Gene transfer into the fungi

Richards, Thomas A.; Leonard, Guy; Soanes, Darren M.; Talbot, Nicholas J.

doi:10.1016/j.fbr.2011.04.003

Cited by 125 publications

(139 citation statements)

References 104 publications

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“…This pattern contrasts that observed by Yanai et al (11), who report 31 transfers of gene fusions from a cohort of 51 gene fusions analyzed. The most likely explanation for this discrepancy is that Yanai et al largely identified transfers between or into prokaryotic genomes, where HGT is thought to occur at high frequency (25,(27)(28)(29); HGT is thought to occur at a lower frequency into fungal genomes (30,31).…”

Section: Resultsmentioning

confidence: 91%

Genome-scale comparative analysis of gene fusions, gene fissions, and the fungal tree of life

Leonard

Richards

2012

Proc. Natl. Acad. Sci. U.S.A.

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During the course of evolution genes undergo both fusion and fission by which ORFs are joined or separated. These processes can amend gene function and represent an important factor in the evolution of protein interaction networks. Gene fusions have been suggested to be useful characters for identifying evolutionary relationships because they constitute synapomorphies or cladistic characters. To investigate the fidelity of gene-fusion characters, we developed an approach for identifying differentially distributed gene fusions among whole-genome datasets: fdfBLAST. Applying this tool to the Fungi, we identified 63 gene fusions present in two or more genomes. Using a combination of phylogenetic and comparative genomic analyses, we then investigated the evolution of these genes across 115 fungal genomes, testing each gene fusion for evidence of homoplasy, including gene fission, convergence, and horizontal gene transfer. These analyses demonstrated 110 gene-fission events. We then identified a minimum of three mechanisms that drive gene fission: separation, degeneration, and duplication. These data suggest that gene fission plays an important and hitherto underestimated role in gene evolution. Gene fusions therefore are highly labile characters, and their use for polarizing evolutionary relationships, without reference to gene and species phylogenies, is limited. Accounting for these considerable sources of homoplasy, we identified fusion characters that provide support for multiple nodes in the phylogeny of the Fungi, including relationships within the deeply derived flagellum-forming fungi (i.e., the chytrids).clade | neofunctionalization | monophyly | systematics | Blastocladiomycota

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Section: Resultsmentioning

confidence: 91%

Genome-scale comparative analysis of gene fusions, gene fissions, and the fungal tree of life

Leonard

Richards

2012

Proc. Natl. Acad. Sci. U.S.A.

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“…S6 in the supplemental material). BLAST searches with individual A domains of EcdA and GLNRPS4 also indicated that an uncharacterized dipeptide NRPS, ANID_03496 (InpB) from A. nidulans (31,32), and its orthologs Aspsy1 12236 in A. sydowii, Aspve1 13511 in A. versicolor, and g10398 in A. mulundensis were related. More-targeted BLAST searches performed with individual catalytic domains with the A, C, and T domains of the NRPSs retrieved only other Ascomycota NRPS domains.…”

Section: Phylogenetic Affinities Of the Echinocandin-producing Fungimentioning

confidence: 99%

“…Multiple evolutionary processes have caused phylogenetic discontinuities and variations in secondary-metabolite pathway organization (31,32). Several studies have shown that the A, thiolation (T), and condensation (C) modules from a single family of NRPS metabolites often form monophyletic lineages; thus, tandem duplication of modules has been proposed as a mechanism by which multimodular synthetases arise (23,24).…”

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confidence: 99%

Evolution of Chemical Diversity in Echinocandin Lipopeptide Antifungal Metabolites

Yue

Chen

et al. 2015

Eukaryot Cell

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The echinocandins are a class of antifungal drugs that includes caspofungin, micafungin, and anidulafungin. Gene clusters encoding most of the structural complexity of the echinocandins provided a framework for hypotheses about the evolutionary history and chemical logic of echinocandin biosynthesis. Gene orthologs among echinocandin-producing fungi were identified. Pathway genes, including the nonribosomal peptide synthetases (NRPSs), were analyzed phylogenetically to address the hypothesis that these pathways represent descent from a common ancestor. The clusters share cooperative gene contents and linkages among the different strains. Individual pathway genes analyzed in the context of similar genes formed unique echinocandinexclusive phylogenetic lineages. The echinocandin NRPSs, along with the NRPS from the inp gene cluster in Aspergillus nidulans and its orthologs, comprise a novel lineage among fungal NRPSs. NRPS adenylation domains from different species exhibited a one-to-one correspondence between modules and amino acid specificity that is consistent with models of tandem duplication and subfunctionalization. Pathway gene trees and Ascomycota phylogenies are congruent and consistent with the hypothesis that the echinocandin gene clusters have a common origin. The disjunct Eurotiomycete-Leotiomycete distribution appears to be consistent with a scenario of vertical descent accompanied by incomplete lineage sorting and loss of the clusters from most lineages of the Ascomycota. We present evidence for a single evolutionary origin of the echinocandin family of gene clusters and a progression of structural diversification in two fungal classes that diverged approximately 290 to 390 million years ago. Lineagespecific gene cluster evolution driven by selection of new chemotypes contributed to diversification of the molecular functionalities.

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“…Selective retention of horizontally acquired genes from exchanges between fungi as well as from prokaryote donors have recently been shown to play an important role in the reconfiguration of carbohydrate metabolism of filamentous plant and animal associated fungi (29)(30)(31). Several gene families related to hemicellulose and pectin degradation and fungal cell-wall modification are significantly enriched in the canker pathogen, M. populorum (SI Appendix, Fig.…”

Section: Gene Content and Expression In M Populorum And M Populicolamentioning

confidence: 99%

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

Dhillon

Feau

Aerts

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

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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 hemicellulosedegrading 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. poplar pathogen | tree disease | fungal genomics | Septoria canker

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Gene transfer into the fungi

Cited by 125 publications

References 104 publications

Genome-scale comparative analysis of gene fusions, gene fissions, and the fungal tree of life

Genome-scale comparative analysis of gene fusions, gene fissions, and the fungal tree of life

Evolution of Chemical Diversity in Echinocandin Lipopeptide Antifungal Metabolites

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

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