequently exhibit host-dependent, atypical phenotypes called non-wild type (nwt), apparently without any host-associated population differentiation. Based on a large survey of genotypes from different hosts, we previously hypothesized that the environment in oak cankers may be responsible for the observed phenotypic diversification in P. ramorum. RESULTS We show that both normal wild type (wt) and nwt phenotypes were obtained when wt P. ramorum isolates from the foliar host California bay (Umbellularia californica) were re-isolated from cankers of artificially-inoculated canyon live oak (Q. chrysolepis). We also found comparable nwt phenotypes in P. ramorum isolates from a bark canker of Lawson cypress (Chamaecyparis lawsoniana) in the UK; previously nwt was not known to occur in this pathogen population. High-throughput sequencing-based analyses identified major genomic alterations including partial aneuploidy and copy-neutral loss of heterozygosity predominantly in nwt isolates. Chromosomal breakpoints were located at or near transposons. CONCLUSION This work demonstrates that major genome alterations of a pathogen can be induced by its host species. This is an undocumented type of plant-microbe interaction, and its contribution to pathogen evolution is yet to be investigated, but one of the potential collateral effects of nwt phenotypes may be host survival.
Collapse
Affiliation(s)
- Takao Kasuga
- Crops Pathology and Genetics Research Unit, USDA Agricultural Research Service, Davis, California, 95616, USA
| | - Mai Bui
- Crops Pathology and Genetics Research Unit, USDA Agricultural Research Service, Davis, California, 95616, USA
| | | | | | - Kamyar Aram
- Department of Plant Pathology, University of California, Davis, California, 95616, USA
| | - Liliana M Cano
- Department of Plant Pathology, University of Florida, IFAS, Indian River Research and Education Center, Fort Pierce, Florida, 34945, USA
| | - Joan Webber
- Forest Research, Farnham, Surrey, GU10 4LH, UK
| | | | - Caroline Press
- Horticultural Crops Research Laboratory, USDA Agricultural Research Service, Corvallis, Oregon, 97330, USA
| | - Niklaus J Grünwald
- Horticultural Crops Research Laboratory, USDA Agricultural Research Service, Corvallis, Oregon, 97330, USA
| | - David M Rizzo
- Department of Plant Pathology, University of California, Davis, California, 95616, USA
| | - Matteo Garbelotto
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, California, 947020, USA.
| |
Collapse
|
6
|
Strain Specific Factors Control Effector Gene Silencing in Phytophthora sojae. PLoS One 2016; 11:e0150530. [PMID: 26930612 PMCID: PMC4773254 DOI: 10.1371/journal.pone.0150530] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Accepted: 02/15/2016] [Indexed: 12/04/2022] Open
Abstract
The Phytophthora sojae avirulence gene Avr3a encodes an effector that is capable of triggering immunity on soybean plants carrying the resistance gene Rps3a. P. sojae strains that express Avr3a are avirulent to Rps3a plants, while strains that do not are virulent. To study the inheritance of Avr3a expression and virulence towards Rps3a, genetic crosses and self-fertilizations were performed. A cross between P. sojae strains ACR10 X P7076 causes transgenerational gene silencing of Avr3a allele, and this effect is meiotically stable up to the F5 generation. However, test-crosses of F1 progeny (ACR10 X P7076) with strain P6497 result in the release of silencing of Avr3a. Expression of Avr3a in the progeny is variable and correlates with the phenotypic penetrance of the avirulence trait. The F1 progeny from a direct cross of P6497 X ACR10 segregate for inheritance for Avr3a expression, a result that could not be explained by parental imprinting or heterozygosity. Analysis of small RNA arising from the Avr3a gene sequence in the parental strains and hybrid progeny suggests that the presence of small RNA is necessary but not sufficient for gene silencing. Overall, we conclude that inheritance of the Avr3a gene silenced phenotype relies on factors that are variable among P. sojae strains.
