Lawrence Berkeley National Laboratory Recent Work Title Desert truffle genomes reveal their reproductive modes and new insights into plant- fungal interaction and ectendomycorrhizal lifestyle. Permalink https://escholarship.org/uc/item/74j9653p Journal The New phytologist, 229(5) ISSN 0028-646X Authors Marqués-Gálvez, José Eduardo Miyauchi, Shingo Paolocci, Francesco et al. Publication Date 2021-03-01 DOI 10.1111/nph.17044 Peer reviewed eScholarship.org Powered by the California Digital Library University of California Research Desert truffle genomes reveal their reproductive modes and new insights into plant–fungal interaction and ectendomycorrhizal lifestyle Jose Eduardo Marques-Galvez1,2* , Shingo Miyauchi2* , Francesco Paolocci3 , Alfonso Navarro-Rodenas 1 , Francisco Arenas1 , Manuela Perez-Gilabert4 , Emmanuelle Morin2 , Lucas Auer2, Kerrie W. Barry5 , Alan Kuo5, Igor V. Grigoriev5,6 , Francis M. Martin2† , Annegret Kohler2† and Asuncion Morte1† 1Departamento de Biologıa Vegetal (Botanica), Facultad de Biologıa, Universidad de Murcia, Campus de Espinardo, Murcia 30100, Spain; 2INRAE, UMR 1136, Interactions Arbres/ Microorganismes (IAM), Centre INRAE GrandEst - Nancy, Universite de Lorraine, Champenoux 54280, France; 3CNR-IBBR, Istituto di Bioscienze e Biorisorse, UOS di Perugia, Perugia 06128, Italy; 4Departamento de Bioquımica y Biologıa Molecular-A, Universidad de Murcia, Campus de Espinardo, Murcia 30100, Spain; 5US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94598, USA; 6Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94598, USA Summary Author for correspondence: Desert truffles are edible hypogeous fungi forming ectendomycorrhizal symbiosis with Asuncion Morte plants of Cistaceae family. Knowledge about the reproductive modes of these fungi and the Email: [email protected] molecular mechanisms driving the ectendomycorrhizal interaction is lacking. Received: 10 April 2020 Genomes of the highly appreciated edible desert truffles Terfezia claveryi Chatin and Accepted: 9 October 2020 Tirmania nivea Trappe have been sequenced and compared with other Pezizomycetes. Tran- scriptomes of T. claveryi 9 Helianthemum almeriense mycorrhiza from well-watered and New Phytologist (2020) drought-stressed plants, when intracellular colonizations is promoted, were investigated. doi: 10.1111/nph.17044 We have identified the fungal genes related to sexual reproduction in desert truffles and desert-truffles-specific genomic and secretomic features with respect to other Pezizomycetes, such as the expansion of a large set of gene families with unknown Pfam domains and a num- Key words: arid environment, desert truffles, drought stress, ectendomycorrhizal ber of species or desert-truffle-specific small secreted proteins differentially regulated in sym- symbiosis, MAT genes, mycorrhiza, plant–mi- biosis. A core set of plant genes, including carbohydrate, lipid-metabolism, and defence- crobe interactions. related genes, differentially expressed in mycorrhiza under both conditions was found. Our results highlight the singularities of desert truffles with respect to other mycorrhizal fungi while providing a first glimpse on plant and fungal determinants involved in ecto to endo symbiotic switch that occurs in desert truffle under dry conditions. nutritional parameters (Morte et al., 2010), such as increased phos- Introduction phorus, nitrogen (N), and potassium uptake (Morte et al., 2000). The so-called desert truffles are a group of edible hypogeous fungi As a result of this interaction, a fine-tune regulation of both plant that establish mycorrhizal symbiosis with annual and perennial and fungal aquaporin expression (Navarro-Rodenas et al., 2013; shrubs belonging to Cistaceae, a plant family adapted to arid and Marques-Galvez et al., 2020) and hydrogen peroxide content in semiarid areas (Kovacs & Trappe, 2014; Roth-Bejerano et al., roots (Marques-Galvez et al., 2019) also occur. The type of mycor- 2014). These areas are characterized by an aridity index AI <0.5— rhiza established by these fungi is known as an ectendomycorrhiza that is, the ratio between the annual precipitation and potential (EEM). EEMs are characterized by the co-occurrence of an intercel- evapotranspiration (United Nations Educational, Scientific and lular Hartig net, intracellular hyphas penetrating the cortex cells, Cultural Organization, 1979)—andbypoorlyfertilesoilswith where they form coil-like structures, and a thin and disordered fun- sandy texture and low inputs of organic matter (Bonifacio & Morte, gal mantle surrounding the colonized roots (Morte et al., 1994; Yu 2014). Under these environmental conditions, mutualistic sym- et al., 2001). The occurrence of either intercellular or intracellular bionts promote growth and survival of their host plants. For exam- mycorrhizal structures depends on several factors. In vitro condi- ple, Terfezia claveryi mycorrhizas promote Helianthemum almeriense tions, high auxin, high phosphate, and/or high water content favour survival during drought periods by altering its physiological and the intercellular mycorrhizal type, whereas field conditions, low auxin, low phosphate, and/or low water availability favour the intra- *These authors contributed equally as first authors. cellular mycorrhizal type (Gutierrez et al., 2003; Zaretsky et al., †These authors contributed equally as senior authors. 