Fungal Genetics and Biology最新文献

{"title":"RHO-3 plays a significant role in hyphal extension rate, conidiation, and the integrity of the Spitzenkörper in Neurospora crassa","authors":"Martha M. Ornelas-Llamas ,&nbsp;Luis L. Pérez-Mozqueda ,&nbsp;Olga A. Callejas-Negrete ,&nbsp;Ernestina Castro-Longoria","doi":"10.1016/j.fgb.2024.103873","DOIUrl":"10.1016/j.fgb.2024.103873","url":null,"abstract":"<div><p>The Rho family of monomeric GTPases act as signaling proteins to establish and maintain cell polarity and other essential cellular processes. Rho3 is a GTPase of the Rho family that is exclusive of fungi that regulate cell polarity in yeast. However, studies have yet to explore its function in filamentous fungi. In this work, we investigated the role of RHO-3 in the model organism <em>Neurospora crassa</em>. Confocal microscopy analysis revealed that RHO-3 localizes in the outer region of the Spitzenkörper (Spk), in the plasma membrane from region II to the beginning of region III, and in the septa of mature hyphae. The phenotypic effect of the <em>rho-3</em> deletion was analyzed. The results revealed that the <em>rho-3</em> null strain showed severe defects in growth rate, aerial hyphae length, and conidia production. The organization of the Spk is also affected in the absence of RHO-3. Co-expression analysis of GFP-RHO-3 with glucan synthase 1 (GS-1-mChFP) and chitin synthase 1 (CHS-1-mChFP) revealed that RHO-3 localizes in the external region of the Spk in the macrovesicles zone. In summary, our results suggest that RHO-3 is not essential for the polarized growth of hyphae but plays a significant role in hyphal extension rate, conidiation, sexual reproduction and the integrity of the Spk, possibly regulating the delivery of macrovesicles to the apical dome.</p></div>","PeriodicalId":55135,"journal":{"name":"Fungal Genetics and Biology","volume":"171 ","pages":"Article 103873"},"PeriodicalIF":3.0,"publicationDate":"2024-01-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139517715","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"AwSclB regulates a network for Aspergillus westerdijkiae asexual sporulation and secondary metabolism independent of the fungal light control","authors":"Gang Wang ,&nbsp;Yibing Liu ,&nbsp;Yafan Hu ,&nbsp;Jiaqi Pan ,&nbsp;Zifan Wei ,&nbsp;Bowen Tai ,&nbsp;Bolei Yang ,&nbsp;Erfeng Li ,&nbsp;Fuguo Xing","doi":"10.1016/j.fgb.2024.103865","DOIUrl":"10.1016/j.fgb.2024.103865","url":null,"abstract":"<div><p>As a prevalent pathogenic fungus, <em>Aspergillus westerdijkiae</em> poses a threat to both food safety and human health. The fungal growth, conidia production and ochratoxin A (OTA) in <em>A. weterdijkiae</em> are regulated by many factors especially transcription factors. In this study, a transcription factor <em>AwSclB</em> in <em>A. westerdijkiae</em> was identified and its function in asexual sporulation and OTA biosynthesis was investigated. In addition, the effect of light control on <em>AwSclB</em> regulation was also tested. The deletion of <em>AwSclB</em> gene could reduce conidia production by down-regulation of conidia genes and increase OTA biosynthesis by up-regulation of cluster genes, regardless under light or dark conditions. It is worth to note that the inhibitory effect of light on OTA biosynthesis was reversed by the knockout of <em>AwSclB</em> gene. The yeast one-hybrid assay indicated that <em>AwSclB</em> could interact with the promoters of <em>BrlA</em>, <em>ConJ</em> and <em>OtaR1</em> genes. This result suggests that <em>AwSclB</em> in <em>A. westerdijkiae</em> can directly regulate asexual conidia formation by activating the central developmental pathway <em>BrlA-AbaA-WetA</em> through up-regulating the expression of <em>AwBrlA</em>, and promote the light response of the strain by activating <em>ConJ</em>. However, <em>AwSclB</em> itself is unable to respond to light regulation. This finding will deepen our understanding of the molecular regulation of <em>A. westerdijkiae</em> development and secondary metabolism, and provide potential targets for the development of new fungicides.