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Open Access Research article

Genome sequencing of four Aureobasidium pullulans varieties: biotechnological potential, stress tolerance, and description of new species

Cene Gostinčar12*, Robin A Ohm3, Tina Kogej1, Silva Sonjak1, Martina Turk1, Janja Zajc1, Polona Zalar1, Martin Grube4, Hui Sun3, James Han3, Aditi Sharma3, Jennifer Chiniquy3, Chew Yee Ngan3, Anna Lipzen3, Kerrie Barry3, Igor V Grigoriev3 and Nina Gunde-Cimerman15

Author Affiliations

1 Department of Biology, Biotechnical Faculty, University of Ljubljana, Večna pot 111, Ljubljana SI-1000, Slovenia

2 National Institute of Biology, Večna pot 111, Ljubljana SI-1000, Slovenia

3 US Department of Energy Joint Genome Institute, 2800 Michell Drive, Walnut Creek, CA 94598, USA

4 Institute of Plant Sciences, Karl-Franzens-University Graz, Holteigasse 6, Graz A-8010, Austria

5 Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins (CIPKeBiP), Jamova 39, Ljubljana SI-1000, Slovenia

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BMC Genomics 2014, 15:549  doi:10.1186/1471-2164-15-549

Published: 1 July 2014

Abstract

Background

Aureobasidium pullulans is a black-yeast-like fungus used for production of the polysaccharide pullulan and the antimycotic aureobasidin A, and as a biocontrol agent in agriculture. It can cause opportunistic human infections, and it inhabits various extreme environments. To promote the understanding of these traits, we performed de-novo genome sequencing of the four varieties of A. pullulans.

Results

The 25.43-29.62 Mb genomes of these four varieties of A. pullulans encode between 10266 and 11866 predicted proteins. Their genomes encode most of the enzyme families involved in degradation of plant material and many sugar transporters, and they have genes possibly associated with degradation of plastic and aromatic compounds. Proteins believed to be involved in the synthesis of pullulan and siderophores, but not of aureobasidin A, are predicted. Putative stress-tolerance genes include several aquaporins and aquaglyceroporins, large numbers of alkali-metal cation transporters, genes for the synthesis of compatible solutes and melanin, all of the components of the high-osmolarity glycerol pathway, and bacteriorhodopsin-like proteins. All of these genomes contain a homothallic mating-type locus.

Conclusions

The differences between these four varieties of A. pullulans are large enough to justify their redefinition as separate species: A. pullulans, A. melanogenum, A. subglaciale and A. namibiae. The redundancy observed in several gene families can be linked to the nutritional versatility of these species and their particular stress tolerance. The availability of the genome sequences of the four Aureobasidium species should improve their biotechnological exploitation and promote our understanding of their stress-tolerance mechanisms, diverse lifestyles, and pathogenic potential.

Keywords:
Aureobasidium pullulans; Dothideomycetes; Genome; Stress; Haloadaptation; Halotolerance; Polyextremotolerant; New species; Opportunistic mycosis; Pullulan