Diversity and Mechanisms of Genomic Adaptation in Penicillium
2016
Ropars, Jeanne | de La Vega, Ricardo C. Rodriguez | Lopez-Villavicencio, Manuela | Dupont, Joëlle | Swennen, Dominique | Dumas, Emilie | Giraud, Tatiana | Branca, Antoine | Ecologie Systématique et Evolution (ESE) ; Université Paris-Sud - Paris 11 (UP11)-AgroParisTech-Centre National de la Recherche Scientifique (CNRS) | Centre National de la Recherche Scientifique (CNRS) | Université Paris-Saclay | Institut de Systématique, Evolution, Biodiversité (ISYEB) ; Muséum national d'Histoire naturelle (MNHN)-Université Pierre et Marie Curie - Paris 6 (UPMC)-École Pratique des Hautes Études (EPHE) ; Université Paris Sciences et Lettres (PSL)-Université Paris Sciences et Lettres (PSL)-Centre National de la Recherche Scientifique (CNRS) | Muséum national d'Histoire naturelle (MNHN) | Université Pierre et Marie Curie - Paris 6 (UPMC) | École Pratique des Hautes Études (EPHE) ; Université Paris Sciences et Lettres (PSL) | MICrobiologie de l'ALImentation au Service de la Santé (MICALIS) ; Institut National de la Recherche Agronomique (INRA)-AgroParisTech | Université Paris Sud (Paris 11)
Penicillium is a diverse fungal genus with hundreds of species occurring worldwide in various substrates, from soil to food, and with various lifestyles, from necrotrophic pathogenicity to endophytic mutualism. Several species are important for human affairs, being widely used in industry, such as the penicillin-producer P. rubens, the two cheese starters P. camemberti and P. roqueforti, and the mould used for fermenting sausages, P. nalgiovense. Other species are food spoilers that produce harmful mycotoxins or cause damages in fruit crops. Currently, 30 genomes of Penicillium belonging to 18 species are available. In this chapter, we reconstruct a phylogenetic tree based on available Penicillium genomes and outline the main features of the genomes, such as gene and transposable element content. We then review the recent advances that the available genomic and transcriptomic resources in the Penicillium genus have allowed regarding our understanding of the genomic processes of adaptation, including changes in gene content, expression and strikingly frequent and recent horizontal gene transfers. In addition, we summarize recent studies using genetic markers on the level of genetic diversity, mode of reproduction and population structure within Penicillium species. Overall, the Penicillium genus appears a highly suitable model for studying the mechanisms of adaptation.
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