</p></div>","PeriodicalId":55135,"journal":{"name":"Fungal Genetics and Biology","volume":"171 ","pages":"Article 103865"},"PeriodicalIF":3.0,"publicationDate":"2024-01-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139509204","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genomic, transcriptomic, and ecological diversity of Penicillium species in cheese rind microbiomes","authors":"Ruby Ye ,&nbsp;Megan Biango-Daniels ,&nbsp;Jacob L. Steenwyk ,&nbsp;Antonis Rokas ,&nbsp;Nicolas L. Louw ,&nbsp;Robert Nardella ,&nbsp;Benjamin E. Wolfe","doi":"10.1016/j.fgb.2023.103862","DOIUrl":"10.1016/j.fgb.2023.103862","url":null,"abstract":"<div><p>Although <em>Penicillium</em> molds can have significant impacts on agricultural, industrial, and biomedical systems, the ecological roles of <em>Penicillium</em> species in many microbiomes are not well characterized. Here we utilized a collection of 35 <em>Penicillium</em> strains isolated from cheese rinds to broadly investigate the genomic potential for secondary metabolism in cheese-associated <em>Penicillium</em> species, the impact of <em>Penicillium</em> on bacterial community assembly, and mechanisms of <em>Penicillium</em>-bacteria interactions. Using antiSMASH, we identified 1558 biosynthetic gene clusters, 406 of which were mapped to known pathways, including several mycotoxins and antimicrobial compounds. By measuring bacterial abundance and fungal mRNA expression when culturing representative <em>Penicillium</em> strains with a cheese rind bacterial community, we observed divergent impacts of different <em>Penicillium</em> strains, from strong inhibitors of bacterial growth to those with no impact on bacterial growth or community composition. Through differential mRNA expression analyses, <em>Penicillium</em> strains demonstrated limited differential gene expression in response to the bacterial community. We identified a few shared responses between the eight tested <em>Penicillium</em> strains, primarily upregulation of nutrient metabolic pathways, but we did not identify a conserved fungal response to growth in a multispecies community. These results in tandem suggest high variation among cheese-associated <em>Penicillium</em> species in their ability to shape bacterial community development and highlight important ecological diversity within this iconic genus.</p></div>","PeriodicalId":55135,"journal":{"name":"Fungal Genetics and Biology","volume":"171 ","pages":"Article 103862"},"PeriodicalIF":3.0,"publicationDate":"2024-01-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139423948","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Methyl jasmonate differentially and tissue-specifically regulated the expression of arginine catabolism–related genes and proteins in Agaricus bisporus mushrooms during storage","authors":"Hanyue Jiang ,&nbsp;Huadong Wang ,&nbsp;Xiuhong Wang ,&nbsp;Yating Wang ,&nbsp;Rui Song ,&nbsp;Shuai Yuan ,&nbsp;Zhenchuan Fan ,&nbsp;Demei Meng","doi":"10.1016/j.fgb.2024.103864","DOIUrl":"10.1016/j.fgb.2024.103864","url":null,"abstract":"<div><p>Methyl jasmonate (MeJA)-regulated postharvest quality retention of <em>Agaricus bisporus</em> fruiting bodies is associated with arginine catabolism. However, the mechanism of MeJA-regulated arginine catabolism in edible mushrooms is still unclear. This study aimed to investigate the regulatory modes of MeJA on the expression of arginine catabolism–related genes and proteins in intact and different tissues of <em>A. bisporus</em> mushrooms during storage. Results showed that exogenous MeJA treatment activated endogenous JA biosynthesis in <em>A. bisporus</em> mushrooms, and differentially and tissue-specifically regulated the expression of arginine catabolism–related genes (<em>AbARG</em>, <em>AbODC</em>, <em>AbSPE-SDH</em>, <em>AbSPDS</em>, <em>AbSAMDC,</em> and <em>AbASL</em>) and proteins (AbARG, AbSPE-SDH, AbASL, and AbASS). MeJA caused no significant change in <em>AbASS</em> expression but resulted in a dramatic increase in AbASS protein level. Neither the expression of the <em>AbSAMS</em> gene nor the AbSAMS protein was conspicuously altered upon MeJA treatment. Additionally, MeJA reduced the contents of arginine and ornithine and induced the accumulation of free putrescine and spermidine, which was closely correlated with MeJA-regulated arginine catabolism–related genes and proteins. Hence, the results suggested that the differential and tissue-specific regulation of arginine catabolism–related genes and proteins by MeJA contributed to their selective involvement in the postharvest continuing development and quality retention of button mushrooms.