Publications by authors named "Stephen B Goodwin"

39 Publications

The wheat pathogen Zymoseptoria tritici senses and responds to different wavelengths of light.

BMC Genomics 2020 Jul 25;21(1):513. Epub 2020 Jul 25.

USDA-Agricultural Research Service, Crop Production and Pest Control Research Unit, Department of Botany and Plant Pathology, Purdue University, 915 West State Street, West Lafayette, IN, 47907-2054, USA.

Background: The ascomycete fungus Zymoseptoria tritici (synonyms: Mycosphaerella graminicola, Septoria tritici) is a major pathogen of wheat that causes the economically important foliar disease Septoria tritici blotch. Despite its importance as a pathogen, little is known about the reaction of this fungus to light. To test for light responses, cultures of Z. tritici were grown in vitro for 16-h days under white, blue or red light, and their transcriptomes were compared with each other and to those obtained from control cultures grown in darkness.

Results: There were major differences in gene expression with over 3400 genes upregulated in one or more of the light conditions compared to dark, and from 1909 to 2573 genes specifically upregulated in the dark compared to the individual light treatments. Differences between light treatments were lower, ranging from only 79 differentially expressed genes in the red versus blue comparison to 585 between white light and red. Many of the differentially expressed genes had no functional annotations. For those that did, analysis of the Gene Ontology (GO) terms showed that those related to metabolism were enriched in all three light treatments, while those related to growth and communication were more prevalent in the dark. Interestingly, genes for effectors that have been shown previously to be involved in pathogenicity also were upregulated in one or more of the light treatments, suggesting a possible role of light for infection.

Conclusions: This analysis shows that Z. tritici can sense and respond to light with a huge effect on transcript abundance. High proportions of differentially expressed genes with no functional annotations illuminates the huge gap in our understanding of light responses in this fungus. Differential expression of genes for effectors indicates that light could be important for pathogenicity; unknown effectors may show a similar pattern of transcription. A better understanding of the effects of light on pathogenicity and other biological processes of Z. tritici could help to manage Septoria tritici blotch in the future.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12864-020-06899-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7382159PMC
July 2020

Genome-scale data resolve ancestral rock-inhabiting lifestyle in Dothideomycetes (Ascomycota).

IMA Fungus 2019 30;10:19. Epub 2019 Oct 30.

Department of Life Sciences, University of Trieste, via Giorgieri 10, 34127 Trieste, Italy.

Dothideomycetes is the most diverse fungal class in Ascomycota and includes species with a wide range of lifestyles. Previous multilocus studies have investigated the taxonomic and evolutionary relationships of these taxa but often failed to resolve early diverging nodes and frequently generated inconsistent placements of some clades. Here, we use a phylogenomic approach to resolve relationships in Dothideomycetes, focusing on two genera of melanized, extremotolerant rock-inhabiting fungi, and , that have been suggested to be early diverging lineages. We assembled phylogenomic datasets from newly sequenced (4) and previously available genomes (238) of 242 taxa. We explored the influence of tree inference methods, supermatrix vs. coalescent-based species tree, and the impact of varying amounts of genomic data. Overall, our phylogenetic reconstructions provide consistent and well-supported topologies for Dothideomycetes, recovering and among the earliest diverging lineages in the class. In addition, many of the major lineages within Dothideomycetes are recovered as monophyletic, and the phylogenomic approach implemented strongly supports their relationships. Ancestral character state reconstruction suggest that the rock-inhabiting lifestyle is ancestral within the class.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1186/s43008-019-0018-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7325674PMC
October 2019

Genetic diversity and population structure of Zymoseptoria tritici in Ethiopia as revealed by microsatellite markers.

Fungal Genet Biol 2020 08 19;141:103413. Epub 2020 May 19.

Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia; Ethiopian Biotechnology Institute. Affiliated with Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia. Electronic address:

Septoria tritici blotch (STB), caused by Zymoseptoria tritici (formerly: Mycosphaerella graminicola or Septoria tritici), is one of the most devastating diseases of wheat globally. Understanding genetic diversity of the pathogen has supreme importance in developing best management strategies. However, there is dearth of information on the genetic structure of Z. tritici populations in Ethiopia. Therefore, the present study was targeted to uncover the genetic diversity and population structure of Z. tritici populations from the major wheat-growing areas of Ethiopia. Totally, 182 Z. tritici isolates representing eight populations were analyzed with 14 microsatellite markers. All the microsatellite loci were polymorphic and highly informative, and hence useful genetic tools to depict the genetic diversity and population structure of the pathogen. A wide range of diversity indices including number of observed alleles, effective number of alleles, Shannon's diversity index, number of private alleles, Nei's gene diversity and percentage of polymorphic loci (PPL) were computed to determine genetic variation within populations. A high within-populations genetic diversity was confirmed with gene diversity index and PPL values ranging from 0.34 - 0.58 and 79-100% with overall mean of 0.45 and 94%, respectively. Analysis of molecular variance (AMOVA) revealed a moderate genetic differentiation where 92% of the total genetic variation resides within populations, leaving only 8% among populations. Cluster (UPGMA), PCoA and STRUCTURE analyses did not group the populations into sharply genetically distinct clusters according to their geographical origins, likely due to high gene flow (Nm = 5.66) and reproductive biology of the pathogen. All individual samples shared alleles from two subgroups (K = 2) evidencing high potential of genetic admixture. In conclusion, the microsatellite markers used in the present study were highly informative and thus, helped to dissect the genetic structures of Z. tritici populations in Ethiopia. Among the studied populations, those of East Shewa, Arsi, South West Shewa and Bale showed a high genetic diversity, and hence these areas can be considered as hot spots for investigations planned on the pathogen and host-pathogen interactions. Therefore, the present study not only enriches missing information in Ethiopia but also provides new insights into the epidemiology and genetic structure of Z. tritici in Africa where the agro-climatic conditions and the wheat cropping systems are different from other parts of the world. Such baseline information is useful for designing and implementing durable and effective management strategies.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.fgb.2020.103413DOI Listing
August 2020

Variable genome evolution in fungi after transposon-mediated amplification of a housekeeping gene.

Mob DNA 2019 27;10:37. Epub 2019 Aug 27.

5U.S. Department of Agriculture-Agricultural Research Service (USDA-ARS), Crop Production and Pest Control Research Unit, Purdue University, West Lafayette, IN USA.

