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Projects / Programmes source: ARRS

Methodology approaches in genome-based diversity and ecological plasticity study of truffles from their natural distribution areas

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Research activity

Code Science Field Subfield
4.01.01  Biotechnical sciences  Forestry, wood and paper technology  Forest - forestry 

Code Science Field
B006  Biomedical sciences  Agronomics 

Code Science Field
4.01  Agricultural and Veterinary Sciences  Agriculture, Forestry and Fisheries 
Keywords
truffles, genomics, genomic diversity, ecological adaptation and distribution, protection of geographic origin
Evaluation (rules)
source: COBISS
Citations Citations for bibliographic records in COBIB.SI that are linked to records in citation databases
source: WoS source: Scopus source: COBISS
Researchers (30)
no. Code Name and surname Research area Role Period No. of publications
1.  29875  Marko Bajc  Forestry, wood and paper technology  Technician  2019 - 2022  273 
2.  51355  Tjaša Baloh  Forestry, wood and paper technology  Researcher  2019 - 2022  30 
3.  15493  PhD Matjaž Čater  Forestry, wood and paper technology  Researcher  2019 - 2022  287 
4.  52663  Rok Damjanić    Technician  2020 - 2022  130 
5.  52869  Natalija Dovč    Technician  2020 - 2022  0 
6.  29164  PhD Mitja Ferlan  Forestry, wood and paper technology  Researcher  2019 - 2022  209 
7.  56599  Mitja Gajšek  Microbiology and immunology  Researcher  2021 - 2022  0 
8.  25974  PhD Cene Gostinčar  Biotechnology  Researcher  2019 - 2022  294 
9.  21242  PhD Tine Grebenc  Plant production  Principal Researcher  2019 - 2022  457 
10.  05935  PhD Nina Gunde-Cimerman  Biotechnology  Researcher  2019 - 2022  1,185 
11.  28855  Melita Hrenko    Technician  2021 - 2022  0 
12.  16067  PhD Andrej Kobler  Forestry, wood and paper technology  Researcher  2019 - 2022  284 
13.  07127  PhD Hojka Kraigher  Forestry, wood and paper technology  Researcher  2019 - 2022  1,300 
14.  50798  PhD Bor Krajnc  Control and care of the environment  Researcher  2019 - 2022  62 
15.  37938  PhD Tijana Martinović  Forestry, wood and paper technology  Researcher  2020 - 2022  30 
16.  24268  PhD Tanja Mrak  Forestry, wood and paper technology  Researcher  2019 - 2022  118 
17.  11279  PhD Nives Ogrinc  Control and care of the environment  Researcher  2019 - 2022  1,046 
18.  38496  PhD Doris Potočnik  Chemistry  Researcher  2019 - 2022  162 
19.  08604  PhD Cvetka Ribarič Lasnik  Plant production  Researcher  2019 - 2022  278 
20.  28327  PhD Nadja Romih  Biology  Researcher  2019 - 2022  49 
21.  31877  PhD Nataša Šibanc  Forestry, wood and paper technology  Researcher  2019 - 2022  74 
22.  54070  David Štefanič    Technician  2020 - 2022  0 
23.  24777  Barbara Štupar    Technician  2019 - 2022  29 
24.  18510  PhD Martina Turk  Biochemistry and molecular biology  Researcher  2019 - 2022  176 
25.  38188  PhD Tina Unuk Nahberger  Forestry, wood and paper technology  Junior researcher  2019 - 2020  42 
26.  31120  PhD Grega Ernest Voglar  Control and care of the environment  Researcher  2019 - 2020  38 
27.  16103  PhD Polona Zalar  Microbiology and immunology  Researcher  2019  437 
28.  56298  Luen Zidar  Biotechnology  Researcher  2021 - 2022  2 
29.  50188  Boštjan Zupanc    Technician  2021 - 2022  0 
30.  28401  PhD Peter Železnik  Forestry, wood and paper technology  Researcher  2019 - 2021  181 
Organisations (4)
no. Code Research organisation City Registration number No. of publications
1.  0106  Jožef Stefan Institute  Ljubljana  5051606000  85,605 
2.  0404  Slovenian Forestry Institute  Ljubljana  5051673000  10,986 
3.  0481  University of Ljubljana, Biotechnical Faculty  Ljubljana  1626914  64,524 
4.  2434  Institute of Environmental and Spatial Planning  Velenje  2194015  286 
Abstract
Truffles are among the most prominent edible ectomycorrhizal fungi and non-timber forest products, valued for their rich and diverse species-specific aromas. The focus of this study are two species, Tuber magnatum and T. aestivum. T. magnatum has the highest value among truffles but a very limited areal spreading from limestone-rich flood-lands in Italy, across the Balkan peninsula to east Romania and Greece. On the other hand, T. aestivum, has the largest areal in Europe among truffles. It occupies ruderal and unproductive ectomycorrhizal forest and shrubs ecosystems from boreal to Mediterranean climate. The two species differ also in their ecology and ability to grow under various environmental conditions and forest types. There are no clear explanations