</p></div>","PeriodicalId":55135,"journal":{"name":"Fungal Genetics and Biology","volume":"170 ","pages":"Article 103864"},"PeriodicalIF":3.0,"publicationDate":"2024-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139409895","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Creating large chromosomal segment deletions in Aspergillus flavus by a dual CRISPR/Cas9 system: Deletion of gene clusters for production of aflatoxin, cyclopiazonic acid, and ustiloxin B","authors":"Perng-Kuang Chang","doi":"10.1016/j.fgb.2023.103863","DOIUrl":"10.1016/j.fgb.2023.103863","url":null,"abstract":"<div><p><em>Aspergillus flavus</em> produces hepatocarcinogenic aflatoxin that adversely impacts human and animal health and international trade. A promising means to manage preharvest aflatoxin contamination of crops is biological control, which employs non-aflatoxigenic <em>A. flavus</em> isolates possessing defective aflatoxin gene clusters to outcompete field toxigenic populations. However, these isolates often produce other toxic metabolites. The CRISPR/Cas9 technology has greatly advanced genome editing and gene functional studies. Its use in deleting large chromosomal segments of filamentous fungi is rarely reported. A system of dual CRISPR/Cas9 combined with a 60-nucleotide donor DNA that allowed removal of <em>A. flavus</em> gene clusters involved in production of harmful specialized metabolites was established. It efficiently deleted a 102-kb segment containing both aflatoxin and cyclopiazonic acid gene clusters from toxigenic <em>A. flavus</em> morphotypes, L-type and S-type. It further deleted the 27-kb ustiloxin B gene cluster of a resulting L-type mutant. Overall efficiencies of deletion ranged from 66.6 % to 85.6 % and efficiencies of deletions repaired by a single copy of donor DNA ranged from 50.5 % to 72.7 %. To determine the capacity of this technique, a pigment-screening setup based on absence of aspergillic acid gene cluster was devised. Chromosomal segments of 201 kb and 301 kb were deleted with efficiencies of 57.7 % to 69.2 %, respectively. This system used natural <em>A. flavus</em> isolates as recipients, eliminated a forced-recycling step to produce recipients for next round deletion, and generated maker-free deletants with sequences predefined by donor DNA. The research provides a method for creating genuine atoxigenic biocontrol strains friendly for field trial release.</p></div>","PeriodicalId":55135,"journal":{"name":"Fungal Genetics and Biology","volume":"170 ","pages":"Article 103863"},"PeriodicalIF":3.0,"publicationDate":"2023-12-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1087184523000944/pdfft?md5=07e0850522dfb1bfca59fceadd36aa1f&pid=1-s2.0-S1087184523000944-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139057421","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Multi-locus sequence typing and phylogenetics of Cryptococcus neoformans AD hybrids","authors":"M. Cogliati ,&nbsp;P.E. Chidebelu ,&nbsp;M. Hitchcock ,&nbsp;M. Chen ,&nbsp;V. Rickerts ,&nbsp;S. Ackermann ,&nbsp;M. Desnos Ollivier ,&nbsp;J. Inácio ,&nbsp;U. Nawrot ,&nbsp;M. Florek ,&nbsp;K.J. Kwon-Chung ,&nbsp;D.-H. Yang ,&nbsp;C. Firacative ,&nbsp;C.A. Puime ,&nbsp;P. Escandon ,&nbsp;S. Bertout ,&nbsp;F. Roger ,&nbsp;J. Xu","doi":"10.1016/j.fgb.2023.103861","DOIUrl":"10.1016/j.fgb.2023.103861","url":null,"abstract":"<div><p>Hybrid AD strains of the human pathogenic <em>Cryptococcus neoformans</em> species complex have been reported from many parts of the world. However, their origin, diversity, and evolution are incompletely understood. In this study, we analyzed 102 AD hybrid strains representing 21 countries on five continents. For each strain, we obtained its mating type and its allelic sequences at each of the seven loci that have