The biology and potential for genetic research of transposable elements in filamentous fungi

Fávaro, Léia Cecília de Lima; Araújo, Welington Luiz; Azevedo, João Lúcio de; Paccola-Meirelles, Luzia Doretto

doi:10.1590/s1415-47572005000500024

Cited by 11 publications

(6 citation statements)

References 105 publications

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“…Excluding deleterious insertions, the mutational activity of TEs may promote genetic diversity and speed up adaptative evolution in the host [ 28 ]. Class I (retroelements) use a ‘copy and paste’ mechanism to transpose via the reverse-transcription of an RNA intermediate and include long terminal repeats (LTRs), non LTRs, and long and short interspersed nuclear elements (LINEs and SINEs, respectively [ 27 , 29 ]. Class II TEs (DNA transposons) ‘cut and paste’ directly through a DNA form, using the enzyme transposase [ 27 , 29 ].…”

Section: Discussionmentioning

confidence: 99%

“…Class I (retroelements) use a ‘copy and paste’ mechanism to transpose via the reverse-transcription of an RNA intermediate and include long terminal repeats (LTRs), non LTRs, and long and short interspersed nuclear elements (LINEs and SINEs, respectively [ 27 , 29 ]. Class II TEs (DNA transposons) ‘cut and paste’ directly through a DNA form, using the enzyme transposase [ 27 , 29 ]. Earlier, we detailed our observations of phenotypic variation within single spored cultures of M. anisopliae (Figure 2 ) .…”

Section: Discussionmentioning

confidence: 99%

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The genome sequence of the biocontrol fungus Metarhizium anisopliae and comparative genomics of Metarhizium species

et al. 2014

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BackgroundMetarhizium anisopliae is an important fungal biocontrol agent of insect pests of agricultural crops. Genomics can aid the successful commercialization of biopesticides by identification of key genes differentiating closely related species, selection of virulent microbial isolates which are amenable to industrial scale production and formulation and through the reduction of phenotypic variability. The genome of Metarhizium isolate ARSEF23 was recently published as a model for M. anisopliae, however phylogenetic analysis has since re-classified this isolate as M. robertsii. We present a new annotated genome sequence of M. anisopliae (isolate Ma69) and whole genome comparison to M. robertsii (ARSEF23) and M. acridum (CQMa 102).ResultsWhole genome analysis of M. anisopliae indicates significant macrosynteny with M. robertsii but with some large genomic inversions. In comparison to M. acridum, the genome of M. anisopliae shares lower sequence homology. While alignments overall are co-linear, the genome of M. acridum is not contiguous enough to conclusively observe macrosynteny. Mating type gene analysis revealed both MAT1-1 and MAT1-2 genes present in M. anisopliae suggesting putative homothallism, despite having no known teleomorph, in contrast with the putatively heterothallic M. acridum isolate CQMa 102 (MAT1-2) and M. robertsii isolate ARSEF23 (altered MAT1-1). Repetitive DNA and RIP analysis revealed M. acridum to have twice the repetitive content of the other two species and M. anisopliae to be five times more RIP affected than M. robertsii. We also present an initial bioinformatic survey of candidate pathogenicity genes in M. anisopliae.ConclusionsThe annotated genome of M. anisopliae is an important resource for the identification of virulence genes specific to M. anisopliae and development of species- and strain- specific assays. New insight into the possibility of homothallism and RIP affectedness has important implications for the development of M. anisopliae as a biopesticide as it may indicate the potential for greater inherent diversity in this species than the other species. This could present opportunities to select isolates with unique combinations of pathogenicity factors, or it may point to instability in the species, a negative attribute in a biopesticide.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-660) contains supplementary material, which is available to authorized users.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

The genome sequence of the biocontrol fungus Metarhizium anisopliae and comparative genomics of Metarhizium species

et al. 2014

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“…The discovery of chromosome location “hot spots” for TE insertion, as well as a “patchy” distribution among isolates of some of the TEs offers tantalizing evidence that TEs may play an important role in modulating genome architecture to allow Verticillium fungi to evolve quickly and adapt to their hosts, as has been suggested for other plant pathogens [17,74]. V. dahliae and V. albo-atrum were previously perceived, on the basis of vegetative compatibility and pathogenicity analyses, to have rather low genetic diversity.…”

Section: Discussionmentioning

confidence: 99%

“…The identification and characterization of Class I and II TEs of Verticillium dahliae (VdLs.17) has allowed further exploration of the genetic diversity existing among the phytopathogenic Verticillium spp., and raised intriguing questions about the role(s) that TEs may have in shaping intra- and inter-specific evolution in this fungal genus. The discovery of chromosome location “hot spots” for TE insertion, as well as a “patchy” distribution among isolates of some of the TEs offers tantalizing evidence that TEs may play an important role in modulating genome architecture to allow Verticillium fungi to evolve quickly and adapt to their hosts, as has been suggested for other plant pathogens [ 17 , 74 ]. V. dahliae and V. albo-atrum were previously perceived, on the basis of vegetative compatibility and pathogenicity analyses, to have rather low genetic diversity.…”

