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. 2021 Nov 15;12(2):jkab398. doi: 10.1093/g3journal/jkab398

Draft genome sequences of strains CBS6241 and CBS6242 of the basidiomycetous yeast Filobasidium floriforme

Marco Alexandre Guerreiro 1, Steven Ahrendt 2, Jasmyn Pangilinan 2, Cindy Chen 2, Mi Yan 2, Anna Lipzen 2, Kerrie Barry 2, Igor V Grigoriev 2,3, Dominik Begerow 1, Minou Nowrousian 4,✉
Editor: A Rokas
PMCID: PMC9210288  PMID: 34791213

Abstract

The Tremellomycetes are a species-rich group within the basidiomycete fungi; however, most analyses of this group to date have focused on pathogenic Cryptococcus species within the order Tremellales. Recent genome-assisted studies of other Tremellomycetes have identified interesting features with respect to biotechnological applications as well as the evolution of genes involved in mating and sexual development. Here, we report genome sequences of two strains of Filobasidium floriforme, a species from the order Filobasidiales, which branches basally to the Tremellales, Trichosporonales, and Holtermanniales. The assembled genomes of strains CBS6241 and CBS6242 are 27.4 Mb and 26.4 Mb in size, respectively, with 8314 and 7695 predicted protein-coding genes. Overall sequence identity at nucleic acid level between the strains is 97%. Among the predicted genes are pheromone precursor and pheromone receptor genes as well as two genes encoding homedomain (HD) transcription factors, which are predicted to be part of the mating type (MAT) locus. Sequence analysis indicates that CBS6241 and CBS6242 carry different alleles for both the pheromone/receptor genes as well as the HD transcription factors. Orthology inference identified 1482 orthogroups exclusively found in F. floriforme, some of which were involved in carbohydrate transport and metabolism. Subsequent CAZyme repertoire characterization identified 267 and 247 enzymes for CBS6241 and CBS6242, respectively, the second highest number of CAZymes among the analyzed Tremellomycete species. In addition, F. floriforme contains five CAZymes absent in other species and several plant-cell-wall degrading CAZymes with the highest copy number in Tremellomycota, indicating the biotechnological potential of this species.

Keywords: Filobasidium floriforme, mating-type locus, basidiomycete, Filobasidiales, CAZymes

Introduction

The basidiomycete group of Tremellomycetes is a species-rich group comprising both filamentous and yeast-like fungi (Liu et al. 2015a, 2015b; Spatafora et al. 2017). In-depth studies in this group have mostly focused on pathogenic Cryptococcus species (order Tremellales) (Sun et al. 2019a; Bahn et al. 2020). However, facilitated by increased genome-sequencing capacities in recent years, additional species within the Tremellomycetes have been investigated, often for their biotechnological potential or to study the evolution of sexual development in this group (Sharma et al. 2015; Bellora et al. 2016; Barredo et al. 2017; Bracharz et al. 2017; Coelho et al. 2017; Sun et al. 2019b; Aliyu et al. 2020).

Mating and sexual development in basidiomycetes is regulated by mating type (MAT) genes encoding pheromone precursors, pheromone receptors, and homeodomain (HD) transcription factors. The ancestral state in basidiomycetes is thought to be tetrapolar, with two nonlinked genetic loci containing pheromone and pheromone receptor genes (P/R locus) and HD transcription factor genes (HD locus), respectively (Kües et al. 2011; Coelho et al. 2017). However, studies of pathogenic Cryptococcus species revealed a single, large MAT locus predicted to have arisen from genomic transitions leading to fusion of the formerly unlinked P/R and HD loci (Lengeler et al. 2002; Fraser et al. 2004), whereas in all other species of the order Tremellales that were analyzed so far, the ancient tetrapolar arrangement of unlinked P/R and HD loci is found (Sun et al. 2019a). In contrast, in the Trichosporonales, the sister order to the Tremellales (Liu et al. 2015b), a recent analysis of MAT loci revealed that in all analyzed species, P/R and HD loci are physically linked in a single MAT locus (Sun et al. 2019b).