Background: Transposable elements (TEs) can be key drivers of evolution, but the mechanisms and scope of how they impact gene and genome function are largely unknown. Previous analyses revealed that TE-mediated gene amplifications can have variable effects on fungal genomes, from inactivation of function to production of multiple active copies. For example, a DNA methyltransferase gene in the wheat pathogen (synonym ) was amplified to tens of copies, all of which were inactivated by Repeat-Induced Point mutation (RIP) including the original, resulting in loss of cytosine methylation. In another wheat pathogen, , a histone H3 gene was amplified to tens of copies with little evidence of RIP, leading to many potentially active copies. To further test the effects of transposon-aided gene amplifications on genome evolution and architecture, the repetitive fraction of the significantly expanded genome of the banana pathogen, , was analyzed in greater detail.

Results: These analyses identified a housekeeping gene, histone H3, which was captured and amplified to hundreds of copies by a DNA transposon, all of which were inactivated by RIP, except for the original. In the original H3 gene probably was not protected from RIP, but most likely was maintained intact due to strong purifying selection. Comparative analyses revealed that a similar event occurred in five additional genomes representing the fungal genera , and .

Conclusions: These results indicate that the interplay of TEs and RIP can result in different and unpredictable fates of amplified genes, with variable effects on gene and genome evolution.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1186/s13100-019-0177-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6710886PMC
August 2019

The mitochondrial genome of the ethanol-metabolizing, wine cellar mold Zasmidium cellare is the smallest for a filamentous ascomycete.

Fungal Biol 2016 08 20;120(8):961-974. Epub 2016 May 20.

U.S. Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA.

Fungi in the class Dothideomycetes often live in extreme environments or have unusual physiology. One of these, the wine cellar mold Zasmidium cellare, produces thick curtains of mycelia in cellars with high humidity, and its ability to metabolize volatile organic compounds is thought to improve air quality. Whether these abilities have affected its mitochondrial genome is not known. To fill this gap, the circular-mapping mitochondrial genome of Z. cellare was sequenced and, at only 23 743 bp, is the smallest reported for a filamentous fungus. Genes were encoded on both strands with a single change of direction, different from most other fungi but consistent with the Dothideomycetes. Other than its small size, the only unusual feature of the Z. cellare mitochondrial genome was two copies of a 110-bp sequence that were duplicated, inverted and separated by approximately 1 kb. This inverted-repeat sequence confused the assembly program but appears to have no functional significance. The small size of the Z. cellare mitochondrial genome was due to slightly smaller genes, lack of introns and non-essential genes, reduced intergenic spacers and very few ORFs relative to other fungi rather than a loss of essential genes. Whether this reduction facilitates its unusual biology remains unknown.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.funbio.2016.05.003DOI Listing
August 2016

Combating a Global Threat to a Clonal Crop: Banana Black Sigatoka Pathogen Pseudocercospora fijiensis (Synonym Mycosphaerella fijiensis) Genomes Reveal Clues for Disease Control.

PLoS Genet 2016 08 11;12(8):e1005876. Epub 2016 Aug 11.

Plant Research International, Wageningen University and Research, Wageningen, The Netherlands.

Black Sigatoka or black leaf streak disease, caused by the Dothideomycete fungus Pseudocercospora fijiensis (previously: Mycosphaerella fijiensis), is the most significant foliar disease of banana worldwide. Due to the lack of effective host resistance, management of this disease requires frequent fungicide applications, which greatly increase the economic and environmental costs to produce banana. Weekly applications in most banana plantations lead to rapid evolution of fungicide-resistant strains within populations causing disease-control failures throughout the world. Given its extremely high economic importance, two strains of P. fijiensis were sequenced and assembled with the aid of a new genetic linkage map. The 74-Mb genome of P. fijiensis is massively expanded by LTR retrotransposons, making it the largest genome within the Dothideomycetes. Melting-curve assays suggest that the genomes of two closely related members of the Sigatoka disease complex, P. eumusae and P. musae, also are expanded. Electrophoretic karyotyping and analyses of molecular markers in P. fijiensis field populations showed chromosome-length polymorphisms and high genetic diversity. Genetic differentiation was also detected using neutral markers, suggesting strong selection with limited gene flow at the studied geographic scale. Frequencies of fungicide resistance in fungicide-treated plantations were much higher than those in untreated wild-type P. fijiensis populations. A homologue of the Cladosporium fulvum Avr4 effector, PfAvr4, was identified in the P. fijiensis genome. Infiltration of the purified PfAVR4 protein into leaves of the resistant banana variety Calcutta 4 resulted in a hypersensitive-like response. This result suggests that Calcutta 4 could carry an unknown resistance gene recognizing PfAVR4. Besides adding to our understanding of the overall Dothideomycete genome structures, the P. fijiensis genome will aid in developing fungicide treatment schedules to combat this pathogen and in improving the efficiency of banana breeding programs.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1371/journal.pgen.1005876DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4981457PMC
August 2016

Generation of Reactive Oxygen Species via NOXa Is Important for Development and Pathogenicity of Mycosphaerella graminicola.

Mycobiology 2016 Mar 31;44(1):38-47. Epub 2016 Mar 31.

USDA-Agricultural Research Service, 915 West State Street, Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907-2054, USA.

The ascomycete fungus Mycosphaerella graminicola (synonym Zymoseptoria tritici) is an important pathogen of wheat causing economically significant losses. The primary nutritional mode of this fungus is thought to be hemibiotrophic. This pathogenic lifestyle is associated with an early biotrophic stage of nutrient uptake followed by a necrotrophic stage aided possibly by production of a toxin or reactive oxygen species (ROS). In many other fungi, the genes CREA and AREA are important during the biotrophic stage of infection, while the NOXa gene product is important during necrotrophic growth. To test the hypothesis that these genes are important for pathogenicity of M. graminicola, we employed an over-expression strategy for the selected target genes CREA, AREA, and NOXa, which might function as regulators of nutrient acquisition or ROS generation. Increased expressions of CREA, AREA, and NOXa in M. graminicola were confirmed via quantitative real-time PCR and strains were subsequently assayed for pathogenicity. Among them, the NOXa over-expression strain, NO2, resulted in significantly increased virulence. Moreover, instead of the usual filamentous growth, we observed a predominance of yeast-like growth of NO2 which was correlated with ROS production. Our data indicate that ROS generation via NOXa is important to pathogenicity as well as development in M. graminicola.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.5941/MYCO.2016.44.1.38DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4838590PMC
March 2016

Determining the order of resistance genes against Stagonospora nodorum blotch, Fusarium head blight and stem rust on wheat chromosome arm 3BS.

