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Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium (2010)

L. J. Ma ; H. C. van der Does ; K. A. Borkovich ; [et al.]

Nature Publishing Group (NPG)

In: Nature. 464(7287): 367-73. doi: 10.1038/nature08850.

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Publication Date: 2010-03-20

Description: Fusarium species are among the most important phytopathogenic and toxigenic fungi. To understand the molecular underpinnings of pathogenicity in the genus Fusarium, we compared the genomes of three phenotypically diverse species: Fusarium graminearum, Fusarium verticillioides and Fusarium oxysporum f. sp. lycopersici. Our analysis revealed lineage-specific (LS) genomic regions in F. oxysporum that include four entire chromosomes and account for more than one-quarter of the genome. LS regions are rich in transposons and genes with distinct evolutionary profiles but related to pathogenicity, indicative of horizontal acquisition. Experimentally, we demonstrate the transfer of two LS chromosomes between strains of F. oxysporum, converting a non-pathogenic strain into a pathogen. Transfer of LS chromosomes between otherwise genetically isolated strains explains the polyphyletic origin of host specificity and the emergence of new pathogenic lineages in F. oxysporum. These findings put the evolution of fungal pathogenicity into a new perspective.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3048781/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉 〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3048781/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ma, Li-Jun -- van der Does, H Charlotte -- Borkovich, Katherine A -- Coleman, Jeffrey J -- Daboussi, Marie-Josee -- Di Pietro, Antonio -- Dufresne, Marie -- Freitag, Michael -- Grabherr, Manfred -- Henrissat, Bernard -- Houterman, Petra M -- Kang, Seogchan -- Shim, Won-Bo -- Woloshuk, Charles -- Xie, Xiaohui -- Xu, Jin-Rong -- Antoniw, John -- Baker, Scott E -- Bluhm, Burton H -- Breakspear, Andrew -- Brown, Daren W -- Butchko, Robert A E -- Chapman, Sinead -- Coulson, Richard -- Coutinho, Pedro M -- Danchin, Etienne G J -- Diener, Andrew -- Gale, Liane R -- Gardiner, Donald M -- Goff, Stephen -- Hammond-Kosack, Kim E -- Hilburn, Karen -- Hua-Van, Aurelie -- Jonkers, Wilfried -- Kazan, Kemal -- Kodira, Chinnappa D -- Koehrsen, Michael -- Kumar, Lokesh -- Lee, Yong-Hwan -- Li, Liande -- Manners, John M -- Miranda-Saavedra, Diego -- Mukherjee, Mala -- Park, Gyungsoon -- Park, Jongsun -- Park, Sook-Young -- Proctor, Robert H -- Regev, Aviv -- Ruiz-Roldan, M Carmen -- Sain, Divya -- Sakthikumar, Sharadha -- Sykes, Sean -- Schwartz, David C -- Turgeon, B Gillian -- Wapinski, Ilan -- Yoder, Olen -- Young, Sarah -- Zeng, Qiandong -- Zhou, Shiguo -- Galagan, James -- Cuomo, Christina A -- Kistler, H Corby -- Rep, Martijn -- BBS/E/C/00004973/Biotechnology and Biological Sciences Research Council/United Kingdom -- DP1 OD003958/OD/NIH HHS/ -- R01 GM086565/GM/NIGMS NIH HHS/ -- R01 GM086565-03/GM/NIGMS NIH HHS/ -- R01 HG000225/HG/NHGRI NIH HHS/ -- England -- Nature. 2010 Mar 18;464(7287):367-73. doi: 10.1038/nature08850.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉The Broad Institute, Cambridge, Massachusetts 02141, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20237561" target="_blank"〉PubMed〈/a〉

Keywords: Chromosomes, Fungal/*genetics ; Evolution, Molecular ; Fusarium/classification/*genetics/*pathogenicity ; Genome, Fungal/*genetics ; *Genomics ; Host-Parasite Interactions/genetics ; Multigene Family/genetics ; Phenotype ; Phylogeny ; Proteome/genetics ; Sequence Analysis, DNA ; Synteny/genetics ; Virulence/genetics

Print ISSN: 0028-0836

Electronic ISSN: 1476-4687

Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics

Published by Nature Publishing Group (NPG)

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The Fusarium graminearum genome reveals a link between localized polymorphism and pathogen specialization (2007)

C. A. Cuomo ; U. Guldener ; J. R. Xu ; [et al.]

American Association for the Advancement of Science (AAAS)

In: Science. 317(5843): 1400-2. doi: 10.1126/science.1143708.