For the Tremellomycete order Filobasidiales, which branches basally to the Tremellales, Trichosporonales, and Holtermanniales (Liu et al. 2015b), genomes have been published for the genera Naganishia and Solicoccozyma, but none were analyzed with respect to the mating type (Close et al. 2016; Vajpeyi and Chandran 2016; Yong et al. 2016; Bijlani et al. 2020; Han et al. 2020; Nizovoy et al. 2021). Here, we present the first draft genome sequences including an analysis of MAT genes for two strains of the genus Filobasidium, Filobasidium floriforme strains CBS6241 and CBS6242.

Carbohydrate-active enzymes (CAZymes) are essential for fungi as heterotrophic organisms. These enzymes are responsible for the biosynthesis, modification, binding, and breakdown of carbohydrates and glycoconjugates (Cantarel et al. 2009). Different fungal species harbor different sets of CAZymes to meet their ecological needs as saprobes, symbionts, endophytes, parasites, or pathogens (Rytioja et al. 2014; Kameshwar and Qin 2018). CAZyme content and diversity is therefore suggested to reflect niche adaptation. CAZymes are widely applied in various biotechnological processes and industries, such as in food, wine, paper, pulp, textile, detergents, biofuels, biorefinery, and bioremediation (Mäkelä et al. 2014). Since Tremellomycetes are known for their ability to colonize and inhabit a vast diversity of substrates, characterizing their set of CAZymes provides a great opportunity to identify and characterize species with biotechnological potential.

Materials and methods

Strains and culture conditions

Strains CBS6241 and CBS6242 were obtained from the Westerdijk Fungal Biodiversity Institute (Utrecht, The Netherlands). Strains were kept on YPD agar medium at 25°C.

DNA extraction and sequencing

For DNA extraction, strains were grown as pre-cultures for 4 days at 25°C on YPD agar medium. From single colonies, 30 ml liquid YPD medium was inoculated and cultures were incubated at 25°C and 100 rpm on a shaker for 24 h (OD600 > 1). DNA was extracted as described previously (Kourist et al. 2015).

The genome of strain CBS6241 was sequenced using Pacific Biosciences Sequel sequencing platform. One microgram of genomic DNA was sheared to 10 kb using Covaris g-TUBE. The sheared DNA was treated with DNA damage repair mix followed by end repair and ligation of blunt adapters using SMRTbell Template Prep Kit 1.0 (Pacific Biosciences). The library was purified with AMPure PB beads. PacBio Sequencing primer was then annealed to the SMRTbell template library and sequencing polymerase was bound to them using Sequel Binding kit 3.0. The prepared SMRTbell template libraries were then sequenced on a Pacific Biosystem’s Sequel sequencer using v3 sequencing primer, 1M v3 SMRT cells, and Version 3.0 sequencing chemistry with 1 × 360 and 1 × 600 sequencing movie run times. A total of 3,594,174 reads were obtained with an average length of 3.8 kb and an N50 of 5.7 kb.

Library preparation and Illumina sequencing of strain CBS6242 was performed by Eurofins (Konstanz, Germany). Paired-end reads of 151 nt were sequenced from a library with an average insert size of 330 nt.

RNA extraction, sequencing, and transcriptome assembly

For RNA extraction, CBS6241 was grown as pre-culture for 4 days at 25°C on YPD agar medium. From single colonies, 30 ml of three different liquid media were inoculated (V8: 50 ml/l vegetable juice, pH 5.2; V8-YPD1: 50 ml/l vegetable juice, 10 g/l tryptone, 5 g/l yeast extract, 10 g/l glucose, pH 5.2; V8-YPD2: 25 ml/l vegetable juice, 20 g/l tryptone, 5 g/l yeast extract, 10 g/l glucose, pH 5.2). Cultures were incubated at 25°C and 100 rpm on a shaker for 24 h. RNA was extracted as described previously (Kourist et al. 2015).