BMC Res Notes 2016 Feb 2;9:58. Epub 2016 Feb 2.

USDA-ARS, Department of Botany and Plant Pathology, Purdue University, 915 West State Street, West Lafayette, IN, 47907-2054, USA.

Background: Stagonospora nodorum blotch (SNB), Fusarium head blight (FHB) and stem rust (SR), caused by the fungi Parastagonospora (synonym Stagonospora) nodorum, Fusarium graminearum and Puccinia graminis, respectively, significantly reduce yield and quality of wheat. Three resistance factors, QSng.sfr-3BS, Fhb1 and Sr2, conferring resistance, respectively, to SNB, FHB and SR, each from a unique donor line, were mapped previously to the short arm of wheat chromosome 3B. Based on published reports, our hypothesis was that Sr2 is the most distal, Fhb1 the most proximal and QSng.sfr-3BS is in between Sr2 and Fhb1 on wheat chromosome arm 3BS.

Results: To test this hypothesis, 1600 F2 plants from crosses between parental lines Arina, Alsen and Ocoroni86, conferring resistance genes QSng.sfr-3BS, Fhb1 and Sr2, respectively, were genotyped and phenotyped for SNB along with the parental lines. Five closely linked single-nucleotide polymorphism (SNP) markers were used to make the genetic map and determine the gene order.

Conclusions: The results indicate that QSng.sfr-3BS is located between the other two resistance genes on chromosome 3BS. Knowing the positional order of these resistance genes will aid in developing a wheat line with all three genes in coupling, which has the potential to provide broad-spectrum resistance preventing grain yield and quality losses.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1186/s13104-016-1859-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4736272PMC
February 2016

Horizontal gene transfer and gene dosage drives adaptation to wood colonization in a tree pathogen.

Proc Natl Acad Sci U S A 2015 Mar 2;112(11):3451-6. Epub 2015 Mar 2.

Department of Forest and Conservation Sciences, The University of British Columbia, Vancouver, BC, Canada V6T 1Z4; Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Québec, QC, Canada G1V 4C7;

Some of the most damaging tree pathogens can attack woody stems, causing lesions (cankers) that may be lethal. To identify the genomic determinants of wood colonization leading to canker formation, we sequenced the genomes of the poplar canker pathogen, Mycosphaerella populorum, and the closely related poplar leaf pathogen, M. populicola. A secondary metabolite cluster unique to M. populorum is fully activated following induction by poplar wood and leaves. In addition, genes encoding hemicellulose-degrading enzymes, peptidases, and metabolite transporters were more abundant and were up-regulated in M. populorum growing on poplar wood-chip medium compared with M. populicola. The secondary gene cluster and several of the carbohydrate degradation genes have the signature of horizontal transfer from ascomycete fungi associated with wood decay and from prokaryotes. Acquisition and maintenance of the gene battery necessary for growth in woody tissues and gene dosage resulting in gene expression reconfiguration appear to be responsible for the adaptation of M. populorum to infect, colonize, and cause mortality on poplar woody stems.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1073/pnas.1424293112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4371944PMC
March 2015

A New Map Location of Gene for Resistance to Septoria Tritici Blotch in Wheat.

Crop Sci 2015 Jan-Feb;55(1):35-43. Epub 2014 Oct 31.

Department of Plant Sciences, University of California, Davis, CA 95616-8515, USA, and Howard Hughes Medical Institute, Chevy Chase, MD 20815-6789, USA.

Septoria tritici blotch (STB), caused by (synonym: ; asexual stage: ), is an important disease of wheat worldwide. Management of the disease usually is by host resistance or fungicides. However, has developed insensitivity to most commonly applied fungicides so there is a continuing need for well-characterized sources of host resistance to accelerate the development of improved wheat cultivars. Gene has been a useful source of major resistance, but its mapping location has not been well characterized. Based on linkage to a single marker, a previous study assigned to a location on the short arm of chromosome 6D. However, the results from the present study show that this reported location is incorrect. Instead, linkage analysis revealed that is located on the short arm of wheat chromosome 7A, completely linked to microsatellite (SSR) locus and flanked by loci (12.4 cM distal) and (2.1 cM proximal). Linkage between and was validated in BCF progeny of other crosses, and analyses of the flanking markers with deletion stocks showed that the gene is located on 7AS between fraction lengths 0.73 and 0.83. This revised location of is different from those for other STB resistance genes previously mapped in hexaploid wheat but is approximately 20 cM proximal to an STB resistance gene mapped on the short arm of chromosome 7A in . The markers described in this study are useful for accelerating the deployment of in wheat breeding programs.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.2135/cropsci2013.11.0766DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5089079PMC
October 2014

The landscape of transposable elements in the finished genome of the fungal wheat pathogen Mycosphaerella graminicola.

BMC Genomics 2014 Dec 17;15:1132. Epub 2014 Dec 17.

USDA-ARS, Crop Production and Pest Control Research Unit, Purdue University, 915 W. State Street, West Lafayette, Indiana, 47907-2054, USA.

Background: In addition to gene identification and annotation, repetitive sequence analysis has become an integral part of genome sequencing projects. Identification of repeats is important not only because it improves gene prediction, but also because of the role that repetitive sequences play in determining the structure and evolution of genes and genomes. Several methods using different repeat-finding strategies are available for whole-genome repeat sequence analysis. Four independent approaches were used to identify and characterize the repetitive fraction of the Mycosphaerella graminicola (synonym Zymoseptoria tritici) genome. This ascomycete fungus is a wheat pathogen and its finished genome comprises 21 chromosomes, eight of which can be lost with no obvious effects on fitness so are dispensable.