Collapse
|
7
|
Dunn AR, Bruening SR, Grünwald NJ, Smart CD. Evolution of an Experimental Population of Phytophthora capsici in the Field. PHYTOPATHOLOGY 2014; 104:1107-1117. [PMID: 24702666 DOI: 10.1094/phyto-12-13-0346-r] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Populations of the vegetable pathogen Phytophthora capsici are often highly diverse, with limited gene flow between fields. To investigate the structure of a newly established, experimental population, an uninfested research field was inoculated with two single-zoospore isolates of P. capsici in September 2008. From 2009 through 2012, ≈50 isolates of P. capsici were collected from the field each year and genotyped using five microsatellite loci. The same two isolates were also crossed in the lab. High levels of diversity were detected in the research field, with 26 to 37 unique multilocus genotypes detected each year. Through 2012, genotypic diversity did not decline and no evidence of genetic drift was observed. However, during the 2011 and 2012 growing seasons, four new alleles not present in either parental isolate were observed in the field. Selfing (but not apomixis) was observed at low frequency among in vitro progeny. In addition, evidence for loss of heterozygosity was observed in half of the in vitro progeny. These results suggest that recombination, mutation, and loss of heterozygosity can affect the genetic structure observed in P. capsici populations.
Collapse
|
8
|
Li Y, van der Lee TAJ, Evenhuis A, van den Bosch GBM, van Bekkum PJ, Förch MG, van Gent-Pelzer MPE, van Raaij HMG, Jacobsen E, Huang SW, Govers F, Vleeshouwers VGAA, Kessel GJT. Population dynamics of Phytophthora infestans in the Netherlands reveals expansion and spread of dominant clonal lineages and virulence in sexual offspring. G3 (BETHESDA, MD.) 2012; 2:1529-40. [PMID: 23275876 PMCID: PMC3516475 DOI: 10.1534/g3.112.004150] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/28/2012] [Accepted: 09/22/2012] [Indexed: 11/18/2022]
Abstract
For a comprehensive survey of the structure and dynamics of the Dutch Phytophthora infestans population, 652 P. infestans isolates were collected from commercial potato fields in the Netherlands during the 10-year period 2000-2009. Genotyping was performed using 12 highly informative microsatellite markers and mitochondrial haplotypes. In addition, for each isolate, the mating type was determined. STRUCTURE analysis grouped the 322 identified genotypes in three clusters. Cluster 1 consists of a single clonal lineage NL-001, known as "Blue_13"; all isolates in this cluster have the A2 mating type and the Ia mitochondrial haplotype. Clusters 2 and 3 display a more elaborate substructure containing many unique genotypes. In Cluster 3, several distinct clonal lineages were also identified. This survey witnesses that the Dutch population underwent dramatic changes in the 10 years under study. The most notable change was the emergence and spread of A2 mating type strain NL-001 (or "Blue_13"). The results emphasize the importance of the sexual cycle in generating genetic diversity and the importance of the asexual cycle as the propagation and dispersal mechanism for successful genotypes. Isolates were also screened for absence of the Avrblb1/ipiO class I gene, which is indicative for virulence on Rpi-blb1. This is also the first report of Rpi-blb1 breakers in the Netherlands. Superimposing the virulence screening on the SSR genetic backbone indicates that lack the Avrblb1/ipiO class I gene only occurred in sexual progeny. So far, the asexual spread of the virulent isolates identified has been limited.
Collapse
Affiliation(s)
- Y. Li
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 100081, Beijing, China
- Bio-interactions and Plant Health, Plant Research International, 6700 AA Wageningen, The Netherlands
| | - T. A. J. van der Lee
- Bio-interactions and Plant Health, Plant Research International, 6700 AA Wageningen, The Netherlands
| | - A. Evenhuis
- Bio-interactions and Plant Health, Plant Research International, 6700 AA Wageningen, The Netherlands
| | - G. B. M. van den Bosch
- Bio-interactions and Plant Health, Plant Research International, 6700 AA Wageningen, The Netherlands
| | - P. J. van Bekkum
- Bio-interactions and Plant Health, Plant Research International, 6700 AA Wageningen, The Netherlands
| | - M. G. Förch