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Publication Date: 2007-09-08

Description: We sequenced and annotated the genome of the filamentous fungus Fusarium graminearum, a major pathogen of cultivated cereals. Very few repetitive sequences were detected, and the process of repeat-induced point mutation, in which duplicated sequences are subject to extensive mutation, may partially account for the reduced repeat content and apparent low number of paralogous (ancestrally duplicated) genes. A second strain of F. graminearum contained more than 10,000 single-nucleotide polymorphisms, which were frequently located near telomeres and within other discrete chromosomal segments. Many highly polymorphic regions contained sets of genes implicated in plant-fungus interactions and were unusually divergent, with higher rates of recombination. These regions of genome innovation may result from selection due to interactions of F. graminearum with its plant hosts.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cuomo, Christina A -- Guldener, Ulrich -- Xu, Jin-Rong -- Trail, Frances -- Turgeon, B Gillian -- Di Pietro, Antonio -- Walton, Jonathan D -- Ma, Li-Jun -- Baker, Scott E -- Rep, Martijn -- Adam, Gerhard -- Antoniw, John -- Baldwin, Thomas -- Calvo, Sarah -- Chang, Yueh-Long -- Decaprio, David -- Gale, Liane R -- Gnerre, Sante -- Goswami, Rubella S -- Hammond-Kosack, Kim -- Harris, Linda J -- Hilburn, Karen -- Kennell, John C -- Kroken, Scott -- Magnuson, Jon K -- Mannhaupt, Gertrud -- Mauceli, Evan -- Mewes, Hans-Werner -- Mitterbauer, Rudolf -- Muehlbauer, Gary -- Munsterkotter, Martin -- Nelson, David -- O'donnell, Kerry -- Ouellet, Therese -- Qi, Weihong -- Quesneville, Hadi -- Roncero, M Isabel G -- Seong, Kye-Yong -- Tetko, Igor V -- Urban, Martin -- Waalwijk, Cees -- Ward, Todd J -- Yao, Jiqiang -- Birren, Bruce W -- Kistler, H Corby -- U54 HG003067/HG/NHGRI NIH HHS/ -- New York, N.Y. -- Science. 2007 Sep 7;317(5843):1400-2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Broad Institute of the Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17823352" target="_blank"〉PubMed〈/a〉

Keywords: DNA, Fungal ; Evolution, Molecular ; Fusarium/*genetics/physiology ; *Genome, Fungal ; Hordeum/microbiology ; Molecular Sequence Data ; Plant Diseases/microbiology ; Point Mutation ; *Polymorphism, Genetic ; Polymorphism, Single Nucleotide ; Sequence Analysis, DNA

Print ISSN: 0036-8075

Electronic ISSN: 1095-9203

Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics

Published by American Association for the Advancement of Science (AAAS)

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Ultrastructure of infection-thread development during the infection of soybean by Rhizobium japonicum (1985)

Turgeon, B. G. ; Bauer, W. D.

Springer

Planta 163 (1985), S. 328-349

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ISSN: 1432-2048

Keywords: Glycine (Rhizobium infection) ; Infection thread ; Rhizobium ; Root hair infection ; Symbiosis (legume-Rhizobium)

Source: Springer Online Journal Archives 1860-2000

Topics: Biology

Notes: Abstract The location and topography of infection sites in soybean (Glycine max (L.) Merr.) root hairs spot-inoculated with Rhizobium japonicum have been studied at the ultrastructural level. Infections commonly developed at sites created when the induced deformation of an emerging root hair caused a portion of the root-hair cell wall to press against an adjacent epidermal cell, entrapping rhizobia within the pocket between the two host cells. Infections were initiated by bacteria which became embedded in the mucigel in the enclosed groove. Infection-thread formation in soybean appears to involve degradation of mucigel material and localized disruption of the outer layer of the folded hair cell wall by one or more entrapped rhizobia. Rhizobia at the site of penetration are separated from the host cytoplasm by the host plasmalemma and by a layer of wall material that appears similar or identical to the normal inner layer of the hair cell wall. Proliferation of the bacteria results in an irregular, wall-bound sac near the site of penetration. Tubular infection threads, bounded by wall material of the same appearance as that surrounding the sac, emerge from the sac to carry rhizobia roughly single-file into the hair cell. Growing regions of the infection sac or thread are surrounded by host cytoplasm with high concentrations of organelles associated with synthesis and deposition of membrane and cell-wall material. The threads follow a highly irregular path toward the base of the hair cell. Threads commonly run along the base of the hair cell for some distance, and may branch and penetrate into subjacent cortical cells at several points in a manner analagous to the initial penetration of the root hair.