Results: Using a combination of four repeat-finding methods, at least 17% of the M. graminicola genome was estimated to be repetitive. Class I transposable elements, that amplify via an RNA intermediate, account for about 70% of the total repetitive content in the M. graminicola genome. The dispensable chromosomes had a higher percentage of repetitive elements as compared to the core chromosomes. Distribution of repeats across the chromosomes also varied, with at least six chromosomes showing a non-random distribution of repetitive elements. Repeat families showed transition mutations and a CpA → TpA dinucleotide bias, indicating the presence of a repeat-induced point mutation (RIP)-like mechanism in M. graminicola. One gene family and two repeat families specific to subtelomeres also were identified in the M. graminicola genome. A total of 78 putative clusters of nested elements was found in the M. graminicola genome. Several genes with putative roles in pathogenicity were found associated with these nested repeat clusters. This analysis of the transposable element content in the finished M. graminicola genome resulted in a thorough and highly curated database of repetitive sequences.

Conclusions: This comprehensive analysis will serve as a scaffold to address additional biological questions regarding the origin and fate of transposable elements in fungi. Future analyses of the distribution of repetitive sequences in M. graminicola also will be able to provide insights into the association of repeats with genes and their potential role in gene and genome evolution.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1186/1471-2164-15-1132DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4522978PMC
December 2014

Comparative genomics of a plant-pathogenic fungus, Pyrenophora tritici-repentis, reveals transduplication and the impact of repeat elements on pathogenicity and population divergence.

G3 (Bethesda) 2013 Jan 1;3(1):41-63. Epub 2013 Jan 1.

Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331-8530, USA.

Pyrenophora tritici-repentis is a necrotrophic fungus causal to the disease tan spot of wheat, whose contribution to crop loss has increased significantly during the last few decades. Pathogenicity by this fungus is attributed to the production of host-selective toxins (HST), which are recognized by their host in a genotype-specific manner. To better understand the mechanisms that have led to the increase in disease incidence related to this pathogen, we sequenced the genomes of three P. tritici-repentis isolates. A pathogenic isolate that produces two known HSTs was used to assemble a reference nuclear genome of approximately 40 Mb composed of 11 chromosomes that encode 12,141 predicted genes. Comparison of the reference genome with those of a pathogenic isolate that produces a third HST, and a nonpathogenic isolate, showed the nonpathogen genome to be more diverged than those of the two pathogens. Examination of gene-coding regions has provided candidate pathogen-specific proteins and revealed gene families that may play a role in a necrotrophic lifestyle. Analysis of transposable elements suggests that their presence in the genome of pathogenic isolates contributes to the creation of novel genes, effector diversification, possible horizontal gene transfer events, identified copy number variation, and the first example of transduplication by DNA transposable elements in fungi. Overall, comparative analysis of these genomes provides evidence that pathogenicity in this species arose through an influx of transposable elements, which created a genetically flexible landscape that can easily respond to environmental changes.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1534/g3.112.004044DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3538342PMC
January 2013

Diverse lifestyles and strategies of plant pathogenesis encoded in the genomes of eighteen Dothideomycetes fungi.

PLoS Pathog 2012 6;8(12):e1003037. Epub 2012 Dec 6.

United States Department of Energy DOE Joint Genome Institute JGI, Walnut Creek, California, United States of America.

The class Dothideomycetes is one of the largest groups of fungi with a high level of ecological diversity including many plant pathogens infecting a broad range of hosts. Here, we compare genome features of 18 members of this class, including 6 necrotrophs, 9 (hemi)biotrophs and 3 saprotrophs, to analyze genome structure, evolution, and the diverse strategies of pathogenesis. The Dothideomycetes most likely evolved from a common ancestor more than 280 million years ago. The 18 genome sequences differ dramatically in size due to variation in repetitive content, but show much less variation in number of (core) genes. Gene order appears to have been rearranged mostly within chromosomal boundaries by multiple inversions, in extant genomes frequently demarcated by adjacent simple repeats. Several Dothideomycetes contain one or more gene-poor, transposable element (TE)-rich putatively dispensable chromosomes of unknown function. The 18 Dothideomycetes offer an extensive catalogue of genes involved in cellulose degradation, proteolysis, secondary metabolism, and cysteine-rich small secreted proteins. Ancestors of the two major orders of plant pathogens in the Dothideomycetes, the Capnodiales and Pleosporales, may have had different modes of pathogenesis, with the former having fewer of these genes than the latter. Many of these genes are enriched in proximity to transposable elements, suggesting faster evolution because of the effects of repeat induced point (RIP) mutations. A syntenic block of genes, including oxidoreductases, is conserved in most Dothideomycetes and upregulated during infection in L. maculans, suggesting a possible function in response to oxidative stress.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1371/journal.ppat.1003037DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3516569PMC
May 2013

The genomes of the fungal plant pathogens Cladosporium fulvum and Dothistroma septosporum reveal adaptation to different hosts and lifestyles but also signatures of common ancestry.

PLoS Genet 2012 29;8(11):e1003088. Epub 2012 Nov 29.

Laboratory of Phytopathology, Wageningen University, Wageningen, The Netherlands.

We sequenced and compared the genomes of the Dothideomycete fungal plant pathogens Cladosporium fulvum (Cfu) (syn. Passalora fulva) and Dothistroma septosporum (Dse) that are closely related phylogenetically, but have different lifestyles and hosts. Although both fungi grow extracellularly in close contact with host mesophyll cells, Cfu is a biotroph infecting tomato, while Dse is a hemibiotroph infecting pine. The genomes of these fungi have a similar set of genes (70% of gene content in both genomes are homologs), but differ significantly in size (Cfu >61.1-Mb; Dse 31.2-Mb), which is mainly due to the difference in repeat content (47.2% in Cfu versus 3.2% in Dse). Recent adaptation to different lifestyles and hosts is suggested by diverged sets of genes. Cfu contains an α-tomatinase gene that we predict might be required for detoxification of tomatine, while this gene is absent in Dse. Many genes encoding secreted proteins are unique to each species and the repeat-rich areas in Cfu are enriched for these species-specific genes. In contrast, conserved genes suggest common host ancestry. Homologs of Cfu effector genes, including Ecp2 and Avr4, are present in Dse and induce a Cf-Ecp2- and Cf-4-mediated hypersensitive response, respectively. Strikingly, genes involved in production of the toxin dothistromin, a likely virulence factor for Dse, are conserved in Cfu, but their expression differs markedly with essentially no expression by Cfu in planta. Likewise, Cfu has a carbohydrate-degrading enzyme catalog that is more similar to that of necrotrophs or hemibiotrophs and a larger pectinolytic gene arsenal than Dse, but many of these genes are not expressed in planta or are pseudogenized. Overall, comparison of their genomes suggests that these closely related plant pathogens had a common ancestral host but since adapted to different hosts and lifestyles by a combination of differentiated gene content, pseudogenization, and gene regulation.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1371/journal.pgen.1003088DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3510045PMC
May 2013

Finished genome of the fungal wheat pathogen Mycosphaerella graminicola reveals dispensome structure, chromosome plasticity, and stealth pathogenesis.