2006a; Navarro-Rodenas et al., 2012, 2013). Ó2020 The Authors New Phytologist (2020) 1 New Phytologist Ó2020 New Phytologist Foundation www.newphytologist.com This is an open access article under the terms of the Creative Commons Attribution-NonCommercial-NoDerivs License, which permits use and distribution in any medium, provided the original work is properly cited, the use is non-commercial and no modifications or adaptations are made. New 2 Research Phytologist Among desert truffles, Terfezia and Tirmania ascocarps (fruit- (Turgeon & Debuchy, 2007). In these fungi, only isolates that ing bodies) are well-known delicacies and largely marketed differ at MAT are sexually compatible. Conversely, in homothal- mainly because of their taste and nutritional values (Kagan-Zur lic species, the isolates carry both MAT1-1 and MAT1-2 genes in et al., 2014). Terfezia claveryi (Honrubia et al., 2002; Morte their genomes, and thus they are self-compatible (Bennett & et al., 2008) and Terfezia boudieri (Slama et al., 2010; Kagan-Zur Turgeon, 2017). So far, MAT loci have not been identified in et al., 2014), both associating with Helianthemum spp. as host any desert truffle, and therefore their mating mode (homothal- plants, are the only ones that have been successfully cultivated, lism vs heterothallism) is unknown (Murat et al., 2018). As the former in Spain and the latter in Tunisia and Israel. Since shown for Tuber melanosporum (Rubini et al., 2011, 2014; Linde most climate models point to increased temperature and lower & Selmes, 2012; Zampieri et al., 2012; Murat et al., 2013; Le precipitation rates for the next decades, areas covered by arid and Tacon et al., 2014), Tuber borchii (Mello et al., 2017; Leonardi semiarid ecosystems are expected to increase (Schlesinger et al., et al., 2019), and Tuber aestivum (Molinier et al., 2016; Splivallo 1990; Lavee et al., 1998; Huang et al., 2016). Thus, desert truf- et al., 2019), the characterization of the MAT locus has been criti- fles are becoming a promising, alternative crop in regions such as cal for disclosing the reproduction mode of these fungi and, in the Mediterranean basin and the Middle East, where desertifica- turn, for designing new cultivation strategies. tion will cause an alarming increase in dry lands (Morte et al., Here, we sequenced the genomes of T. claveryi strain T7 and 2017). Helianthemum almeriense Pau is a drought deciduous Tirmania nivea strain G3 and compared them with those of other shrub that is well represented in the Mediterranean basin. This Pezizomycetes. We also assessed both plant and fungal transcrip- species establishes EEM symbiosis with several desert truffles in tomes of the symbiosis between T. claveryi and H. almeriense the wild, including T. claveryi. The symbiotic relationship under well-watered (favouring intercellular colonization) and between H. almeriense and T. claveryi has been widely used as a drought-stress (favouring intracellular colonization) conditions. model for the research of desert truffle symbiosis at a basic and We aimed to decipher the specific genomic and transcriptomic applied level—see Morte et al. (2017) for review. However, at features of desert truffles compared with other Pezizaceae species. the present time, the information on the molecular mechanics Our findings pave the way for a better understanding of sexual involved in this particular symbiosis is scarce. and vegetative propagation modes of the desert truffles and high- Several studies have revealed the specific genomic signature of light singularities in their genomes and transcriptomes that may ectomycorrhizal, arbuscular mycorrhizal, or ericoid mycorrhizal shape the ectendomycorrhizal interaction between these fungi fungi (Martin et al., 2008, 2010; Tisserant et al., 2013; Kohler and their host plants. et al., 2015; Chen et al., 2018; Martino et al., 2018; Murat et al., 2018; Morin et al., 2019; Sun et al., 2019; Venice et al., 2020), Materials and methods but similar studies have not yet been carried out on EEM fungi. These genome and transcriptome analyses have identified hall- Strains and fungal material