been used for genotyping haploid serotypes A and D strains of the species complex by the <em>Cryptococcus</em> research community. Our results showed that most AD hybrids exhibited loss of heterozygosity at one or more of the seven analyzed loci. Phylogenetic and population genetic analyses of the allelic sequences revealed multiple origins of the hybrids within each continent, dating back to one million years ago in Africa and up to the present in other continents. We found evidence for clonal reproduction and long-distance dispersal of these hybrids in nature. Comparisons with the global haploid serotypes A and D strains identified new alleles and new haploid multi-locus genotypes in AD hybrids, consistent with the presence of yet-to-be discovered genetic diversity in haploid populations of this species complex in nature. Together, our results indicate that AD hybrids can be effectively genotyped using the same multi-locus sequencing type approach as that established for serotypes A and D strains. Our comparisons of the AD hybrids among each other as well as with the global haploid serotypes A and D strains revealed novel genetic diversity as well as evidence for multiple origins and dynamic evolution of these hybrids in nature.</p></div>","PeriodicalId":55135,"journal":{"name":"Fungal Genetics and Biology","volume":"170 ","pages":"Article 103861"},"PeriodicalIF":3.0,"publicationDate":"2023-12-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1087184523000920/pdfft?md5=95f92c11deffa51bb10ea69034028776&pid=1-s2.0-S1087184523000920-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138833112","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Unidirectional mating-type switching is underpinned by a conserved MAT1 locus architecture","authors":"P. Markus Wilken,&nbsp;Frances A. Lane,&nbsp;Emma T. Steenkamp,&nbsp;Michael J. Wingfield,&nbsp;Brenda D. Wingfield","doi":"10.1016/j.fgb.2023.103859","DOIUrl":"10.1016/j.fgb.2023.103859","url":null,"abstract":"<div><p>Unidirectional mating-type switching is a form of homothallic reproduction known only in a small number of filamentous ascomycetes. Their ascospores can give rise to either self-sterile isolates that require compatible partners for subsequent sexual reproduction, or self-fertile individuals capable of completing this process in isolation. The limited studies previously conducted in these fungi suggest that the differences in mating specificity are determined by the architecture of the <em>MAT1</em> locus. In self-fertile isolates that have not undergone unidirectional mating-type switching, the locus contains both <em>MAT1-1</em> and <em>MAT1-2</em> mating-type genes, typical of primary homothallism. In the self-sterile isolates produced after a switching event, the <em>MAT1-2</em> genes are lacking from the locus, likely due to a recombination-mediated deletion of the <em>MAT1-2</em> gene information. To determine whether these arrangements of the <em>MAT1</em> locus support unidirectional mating-type switching in the <em>Ceratocystidaceae</em>, the largest known fungal assemblage capable of this reproduction strategy, a combination of genetic and genomic approaches were used. The <em>MAT1</em> locus was annotated in representative species of <em>Ceratocystis, Endoconidiophora,</em> and <em>Davidsoniella</em>. In all cases, <em>MAT1-2</em> genes interrupted the <em>MAT1-1</em>–<em>1</em> gene in self-fertile isolates. The <em>MAT1-2</em> genes were flanked by two copies of a direct repeat that accurately predicted the boundaries of the deletion event that would yield the <em>MAT1</em> locus of self-sterile isolates. Although the relative position of the <em>MAT1-2</em> gene region differed among species, it always disrupted the <em>MAT1-1</em>–<em>1</em> gene and/or its expression in the self-fertile <em>MAT1</em> locus. Following switching, this gene and/or its expression was restored in the self-sterile arrangement of the locus. This mirrors what has been reported in other species capable of unidirectional mating-type switching, providing the strongest support for a conserved <em>MAT1</em> locus structure that is associated with this process. This study contributes to our understanding of the evolution of unidirectional mating-type switching.