The transcriptome of strain CBS6241 was sequenced using Illumina 2 × 150 paired-end reads. Stranded cDNA library was generated using the Illumina Truseq Stranded RNA LT kit. mRNA was purified from 1 µg of total RNA using magnetic beads containing poly-T oligonucleotides. mRNA was fragmented and reversed transcribed using random hexamers and SSII (Invitrogen) followed by second strand synthesis. The fragmented cDNA was treated with end-pair, A-tailing, adapter ligation, and eight cycles of PCR. The prepared library was quantified using KAPA Biosystems’ next-generation sequencing library qPCR kit and run on a Roche LightCycler 480 real-time PCR instrument. Sequencing of the library was performed on the Illumina NovaSeq sequencer using NovaSeq XP V1 reagent kits, S4 flowcell, following a 2 × 150 dependent indexed run recipe. Raw reads were filtered and trimmed. Using BBDuk (https://sourceforge.net/projects/bbmap/, Accessed: 2021 November 19), raw reads were evaluated for artifact sequence by kmer matching (kmer = 25), allowing 1 mismatch and detected artifact was trimmed from the 3′ end of the reads. RNA spike-in reads, PhiX reads and reads containing any Ns were removed. Quality trimming was performed using the phred trimming method set at Q6. Finally, following trimming, reads under the length threshold were removed (minimum length 25 bases or 1/3 of the original read length—whichever is longer). Filtered reads were assembled into consensus sequences using Trinity (v2.3.2) (Grabherr et al. 2011), run with the –normalize_reads (In-silico normalization routine) and –jaccard_clip (Minimizing fusion transcripts derived from gene dense genomes) options. The transcriptome data were used for annotation.

Genome assembly and annotation

Filtered Pacific Biosciences subread data for strain CBS6241 was filtered for artifacts and assembled with Falcon version pb-assembly = 0.0.2|falcon-kit = 1.2.3|pypeflow = 2.1.0 (https://github.com/PacificBiosciences/FALCON, Accessed: 2021 November 19) and polished with Arrow version SMRTLink v7.0.1.66975 (https://www.pacb.com/support/software-downloads, Accessed: 2021 November 19), improved with finisherSC version 2.1 (Lam et al. 2015), and polished with Arrow version SMRTLINK v7.0.1.66975 (https://www.pacb.com/support/software-downloads, Accessed: 2021 November 19). The genome was annotated using the JGI Annotation pipeline (Grigoriev et al. 2014).

For strain CBS6242, Illumina reads were quality-trimmed with Trimmomatic v0.36 (Bolger et al. 2014) and assembled with SPAdes v3.14.0 (Prjibelski et al. 2020). Contigs >1 kb were kept for downstream analyses. Contigs were error-corrected with Pilon v1.22 (Walker et al. 2014) based on the Illumina reads mapped to the assembly with Bowtie2 v2.2.6 (Langmead and Salzberg 2012). For CBS6242, genes were predicted with Maker v2.31.8 (Cantarel et al. 2008) based on the predicted genes of CBS6241. Pheromone genes in both strains were identified with a custom-made Perl script (Supplementary Text S1) to search for the consensus sequence M-X(15-60)-CAAX-Stop, with X representing any amino acid and A representing the amino acids valine, leucine, isoleucine, methionine, threonine or serine. Putative telomeric repeats (sequence TTAGGGG occurring consecutively at least three times) were identified with a custom-made Perl script (Supplementary Text S2).

Phylogenetic analysis and functional annotation

Published genome assembly data of tremellomycetous species were collected from NCBI and JGI databases (Supplementary Table S1). The respective proteomes were predicted by Augustus version 3.3.3 (Stanke et al. 2008), with Cryptococcus neoformans as reference organism. Orthologous protein sequences were identified with OrthoFinder v2.5.2 (Emms and Kelly 2019). Single-copy orthologous sequences present in all species were individually aligned with MAFFT v7.273 (Katoh and Standley 2013) and concatenated. The maximum likelihood phylogenetic tree was calculated based on a single alignment of 142 single-copy orthologous genes by RAxML v8.2.12 (Stamatakis 2014) using 500 bootstrap replications, the PROTGAMMAWAG model, 123 as seed number for the parsimony inferences and a random seed of 321.

The strains Cryptococcus deneoformans JEC21 (Loftus et al. 2005), Cutaneotrichosporon oleaginosum IBC0246 (Kourist et al. 2015) and Cystofilobasidium capitatum CBS7420 (David-Palma et al. 2020) were selected for further analyses as representatives of Tremellales, Trichosporonales and Cystofilobasidiales, respectively (one species per order). Orthology comparisons were calculated with ComplexUpset (v1.3.1) package for R v4.1.0 and “exclusive intersection” mode.

Genes comprised in orthogroups exclusively found in F. floriforme were extracted and functionally annotated with PFAM v34.0 online database (Mistry et al. 2021) and eggNOG-mapper v2.1.0-1 (Huerta-Cepas et al. 2019; Cantalapiedra et al. 2021).