PLoS Genet 2011 Jun 9;7(6):e1002070. Epub 2011 Jun 9.

USDA-Agricultural Research Service, Purdue University, West Lafayette, Indiana, United States of America.

The plant-pathogenic fungus Mycosphaerella graminicola (asexual stage: Septoria tritici) causes septoria tritici blotch, a disease that greatly reduces the yield and quality of wheat. This disease is economically important in most wheat-growing areas worldwide and threatens global food production. Control of the disease has been hampered by a limited understanding of the genetic and biochemical bases of pathogenicity, including mechanisms of infection and of resistance in the host. Unlike most other plant pathogens, M. graminicola has a long latent period during which it evades host defenses. Although this type of stealth pathogenicity occurs commonly in Mycosphaerella and other Dothideomycetes, the largest class of plant-pathogenic fungi, its genetic basis is not known. To address this problem, the genome of M. graminicola was sequenced completely. The finished genome contains 21 chromosomes, eight of which could be lost with no visible effect on the fungus and thus are dispensable. This eight-chromosome dispensome is dynamic in field and progeny isolates, is different from the core genome in gene and repeat content, and appears to have originated by ancient horizontal transfer from an unknown donor. Synteny plots of the M. graminicola chromosomes versus those of the only other sequenced Dothideomycete, Stagonospora nodorum, revealed conservation of gene content but not order or orientation, suggesting a high rate of intra-chromosomal rearrangement in one or both species. This observed "mesosynteny" is very different from synteny seen between other organisms. A surprising feature of the M. graminicola genome compared to other sequenced plant pathogens was that it contained very few genes for enzymes that break down plant cell walls, which was more similar to endophytes than to pathogens. The stealth pathogenesis of M. graminicola probably involves degradation of proteins rather than carbohydrates to evade host defenses during the biotrophic stage of infection and may have evolved from endophytic ancestors.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1371/journal.pgen.1002070DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3111534PMC
June 2011

Genetic differentiation at microsatellite loci among populations of Mycosphaerella graminicola from California, Indiana, Kansas, and North Dakota.

Phytopathology 2011 Oct;101(10):1251-9

Department of Plant Pathology, North Dakota State University, Fargo, ND, USA.

Mycosphaerella graminicola causes Septoria tritici blotch (STB) in wheat (Triticum aestivum) and is considered one of the most devastating pathogens of that crop in the United States. Although the genetic structures of M. graminicola populations from different countries have been analyzed using various molecular markers, relatively little is known about M. graminicola populations from geographically distinct areas of the United States and, in particular, of those from spring versus winter wheat. These are exposed to great differences in environmental conditions, length and season of host-free periods, and resistance sources used in geographically separated wheat breeding programs. Thus, there is more likely to be genetic differentiation between populations from spring versus winter wheat than there is among those within each region. To test this hypothesis, 330 single-spore isolates of M. graminicola representing 11 populations (1 from facultative winter wheat in California, 2 from spring wheat in North Dakota, and 8 from winter wheat in Indiana and Kansas) were analyzed for mating type frequency and for genetic variation at 17 microsatellite or simple-sequence repeat (SSR) loci. Analysis of clone-corrected data revealed an equal distribution of both mating types in the populations from Kansas, Indiana, and North Dakota, but a deviation from a 1:1 ratio in the California population. In total, 306 haplotypes were detected, almost all of which were unique in all 11 populations. High levels of gene diversity (H = 0.31 to 0.56) were observed within the 11 populations. Significant (P ≤ 0.05) gametic disequilibrium, as measured by the index of association (rBarD), was observed in California, one Indiana population (IN1), and three populations (KS1, KS2, and KS3) in Kansas that could not be explained by linkage. Corrected standardized fixation index (G″(ST)) values were 0.000 to 0.621 between the 11 populations and the majority of pairwise comparisons were statistically significant (P ≤ 0.001), suggesting some differentiation between populations. Analysis of molecular variance showed that there was a small but statistically significant level of genetic differentiation between populations from spring versus winter wheat. However, most of the total genetic variation (>98%) occurred within spring and winter wheat regions while <2% was due to genetic differentiation between these regions. Taken together, these results provide evidence that sexual recombination occurs frequently in the M. graminicola populations sampled and that most populations are genetically differentiated over the major spring- and winter-wheat-growing regions of the United States.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1094/PHYTO-08-10-0212DOI Listing
October 2011

A novel mode of chromosomal evolution peculiar to filamentous Ascomycete fungi.

Genome Biol 2011 24;12(5):R45. Epub 2011 May 24.

Australian Centre for Necrotrophic Fungal Pathogens, Curtin University, Perth, 6845, Australia.

Background: Gene loss, inversions, translocations, and other chromosomal rearrangements vary among species, resulting in different rates of structural genome evolution. Major chromosomal rearrangements are rare in most eukaryotes, giving large regions with the same genes in the same order and orientation across species. These regions of macrosynteny have been very useful for locating homologous genes in different species and to guide the assembly of genome sequences. Previous analyses in the fungi have indicated that macrosynteny is rare; instead, comparisons across species show no synteny or only microsyntenic regions encompassing usually five or fewer genes. To test the hypothesis that chromosomal evolution is different in the fungi compared to other eukaryotes, synteny was compared between species of the major fungal taxa.

Results: These analyses identified a novel form of evolution in which genes are conserved within homologous chromosomes, but with randomized orders and orientations. This mode of evolution is designated mesosynteny, to differentiate it from micro- and macrosynteny seen in other organisms. Mesosynteny is an alternative evolutionary pathway very different from macrosyntenic conservation. Surprisingly, mesosynteny was not found in all fungal groups. Instead, mesosynteny appears to be restricted to filamentous Ascomycetes and was most striking between species in the Dothideomycetes.