</p></div>","PeriodicalId":55135,"journal":{"name":"Fungal Genetics and Biology","volume":"170 ","pages":"Article 103859"},"PeriodicalIF":3.0,"publicationDate":"2023-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1087184523000907/pdfft?md5=82f0f3ed686f38efa920b3fdc06cc897&pid=1-s2.0-S1087184523000907-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138744426","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Pathogenicity chromosome of Fusarium oxysporum f. sp. cepae","authors":"Kosei Sakane ,&nbsp;Mitsunori Akiyama ,&nbsp;Sudisha Jogaiah ,&nbsp;Shin-ichi Ito ,&nbsp;Kazunori Sasaki","doi":"10.1016/j.fgb.2023.103860","DOIUrl":"10.1016/j.fgb.2023.103860","url":null,"abstract":"<div><p><em>Fusarium oxysporum</em> f. sp. <em>cepae</em> (<em>Foc</em>) is the causative agent of Fusarium basal rot disease in onions, which leads to catastrophic global crop production losses. Therefore, the interaction of <em>Foc</em> with its host has been actively investigated, and the pathogen-specific (PS) regions of the British strain <em>Foc</em>_FUS2 have been identified. However, it has not been experimentally determined whether the identified PS region plays a role in pathogenicity. To identify the pathogenicity chromosome in the Japanese strain <em>Foc</em>_TA, we initially screened effector candidates, defined as small proteins with a signal peptide that contain two or more cysteines, from genome sequence data. Twenty-one candidate effectors were identified, five of which were expressed during infection. Of the expressed effector candidates, four were located on the 4-Mb-sized chromosome in <em>Foc</em>_TA. To clarify the relationship between pathogenicity and the 4-Mb-sized chromosome in <em>Foc</em>_TA, nine putative 4-Mb-sized chromosome loss strains were generated by treatment with benomyl (a mitotic inhibitor drug). A pathogenicity test with putative 4-Mb-sized chromosome loss strains showed that these strains were impaired in their pathogenicity toward onions. Genome analysis of three putative 4-Mb-sized chromosome loss strains revealed that two strains lost a 4-Mb-sized chromosome in common, and another strain maintained a 0.9-Mb region of the 4-Mb-sized chromosome. Our findings show that the 4-Mb-sized chromosome is the pathogenicity chromosome in <em>Foc</em>_TA, and the 3.1-Mb region within the 4-Mb-sized chromosome is required for full pathogenicity toward onion.</p></div>","PeriodicalId":55135,"journal":{"name":"Fungal Genetics and Biology","volume":"170 ","pages":"Article 103860"},"PeriodicalIF":3.0,"publicationDate":"2023-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138813691","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Pathogenicity chromosome of Fusarium oxysporum f. sp. cepae","authors":"Kosei Sakane, Mitsunori Akiyama, Sudisha Jogaiah, Shin-ichi Ito, Kazunori Sasaki","doi":"10.1016/j.fgb.2023.103860","DOIUrl":"https://doi.org/10.1016/j.fgb.2023.103860","url":null,"abstract":"<p><em>Fusarium oxysporum</em> f. sp. <em>cepae</em> (<em>Foc</em>) is the causative agent of Fusarium basal rot disease in onions, which leads to catastrophic global crop production losses. Therefore, the interaction of <em>Foc</em> with its host has been actively investigated, and the pathogen-specific (PS) regions of the British strain <em>Foc</em>_FUS2 have been identified. However, it has not been experimentally determined whether the identified PS region plays a role in pathogenicity. To identify the pathogenicity chromosome in the Japanese strain <em>Foc</em>_TA, we initially screened effector candidates, defined as small proteins with a signal peptide that contain two or more cysteines, from genome sequence data. Twenty-one candidate effectors were identified, five of which were expressed during infection. Of the expressed effector candidates, four were located on the 4-Mb-sized chromosome in <em>Foc</em>_TA. To clarify the relationship between pathogenicity and the 4-Mb-sized chromosome in <em>Foc</em>_TA, nine putative 4-Mb-sized chromosome loss strains were generated by treatment with benomyl (a mitotic inhibitor drug). A pathogenicity test with putative 4-Mb-sized chromosome loss strains showed that these strains were impaired in their pathogenicity toward onions. Genome analysis of three putative 4-Mb-sized chromosome loss strains revealed that two strains lost a 4-Mb-sized chromosome in common, and another strain maintained a 0.9-Mb region of the 4-Mb-sized chromosome. Our findings show that the 4-Mb-sized chromosome is the pathogenicity chromosome in <em>Foc</em>_TA, and the 3.1-Mb region within the 4-Mb-sized chromosome is required for full pathogenicity toward onion.