Analysis of the MAT regions

Homologs to MAT genes were identified with BLAST analyses (Altschul et al. 1997) using MAT proteins from Cryptococcus neoformans (Lengeler et al. 2002) as queries. Phylogenetic trees of Ste3 proteins from F. floriforme strains and from published sequences of Trichosporonales and Tremellales species (Lengeler et al. 2000, 2002; Kourist et al. 2015; Takashima et al. 2015, 2018; Cho et al. 2016; Sriswasdi et al. 2016; Sun et al. 2019b) were generated with PAUP version 4.0b10 for Windows (D.L. Swofford, distributed by Sinauer Associates, copyright 2001 Smithsonian Institution) for Neighbor joining analyses or with MrBayes (Huelsenbeck and Ronquist 2001; Ronquist and Huelsenbeck 2003) based on multiple alignments generated with CLUSTALX (Thompson et al. 1997). Comparisons of genomic regions at nucleic acid level were performed with nucmer from the MUMmer package (Kurtz et al. 2004).

Prediction of CAZymes

Proteomes of published datasets in Filobasidiales and of representative members of Tremellales, Trichosporonales and Cystofilobasidiales were scanned against dbCAN2 v9.0 database (Zhang et al. 2018) using HMMER v3.3.2 (Eddy 2011). Matches with an e-value lower than 1e-15 and a coverage higher than 0.35 were used for further analyses.

Results and discussion

Genome assembly and assessment

The genome of the F. floriforme strain CBS6241 was sequenced as part of the 1000 Fungal Genomes project (http://1000.fungalgenomes.org) (Grigoriev et al. 2011, 2014) using PacBio sequencing, while strain CBS6242 was sequenced with Illumina sequencing. With assembly sizes of 26–27 Mb and 7695 and 8314 predicted genes (Table 1), the genomes of the two F. floriforme strains are in the same range as the previously sequenced 24.8 Mb genomes of two strains of the Filobasidiales species Naganishia albida, for which 7375 and 8637 genes were predicted (Vajpeyi and Chandran 2016; Yong et al. 2016).

Table 1.

Genome assembly statistics for CBS6241 and CBS6242

CBS6241 CBS6242
Assembly size (Mb) 27.5 26.4
No. of scaffolds 42 700
N50 (kb) 9388 120
GC content (%) 52.9 52.9
Predicted genes 8314 7695
completeness (%)a 94.9 92.6
Coding regions (%) 46.0 44.3
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a

Completeness was analyzed with BUSCO v5.2.1 (Manni et al. 2021).

Searches for putative telomeric repeats identified seven contigs in CBS6241 with putative telomeric repeats at both ends, and 23 contigs with putative telomeric repeats at one end (Supplementary Table S2). This suggests that the genome of CBS6241 consists of (at least) 19 chromosomes. In the Illumina-sequenced genome of CBS6242, no putative telomeric repeats were identified, as is to be expected in a genome assembled from short reads.

Phylogenetic analysis

The maximum likelihood analysis of the 142 single-copy orthologous protein sequences produced a highly resolved phylogeny of Tremellomycota, in which most clades were supported by bootstrap values of 100% (Figure 1, Supplementary Figure S1). The Filobasidiales order is monophyletic and basal to the orders Tremellales and Trichosporonales. Cystofilobasidiales is the most basal order in Tremellomycota. The calculated phylogeny is consistent with previous reconstructions (Liu et al. 2015a, 2015b). Currently, classifications suggest that the Filobasidium genus is likely monophyletic and closely related to Naganishia and Solicoccozyma genera (Kwon-Chung 2011; Liu et al. 2015a), supporting our results. Due to their placement in the phylogeny (Figure 1, Supplementary Figure S1), a taxonomic revision of available Naganishia genomes might be advisable for future studies.

Figure 1.

Figure 1

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Phylogenetic analysis of Tremellomycetes. A maximum likelihood analysis of 142 single-copy orthologous protein sequences was performed with 500 bootstrap replicates using Ustilago maydis as an outgroup. All depicted nodes showed 100% bootstrap support except when noted. Accession numbers for the genome assembly data is provided in Supplementary Table S1. Groups outside of the Filobasidiales are collapsed, for the full phylogeny, see Supplementary Figure S1. The scale bar gives substitutions per site.