- Bio-interactions and Plant Health, Plant Research International, 6700 AA Wageningen, The Netherlands
| | - M. P. E van Gent-Pelzer
- Bio-interactions and Plant Health, Plant Research International, 6700 AA Wageningen, The Netherlands
| | - H. M. G. van Raaij
- Bio-interactions and Plant Health, Plant Research International, 6700 AA Wageningen, The Netherlands
| | - E. Jacobsen
- Laboratory of Plant Breeding, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - S. W. Huang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 100081, Beijing, China
| | - F. Govers
- Laboratory of Phytopathology, Wageningen University, 6700 EE Wageningen, The Netherlands
- Centre for BioSystems Biology, 6700 AB Wageningen, The Netherlands
| | | | - G. J. T. Kessel
- Bio-interactions and Plant Health, Plant Research International, 6700 AA Wageningen, The Netherlands
| |
Collapse
|
9
|
Aberrant genome size and instability of Phytophthora ramorum oospore progenies. Fungal Genet Biol 2011; 48:537-43. [DOI: 10.1016/j.fgb.2011.01.008] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2010] [Revised: 01/17/2011] [Accepted: 01/18/2011] [Indexed: 11/22/2022]
|
10
|
Heesch S, Cho GY, Peters AF, Le Corguillé G, Falentin C, Boutet G, Coëdel S, Jubin C, Samson G, Corre E, Coelho SM, Cock JM. A sequence-tagged genetic map for the brown alga Ectocarpus siliculosus provides large-scale assembly of the genome sequence. THE NEW PHYTOLOGIST 2010; 188:42-51. [PMID: 20456050 DOI: 10.1111/j.1469-8137.2010.03273.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
• Ectocarpus siliculosus has been proposed as a genetic and genomic model for the brown algae and the 214 Mbp genome of this organism has been sequenced. The aim of this project was to obtain a chromosome-scale view of the genome by constructing a genetic map using microsatellite markers that were designed based on the sequence supercontigs. • To map genetic markers, a segregating F(2) population was generated from a cross between the sequenced strain (Ec 32) and a compatible strain from northern Chile. Amplified fragment length polymorphism (AFLP) analysis indicated a significant degree of polymorphism (41%) between the genomes of these two parental strains. Of 1,152 microsatellite markers that were selected for analysis based on their location on long supercontigs, their potential as markers and their predicted ability to amplify a single genomic locus, 407 were found to be polymorphic. • A genetic map was constructed using 406 markers, resulting in 34 linkage groups. The 406 markers anchor 325 of the longest supercontigs on to the map, representing 70.1% of the genome sequence. • The Ectocarpus genetic map described here not only provides a large-scale assembly of the genome sequence, but also represents an important tool for future genetic analysis using this organism.
Collapse
Affiliation(s)
- Svenja Heesch
- UPMC Univ. Paris 06, The Marine Plants and Biomolecules Laboratory, UMR 7139, Station Biologique de Roscoff, Place Georges Teissier, BP74, 29682 Roscoff Cedex, France
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
11
|
Hulvey J, Young J, Finley L, Lamour K. Loss of heterozygosity in Phytophthora capsici after N-ethyl-nitrosourea mutagenesis. Mycologia 2010; 102:27-32. [PMID: 20120225 DOI: 10.3852/09-102] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Loss of heterozygosity (LOH) occurs in a variety of diploid organisms after chemical mutagenesis and was observed in the vegetable pathogen Phytophthora capsici after N-ethyl-nitrosourea (ENU) mutagenesis at three loci during reverse genetic screening. Our objectives were to determine (i) the frequency of LOH among mutants, (ii) the directionality of the LOH events and (iii) the length of the genomic tracts exhibiting LOH. Of the 1152 ENU mutants screened, LOH was most frequent at locus 3 (99 ENU mutants), with locus 1 (10 ENU mutants) and locus 2 (9 ENU mutants) undergoing LOH at similar frequencies. LOH was bidirectional for all three loci, with locus 3 mutants biased toward one haplotype. Analysis of upstream and downstream heterozygosity indicates that the LOH events spanned up to at least 4.6 kb. The implications of mitotic recombination and LOH for reverse genetics and natural variation in Phytophthora are discussed.
Collapse
Affiliation(s)
- Jon Hulvey
- Genome Science and Technology Graduate Program, University of Tennessee, Knoxville, Tennessee, USA.