for the observed differences. Despite the relatively wide distribution of T. aestivum, the price of specimens reflects their geographic origin, being highest in the areas with tradition of truffle hunting - even though no phylogenetic or population study so far provided any substantial basis for such differentiation. Similarly, no population genomic data exist on truffles. In the proposed project we will for the first time in Slovenian forestry sector sequence genomes of at least 30 strains of T. aestivum and at least 30 strains of T. magnatum. The comparison of a large collection of genomes and their association with ecological, geographic and truffle quality (aroma) data, using state-of-the-art bioinformatic approaches will enable us to (i) investigate a detailed population structure of T. aestivum and T. magnatum; (ii) attempt to associate this population structure with host/geographic/climate data and set-up markers for tracing of samples origin; (iii) correlate diversity of aromas with metabolic potential at genome level and (iv) offer population or genome-level insights of the different specialisation of the two species: why the generalist T. aestivum is broadly distributed and successfully cultivated but the specialised T. magnatum is limited in its areal and notoriously difficult to cultivate. Genomic DNA will be isolated from readily available and pre-characterised sporocarps with a method for routine isolation of genomic DNA of sufficient quality for genome resequencing. Sequencing will be performed with an Illumina platform at approximately 30× coverage. Selected bioinformatic tools and pipelines will be used to investigate the phylogenomics and population genetics of sequenced strains and associate these data with available metadata. The proposed project is expected to have important benefits at several levels. Globally it will contribute to better understanding of infraspecific diversity. If our hypothesis about the existence of a consistent population structure linked to the geographical origin is true, this will provide reliable tools to uncover the fraudulent claims of geographical origin and promote the branding of truffles with their geographic origin. If, on the other hand, the no population structure will be discovered, this would mean that the pricing truffles based on their geographic origin has no firm basis. Any genomic evidence of habitat adaptation can be used for informed modification of cultivation activities towards the use of better adapted and site-specific genotypes, thus increasing the success of cultivation and decreasing the hazards of introducing foreign genotypes for the indigenous truffle strains. Both at global and regional level, the comparison of a species with broad areal may reveal mechanisms for their adaptability or suggest markers that are responsible for such characteristics. As truffles are gaining popularity at a global scale we propose a range of dissemination activities from high-ranking scientific papers to presentation of results in education, technology development, in the form of support to truffle growers support and a contribution to principles of green (myco)tourism.
Significance for science
Truffles are well-known commercial ectomycorrhizal fungi famous for their distinct aromas. They have probably best characterised ecological niche, growth requirements and limiting factors affecting their survival and distribution among all fungi. The knowledge originates from centuries of field experiences and urge for their cultivation or better exploitation of natural habitats. Mechanism behind their ecology and distribution patterns remain unknown. Whole genome sequencing and resequencing is an up-to date approach in studying the complete genome information enabling us to yield a vast amount of data and presumably most of information required for living of target organisms. The concept of this research is to bring together and efficiently extract relevant conclusions of using modern molecular techniques that enable us to read complete genome information with ecological aspects of truffles lives and aromas, in a so far unique association study. Study will result in a large-scale genome re-sequencing and analysis at the intra-specific level for the two species. Intra-specific comparison and between-two species analyses will help us in understanding ecological strategies of two species. Gained genome sequences will also enable us to correlate either specific markers polymorphism or overall intraspecific genome differences with several site characteristics (soil, climate, ecosystem or associated mycorrhizal