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File S1: Draft genome assembly forCladonia perforata(mycobiont of the Florida Perforate Cladonia’ specimen ‘Arbors7’ [Herbarium BRY-C]), comprising 72 fragments and spanning 33.61 Mb, with an N50 score of 1.1 Mb (describes the length of the shortest contig in the group of the longest contigs which together represent 50% of the assembled genome) and a L50 of 12 (the smallest number of contigs that includes 50% of the total sequence assembly length); File S2: the 1250 complete, single-copy BUSCO nuclear markers (95.1% complete) extracted from the draftCladonia perforataassembly (specimen ‘Arbors7’ [Herbarium BRY-C]); File S3: draftCladonia perforatamitochondrial genome (specimen ‘Arbors7’ [Herbarium BRY-C]); File S4: Circular gene map of the mitochondrial genome ofCladonia perforata(mycobiont of the Florida Perforate Cladonia’, specimen ‘Arbors7’ [Herbarium BRY-C]). Genes drawn inside the circle are transcribed clockwise, and those outside the circle are transcribed counterclockwise. The darker grey in the inner circle represents the GC content; conversely, the lighter one represents the AT content. Gene function or gene identifiers are displayed using colors indicated by the inner legend. The symbol ‘*' indicates genes with introns; File S5: draftAsterochlorisspecies chloroplast genome (photobiont of the Florida Perforate Cladonia’ specimen ‘Arbors7’ [Herbarium BRY-C]); File S6: Circular gene map of the chloroplast genome ofCladonia perforata(photobiont of the Florida Perforate Cladonia’, specimen ‘Arbors7’ [Herbarium BRY-C]). Genes drawn inside the circle are transcribed clockwise, and those outside the circle are transcribed counterclockwise. The darker grey in the inner circle represents the GC content; conversely, the lighter one represents the AT content. Gene function or gene identifiers are displayed using colors indicated by the inner legend. The symbol ‘*' indicates genes with introns; File S7: Multiple sequence alignments used in this study. Nuclear phylogenomic data matrix based on the all sequences larger than 100 Kb in the draft ONT Flye assembly – “cladonia_perforata_NUC_32mb_realphy_alignment.phy”; nuclear phylogenomic data matrix based on annotated coding regions from the draft ONT Flye assembly – “cladonia_perforata_NUC_cds_transcripts_realphy_alignment.phy”; matrix based on a fragment of theCladonia perforatanuclear ribosomal cistron – “cladonia_perforata_NUC_cistron.fas”; matrix based on the ITS regions of theCladonia perforatanuclear ribosomal cistron “cladonia_perforata_NUC_ITS.fas”; mitochondrial phylogenomic data matrix based on complete mitochondrial genomes – “cladonia_perforata_MT_alignment.fas”.

Chapter 2

Chapter 4 thesis

Lichens are well-known examples of complex symbiotic associations between organisms from different Kingdoms. Microfungi in particular, establish diverse associations with the hosting lichen thallus, as species-specific parasites or transient co-inhabitants. The whole community of lichen-associated fungi constitute the 'lichen mycobiome' comprising both ascomycetes and basidiomycetes, including filamentous and yeast taxa. Metabarcoding results and microscopy analyses show that in some thalli, basidiomycetes are frequent lichen-associated fungi but still only a few species could be axenically isolated and morphologically characterized. Within a broad project aiming at characterizing the mycobiome diversity by culture-dependent and independent approaches in two lichen species selected as reference models - Rhizoplaca melanophthalma and Tephromela atra, we succeed in isolating and culturing 76 new strains of basidiomycetous yeasts. The lichen thalli were collected in different mountain regions worldwide and at relatively high elevation. The yeast strains were isolated on different growth media and were studied for their morphological and genetic diversity. Nuclear internal transcribed spacer (ITS) and ribosomal large subunit (LSU) sequence analyses identified them to belong to ten families within the orders Agaricostilbomycetes, Cystobasidiomycetes, Microbotryomycetes, Tremellomycetes and Ustilaginomycetes. The yeasts here detected showed patterns of host-preference in a few cases and they are potentially related to the ecological conditions.