Orthologous genes and functional assignment

Orthology inference analysis revealed that 2526 orthogroups were shared among all the selected Tremellomycetes species (Figure 2). Furthermore, 123 were exclusively found among members of Filobasidiales, while 236 were exclusive to the Naganishia genus. A total of 1485 unique orthogroups were exclusively found in the two strains of F. floriforme, from which 83 orthogroups (comprising 224 orthologous sequences) were successfully functionally assigned by both PFAM and eggNOG databases (Supplementary Table S3). The most represented eggNOG functional categories included unknown function (31 orthogroups), carbohydrate transport and metabolism (13), post-translational modification, protein turnover, and chaperones (10), and replication, recombination, and repair (8). Functional description resulted, among others, in glycosyl hydrolases, dehydrogenases, kinases and proteases, that were specific to F. floriforme. These unique features might indicate a unique evolutionary adaptation to the environment (Rytioja et al. 2014; Nizovoy et al. 2021). Both strains comprised similar copy numbers, with a few exceptions in some domains, which could be explained by the different assembly quality of both genomes (Table 1). Orthology inference analysis and functional assignment suggest that F. floriforme might comprise unique genomic traits that might be valuable for further functional studies (Nizovoy et al. 2021).

Figure 2.

Figure 2

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Orthogroup analysis to identify shared orthogroups between F. floriforme strains and other Tremellomycetes. Black dots indicate species/strains that share the indicated number of orthogroups. Indicated orthogroups are exclusively found in the indicated set of species [shared orthogroups were compared among orders (Tremellales, Trichosporonales, Filobasidiales, and Cystofilobasidiales) and within the Naganisha genus].

Analysis of MAT genes

Putative pheromone receptor genes and HD genes were identified by BLAST searches with the corresponding C. neoformans genes, whereas putative pheromone precursor genes were identified through searches for a consensus sequence with a custom-made Perl script. In each of the F. floriforme strains, one STE3 pheromone receptor gene, one pheromone precursor gene, and two HD transcription factor genes (SXI1 and SXI2) were identified (Supplementary Figures S2 and S3). The pheromone receptor gene and pheromone precursor gene of CBS6241 are located in a 21 kb region on contig 14, whereas the HD genes are located in a 4 kb region on contig 3. Both contigs have telomeric repeats at both ends (Supplementary Table S2), making it likely that they represent different chromosomes. This suggests that the P/R and HD loci of CBS6241 are genetically unlinked and that therefore the mating type configuration of F. floriforme might be tetrapolar.

The genomic regions containing the HD genes are syntenic in CBS6241 and CBS6242 (Supplementary Figure S4). The predicted pheromone precursor gene of CBS6242 is located toward one end of contig 18, and the region is syntenic to the corresponding region in CBS6241 (Supplementary Figure S4). However, the pheromone receptor genes STE3 is located on a separate, short contig that shows two inversions compared to CBS6241 (Supplementary Figure S4). Furthermore, a repeat-rich region of 15 kb that is present close to STE3 in CBS6241 was not assembled in CBS6242, probably due to the short read-based assembly. Repeat expansions and sequence divergence have been observed previously in the MAT regions of other basidiomycetes and are often associated with sex- or mating type-determining regions with reduced recombination (Lengeler et al. 2002; Loftus et al. 2005; Branco et al. 2017, 2018; Coelho et al. 2017).

The STE3 gene of CBS6241 belongs to the MATa group of STE3 pheromone receptor genes, whereas the STE3 gene of CBS6242 belongs to the MATα group of STE3 genes (Figure 3, Supplementary Figure S2). A phylogenetic analysis of STE3 alleles from the two F. floriforme strains as well as STE3 genes from Trichosporonales and Tremellales showed trans-species polymorphism already observed for Trichosporonales and Tremellales (Metin et al. 2010; Findley et al. 2012; Sun et al. 2019b), indicating that the trans-species polymorphism of STE3 alleles was present already in the last common ancestor of the Filobasidiales and its sister orders (Figure 3).

Figure 3.