Type of Medium: Electronic Resource

URL: http://dx.doi.org/10.1007/BF00395142

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Transcripts at the mating type locus of Cochliobolus heterostrophus (1997)

Leubner-Metzger, G. ; Horwitz, B. A. ; Yoder, O. C. ; [et al.]

Springer

Molecular genetics and genomics 256 (1997), S. 661-673

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ISSN: 1617-4623

Keywords: Key words Ascomycete ; Intron ; uORF ; UTR ; mRNA leader

Source: Springer Online Journal Archives 1860-2000

Topics: Biology

Notes: Abstract The single mating type locus (MAT ) of the heterothallic ascomycete Cochliobolus heterostrophus is composed of a pair of unlike sequences called idiomorphs, each of which encodes one MAT-specific gene (MAT-1 and MAT-2). MAT transcripts were observed in blots of poly(A)+ RNA isolated from cultures grown in minimal medium, but were not detectable after growth of the fungus in complete medium, suggesting that transcription of MAT is tightly regulated. The idiomorphs (MAT-1 = 1297-bp, MAT-2 = 1171-bp) encode transcripts of 2.2 kb (MAT-1) and 2.1 kb (MAT-2), which start 5′ and end 3′ of the idiomorph within sequences common to both mating types. Analyses of MAT-1 and MAT-2 cDNAs revealed obligatory splicing of one intron (55-bp in MAT-1, 52-bp in MAT-2) within each MAT-specific ORF and optional splicing of two introns (63 and 79-bp) in the long (approximately 0.55 kb) 5′ untranslated leader sequences; the 3′ untranslated region is 0.46 kb long. Transcription start sites were found 5′ of, and within, the 79-bp intron. Optional splicing of the upstream introns and at least two transcription start sites result in three types of transcript: Type I with both 5′ introns spliced, Type II with only the 63-bp intron spliced, and Type III with neither 5′ intron spliced. The three transcript types are distinguished by various combinations of four short ORFs encoded by the corresponding genomic DNA, in the leader sequences of the MAT mRNAs. The transcript structure suggests several mechanisms by which expression of the MAT genes might be regulated at the level of translation during sexual development.

Type of Medium: Electronic Resource

URL: http://dx.doi.org/10.1007/s004380050614

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Single mating type-specific genes and their 3′ UTRs control mating and fertility in Cochliobolus heterostrophus (1998)

Wirsel, S. ; Horwitz, B. ; Yamaguchi, K. ; [et al.]

Springer

Molecular genetics and genomics 259 (1998), S. 272-281

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ISSN: 1617-4623

Keywords: Key words HMG box ; Transcriptional regulator ; 3′ UTR ; DNA-binding protein ; Heterothallic ascomycete

Source: Springer Online Journal Archives 1860-2000

Topics: Biology

Notes: Abstract To determine the number of proteins required for mating type (MAT) locus-regulated control of mating in Cochliobolus heterostrophus, MAT fragments of various sizes were expressed in MAT deletion strains. As little as 1.5 kb of MAT sequence, encoding a single unique protein in each mating type (MAT-1 and MAT-2), conferred mating ability, although an additional 160 bp of 3′ UTR was needed for production of ascospores. No other mating type-specific genes involved in mating identity or fertility were found. Thus, although homologs of the C. heterostrophus MAT-1 and MAT-2 genes exist in the filamentous ascomycetes Neurospora crassa and Podospora anserina, C. heterostrophus does not appear to have mating type-specific homologs of two additional genes required by both N. crassa and P.␣anserina for successful sexual reproduction. Three genes were identified in the common DNA flanking the MAT locus: a gene encoding a GTPase-activating protein and an ORF of unknown function lie 5′ while a β-glucosidase encoding gene lies found 3′. None of these genes appears to be involving in the mating process.

Type of Medium: Electronic Resource

URL: http://dx.doi.org/10.1007/s004380050813

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An asexual fungus has the potential for sexual development (1996)

Sharon, A. ; Yamaguchi, K. ; Christiansen, S. ; [et al.]