Cladia tasmanica Parnmen & Lumbsch, sp. nov. (Fig. 3C). Mycobank No.: 803450 Characterized by swollen sterile pseudopodetia, areolate, 3–6 cm tall, glossy and usually smooth, chestnut-brown to blackish brown, not perforated, and di- or trichotomously branched. Conidiomata on terminal branches of sterile pseudopodetia, conidia 4–7 µm long, bacilliform. Fertile pseudopodetia robust and taller than sterile pseudopodetia, necrotic at the base, racemosely branched. Apothecia on terminal branches of fertile pseudopodetia, 0.5–1.0 mm wide, disk concave to plane, blackish; ascospores not seen. Secondary chemistry: Fumarprotocetraric acid. Type: — AUSTRALIA. Tasmania: Lake St. Clair National Park, Trail to Frenchman's cap, 42°12'S 145°59'E, 770 m, Lumbsch 20011c (holotype HO!; isotype F!) Phylogenetic notes: —Strongly supported as a monophyletic lineage in concatenated multilocus gene tree (ML bootstrap = 100%, posterior probability = 1.0). Cladia tasmanica was previously called clade 9 (Parnmen et al. 2012). This species belongs to an early diverging lineage within the C. aggregata complex sister to all other species in the group. Reference sequence: — GenBank No. JN115301. Distribution and habitat: This species is only known from Tasmania, where it grows on soil in wet sclerophyll forests and buttongrass moorland. Etymology: —Referring to the island of Tasmania where the species is found. Additional specimens examined (paratypes): — AUSTRALIA. Tasmania: Southwest National Park, March 2009, Lumbsch, Widhelm & Parnmen 19989o, 19994k (F, RAMK).

Cladia neocaledonica (Räsänen) Parnmen & Lumbsch, comb. nov. Mycobank No.: 803446 Cladonia neocaledonica Räsänen (1944: 20). Type: NEW CALEDONIA. Wagap, 1863, Vieillard s.n. (lectotype H!, designated by Filson [1981]; isolectotypes CANB, H, KUO, TNS, US)., Published as part of Parnmen, Sittiporn, Leavitt, Steven D., Rangsiruji, Achariya & Lumbsch, H. Thorsten, 2013, Identification of species in the Cladia aggregata group using DNA barcoding (Ascomycota: Lecanorales), pp. 1-14 in Phytotaxa 115 (1) on page 7, DOI: 10.11646/phytotaxa.115.1.1, http://zenodo.org/record/5078997, {"references":["Rasanen, V. (1944) Lichenes Novi I. Annales Botanici Societatis Zoologicae-Botanicae Fennicae \" Vanamo \" 20: 1 - 34.","Filson, R. B. (1981) A revision of the lichen genus Cladia Nyl. Journal of the Hattori Botanical Laboratory 49: 1 - 75."]}

Cladia tasmanica Parnmen & Lumbsch, sp. nov. (Fig. 3C). Mycobank No.: 803450 Characterized by swollen sterile pseudopodetia, areolate, 3–6 cm tall, glossy and usually smooth, chestnut-brown to blackish brown, not perforated, and di- or trichotomously branched. Conidiomata on terminal branches of sterile pseudopodetia, conidia 4–7 µm long, bacilliform. Fertile pseudopodetia robust and taller than sterile pseudopodetia, necrotic at the base, racemosely branched. Apothecia on terminal branches of fertile pseudopodetia, 0.5–1.0 mm wide, disk concave to plane, blackish; ascospores not seen. Secondary chemistry: Fumarprotocetraric acid. Type: — AUSTRALIA. Tasmania: Lake St. Clair National Park, Trail to Frenchman's cap, 42°12'S 145°59'E, 770 m, Lumbsch 20011c (holotype HO!; isotype F!) Phylogenetic notes: —Strongly supported as a monophyletic lineage in concatenated multilocus gene tree (ML bootstrap = 100%, posterior probability = 1.0). Cladia tasmanica was previously called clade 9 (Parnmen et al. 2012). This species belongs to an early diverging lineage within the C. aggregata complex sister to all other species in the group. Reference sequence: — GenBank No. JN115301. Distribution and habitat: This species is only known from Tasmania, where it grows on soil in wet sclerophyll forests and buttongrass moorland. Etymology: —Referring to the island of Tasmania where the species is found. Additional specimens examined (paratypes): — AUSTRALIA. Tasmania: Southwest National Park, March 2009, Lumbsch, Widhelm & Parnmen 19989o, 19994k (F, RAMK)., Published as part of Parnmen, Sittiporn, Leavitt, Steven D., Rangsiruji, Achariya & Lumbsch, H. Thorsten, 2013, Identification of species in the Cladia aggregata group using DNA barcoding (Ascomycota: Lecanorales), pp. 1-14 in Phytotaxa 115 (1) on page 11, DOI: 10.11646/phytotaxa.115.1.1, http://zenodo.org/record/5078997, {"references":["Parnmen, S., Rangsiruji, A., Mongkolsuk, P., Boonpragob, K., Nutakki, A. & Lumbsch, H. T. (2012) Using phylogenetic and coalescent methods to understand the species diversity in the Cladia aggregata complex (Ascomycota, Lecanorales). PLoS ONE 7: e 52245. http: // dx. doi. org / 10.1371 / journal. pone. 0052245"]}