Figure 3

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Phylogenetic analysis of Ste3 proteins from several Tremellomycetes. Analysis was done by MrBayes (A) or Neighbor joining (NJ, in B). Bayesian probabilities (A) or bootstrap percentages for 1000 bootstrap replications (B) are given at the branches. The pheromone-receptor-like Cpr2 proteins from C. neoformans and C. gattii were used as outgroups. The phylogenetic trees show a deep trans-species polymorphism for the Ste3 proteins within the Tremellomycetes that not only includes the sister orders Tremellales and Trichosporonales, but also includes the early-branching Filobasidiales represented by the two F. floriforme strains. Species abbreviations and accession numbers or locus tag numbers: A. dom, Apiotrichum domesticum (T. domesticum_002_745, genome accession BCFW01000000); C. neo, Cryptococcus neoformans (Ste3a: AAN75624.1, Ste3α: XP_012049557.1, Cpr2: XP_012047561.1); C. gat, Cryptococcus gattii (Ste3a: AEG78597.1, Ste3α: XP_003196044.1, Cpr2: XP_003191200.1); C. ole, Cutaneotrichosporon oleaginosum (XP_018276494.1); F. flo, Filobasidium floriforme (CBS6241: gene_1555, CBS6242: CBS6242_07693 = FFLO_06159), T. fae, Trichosporon faecale (T. faecale_002_949, genome accession JXYK01000000), T. ink. Trichosporon inkin (T. inkin_003_120, genome accession JXYM01000000); V. hum, Vanrija humicola (Ste3a: JCM1475_001_295, genome accession BCJF01000000, Ste3α: TXT13458.1).

Both strains carry two HD genes (SXI1 and SXI2) next to each other but divergently transcribed, which is the typical genomic arrangement for basidiomycete HD genes (Coelho et al. 2017). Sequence comparison of the HD region of CBS6241 and CBS6242 showed that the region is similar in both strains except for a part encompassing the intergenic region and the N-terminal regions of SXI1 and SXI2, which is highly divergent (Figure 4). This is similar to previous findings in other basidiomycetes, where it was shown that the divergent N-termini of the SXI1 and SXI2 proteins are relevant for the interactions of the two different types of HD transcription factors, and that allele specificity is conferred by these regions (Banham et al. 1995; Kämper et al. 1995, 2020; Metin et al. 2010; Findley et al. 2012).

Figure 4.

Figure 4

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Dot plot of HD transcription factor gene regions of F. floriforme strains CBS6241 and CBS6242. The comparison was performed with nucmer from the MUMmer package (Kurtz et al. 2004). Nucleic acid sequence identity in the first aligned region (nt 1–356) is 96.4%, in the second aligned region (nt ∼2000–4200) it is 84.0%. No sequence similarity was detected in the region shaded in gray, which comprises the intergenic region and the N-terminal regions of SXI1 and SXI2. The regions encoding the conserved homeodomains in Sxi1 and Sxi2 are shown in light blue and light green, respectively. Gene regions outside of the conserved homeodomain-encoding regions are given in dark blue and dark green for SXI1 and SXI2, respectively. The sequences used for comparison comprise the following genomic regions in the CBS6241 and CBS6242 assemblies, respectively: CBS6241 contig14 nt 669,525–673,807, CBS6242 contig45 nt 55,021–59,216.

Thus, the two strains carry different and potentially mating-compatible alleles at the P/R as well as the HD locus, and one can conclude that there are at least two alleles for each MAT locus present in the population. Mating between CBS6241 and CBS6242 was observed in 1972 (Rodrigues De Miranda 1972). However, in our laboratories, we were not able to observe sexual structures in co-cultures of the two strains. It is possible that we were not able to recreate the conditions required for mating of the two strains, or that the strains have lost the ability for sexual reproduction through accumulation of mutations after several decades of being cultured under laboratory conditions. The availability of genome sequences for two strains of F. floriforme should facilitate the analysis of MAT alleles of additional strains of this species that might be used in future mating experiments.

Characterization of CAZymes repertoire

Characterization of CAZymes content revealed that F. floriforme contains a high diversity of CAZymes, which includes 267 and 247 genes for CBS6241 and CBS6242, respectively (Figure 5). Solicoccozyma terricola, a promising biotechnological strain (Tanimura et al. 2014; Close et al. 2016) contained the highest number of CAZymes (277), but a similar number (149) of glycoside hydrolases (GHs) compared to the F. floriforme strains (143 and 134). Filobasidium floriforme contained the highest number of carbohydrate esterases (CEs), while Cystofilobasidium capitatum contained the most glycosyltransferases (GTs) and polysaccharide lyases (PLs). Filobasidium floriforme comprised 5 CAZymes that were absent in the other organisms (PL3, PL27, GH39, GT28, and GT34) and 8 with a higher number of copies than any of the other species (AA9, CE5, CE9, GH3, GH10, GH31, GH35, and GH43) (Supplementary Figures S5–S10). Interestingly, most of these (AA9, CE5, CE9, GH3, GH10, GH31, GH35, GH39, GH43, GT34, and PL3) are important plant-cell-wall degrading enzymes (Zhao et al. 2013; Chang et al. 2016). This highlights the promising vast potential of F. floriforme in industrial and biotechnological application (Bosetto et al. 2016).

