Mitochondrial genomes from the lichenized fungi Peltigera membranacea and Peltigera malacea: Features and phylogeny

Xavier, Basil Britto; Miao, Vivian; Jónsson, Zophonı́as O.; Andrésson, Ólafur S.

doi:10.1016/j.funbio.2012.04.013

Cited by 38 publications

(33 citation statements)

References 76 publications

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“…1 A-D). Total lichen DNA extracted from field samples collected in Iceland processed for whole genome sequencing (WGS) (11) revealed approximately equal contributions from the mycobiont, the photobiont, and the community of intrathalline microbes. Bioinformatic mining of the initial metagenome assembly yielded 18 candidate clusters containing genes that encode PKS enzymes (SI Appendix, Table S1).…”

Section: Resultsmentioning

confidence: 99%

Metagenomic natural product discovery in lichen provides evidence for a family of biosynthetic pathways in diverse symbioses

Kampa

Gagunashvili

Gulder

et al. 2013

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

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Bacteria are a major source of natural products that provide rich opportunities for both chemical and biological investigation. Although the vast majority of known bacterial metabolites derive from free-living organisms, increasing evidence supports the widespread existence of chemically prolific bacteria living in symbioses. A strategy based on bioinformatic prediction, symbiont cultivation, isotopic enrichment, and advanced analytics was used to characterize a unique polyketide, nosperin, from a lichen-associated Nostoc sp. cyanobacterium. The biosynthetic gene cluster and the structure of nosperin, determined from 30 μg of compound, are related to those of the pederin group previously known only from nonphotosynthetic bacteria associated with beetles and marine sponges. The presence of this natural product family in such highly dissimilar associations suggests that some bacterial metabolites may be specific to symbioses with eukaryotes and encourages exploration of other symbioses for drug discovery and better understanding of ecological interactions mediated by complex bacterial metabolites.biosynthesis | Peltigera membranacea | trans-acyltransferase polyketide synthase | 13 C nuclear magnetic resonance

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Section: Resultsmentioning

confidence: 99%

Metagenomic natural product discovery in lichen provides evidence for a family of biosynthetic pathways in diverse symbioses

Kampa

Gagunashvili

Gulder

et al. 2013

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

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126

127

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“…Also, some DNA polymerase genes were present in the mtDNA of the ascomycete fungal partner of the lichen Peltigera malacea (Xavier et al 2012). Those sequences clustered within the other fungi group in the global DPO protein network.…”

Section: Discussionmentioning

confidence: 99%

Mitochondrial Genome Rearrangements in Glomus Species Triggered by Homologous Recombination between Distinct mtDNA Haplotypes

Beaudet

Terrat

Halary

et al. 2013

Genome Biology and Evolution

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Comparative mitochondrial genomics of arbuscular mycorrhizal fungi (AMF) provide new avenues to overcome long-lasting obstacles that have hampered studies aimed at understanding the community structure, diversity, and evolution of these multinucleated and genetically polymorphic organisms. AMF mitochondrial (mt) genomes are homogeneous within isolates, and their intergenic regions harbor numerous mobile elements that have rapidly diverged, including homing endonuclease genes, small inverted repeats, and plasmid-related DNA polymerase genes (dpo), making them suitable targets for the development of reliable strain-specific markers. However, these elements may also lead to genome rearrangements through homologous recombination, although this has never previously been reported in this group of obligate symbiotic fungi. To investigate whether such rearrangements are present and caused by mobile elements in AMF, the mitochondrial genomes from two Glomeraceae members (i.e., Glomus cerebriforme and Glomus sp.) with substantial mtDNA synteny divergence, were sequenced and compared with available glomeromycotan mitochondrial genomes. We used an extensive nucleotide/protein similarity network-based approach to investigate dpo diversity in AMF as well as in other organisms for which sequences are publicly available. We provide strong evidence of dpo-induced inter-haplotype recombination, leading to a reshuffled mitochondrial genome in Glomus sp. These findings raise questions as to whether AMF single spore cultivations artificially underestimate mtDNA genetic diversity. We assessed potential dpo dispersal mechanisms in AMF and inferred a robust phylogenetic relationship with plant mitochondrial plasmids. Along with other indirect evidence, our analyses indicate that members of the Glomeromycota phylum are potential donors of mitochondrial plasmids to plants.

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“…A metagenomic sequence library was constructed from a P. dolichorhiza thallus (extract: DNA-2289) using Roche 454 sequencing as described by Magain et al (2010). Peltigera malacea and P. membranacea metagenomic assemblies were constructed from Roche 454 sequence reads as described by Xavier et al (2012). The nucleotide sequence of a full-length cyanobacterial vnf operon was retrieved from the NCBI nr/nt collection (A. variabilis ATCC 29413; GenBank accession: CP000117, GI: 75699950; bases 5009717 to 5019000 were extracted in FASTA format) and a BLASTn search was conducted using BLAST+ 2.2.24 against the metagenomic sequence libraries (Altschul et al, 1997), which had been formatted as BLAST databases using the mpiformatdb command in MPIBLAST 1.6.0.…”

Section: Metagenomic Analysesmentioning

confidence: 99%

Lichen-symbiotic cyanobacteria associated withPeltigerahave an alternative vanadium-dependent nitrogen fixation system

Hodkinson

Allen

Forrest

et al. 2014

European Journal of Phycology

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In past decades, environmental nitrogen fixation has been attributed almost exclusively to the action of enzymes in the wellstudied molybdenum-dependent nitrogen fixation system. However, recent evidence has shown that nitrogen fixation by alternative pathways may be more frequent than previously suspected. In this study, the nitrogen fixation systems employed by lichen-symbiotic cyanobacteria were examined to determine whether their diazotrophy can be attributed, in part, to an alternative pathway. The mining of metagenomic data (generated through pyrosequencing) and PCR assays were used to determine which nitrogen-fixation systems are present in cyanobacteria from the genus Nostoc associated with four samples from different geographical regions, representing different lichen-forming fungal species in the genus Peltigera. A metatranscriptomic sequence library from an additional specimen was examined to determine which genes associated with N 2 fixation are transcriptionally expressed. Results indicated that both the standard molybdenum-dependent system and an alternative vanadium-dependent system are present and actively transcribed in the lichen symbiosis. This study shows for the first time that an alternative system is utilized by cyanobacteria associated with fungi. The ability of lichen-associated cyanobacteria to switch between pathways could allow them to colonize a wider array of environments, including habitats characterized by low temperature and trace metal (e.g. molybdenum) availability. We discuss the implications of these findings for environmental studies that incorporate acetylenereduction assay data.

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Mitochondrial genomes from the lichenized fungi Peltigera membranacea and Peltigera malacea: Features and phylogeny

Cited by 38 publications

References 76 publications

Metagenomic natural product discovery in lichen provides evidence for a family of biosynthetic pathways in diverse symbioses

Metagenomic natural product discovery in lichen provides evidence for a family of biosynthetic pathways in diverse symbioses

Mitochondrial Genome Rearrangements in Glomus Species Triggered by Homologous Recombination between Distinct mtDNA Haplotypes

Lichen-symbiotic cyanobacteria associated withPeltigerahave an alternative vanadium-dependent nitrogen fixation system

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