| | | | | | | |
Collapse
|
12
|
Xavier B, Annelies V, Kurt H, Fréderic L, Anne C. Oospores progenies from Phytophthora ramorum. Fungal Biol 2010; 114:369-78. [DOI: 10.1016/j.funbio.2010.02.009] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2009] [Revised: 02/11/2010] [Accepted: 02/23/2010] [Indexed: 11/26/2022]
|
13
|
Catal M, King L, Tumbalam P, Wiriyajitsomboon P, Kirk WW, Adams GC. Heterokaryotic nuclear conditions and a heterogeneous nuclear population are observed by flow cytometry in Phytophthora infestans. Cytometry A 2010; 77:769-75. [DOI: 10.1002/cyto.a.20888] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|
14
|
Klarfeld S, Rubin AE, Cohen Y. Pathogenic Fitness of Oosporic Progeny Isolates of Phytophthora infestans on Late-Blight-Resistant Tomato Lines. PLANT DISEASE 2009; 93:947-953. [PMID: 30754538 DOI: 10.1094/pdis-93-9-0947] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Four A1 field isolates and one A2 field isolate of Phytophthora infestans were crossed to produce oospores in tomato leaves. The oospores were extracted and mixed with perlite and water, and healthy tomato leaves were used as bait for oospore-progeny infection. Twenty-nine lesions were obtained from the four crosses and 283 single-sporangium isolates were recovered and tested on four tomato differential lines carrying different major genes (Ph-0, Ph-1, Ph-2, and 3707) for late blight resistance. The pathogenic fitness (number of sporangia per unit leaf area) of parental and progeny isolates was strongly dependent on the host genotype; it decreased in the order Ph-0 > Ph-1 > Ph-2 > 3707. The A2 parent had a higher pathogenic fitness than the A1 parents on Ph-0 and Ph-1 but similar, lower fitness on Ph-2. Different levels of pathogenic fitness were observed across all isolates on Ph-0, although Ph-0 lacks resistance genes. Pathogenic fitness on one tomato genotype was not related to the pathogenic fitness on the other tomato genotypes. Some isolates exhibited reduced pathogenic fitness relative to the respective A1 parent, whereas others demonstrated a higher pathogenic fitness compared with the A2 parent. The tomato genotype Solanum pimpinellifolium L3707/5 was resistant to all five parental isolates of P. infestans. However, 37 of the 283 progeny isolates from 11 different lesions had compatible reactions with this line, producing up to 31 × 103 sporangia/cm2. Overall, reduced fitness was more frequent among the progeny isolates than increased fitness.
Collapse
Affiliation(s)
- Shiri Klarfeld
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Avia Evgenia Rubin
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Yigal Cohen
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| |
Collapse
|
15
|
Abstract
Three common systemic human fungal pathogens--Cryptococcus neoformans, Candida albicans and Aspergillus fumigatus--have retained all the machinery to engage in sexual reproduction, and yet their populations are often clonal with limited evidence for recombination. Striking parallels have emerged with four protozoan parasites that infect humans: Toxoplasma gondii, Trypanosoma brucei, Trypanosoma cruzi and Plasmodium falciparum. Limiting sexual reproduction appears to be a common virulence strategy, enabling generation of clonal populations well adapted to host and environmental niches, yet retaining the ability to engage in sexual or parasexual reproduction and respond to selective pressure. Continued investigation of the sexual nature of microbial pathogens should facilitate both laboratory investigation and an understanding of the complex interplay between pathogens, hosts, vectors, and their environments.
Collapse
Affiliation(s)
- Joseph Heitman
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina 27710, USA.
| |
Collapse
|
16
|
Jiang RHY, Weide R, van de Vondervoort PJI, Govers F. Amplification generates modular diversity at an avirulence locus in the pathogen Phytophthora. Genome Res 2006; 16:827-40. [PMID: 16818726 DOI: 10.1101/gr.5193806] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The destructive late blight pathogen Phytophthora infestans is notorious for its rapid adaptation to circumvent detection mediated by plant resistance (R) genes. We performed comparative genomic hybridization on microarrays (array-CGH) in a near genome-wide survey to identify genome rearrangements related to changes in virulence. Six loci with copy number variation were found, one of which involves an amplification colocalizing with a previously identified locus that confers avirulence in combination with either R gene R3b, R10, or R11. Besides array-CGH, we used three independent approaches to find candidate genes at the Avr3b-Avr10-Avr11 locus: positional cloning, cDNA-AFLP analysis, and Affymetrix array expression profiling. This resulted in one candidate, pi3.4, that encodes a protein of 1956 amino acids with regulatory domains characteristic for transcription factors. Amplification is restricted to the 3' end of the full-length gene but the amplified copies still contain the hallmarks of a regulatory protein. Sequence comparison showed that the amplification may generate modular diversity and assist in the assembly of novel full-length genes via unequal crossing-over. Analyses of P. infestans field isolates revealed that the pi3.4 amplification correlates with avirulence; isolates virulent on R3b, R10, and R11 plants lack the amplified gene cluster. The ancestral state of 3.4 in the Phytophthora lineage is a full-length, single-copy gene. In P. infestans, however, pi3.4 is a dynamic gene that is amplified and has moved to other locations. Modular diversity could be a novel mechanism for pathogens to quickly adapt to changes in the environment.