Conclusions: The existence of mesosynteny between relatively distantly related Ascomycetes could be explained by a high frequency of chromosomal inversions, but translocations must be extremely rare. The mechanism for this phenomenon is not known, but presumably involves generation of frequent inversions during meiosis.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1186/gb-2011-12-5-r45DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3219968PMC
February 2012

Identification and annotation of repetitive sequences in fungal genomes.

Methods Mol Biol 2011 ;722:33-50

USDA-ARS, Crop Production and Pest Control Research Unit, Purdue University, West Lafayette, IN, USA.

Advances in sequencing technologies have fundamentally changed the pace of genome sequencing projects and have contributed to the ever-increasing volume of genomic data. This has been paralleled by an increase in computational power and resources to process and translate raw sequence data into meaningful information. In addition to protein coding regions, an integral part of all the genomes studied so far has been the presence of repetitive sequences. Previously considered as "junk," numerous studies have implicated repetitive sequences in important biological and structural roles in the genome. Therefore, the identification and characterization of these repetitive sequences has become an indispensable part of genome sequencing projects. Numerous similarity-based and de novo methods have been developed to search for and annotate repeats in the genome, many of which have been discussed in this chapter.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1007/978-1-61779-040-9_3DOI Listing
September 2011

Effector diversification within compartments of the Leptosphaeria maculans genome affected by Repeat-Induced Point mutations.

Nat Commun 2011 Feb 15;2:202. Epub 2011 Feb 15.

INRA-Bioger, UR1290, Avenue Lucien Brétignières, BP 01, Thiverval-Grignon F-78850, France.

Fungi are of primary ecological, biotechnological and economic importance. Many fundamental biological processes that are shared by animals and fungi are studied in fungi due to their experimental tractability. Many fungi are pathogens or mutualists and are model systems to analyse effector genes and their mechanisms of diversification. In this study, we report the genome sequence of the phytopathogenic ascomycete Leptosphaeria maculans and characterize its repertoire of protein effectors. The L. maculans genome has an unusual bipartite structure with alternating distinct guanine and cytosine-equilibrated and adenine and thymine (AT)-rich blocks of homogenous nucleotide composition. The AT-rich blocks comprise one-third of the genome and contain effector genes and families of transposable elements, both of which are affected by repeat-induced point mutation, a fungal-specific genome defence mechanism. This genomic environment for effectors promotes rapid sequence diversification and underpins the evolutionary potential of the fungus to adapt rapidly to novel host-derived constraints.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/ncomms1189DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3105345PMC
February 2011

Gene encoding a c-type cyclin in Mycosphaerella graminicola is involved in aerial mycelium formation, filamentous growth, hyphal swelling, melanin biosynthesis, stress response, and pathogenicity.

Mol Plant Microbe Interact 2011 Apr;24(4):469-77

United States Department of Agriculture–Agricultural Research Service, 915 West State Street, IN, USA.

Mycosphaerella graminicola is an important wheat pathogen causing Septoria tritici blotch. To date, an efficient strategy to control M. graminicola has not been developed. More significantly, we have a limited understanding of the molecular mechanisms of M. graminicola pathogenicity. In this study, we attempted to characterize an MCC1-encoding c-type cyclin, a gene homologous to FCC1 in Fusarium verticillioides. Four independent MCC1 knock-out mutants were generated via Agrobacterium tumefaciens-mediated transformation. All of the MCC1 mutants showed consistent multiple phenotypes. Significant reductions in radial growth on potato dextrose agar (PDA) were observed in all of the MCC1 mutants. In addition, MCC1 gene-deletion mutants produced less aerial mycelium on PDA, showed delayed filamentous growth, had unusual hyphal swellings, produced more melanin, showed an increase in their stress tolerance response, and were reduced significantly in pathogenicity. These results indicate that the MCC1 gene is involved in multiple signaling pathways, including those involved in pathogenicity in M. graminicola.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1094/MPMI-04-10-0090DOI Listing
April 2011

MVE1, encoding the velvet gene product homolog in Mycosphaerella graminicola, is associated with aerial mycelium formation, melanin biosynthesis, hyphal swelling, and light signaling.

Appl Environ Microbiol 2011 Feb 29;77(3):942-53. Epub 2010 Nov 29.

Department of Botany and Plant Pathology, Purdue University, USDA-ARS, Crop Production and Pest Control Research Unit, 915 West State Street, West Lafayette, IN 47907-2054, USA.

The ascomycete fungus Mycosphaerella graminicola is an important pathogen of wheat that causes Septoria tritici blotch. Despite the serious impact of M. graminicola on wheat production worldwide, knowledge about its molecular biology is limited. The velvet gene, veA, is one of the key regulators of diverse cellular processes, including development and secondary metabolism in many fungi. However, the species analyzed to date are not related to the Dothideomycetes, the largest class of plant-pathogenic fungi, and the function of veA in this group is not known. To test the hypothesis that the velvet gene has similar functions in the Dothideomycetes, a veA-homologous gene, MVE1, was identified and gene deletion mutations (Δmve1) were generated in M. graminicola. All of the MVE1 mutants exhibited consistent pleiotropic phenotypes, indicating the involvement of MVE1 in multiple signaling pathways. Δmve1 strains displayed albino phenotypes with significant reductions in melanin biosynthesis and less production of aerial mycelia on agar plates. In liquid culture, Δmve1 strains showed abnormal hyphal swelling, which was suppressed completely by osmotic stress or lower temperature. In addition, MVE1 gene deletion led to hypersensitivity to shaking, reduced hydrophobicity, and blindness to light-dependent stimulation of aerial mycelium production. However, pathogenicity was not altered in Δmve1 strains. Therefore, the light-signaling pathway associated with MVE1 does not appear to be important for Septoria tritici blotch disease. Our data suggest that the MVE1 gene plays crucial roles in multiple key signaling pathways and is associated with light signaling in M. graminicola.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1128/AEM.01830-10DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3028728PMC
February 2011

Accidental amplification and inactivation of a methyltransferase gene eliminates cytosine methylation in Mycosphaerella graminicola.

Genetics 2010 Sep 6;186(1):67-77. Epub 2010 Jul 6.

Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana 47907, USA.