Cladia blanchonii Parnmen & Lumbsch, sp. nov. (Fig. 3A). Mycobank No.: 803448 Characterized by inflated and tapered sterile pseudopodetia, with glossy, pale yellow to greenish brown surface, mostly dichotomously branched toward the apex. Perforations rare to abundant. Fertile pseudopodetia robust and either inflated or not, and racemosely branched. Perforations abundant. Conidiomata on terminal branches of sterile pseudopodetia, conidia 5–7.5 µm long, bacilliform. Apothecia on short terminal branches of fertile pseudopodetia, 0.5–1.0 mm wide, disk concave to plane, brownish black; ascospores ellipsoid, non-septate, hyaline, 6.25–7.50 × 2.5 µm, 8 per ascus. Secondary chemistry: Barbatic acid and 4- O -demethylbarbatic acid. Type: — NEW ZEALAND. North Island: West Auckland, Mt. Albert, October 2011, Blanchon 4629 (holotype AK!, isotype F!, UNITEC!). Phylogenetic notes: —Strongly supported as a monophyletic lineage in concatenated multilocus gene tree (ML bootstrap = 100%; posterior probability = 1.0). Cladia blanchonii was named clade 2 previously (Parnmen et al. 2012). Reference sequence: — GenBank No. KC148367. Distribution and habitat: —Widespread in New Zealand and also found in Tasmania and south-eastern continental Australia. Mostly specimens were found on mossy soil and rocky outcrops. Etymology: —The new species is named after our colleague and friend, the New Zealand lichenologist, Dan Blanchon, who has collected the type material of this species. Additional specimens examined (paratypes): — AUSTRALIA. Australian Capital Territory: Canberra Nature Park, August 2008, Elix 39061 (CANB); Tasmania: Ben Lomond National Park, Tasmania, March 2009, Lumbsch, Widhelm & Parnmen 19994c, 19975e, 19975g, 20039a (F, RAMK). NEW ZEALAND. North Island: West Auckland, Omanawanui track, August 2011, Hayward 004634 (F); ibid., Wellington Ngaio, October 2011, Blanchon & Edmonds 004630 (F); ibid., Destruction Gully track, Hayward 004635 (F). South Island: Charming Creek, Ngakawau, West coast, January 2009, Knight 61711 (OTA); ibid., Catlins river, Coastal Otago, May 2009, Knight 61712 (OTA)., Published as part of Parnmen, Sittiporn, Leavitt, Steven D., Rangsiruji, Achariya & Lumbsch, H. Thorsten, 2013, Identification of species in the Cladia aggregata group using DNA barcoding (Ascomycota: Lecanorales), pp. 1-14 in Phytotaxa 115 (1) on page 9, DOI: 10.11646/phytotaxa.115.1.1, http://zenodo.org/record/5078997, {"references":["Parnmen, S., Rangsiruji, A., Mongkolsuk, P., Boonpragob, K., Nutakki, A. & Lumbsch, H. T. (2012) Using phylogenetic and coalescent methods to understand the species diversity in the Cladia aggregata complex (Ascomycota, Lecanorales). PLoS ONE 7: e 52245. http: // dx. doi. org / 10.1371 / journal. pone. 0052245"]}

Parnmen, Sittiporn, Leavitt, Steven D., Rangsiruji, Achariya, Lumbsch, H. Thorsten (2013): Identification of species in the Cladia aggregata group using DNA barcoding (Ascomycota: Lecanorales). Phytotaxa 115 (1): 1-14, DOI: 10.11646/phytotaxa.115.1.1, URL: http://dx.doi.org/10.11646/phytotaxa.115.1.1