Collapse
Affiliation(s)
- Rays H Y Jiang
- Laboratory of Phytopathology, Plant Sciences Group, Wageningen University, NL-5-6709 PD Wageningen and Graduate School Experimental Plant Sciences, The Netherlands
| | | | | | | |
Collapse
|
17
|
Rubin E, Cohen Y. An Improved Method for Infecting Tomato Leaves or Seedlings with Oospores of Phytophthora infestans Used to Investigate F1 Progeny. PLANT DISEASE 2006; 90:741-749. [PMID: 30781233 DOI: 10.1094/pd-90-0741] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
An improved, soil-free laboratory method was developed to induce late blight infection in detached tomato leaves or tomato seedlings with in vivo-produced oospores of Phytophthora infestans. Oospores were produced in detached tomato leaves infected with an inoculum mixture of A1 and A2 isolates. The infected leaves were homogenized in distilled water. The homogenates were exposed to two cycles of drying and wetting to kill sporangia, zoospores, and mycelia and, thereafter, mixed with perlite and water. Tomato leaves or seed were floated on the perlite mixture in petri dishes and incubated for up to 30 days. Results from 13 experiments showed that, in dishes containing oospores, 96 of 820 leaflets (11.7%) developed late blight lesions within 6 to 30 days; whereas, in 3 experiments with seedlings, 12 of 1,400 plants (0.9%) were blighted within 17 to 26 days. No late blight developed in leaflets or seedlings maintained in dishes containing homogenates of the control leaves infected with either A1 or A2 inoculum. In all, 234 single-sporangium F1 isolates recovered from 24 leaf lesions produced by four crosses and 27 isolates recovered from 12 seedlings infected with two crosses were examined for sensitivity to metalaxyl and mating type. Results showed that, although the parent isolates were either S (sensitive) or R (resistant) to metalaxyl, most F1 progeny isolates exhibited various levels of intermediate resistance to metalaxyl. Most isolates belonged to either the A1 or the A2 mating type, depending on the cross and lesion. However, some isolates belonged to the unusual mating type A1A2 or were sterile. Current experiments are intended to elucidate the virulence and aggressiveness of these F1 progenies to tomato. This improved method may facilitate our understanding of the role of in vivo-produced oospores in the epidemiology of late blight in tomato.
Collapse
Affiliation(s)
- Evgenia Rubin
- Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Yigal Cohen
- Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| |
Collapse
|
18
|
van der Lee T, Testa A, Robold A, van 't Klooster J, Govers F. High-density genetic linkage maps of Phytophthora infestans reveal trisomic progeny and chromosomal rearrangements. Genetics 2005; 167:1643-61. [PMID: 15342505 PMCID: PMC1470988 DOI: 10.1534/genetics.104.029652] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Detailed analysis of the inheritance of molecular markers was performed in the oomycete plant pathogen Phytophthora infestans. Linkage analysis in the sexual progeny of two Dutch field isolates (cross 71) resulted in a high-density map containing 508 markers on 13 major and 10 minor linkage groups. The map showed strong clustering of markers, particularly of markers originating from one parent, and dissimilarity between the parental isolates on linkage group III in the vicinity of the mating-type locus, indicating a chromosomal translocation. A second genetic map, constructed by linkage analysis in sexual progeny of two Mexican isolates (cross 68), contained 363 markers and is thus less dense than the cross 71 map. For some linkage groups the two independent linkage maps could be aligned, but sometimes markers appeared to be in a different order, or not linked at all, indicating chromosomal rearrangements between genotypes. Graphical genotyping showed that some progeny contained three copies of a homologous linkage group. This trisomy was found for several linkage groups in both crosses. Together, these analyses suggest a genome with a high degree of flexibility, which may have implications for evolution of new races and resistance development to crop protection agents.