Section: Discussionmentioning

confidence: 99%

Transposable elements in phytopathogenic Verticillium spp.: insights into genome evolution and inter- and intra-specific diversification

et al. 2012

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BackgroundVerticillium dahliae (Vd) and Verticillium albo-atrum (Va) are cosmopolitan soil fungi causing very disruptive vascular diseases on a wide range of crop plants. To date, no sexual stage has been identified in either microorganism suggesting that somatic mutation is a major force in generating genetic diversity. Whole genome comparative analysis of the recently sequenced strains VdLs.17 and VaMs.102 revealed that non-random insertions of transposable elements (TEs) have contributed to the generation of four lineage-specific (LS) regions in VdLs.17.ResultsWe present here a detailed analysis of Class I retrotransposons and Class II “cut-and-paste” DNA elements detected in the sequenced Verticillium genomes. We report also of their distribution in other Vd and Va isolates from various geographic origins. In VdLs.17, we identified and characterized 56 complete retrotransposons of the Gypsy-, Copia- and LINE-like types, as well as 34 full-length elements of the “cut-and-paste” superfamilies Tc1/mariner, Activator and Mutator. While Copia and Tc1/mariner were present in multiple identical copies, Activator and Mutator sequences were highly divergent. Most elements comprised complete ORFs, had matching ESTs and showed active transcription in response to stress treatment. Noticeably, we found evidences of repeat-induced point mutation (RIP) only in some of the Gypsy retroelements. While Copia-, Gypsy- and Tc1/mariner-like transposons were prominent, a large variation in presence of the other types of mobile elements was detected in the other Verticillium spp. strains surveyed. In particular, neither complete nor defective “cut-and-paste” TEs were found in VaMs.102.ConclusionsCopia-, Gypsy- and Tc1/mariner-like transposons are the most wide-spread TEs in the phytopathogens V. dahliae and V. albo-atrum. In VdLs.17, we identified several retroelements and “cut-and-paste” transposons still potentially active. Some of these elements have undergone diversification and subsequent selective amplification after introgression into the fungal genome. Others, such as the ripped Copias, have been potentially acquired by horizontal transfer. The observed biased TE insertion in gene-rich regions within an individual genome (VdLs.17) and the “patchy” distribution among different strains point to the mobile elements as major generators of Verticillium intra- and inter-specific genomic variation.

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“…Such genetic diversity may result from TE activity, which is recognized as an important cause of genetic variation, particularly in the organisms without a sexual phase [23]. Previous studies have demonstrated that class I TEs (Boty) [24] and class II TEs (Flipper) [25] examined in B. cinerea partially contributed to genetic variation between the B. cinerea populations tested [26].…”

Section: Introductionmentioning

confidence: 99%

Scatter: a novel family of miniature inverted‐repeat transposable elements in the fungus Botrytis cinerea

Deng

Shu

Luo

et al. 2013

J. Basic Microbiol.

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Miniature inverted-repeat transposable elements (MITEs) are short non-autonomous DNA transposons that play an important role in genome structure and function. Here, we described a novel family of MITEs, named Scatter, identified from the genomes of three strains of the fungus Botrytis cinerea (T4, B05.10, and TBC-A). Intact Scatter elements are typically an average of 247 bp, and contain 41 bp terminal inverted repeats (TIRs) and 2-bp "TA" target site duplications (TSDs). Based a search against the transposable elements database and GenBank, Scatter is a novel and potentially species-specific family of MITEs. Moderate heterogeneity in sequence and size of individual Scatter copies suggests that Scatter elements were not recently proliferated. Most integrated sites were conserved across all three strains tested and elements inserted at equivalent sites shared high identity at the nucleotide level. This conservation, in combination with the presence of a similar copy number (22-24), in B. cinerea strains tested suggests that Scatter may be a relic of an ancient transposition developed prior to the strain divergence of B. cinerea. Two unique insertion instances were observed, indicating that some copies of Scatter may have remained active following strain divergence of B. cinerea. Because only a few subtle insertion differences among B. cinerea strains were observed, Scatter may play only a minor role in the genetic diversity in B. cinerea species. Most Scatter elements appear to be inserted in potential regulatory regions of adjacent coding regions, highlighting their role in transcriptional regulation. The origin of Scatter remains to be addressed. Scatter is the first well-characterized family of MITEs in B. cinerea.: Additional supporting information may be found in the online version of this article at the publisher's web-site IntroductionTransposable elements (TEs), characterized by their ability to "jump" or transpose within genome, make up a large fraction of the eukaryotic genome and have a substantial impact on genome function and evolution [1][2][3][4]. Given the abundance and diversity of TEs, the classification and naming system of TEs has been inconsistent [5]. Although currently used classification systems for TEs largely differ from one another on a lower level, it has been commonly accepted that, at the highest level, Miniature inverted-repeat transposable elements (MITEs), first discovered in maize [7] and found to be widespread in eukaryotes and prokaryotes [6], are a heterogeneous group of non-autonomous DNA transposons that share structural characteristics, including short length (<600 bp), conserved terminal inverted repeats (TIRs), non-coding capacity of internal sequence, target site duplications (TSDs), high A þ T content, tendency to insert into intergenic regions, and the potential to form stable secondary structure [6]. Base on their TIR and TSD sequence signatures, most MITEs can be assigned to one of two major superfamilies, Tourist and Stowaway, although a few ones cannot be classifi...

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The biology and potential for genetic research of transposable elements in filamentous fungi

Cited by 11 publications

References 105 publications

The genome sequence of the biocontrol fungus Metarhizium anisopliae and comparative genomics of Metarhizium species

The genome sequence of the biocontrol fungus Metarhizium anisopliae and comparative genomics of Metarhizium species

Transposable elements in phytopathogenic Verticillium spp.: insights into genome evolution and inter- and intra-specific diversification

Scatter: a novel family of miniature inverted‐repeat transposable elements in the fungus Botrytis cinerea

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