Multiple recent horizontal transfers of a large genomic region in cheese making fungi

Cheeseman, Kevin; Ropars, Jeanne; Renault, Pierre; Dupont, Joëlle; Gouzy, Jérôme; Branca, Antoine; Abraham, Anne-Laure; Ceppi, Maurizio; Conseiller, Emmanuel; Debuchy, Robert; Malagnac, Fabienne; Goarin, Anne; Silar, Philippe; Lacoste, Sandrine; Sallet, Erika; Bensimon, Aaron; Giraud, Tatiana; Brygoo, Yves

doi:10.1038/ncomms3876

Cited by 190 publications

(253 citation statements)

References 53 publications

Supporting

Mentioning

224

Contrasting

Unclassified

Order By: Relevance

“…Given the short timescales required to form communities, there may be fewer opportunities for species to coevolve. However, horizontal gene transfer between species that co-occur in MCoFFs suggests that at least some members of these communities have coexisted long enough to allow for gene exchange (Cheeseman et al, 2014;Rossi et al, 2014). In fact, some MCoFFs are maintained for many years through serial transfer (Table 1), providing ample opportunities for long-term coevolution within communities.…”

Section: Fermented Foods As Experimentally Tractable Ecosystemsmentioning

confidence: 97%

Fermented Foods as Experimentally Tractable Microbial Ecosystems

Wolfe

Dutton

2015

Cell

312

230

View full text Add to dashboard Cite

show abstract

Section: Fermented Foods As Experimentally Tractable Ecosystemsmentioning

confidence: 97%

Fermented Foods as Experimentally Tractable Microbial Ecosystems

Wolfe

Dutton

2015

Cell

312

230

View full text Add to dashboard Cite

show abstract

Section: Strains and Culture Conditionsmentioning

confidence: 99%

“…Construction of the mat2 library DNA from the P. anserina S mat2 strain was extracted as described in Cheeseman et al (2014). The P. anserina S mat2 DNA was nebulized and 1.7 mg of fragmented DNA was used for library preparation according to the protocol for multiplexed paired-end sequencing of Illumina (part 1005361 RevB, December 2008).…”

Section: Strains and Culture Conditionsmentioning

confidence: 99%

“…Primary transformants were crossed with wild type and progeny analysis permitted selection of transgenes segregating independently from the mating type and harboring no phenotypic alteration. In the progeny of these crosses, the same transgenes were associated with either mat+ or mat2.Construction of the mat2 library DNA from the P. anserina S mat2 strain was extracted as described in Cheeseman et al (2014). The P. anserina S mat2 DNA was nebulized and 1.7 mg of fragmented DNA …”

mentioning

confidence: 99%

See 1 more Smart Citation

Maintaining Two Mating Types: Structure of the Mating Type Locus and Its Role in Heterokaryosis inPodospora anserina

et al. 2014

Self Cite

View full text Add to dashboard Cite

Pseudo-homothallism is a reproductive strategy elected by some fungi producing heterokaryotic sexual spores containing genetically different but sexually compatible nuclei. This lifestyle appears as a compromise between true homothallism (self-fertility with predominant inbreeding) and complete heterothallism (with exclusive outcrossing). However, pseudohomothallic species face the problem of maintaining heterokaryotic mycelia to fully benefit from this lifestyle, as homokaryons are self-sterile. Here, we report on the structure of chromosome 1 in mat+ and mat2 isolates of strain S of the pseudohomothallic fungus Podospora anserina. Chromosome 1 contains either one of the mat+ and mat2 mating types of P. anserina, which is mostly found in nature as a mat+/mat2 heterokaryotic mycelium harboring sexually compatible nuclei. We identified a "mat" region 0.8 Mb long, devoid of meiotic recombination and containing the mating-type idiomorphs, which is a candidate to be involved in the maintenance of the heterokaryotic state, since the S mat+ and S mat2 strains have different physiology that may enable hybrid-vigor-like phenomena in the heterokaryons. The mat region contains 229 coding sequences. A total of 687 polymorphisms were detected between the S mat+ and S mat2 chromosomes. Importantly, the mat region is colinear between both chromosomes, which calls for an original mechanism of recombination inhibition. Microarray analyses revealed that 10% of the P. anserina genes have different transcriptional profiles in S mat+ and S mat2, in line with their different phenotypes. Finally, we show that the heterokaryotic state is faithfully maintained during mycelium growth of P. anserina, yet mat+/mat+ and mat2/mat2 heterokaryons are as stable as mat+/mat2 ones, evidencing a maintenance of heterokaryosis that does not rely on fitness-enhancing complementation between the S mat+ and S mat2 strains.A dikaryotic stage during a significant portion of the lifecycle is the hallmark of the higher fungi (Ascomycota and Basidiomycota), called for this reason the Dikarya. The dikaryotic part of the life cycle is different in the two groups. In Basidiomycota, mating-competent mycelia fuse and yield the secondary dikaryotic mycelium, upon which basidiosporebearing dikaryotic fruiting bodies are differentiated. In Ascomycota, fruiting bodies are differentiated around a monokaryotic female gametangium (the ascogonium), which is fertilized by a male gamete (antheridium or spermatium) to yield the dikaryon, which undergoes further development and produces numerous ascospore-containing asci. In Ascomycota, the dikaryotic stage is thus restricted to the sexual lineage inside the fruiting body. There is one exception to this in the Taphrinomycetes, where a dikaryotic mycelium is formed as part of the life cycle (Martin 1940). Ascomycota are nonetheless able to exhibit heterokaryotic mycelia following somatic fusion between genetically different individuals (Buller 1933). In Basidiomycota, a special structure (the clamp) enables the mai...

show abstract

“…Sequencing of Penicillium species isolated from the cheesemaking environment identified HGT of large genomic islands between these key fungal inhabitants of cheese (Cheeseman et al, 2014;Ropars et al, 2015;Gibbons and Rinker, 2015).…”

Section: Introductionmentioning

confidence: 99%

Extensive Horizontal Gene Transfer in Cheese-Associated Bacteria

Bonham

Wolfe

Dutton

2016

Preprint

View full text Add to dashboard Cite

Acquisition of genes through horizontal gene transfer (HGT) allows microbes to rapidly gain new capabilities and adapt to new or changing environments. Identifying widespread HGT regions within multispecies microbiomes can pinpoint the molecular mechanisms that play key roles in microbiome assembly. We sought to identify horizontally transferred genes within a model microbiome, the cheese rind. Comparing 31 newly sequenced and 134 previously sequenced bacterial isolates from cheese rinds, we identified over 200 putative horizontally transferred genomic regions containing 4733 protein coding genes. The largest of these regions are enriched for genes involved in siderophore acquisition, and are widely distributed in cheese rinds in both Europe and the US. These results suggest that HGT is prevalent in cheese rind microbiomes, and that identification of genes that are frequently transferred in a particular environment may provide insight into the selective forces shaping microbial communities.

show abstract

Multiple recent horizontal transfers of a large genomic region in cheese making fungi

Cited by 190 publications

References 53 publications

Fermented Foods as Experimentally Tractable Microbial Ecosystems

Fermented Foods as Experimentally Tractable Microbial Ecosystems

Maintaining Two Mating Types: Structure of the Mating Type Locus and Its Role in Heterokaryosis inPodospora anserina

Extensive Horizontal Gene Transfer in Cheese-Associated Bacteria

Contact Info

Product

Resources

About