Cladia cryptica Parnmen & Lumbsch, sp. nov. (Fig. 3B). Mycobank No.: 803449 Characterized by inflated sterile pseudopodetia, with glossy, yellow to brownish surface, mostly dichotomously branched toward the apex. Perforations abundant. Conidiomata on terminal branches of sterile pseudopodetia, conidia 5–7.5 µm long, bacilliform. The sizes of fertile pseudopodetia are variable, with yellow to brownish yellow surfaces, racemosely branched. Apothecia on terminal branches of fertile pseudopodetia, 0.5–1.0 mm wide, disk concave to plane, brownish black; ascospores ellipsoid, non-septate, hyaline, 7–10 × 2.5 µm, 8 per ascus. Secondary chemistry: two chemical races were found: I) Barbatic acid and 4- O -demethylbarbatic acid, and II) stictic acid chemosyndrome. Type: — NEW ZEALAND. South Island: Southland, Mistletoe Lake, Te Anau Downs, 45°12'S 167°49'E, 218 m, Knight 61705 (holotype AK!; isotype F!). Phylogenetic notes: —Strongly to moderately supported monophyletic lineage in concatenated multilocus gene tree (ML bootstrap = 83%, posterior probability = 1.0). Cladia cryptica is identical to clade 3 in Parnmen et al. (2012). Reference sequence: — GenBank No. KC148368. Distribution and habitat: —Known from Australia, New Zealand and Malaysia. It is found on soil, grassy soil and rocks. In Tasmania, we found this species in dry sclerophyll forests. Etymology: —The epithet cryptica refers to the fact that the species has been hidden under the name of the species complex C. aggregata. Additional specimens examined (paratypes): — AUSTRALIA. Australian Capital Territory: Canberra Nature Park, 28 August 2008, Elix 39060 (CANB); Tasmania: Ben Lomond National Park, March 2009, Lumbsch, Widhelm & Parnmen 20034f (F, RAMK); ibid., West of Oxford, March 2009, Lumbsch, Widhelm & Parnmen 19975h, 19975f (F, RAMK); MALAYSIA. Penang: Kedah Peak, March 2010, Buaruang & Polyiam s.n. (RAMK); NEW ZEALAND. South Island: Otago, Swampy summit, August 2011, Ludwig 61724 (F).

Cladia cryptica Parnmen & Lumbsch, sp. nov. (Fig. 3B). Mycobank No.: 803449 Characterized by inflated sterile pseudopodetia, with glossy, yellow to brownish surface, mostly dichotomously branched toward the apex. Perforations abundant. Conidiomata on terminal branches of sterile pseudopodetia, conidia 5–7.5 µm long, bacilliform. The sizes of fertile pseudopodetia are variable, with yellow to brownish yellow surfaces, racemosely branched. Apothecia on terminal branches of fertile pseudopodetia, 0.5–1.0 mm wide, disk concave to plane, brownish black; ascospores ellipsoid, non-septate, hyaline, 7–10 × 2.5 µm, 8 per ascus. Secondary chemistry: two chemical races were found: I) Barbatic acid and 4- O -demethylbarbatic acid, and II) stictic acid chemosyndrome. Type: — NEW ZEALAND. South Island: Southland, Mistletoe Lake, Te Anau Downs, 45°12'S 167°49'E, 218 m, Knight 61705 (holotype AK!; isotype F!). Phylogenetic notes: —Strongly to moderately supported monophyletic lineage in concatenated multilocus gene tree (ML bootstrap = 83%, posterior probability = 1.0). Cladia cryptica is identical to clade 3 in Parnmen et al. (2012). Reference sequence: — GenBank No. KC148368. Distribution and habitat: —Known from Australia, New Zealand and Malaysia. It is found on soil, grassy soil and rocks. In Tasmania, we found this species in dry sclerophyll forests. Etymology: —The epithet cryptica refers to the fact that the species has been hidden under the name of the species complex C. aggregata. Additional specimens examined (paratypes): — AUSTRALIA. Australian Capital Territory: Canberra Nature Park, 28 August 2008, Elix 39060 (CANB); Tasmania: Ben Lomond National Park, March 2009, Lumbsch, Widhelm & Parnmen 20034f (F, RAMK); ibid., West of Oxford, March 2009, Lumbsch, Widhelm & Parnmen 19975h, 19975f (F, RAMK); MALAYSIA. Penang: Kedah Peak, March 2010, Buaruang & Polyiam s.n. (RAMK); NEW ZEALAND. South Island: Otago, Swampy summit, August 2011, Ludwig 61724 (F)., Published as part of Parnmen, Sittiporn, Leavitt, Steven D., Rangsiruji, Achariya & Lumbsch, H. Thorsten, 2013, Identification of species in the Cladia aggregata group using DNA barcoding (Ascomycota: Lecanorales), pp. 1-14 in Phytotaxa 115 (1) on page 11, DOI: 10.11646/phytotaxa.115.1.1, http://zenodo.org/record/5078997, {"references":["Parnmen, S., Rangsiruji, A., Mongkolsuk, P., Boonpragob, K., Nutakki, A. & Lumbsch, H. T. (2012) Using phylogenetic and coalescent methods to understand the species diversity in the Cladia aggregata complex (Ascomycota, Lecanorales). PLoS ONE 7: e 52245. http: // dx. doi. org / 10.1371 / journal. pone. 0052245"]}