In 2013 IC Mycosmo was instrumental for sequencing the whole genome of the first eukaryotic organism in Slovenia. In the following years IC Mycosmo developed into an important centre for genomic and transcriptomic research, which is not only sequencing the genomes of microorganisms in its own collection with increasing speed, but also has the required expertise for their analysis. One of the trademarks of the centre is also the specialisation for genomic data of extremophilic fungi, which are studied by only a handful of groups worldwide. The resulting knowledge and data are both publicly acessible.


The first genomes were sequenced in collaboration with Canadian scientists from the University of UBC and the Canadian Centre for Genomics - GSC (the genome of the extremely halotolerant black yeast Hortaea werneckii), with scientists from the scientists from the Beijing Genomics Institute (BGI) in China (the genome of the obligately halophilic fungus Wallemia ichthyophaga), and with the Joint Genome Institute (JGI) of the US Department of Energy (genomes of four black yeast species of the genus Aureobasidium). The genomes of these unique organisms were the first completely sequenced genomes of extremely halotolerant and halophilic fungi in the world. These data were later expanded with sequencing of tens of genomes of environmental strains of the same species and with comparative and population genomics.


In 2021 IC Mycosmo and a Chinese-Danish institute QEI started a shared project 10k Extremophiles, which aims to sequence the genomes of 10 000 fungi from the collection Ex.


The genomes of four varieties of the black yeast Aureobasidium pullulans. 

These black yeast were isolated from different environments around the world. (, through a collaboration with the Joint Genome Institute (JGI) within the US Agency for Energy. 



Cene Gostinčar, Martina Turk, Janja Zajc, Nina Gunde-Cimerman (2019). Fifty Aureobasidium pullulans genomes reveal a recombining polyextremotolerant generalist. Environmental microbiology 21(10): 3638-3652. doi: 10.1111/1462-2920.14693

Cene Gostinčar, Xiaohuan Sun, Janja Zajc, Chao Fang, Hou Yong, Yonglun Luo, Nina Gunde-Cimerman, Zewei Song (2019). Population genomics of an obligately halophilic basidiomycete Wallemia ichthyophaga. Frontiers in microbiology 10: 1-12. doi: 10.3389/fmicb.2019.02019

Sun Xiaohuan, Cene Gostinčar, Chao Fang, Janja Zajc, Yong Hou, Zewei Song, Nina Gunde-Cimerman (2019). Genomic evidence of recombination in the basidiomycete Wallemia mellicola. Genes 10(6): 1-15. doi: 10.3390/genes10060427

Cene Gostinčar, Jason Eric Stajich, Jerneja Zupančič, Polona Zalar, Nina Gunde-Cimerman (2018). Genomic evidence for intraspecific hybridization in a clonal and extremely halotolerant yeast. BMC Genomics 19: 1-12. doi: 10.1186/s12864-018-4751-5

Cene Gostinčar, Robin A Ohm, Tina Kogej, Silva Sonjak, Martina Turk, Janja Zajc, Polona Zalar, Martin Grube, Hui Sun, James Han, Aditi Sharma, Jennifer Chiniquy, Chew Yee Ngan, Anna Lipzen, Kerrie Barry, Igor V Grigoriev, Nina Gunde-Cimerman (2014) Genome sequencing of four Aureobasidium pullulans varieties: biotechnological potential, stress tolerance, and description of new species. BMC Genomics 15:549. doi:10.1186/1471-2164-15-549

Metka Lenassi*, Cene Gostinčar*, Shaun Jackman, Martina Turk, Ivan Sadowski, Corey Nislow, Steven Jones, Inanc Birol, Nina Gunde Cimerman, Ana Plemenitaš (2013) Whole genome duplication and enrichment of metal cation transporters revealed by de novo genome sequencing of extremely halotolerant black yeast Hortaea werneckii. PLoS ONE 8(8): e71328. --- *equally contributed doi:10.1371/journal.pone.0071328

Sunita Sinha, Stephane Flibotte, Mauricio Neira, Sean Formby, Ana Plemenitaš, Nina Gunde-Cimerman, Metka Lenassi, Cene Gostinčar, Jason Eric Stajich, Corey Nislow (2017) Insight into the recent genome duplication of the halophilic yeast Hortaea werneckii: combining an improved genome with gene expression and chromatin structure. G3 7(7):2015-2022. doi: 10.1534/g3.117.040691

Janja Zajc, Yongfeng Liu, Wenkui Dai, Zhenyu Yang, Jingzhi Hu, Cene Gostinčar and Nina Gunde-Cimerman (2013) Genome and transcriptome sequencing of the halophilic fungus Wallemia ichthyophaga: haloadaptations present and absent. BMC Genomics 14:617. e71328. doi:10.1186/1471-2164-14-617

Vera Y. Matrosova, Elena K. Gaidamakova, Kira S. Makarova, Olga Grichenko, Polina Klimenkova, Robert P. Volpe, Rok Tkavc, Gözen Ertem, Isabel H. Conze, Evelyne Brambilla, [24 other authors], Nina Gunde-Cimerman, Tine Grebenc, Cene Gostinčar, Michael J. Daly (2017) High-quality genome sequence of the radioresistant bacterium Deinococcus ficus KS 0460. Standards in genomic sciences 12:46. doi: 10.1186/s40793-017-0258-y


Lenassi, M., Gostinčar, C., Jackman, S., Turk, M., Sadowski, I.,Nislow, C., Gunde-Cimerman, N., Plemenitaš, A., et al. Whole genome duplication and enrichment of metal cation transporters revealed by de-novo genome sequencing of extremely halotolerant black yeast Hortaea werneckii. PLoS ONE, 2013, 8(8).

doi: 10.1371/journal.pone.0071328; COBISS.SI-ID 30761177; ISSN 1932-6203;

Zajc, J., Liu, Y., Dai, W., Yang, Z., Hu, J., Gostinčar, C., Gunde-Cimerman, N. Genome and transcriptome sequencing of the halophilic fungus Wallemia ichthyophaga: haloadaptations present and absent. BMC Genom., 2013, 14, 617

doi: 10.1186/1471-2164-14-617; COBISS.SI-ID 2916687; ISSN 1471-2164;

Gostinčar, C., Ohm, R., Kogej, T. , Sonjak, S., Turk, M., Zajc, J., Zalar, P., Grube, M., Sun, H., Han, J., Sharma, A, Chiniquy, J., Ngan, C.Y., Lipzen, A., Barry, K., Grigoriev, I., Gunde-Cimerman, N. Genome sequencing of four aureobasidium pullulans varieties : biotechnological potential, stress tolerance, and description of new species. Bmc genomics, issn 1471-2164, 2014, vol. 15, str. 1-28. Http://, doi: 10.1186/1471-2164-15-549.