Collapse
Affiliation(s)
- Theo van der Lee
- Laboratory of Phytopathology, Wageningen University, and Graduate School of Experimental Plant Sciences, 6709 PD Wageningen, The Netherlands
| | | | | | | | | |
Collapse
|
19
|
Dobrowolski MP, Tommerup IC, Shearer BL, O'Brien PA. Three Clonal Lineages of Phytophthora cinnamomi in Australia Revealed by Microsatellites. PHYTOPATHOLOGY 2003; 93:695-704. [PMID: 18943056 DOI: 10.1094/phyto.2003.93.6.695] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
ABSTRACT The genetic structure of populations of Phytophthora cinnamomi, a pathogen of an enormous variety of woody plants, was investigated using microsatellites. Three intensively sampled disease sites in southwest Australia were analyzed along with a large culture collection of Austra-lian isolates and some isolates from elsewhere in the world. The mutation in the four microsatellite loci analyzed revealed spatial patterns at the disease sites that correlated with the age of the infestation. Only three clonal lineages were identified in Australian populations and these same clonal lineages were present in worldwide populations, where it is suggested that a limited number of clonal lineages have spread in most regions. No evidence for sexual reproduction between these clonal lineages in Australia has been found even though the pathogen has the opportunity. Instead, mitotic recombination is frequent within the clonal lineages. The implications of this are discussed.
Collapse
|
20
|
Shattock RC. Phytophthora infestans: populations, pathogenicity and phenylamides. PEST MANAGEMENT SCIENCE 2002; 58:944-950. [PMID: 12233186 DOI: 10.1002/ps.527] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Isolates of Phytophthora infestans (Mont) de Bary (the potato and tomato late blight pathogen) resistant to phenylamides appeared in Europe and North America in the late 1970s and early 1990s respectively. Concurrent, but coincidentally, with both these events there were radical structural shifts in the pathogen populations as immigrant genotypes from Mexico displaced the indigenous populations. Both A1 and A2 mating type isolates are now present in blighted crops, permitting alternative inoculum via germinating sexually produced oospores to influence dynamics of late blight populations. Studies of inheritance of ploidy, host-specific pathogenicity, mating type and resistance to antibiotics and phenylamide fungicides have provided insight into mechanisms of variation in this potent pathogen.
Collapse
Affiliation(s)
- Richard C Shattock
- School of Biological Sciences, University of Wales, Bangor, Gwynedd LL57 2UW, UK.
| |
Collapse
|
21
|
Dobrowolski MP, Tommerup IC, Blakeman HD, O'Brien PA. Non-Mendelian inheritance revealed in a genetic analysis of sexual progeny of Phytophthora cinnamomi with microsatellite markers. Fungal Genet Biol 2002; 35:197-212. [PMID: 11929210 DOI: 10.1006/fgbi.2001.1319] [Citation(s) in RCA: 60] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We report the development of four microsatellite loci into genetic markers for the diploid oomycete plant pathogen Phytophthora cinnamomi and that (AC)(n) and (AG)(n) microsatellites are significantly less frequent than in plant and mammal genomes. A minisatellite motif 14 bp long was also discovered. The four microsatellite loci were used to analyze sexual progeny from four separate crosses of P. cinnamomi. A large proportion of non-Mendelian inheritance was observed across all loci in all four crosses, including inheritance of more than two alleles at a locus and noninheritance of alleles from either parent at a locus. The aberrant inheritance is best explained by nondisjunction at meiosis in both the A1 parent and the A2 trisomic parents, resulting in aneuploid progeny. Two loci on the putative trisomic chromosome showed linkage and no loci were linked to mating type. One aneuploid offspring was shown to have lost alleles at two loci following subculture over 4 years, indicating that aneuploid progeny may not be mitotically stable.
Collapse
Affiliation(s)
- Mark P Dobrowolski
- School of Biological Sciences and Biotechnology, Murdoch University, Perth, Western Australia, 6150, Australia
| | | | | | | |
Collapse
|
22
|
Chamnanpunt J, Shan WX, Tyler BM. High frequency mitotic gene conversion in genetic hybrids of the oomycete Phytophthora sojae. Proc Natl Acad Sci U S A 2001; 98:14530-5. [PMID: 11724938 PMCID: PMC64716 DOI: 10.1073/pnas.251464498] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2001] [Indexed: 11/18/2022] Open
Abstract
Microbial populations depend on genetic variation to respond to novel environmental challenges. Plant pathogens are notorious for their ability to overcome pesticides and host resistance genes as a result of genetic changes. We report here that in particular hybrid strains of Phytophthora sojae, an oomycete pathogen of soybean, high frequency mitotic gene conversion rapidly converts heterozygous loci to homozygosity, resulting in heterokaryons containing highly diverse populations of diploid nuclei. In hybrids involving strain P7076, conversion rates of up to 3 x 10(-2) per locus per nucleus per generation were observed. In other hybrids, rates were of the order of 5 x 10(-5). Independent gene conversion was observed within a selected linkage group including loci as close as 0.7 kb apart and in unlinked markers throughout the genome. Gene conversions continued throughout vegetative growth and were stimulated by further sexual reproduction. At many loci, conversion showed extreme disparity, with one allele always being lost, suggesting that conversion was initiated by allele-specific double-stranded breaks. Pedigree analysis indicated that individual loci undergo multiple independent conversions within the nuclei of a vegetative clone and that conversion may be preceded by a heritable "activation" state.