A de novo search for repetitive elements in the genome sequence of the wheat pathogen Mycosphaerella graminicola identified a family of repeats containing a DNA cytosine methyltransferase sequence (MgDNMT). All 23 MgDNMT sequences identified carried signatures of repeat induced point mutation (RIP). All copies were subtelomeric in location except for one on chromosome 6. Synteny with M. fijiensis implied that the nontelomeric copy on chromosome 6 served as a template for subsequent amplifications. Southern analysis revealed that the MgDNMT sequence also was amplified in 15 additional M. graminicola isolates from various geographical regions. However, this amplification event was specific to M. graminicola; a search for MgDNMT homologs identified only a single, unmutated copy in the genomes of 11 other ascomycetes. A genome-wide methylation assay revealed that M. graminicola lacks cytosine methylation, as expected if its MgDNMT gene is inactivated. Methylation was present in several other species tested, including the closest known relatives of M. graminicola, species S1 and S2. Therefore, the observed changes most likely occurred within the past 10,500 years since the divergence between M. graminicola and S1. Our data indicate that the recent amplification of a single-copy MgDNMT gene made it susceptible to RIP, resulting in complete loss of cytosine methylation in M. graminicola.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1534/genetics.110.117408DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2940312PMC
September 2010

Gearing up for comparative genomics: analyses of the fungal class Dothideomycetes.

New Phytol 2009 ;183(2):250-254

Plant Research International B.V., Wageningen University and Research Centre, P.O. Box 16, 6700 AA Wageningen, The Netherlands.

View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1111/j.1469-8137.2009.02906.xDOI Listing
September 2009

Meiosis drives extraordinary genome plasticity in the haploid fungal plant pathogen Mycosphaerella graminicola.

PLoS One 2009 Jun 10;4(6):e5863. Epub 2009 Jun 10.

Plant Research International BV, Wageningen University and Research Centre, Wageningen, The Netherlands.

Meiosis in the haploid plant-pathogenic fungus Mycosphaerella graminicola results in eight ascospores due to a mitotic division following the two meiotic divisions. The transient diploid phase allows for recombination among homologous chromosomes. However, some chromosomes of M. graminicola lack homologs and do not pair during meiosis. Because these chromosomes are not present universally in the genome of the organism they can be considered to be dispensable. To analyze the meiotic transmission of unequal chromosome numbers, two segregating populations were generated by crossing genetically unrelated parent isolates originating from Algeria and The Netherlands that had pathogenicity towards durum or bread wheat, respectively. Detailed genetic analyses of these progenies using high-density mapping (1793 DArT, 258 AFLP and 25 SSR markers) and graphical genotyping revealed that M. graminicola has up to eight dispensable chromosomes, the highest number reported in filamentous fungi. These chromosomes vary from 0.39 to 0.77 Mb in size, and represent up to 38% of the chromosomal complement. Chromosome numbers among progeny isolates varied widely, with some progeny missing up to three chromosomes, while other strains were disomic for one or more chromosomes. Between 15-20% of the progeny isolates lacked one or more chromosomes that were present in both parents. The two high-density maps showed no recombination of dispensable chromosomes and hence, their meiotic processing may require distributive disjunction, a phenomenon that is rarely observed in fungi. The maps also enabled the identification of individual twin isolates from a single ascus that shared the same missing or doubled chromosomes indicating that the chromosomal polymorphisms were mitotically stable and originated from nondisjunction during the second division and, less frequently, during the first division of fungal meiosis. High genome plasticity could be among the strategies enabling this versatile pathogen to quickly overcome adverse biotic and abiotic conditions in wheat fields.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0005863PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2689623PMC
June 2009

Analyses of expressed sequence tags from the maize foliar pathogen Cercospora zeae-maydis identify novel genes expressed during vegetative, infectious, and reproductive growth.

BMC Genomics 2008 Nov 4;9:523. Epub 2008 Nov 4.

Department of Plant Pathology, University of Arkansas, Fayetteville, Arkansas 72701, USA.

Background: The ascomycete fungus Cercospora zeae-maydis is an aggressive foliar pathogen of maize that causes substantial losses annually throughout the Western Hemisphere. Despite its impact on maize production, little is known about the regulation of pathogenesis in C. zeae-maydis at the molecular level. The objectives of this study were to generate a collection of expressed sequence tags (ESTs) from C. zeae-maydis and evaluate their expression during vegetative, infectious, and reproductive growth.

Results: A total of 27,551 ESTs was obtained from five cDNA libraries constructed from vegetative and sporulating cultures of C. zeae-maydis. The ESTs, grouped into 4088 clusters and 531 singlets, represented 4619 putative unique genes. Of these, 36% encoded proteins similar (E value < or = 10(-05)) to characterized or annotated proteins from the NCBI non-redundant database representing diverse molecular functions and biological processes based on Gene Ontology (GO) classification. We identified numerous, previously undescribed genes with potential roles in photoreception, pathogenesis, and the regulation of development as well as Zephyr, a novel, actively transcribed transposable element. Differential expression of selected genes was demonstrated by real-time PCR, supporting their proposed roles in vegetative, infectious, and reproductive growth.

Conclusion: Novel genes that are potentially involved in regulating growth, development, and pathogenesis were identified in C. zeae-maydis, providing specific targets for characterization by molecular genetics and functional genomics. The EST data establish a foundation for future studies in evolutionary and comparative genomics among species of Cercospora and other groups of plant pathogenic fungi.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1186/1471-2164-9-523DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2596140PMC
November 2008

Molecular Mapping of the Stb4 Gene for Resistance to Septoria tritici Blotch in Wheat.