Figure 5.

Figure 5

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Overview of CAZymes identified in F. floriforme compared to other Tremellomycetes. Abbreviations of CAZyme categories: AA, auxiliary activities; CBM, carbohydrate binding modules; CE, carbohydrate esterases; GH, glycoside hydrolases; GT, glycosyltransferases; PL, polysaccharide lyases.

Data availability

PacBio reads from CBS6241 (genome sequencing) were deposited in the NCBI SRA database under accession number SRP256613. Illumina reads from CBS6241 (RNA-seq) were deposited at the NCBI SRA database under accession number SRP256618. Illumina reads from CBS6242 (genome sequencing) were deposited in the NCBI SRA database under accession number SRP258233. The CBS6241 genome sequence (BioProject ID PRJNA621322) was deposited at DDBJ/ENA/GenBank under the accession JAIFAB000000000, and the CBS6242 genome sequence (BioProject ID PRJNA627804) under the accession JABELV000000000. Supplemental material (Supplementary Figures S1–S10, Tables S1–S3, Supplementary Texts S1–S2) is part of the manuscript submission. Supplementary Figure S1: Phylogenetic analysis of Tremellomycetes. Supplementary Figure S2: Multiple alignment of Ste3 homologs in the MAT loci of several Tremellomycetes. Supplementary Figure S3: Analysis of Sxi proteins from Tremellomycetes. Supplementary Figure S4: MAT loci of CBS6241 and CBS6242. Supplementary Figure S5: Overview of CAZyme category AA. Supplementary Figure S6: Overview of CAZyme category CBM. Supplementary Figure S7: Overview of CAZyme category CE. Supplementary Figure S8: Overview of CAZyme category GH. Supplementary Figure S9: Overview of CAZyme category GT. Supplementary Figure S10: Overview of CAZyme category PL. Supplementary Table S1: Genome assemblies that were used in this study. Supplementary Table S2: Analysis of putative telomeric repeats at contig ends of CBS6241. Supplementary Table S3: Analysis of unique orthogroups in F. floriforme. Supplementary Text S1: Perl script for searching for putative pheromone genes. Supplementary Text S2: Perl script for searching for putative telomeric repeats.

Supplementary material is available at G3 online.

Supplementary Material

jkab398_Supplementary_Data
Click here for additional data file. (982.5KB, pdf)

Acknowledgments

The authors would like to thank Silke Nimtz for excellent technical assistance. MN would like to thank Christopher Grefen for support at the Department of Molecular and Cellular Botany.

Funding

This work was funded by the German Research Foundation (DFG, grant NO407/7-2 to MN). The work conducted by the U.S. Department of Energy Joint Genome Institute, a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231.

Conflicts of interest

The authors declare that there is no conflict of interest.