partners, aromas), which are currently recognised as drivers of truffle distribution mechanisms. Research will contribute new knowledge is several general areas such as basic fungal biology, fungi distribution and genomics, etc. The proposed approach was so far only used on a handful of Tuber melanosporum collections. Target species of this study, Tuber magnatum and T. aestivum, differ considerably in their ecology and requirements. If we will be able to confirm that there is genome information-based reasoning for this striking difference in truffles (confirming hypothesis on genomic heterogeneity of geographically and/or ecologically distant populations), that would be a crucial first step in potential future selections in direction of easier cultivation, in particularly of T. magnatum. The selection of commercial truffle species for proposed study was not accidental, as truffles not only are well characterised but also have importance in many communities, thus the expected scientific results should be accepted in broader scientific and non-scientific audience. Due to the mentioned reasons we expect that the project will have a major influence on other researchers in the fields of mycology, fungal physiology, ecology, and genomics. Original scientific results of the project will be published in high impact high quality international scientific journals aimed at a wider scientific audience (journals targeting general mycology, microbiology or ecology communities). The knowledge will also be disseminated to professional audience and end users.
Significance for the country
Truffles are well-known commercial ectomycorrhizal fungi famous for their distinct aromas. They have probably best characterised ecological niche, growth requirements and limiting factors affecting their survival and distribution among all fungi. The knowledge originates from centuries of field experiences and urge for their cultivation or better exploitation of natural habitats. Mechanism behind their ecology and distribution patterns remain unknown. Whole genome sequencing and resequencing is an up-to date approach in studying the complete genome information enabling us to yield a vast amount of data and presumably most of information required for living of target organisms. The concept of this research is to bring together and efficiently extract relevant conclusions of using modern molecular techniques that enable us to read complete genome information with ecological aspects of truffles lives and aromas, in a so far unique association study. Study will result in a large-scale genome re-sequencing and analysis at the intra-specific level for the two species. Intra-specific comparison and between-two species analyses will help us in understanding ecological strategies of two species. Gained genome sequences will also enable us to correlate either specific markers polymorphism or overall intraspecific genome differences with several site characteristics (soil, climate, ecosystem or associated mycorrhizal partners, aromas), which are currently recognised as drivers of truffle distribution mechanisms. Research will contribute new knowledge is several general areas such as basic fungal biology, fungi distribution and genomics, etc. The proposed approach was so far only used on a handful of Tuber melanosporum collections. Target species of this study, Tuber magnatum and T. aestivum, differ considerably in their ecology and requirements. If we will be able to confirm that there is genome information-based reasoning for this striking difference in truffles (confirming hypothesis on genomic heterogeneity of geographically and/or ecologically distant populations), that would be a crucial first step in potential future selections in direction of easier cultivation, in particularly of T. magnatum. The selection of commercial truffle species for proposed study was not accidental, as truffles not only are well characterised but also have importance in many communities, thus the expected scientific results should be accepted in broader scientific and non-scientific audience. Due to the mentioned reasons we expect that the project will have a major influence on other researchers in the fields of mycology, fungal physiology, ecology, and genomics. Original scientific results of the project will be published in high impact high quality international scientific journals aimed at a wider scientific audience (journals targeting general mycology, microbiology or ecology communities). The knowledge will also be disseminated to professional audience and end users.
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