Phytopathology 2004 Nov;94(11):1198-206

ABSTRACT Breeding wheat for resistance is the most effective means to control Septoria tritici blotch (STB), caused by the ascomycete Mycosphaerella graminicola (anamorph Septoria tritici). At least eight genes that confer resistance to STB in wheat have been identified. Among them, the Stb4 locus from the wheat cv. Tadinia showed resistance to M. graminicola at both seedling and adult-plant stages. However, no attempt has been made to map the Stb4 locus in the wheat genome. A mapping population of 77 F10 recombinant-inbred lines (RILs) derived from a three-way cross between the resistant cv. Tadinia and the susceptible parent (Yecora Rojo x UC554) was evaluated for disease resistance and molecular mapping. The RILs were tested with Argentina isolate I 89 of M. graminicola for one greenhouse season in Brazil during 1999, with an isolate from Brazil (IPBr1) for one field season in Piracicaba (Brazil) during 2000, and with Indiana tester isolate IN95-Lafayette-1196-WW-1-4 in the greenhouse during 2000 and 2001. The ratio of resistant:susceptible RILs was 1:1 in all three tests, confirming the single-gene model for control of resistance to STB in Tadinia. However, the patterns of resistance and susceptibility were different between the Indiana isolate and those from South America. For example, the ratio of RILs resistant to both the Indiana and Argentina isolates, resistant to one but susceptible to the other, and susceptible to both isolates was approximately 1:1:1:1, indicating that Tadinia may contain at least two genes for resistance to STB. A similar pattern was observed between the Indiana and Brazil isolates. The gene identified with the Indiana tester isolate was assumed to be the same as Stb4, whereas that revealed by the South American isolates may be new. Bulked-segregant analysis was used to identify amplified fragment length polymorphism (AFLP) and microsatellite markers linked to the presumed Stb4 gene. The AFLP marker EcoRI-ACTG/MseI-CAAA5 and microsatellite Xgwm111 were closely linked to the Stb4 locus in coupling at distances of 2.1 and 0.7 centimorgans (cM), respectively. A flanking marker, AFLP EAGG/ M-CAT10, was 4 cM from Stb4. The Stb4 gene was in a potential supercluster of resistance genes near the centromere on the short arm of wheat chromosome 7D that also contained Stb5 plus five previously identified genes for resistance to Russian wheat aphid. The microsatellite marker Xgwm111 identified in this study may be useful for facilitating the transfer of Stb4 into improved cultivars of wheat.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1094/PHYTO.2004.94.11.1198DOI Listing
November 2004

Identification and Molecular Mapping of a Gene in Wheat Conferring Resistance to Mycosphaerella graminicola.

Phytopathology 2003 Sep;93(9):1158-64

ABSTRACT Septoria tritici leaf blotch (STB), caused by the ascomycete Mycosphaerella graminicola (anamorph Septoria tritici), is an economically important disease of wheat. Breeding for resistance to STB is the most effective means to control this disease and can be facilitated through the use of molecular markers. However, molecular markers linked to most genes for resistance to STB are not yet available. This study was conducted to test for resistance in the parents of a standard wheat mapping population and to map any resistance genes identified. The population consisted of 130 F(10) recombinant-inbred lines (RILs) from a cross between the synthetic hexaploid wheat W7984 and cv. Opata 85. Genetic analysis indicated that a single major gene controls resistance to M. graminicola in this population. This putative resistance gene is now designated Stb8 and was mapped with respect to amplified fragment length polymorphism (AFLP) and microsatellite markers. An AFLP marker, EcoRI-ACG/MseI-CAG5, was linked in repulsion with the resistance gene at a distance of approximately 5.3 centimorgans (cM). Two flanking microsatellite markers, Xgwm146 and Xgwm577, were linked to the Stb8 gene on the long arm of wheat chromosome 7B at distances of 3.5 and 5.3 cM, respectively. The microsatellite markers identified in this study have potential for use in marker-assisted selection in breeding programs and for pyramiding of Stb8 with other genes for resistance to M. graminicola in wheat.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1094/PHYTO.2003.93.9.1158DOI Listing
September 2003

Minimum phylogenetic coverage: an additional criterion to guide the selection of microbial pathogens for initial genomic sequencing efforts.

Phytopathology 2004 Aug;94(8):800-4

ABSTRACT The scientific community has made a persuasive case to increase funding for genomic sequencing of microbial plant pathogens, and a number of objective criteria were developed to guide the selection of sequencing targets. However, this task still is complicated for fungi and Oomycetes, which are extremely diverse evolutionarily. Lack of a definite target number of organisms to be sequenced and inclusion of only a small segment of fungal diversity weaken the effort, which may reduce support and hinder efforts to increase the level of funding. These problems can be minimized by inclusion of phylogenetic relationship as an additional criterion to prioritize organisms for genomic sequencing. A phylogenetic analysis of 18S ribosomal DNA sequences revealed that many of the species proposed for genomic sequencing are very closely related, while other evolutionarily important groups, such as the Taphrinales, are underrepresented or ignored. By choosing one representative from each of the major clusters on the 18S tree, a minimum phylogenetic coverage (MPC) of the fungi and Oomycetes that have been proposed for genomic sequencing can be achieved by including seven Ascomycetes, four Basidiomycetes, and one Oomycete. A second round of 14 species could be sequenced to cover the major sub-branches within each of the 12 major clusters. This approach defines a tangible, achievable goal for genomic sequencing that could be used to lobby for additional funding. MPC also would assure support and participation by the largest number of plant pathologists because most would have access to a sequenced genome from a close relative of their organism of interest. Allocating funds for this effort might be achieved best through a competitive bidding process among sequencing centers rather than the traditional grants programs. MPC provides a logical criterion to help prioritize fungi, Oomycetes, and other microbial pathogens for genomic sequencing that generates a defined, tractable number of sequencing targets and could serve as a rallying point to unify plant pathologists toward achieving a common goal.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1094/PHYTO.2004.94.8.800DOI Listing
August 2004

Analysis of genotypic diversity data for populations of microorganisms.

Phytopathology 2003 Jun;93(6):738-46

ABSTRACT Estimation of genotypic diversity is an important component of the analysis of the genetic structure of plant pathogen and microbial populations. Estimates of genotypic diversity are a function of both the number of genotypes observed in a sample (genotype richness) and the evenness of distribution of genotypes within the sample. Currently used measures of genotypic diversity have inherent problems that could lead to incorrect conclusions, particularly when diversity is low or sample sizes differ. The number of genotypes observed in a sample depends on the technique used to assay for genetic variation; each technique will affect the maximum number of genotypes that can be detected. We developed an approach to analysis of genotypic diversity in plant pathology that makes specific reference to the techniques used for identifying genotypes. Preferably, populations that are being compared should be very similar in sample size. In this case, the number of genotypes observed can be used directly for comparing richness. In most cases, sample sizes differ and use of the rarefaction method to calculate richness is more appropriate. In all cases, scaling either Stoddart and Taylor's G or Shannon and Wiener's H' by sample size should be avoided. Under those circumstances where it might be important to distinguish whether richness or evenness contribute more to diversity, a bootstrapping approach, where confidence intervals are calculated for indices of diversity and evenness, is recommended.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1094/PHYTO.2003.93.6.738DOI Listing
June 2003