Springer

Molecular genetics and genomics 251 (1996), S. 60-68

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ISSN: 1617-4623

Keywords: Key words Idiomorph ; DNA binding ; Mating type ; Bipolaris sacchari ; Cochliobolus heterostrophus

Source: Springer Online Journal Archives 1860-2000

Topics: Biology

Notes: Abstract The availability of cloned genes that control sexual reproducti on (mating type genes) in higher fungi has allowed us to consider the causes of failure to mate in asexual fungi. We report here that the asexual fungus Bipolaris sacchari has a homolog of the MAT-2 gene of its sexual ascomycete relative Cochliobolus heterostrophus. The B. sacchari MAT-2 sequence is highly similar to that of C. heterostrophus MAT-2 and, in fact, functions in transgenic C. heterostrophus. Thus, the asexual nature of B. sacchari is not due to absence or mutation of MAT. When either of the C. heterostrophus MAT genes was transformed into B. sacchari, the recipient could neither self nor cross with other B. sacchari strains, in contrast to transgenic C. heterostrophus strains which can do both. Persistent asexuality of B. sacchari, in spite of the presence of complementary functional MAT genes, suggests that this fungus lacks genes other than MAT which are essential for mating. Notably, the transgenic B. sacchari strains were sometimes able to initiate, but not complete, sexual development in interspecific pairings with C. heterostrophus. Transcript analysis showed that the B. sacchari MAT-2 gene is expressed in transgenic C. heterostrophus and that the C. heterostrophus MAT genes are expressed in transgenic B. sacchari. No transcript of the native B. sacchari MAT-2 gene was detected under any growth condition tested.

Type of Medium: Electronic Resource

URL: http://dx.doi.org/10.1007/BF02174345

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Electronic Resource

An asexual fungus has the potential for sexual development (1996)

Sharon, A. ; Yamaguchi, K. ; Christiansen, S. ; [et al.]

Springer

Molecular genetics and genomics 251 (1996), S. 60-68

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ISSN: 1617-4623

Keywords: Idiomorph ; DNA binding ; Mating type ; Bipolaris sacchari ; Cochliobolus heterostrophus

Source: Springer Online Journal Archives 1860-2000

Topics: Biology

Notes: Abstract The availability of cloned genes that control sexual reproduction (mating type genes) in higher fungi has allowed us to consider the causes of failure to mate in asexual fungi. We report here that the asexual fungusBipolaris sacchari has a homolog of theMAT-2 gene of its sexual ascomycete relativeCochliobolus heterostrophus. TheB. sacchari MAT-2 sequence is highly similar to that ofC. heterostrophus MAT-2 and, in fact, functions in transgenicC. heterostrophus. Thus, the asexual nature ofB. sacchari is not due to absence or mutation ofMAT. When either of theC. heterostrophus MAT genes was transformed intoB. sacchari, the recipient could neither self nor cross with otherB. sacchari strains, in contrast to transgenicC. heterostrophus strains which can do both. Persistent asexuality ofB. sacchari, in spite of the presence of complementary functionalMAT genes, suggests that this fungus lacks genes other thanMAT which are essential for mating. Notably, the transgenicB. sacchari strains were sometimes able to initiate, but not complete, sexual development in interspecific pairings withC. heterostrophus. Transcript analysis showed that theB. sacchari MAT-2 gene is expressed in transgenicC. heterostrophus and that theC. heterostrophus MAT genes are expressed in transgenicB. sacchari. No transcript of the nativeB. sacchari MAT-2 gene was detected under any growth condition tested.

Type of Medium: Electronic Resource

URL: http://dx.doi.org/10.1007/BF02174345

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Spot inoculation of soybean roots withRhizobium japonicum (1983)

Turgeon, B. G. ; Bauer, W. D.

Springer

Protoplasma 115 (1983), S. 122-128

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ISSN: 1615-6102

Keywords: Inoculation ; Nodulation ; Rhizobium japonicum ; Soybean ; Symbiosis

Source: Springer Online Journal Archives 1860-2000

Topics: Biology

Notes: Summary A method has been developed to inoculate soybean roots in the zone of susceptible root cells with nanoliter droplets containing the symbiont,Rhizobium japonicum. The position of inoculation is marked by means of ion exchange beads which adhere to the root surface. InoculatedR. japonicum cells from a nanoliter droplet spread over an area of approximately 35 host epidermal cells and have a high probability (∼ 80%) of inducing nodule formation at exactly the point of inoculation. The spot inoculation method is highly efficient in terms of the number of bacteria required to achieve a given probability of nodule formation. The method greatly facilitates ultrastructural analysis of the infection process and is useful for certain physiological studies of infection.

Type of Medium: Electronic Resource

URL: http://dx.doi.org/10.1007/BF01279804

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