Collapse
Affiliation(s)
- J Chamnanpunt
- Department of Plant Pathology, University of California, Davis, CA 95616, USA
| | | | | |
Collapse
|
23
|
van der Lee T, Testa A, van 't Klooster J, van den Berg-Velthuis G, Govers F. Chromosomal deletion in isolates of Phytophthora infestans correlates with virulence on R3, R10, and R11 potato lines. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2001; 14:1444-1452. [PMID: 11768540 DOI: 10.1094/mpmi.2001.14.12.1444] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
In Phytophthora infestans, a cluster of three dominant avirulence genes is located on the distal part of linkage group VIII. In a mapping population from a cross between two Dutch field isolates, probe M5.1, derived from an amplified fragment length polymorphism (AFLP) marker linked to the Avr3-Avr10-Avr11 cluster, hybridized only to DNA from the parent and F1 progeny that is avirulent on potato lines carrying the R3, R10, and R11 resistance gene. In the virulent parent and the virulent progeny, no M5.1 homologue was detected, demonstrating a deletion on that part of linkage group VIII. P. infestans is diploid, so the avirulent strains must be hemizygous for the region concerned. A similar situation was found in another mapping population from two Mexican strains. The deletion was also found to occur in many field isolates. In a large set of unique isolates collected in The Netherlands from 1980 to 1991, 37% had no M5.1 homologue and the deletion correlated strongly with gain of virulence on potato lines carrying R3, R10, and R11. Also, in some old isolates that belong to a single clonal lineage (US-1) and are thus highly homogenous, deletions at the M5.1 locus were detected, indicating that this region is unstable.
Collapse
Affiliation(s)
- T van der Lee
- Laboratory of Phytopathology, Wageningen University, Graduate School Experimental Plant Sciences, The Netherlands
| | | | | | | | | |
Collapse
|
24
|
AFLP and RFLP (RG57) fingerprints can give conflicting evidence about the relatedness of isolates of Phytophthora infestans. ACTA ACUST UNITED AC 2001. [DOI: 10.1017/s0953756201005135] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|
25
|
van der Lee T, Robold A, Testa A, van 't Klooster JW, Govers F. Mapping of avirulence genes in Phytophthora infestans with amplified fragment length polymorphism markers selected by bulked segregant analysis. Genetics 2001; 157:949-56. [PMID: 11238385 PMCID: PMC1461542 DOI: 10.1093/genetics/157.3.949] [Citation(s) in RCA: 62] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
In this study we investigated the genetic control of avirulence in the diploid oomycete pathogen Phytophthora infestans, the causal agent of late blight on potato. The dominant avirulence (Avr) genes matched six race-specific resistance genes introgressed in potato from a wild Solanum species. AFLP markers linked to Avr genes were selected by bulked segregant analysis and used to construct two high-density linkage maps, one containing Avr4 (located on linkage group A2-a) and the other containing a cluster of three tightly linked genes, Avr3, Avr10, and Avr11 (located on linkage group VIII). Bulked segregant analysis also resulted in a marker linked to Avr1 and this allowed positioning of Avr1 on linkage group IV. No bulked segregant analysis was performed for Avr2, but linkage to a set of random markers placed Avr2 on linkage group VI. Of the six Avr genes, five were located on the most distal part of the linkage group, possibly close to the telomere. The high-density mapping was initiated to facilitate future positional cloning of P. infestans Avr genes.
Collapse
Affiliation(s)
- T van der Lee
- Laboratory of Phytopathology, Wageningen University and Graduate School of Experimental Plant Sciences, Binnenhaven 9, 6709 PD Wageningen, The Netherlands
| | | | | | | | | |
Collapse
|