</p>","PeriodicalId":55135,"journal":{"name":"Fungal Genetics and Biology","volume":"22 1","pages":""},"PeriodicalIF":3.0,"publicationDate":"2023-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138820821","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Sequence capture identifies fastidious chytrid fungi directly from host tissue","authors":"Kevin P. Mulder ,&nbsp;Anna E. Savage ,&nbsp;Brian Gratwicke ,&nbsp;Joyce E. Longcore ,&nbsp;Ed Bronikowski ,&nbsp;Matthew Evans ,&nbsp;Ana V. Longo ,&nbsp;Naoko P. Kurata ,&nbsp;Tim Walsh ,&nbsp;Frank Pasmans ,&nbsp;Nancy McInerney ,&nbsp;Suzan Murray ,&nbsp;An Martel ,&nbsp;Robert C. Fleischer","doi":"10.1016/j.fgb.2023.103858","DOIUrl":"10.1016/j.fgb.2023.103858","url":null,"abstract":"<div><p>The chytrid fungus <em>Batrachochytrium dendrobatidis</em> (Bd) was discovered in 1998 as the cause of chytridiomycosis, an emerging infectious disease causing mass declines in amphibian populations worldwide. The rapid population declines of the 1970s-1990s were likely caused by the spread of a highly virulent lineage belonging to the Bd-GPL clade that was introduced to naïve susceptible populations. Multiple genetically distinct and regional lineages of Bd have since been isolated and sequenced, greatly expanding the known biological diversity within this fungal pathogen. To date, most Bd research has been restricted to the limited number of samples that could be isolated using culturing techniques, potentially causing a selection bias for strains that can grow on media and missing other unculturable or fastidious strains that are also present on amphibians. We thus attempted to characterize potentially non-culturable genetic lineages of Bd from distinct amphibian taxa using sequence capture technology on DNA extracted from host tissue and swabs. We focused our efforts on host taxa from two different regions that likely harbored distinct Bd clades: (1) wild-caught leopard frogs (<em>Rana</em>) from North America, and (2) a Japanese Giant Salamander (<em>Andrias japonicus</em>) at the Smithsonian Institution’s National Zoological Park that exhibited signs of disease and tested positive for Bd using qPCR, but multiple attempts failed to isolate and culture the strain for physiological and genetic characterization. We successfully enriched for and sequenced thousands of fungal genes from both host clades, and Bd load was positively associated with number of recovered Bd sequences. Phylogenetic reconstruction placed all the <em>Rana</em>-derived strains in the Bd-GPL clade. In contrast, the <em>A. japonicus</em> strain fell within the Bd-Asia3 clade, expanding the range of this clade and generating additional genomic data to confirm its placement. The retrieved ITS locus matched public barcoding data from wild <em>A. japonicus</em> and Bd infections found on other amphibians in India and China, suggesting that this uncultured clade is widespread across Asia. Our study underscores the importance of recognizing and characterizing the hidden diversity of fastidious strains in order to reconstruct the spatiotemporal and evolutionary history of Bd. The success of the sequence capture approach highlights the utility of directly sequencing pathogen DNA from host tissue to characterize cryptic diversity that is missed by culture-reliant approaches.</p></div>","PeriodicalId":55135,"journal":{"name":"Fungal Genetics and Biology","volume":"170 ","pages":"Article 103858"},"PeriodicalIF":3.0,"publicationDate":"2023-12-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138687375","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}