Literature cited

  1. Aliyu H, Gorte O, Zhou X, Neumann A, Ochsenreither K.. 2020. In silico proteomic analysis provides insights into phylogenomics and plant biomass deconstruction potentials of the Tremelalles. Front Bioeng Biotechnol. 8:226. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, et al. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25:3389–3402. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Bahn YS, Sun S, Heitman J, Lin X.. 2020. Microbe profile: Cryptococcus neoformans species complex. Microbiology (Reading). 166:797–799. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Banham AH, Asante-Owusu RN, Göttgens B, Thompson S. A J, Kingsnorth CS, et al. 1995. An N-terminal dimerization domain permits homeodomain proteins to choose compatible partners and initiate sexual development in the mushroom Coprinus cinereus. Plant Cell. 7:773–783. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Barredo JL, García-Estrada C, Kosalkova K, Barreiro C.. 2017. Biosynthesis of astaxanthin as a main carotenoid in the heterobasidiomycetous yeast Xanthophyllomyces dendrorhous. J Fungi (Basel). 3:44. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Bellora N, Moliné M, David-Palma M, Coelho MA, Hittinger CT, et al. 2016. Comparative genomics provides new insights into the diversity, physiology, and sexuality of the only industrially exploited tremellomycete: Phaffia rhodozyma. BMC Genomics. 17:901. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Bijlani S, Singh NK, Mason CE, Wang CCC, Venkateswaran K.. 2020. Draft genome sequences of Tremellomycetes strains isolated from the International Space Station. Microbiol Resour Announc. 9:e00504-20. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Bolger AM, Lohse M, Usadel B.. 2014. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 30:2114–2120. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Bosetto A, Justo PI, Zanardi B, Venzon SS, Graciano L, et al. 2016. Research progress concerning fungal and bacterial β-xylosidases. Appl Biochem Biotechnol. 178:766–795. [DOI] [PubMed] [Google Scholar]
  10. Bracharz F, Beukhout T, Mehlmer N, Brück T.. 2017. Opportunities and challenges in the development of Cutaneotrichosporon oleaginosus ATCC 20509 as a new cell factory for custom tailored microbial oils. Microb Cell Fact. 16:178. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Branco S, Badouin H, Rodríguez De La Vega RC, Gouzy J, Carpentier F, et al. 2017. Evolutionary strata on young mating-type chromosomes despite the lack of sexual antagonism. Proc Natl Acad Sci U S A. 114:7067–7072. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Branco S, Carpentier F, Rodríguez De La Vega RC, Badouin H, Snirc A, et al. 2018. Multiple convergent supergene evolution events in mating-type chromosomes. Nat Commun. 9:2000. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Cantalapiedra CP, Hernandez-Plaza A, Letunic I, Bork P, Huerta-Cepas J.. 2021. eggNOG-mapper v2: functional annotation, orthology assignments, and domain prediction at the metagenomic scale. bioRxiv. doi: 10.1101/2021.1106.1103.446934. [DOI] [PMC free article] [PubMed]
  14. Cantarel BL, Coutinho PM, Rancurel C, Bernard T, Lombard V, et al. 2009. The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics. Nucleic Acids Res. 37:D233–D238. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Cantarel BL, Korf I, Robb SMC, Parra G, Ross E, et al. 2008. MAKER: an easy-to-use annotation pipeline designed for emerging model organism genomes. Genome Res. 18:188–196. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Chang HX, Yendrek CR, Caetano-Anolles G, Hartman GL.. 2016. Genomic characterization of plant cell wall degrading enzymes and in silico analysis of xylanses and polygalacturonases of Fusarium virguliforme. BMC Microbiol. 16:147. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Cho O, Ichikawa T, Kurakado S, Takashima M, Manabe R, et al. 2016. Draft genome sequence of the causative antigen of summer-type hypersensitivity pneumonitis, Trichosporon domesticum JCM 9580. Genome Announc. 4:e00651-16. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Close D, Ojumu J, Zhang G.. 2016. Draft genome sequence of Cryptococcus terricola JCM 24523, an oleaginous yeast capable of expressing exogenous DNA. Genome Announc. 4:e01238-16. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Coelho MA, Bakkeren G, Sun S, Hood ME, Giraud T.. 2017. Fungal Sex: the Basidiomycota. Microbiol. Spectr. 5. 10.1128/microbiolspec.FUNK-0046-2016. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. David-Palma M, Libkind D, Brito PH, Silva M, Bellora N, et al. 2020. The untapped Australasian diversity of astaxanthin-producing yeasts with biotechnological potential—Phaffia australis sp. nov. and Phaffia tasmanica sp. nov. Microorganisms. 8:1651. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Eddy SR. 2011. Accelerated profile HMM searches. PLoS Comput Biol. 7:e1002195. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Emms DM, Kelly S.. 2019. OrthoFinder: phylogenetic orthology inference for comparative genomics. Genome Biol. 20:238. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Findley K, Sun S, Fraser JA, Hsueh YP, Averette AF, et al. 2012. Discovery of a modified tetrapolar sexual cycle in Cryptococcus amylolentus and the evolution of MAT in the Cryptococcus species complex. PLoS Genet. 8:e1002528. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Fraser JA, Diezmann S, Subaran RL, Allen A, Lengeler KB, et al. 2004. Convergent evolution of chromosomal sex-determining regions in the animal and fungal kingdoms. PLoS Biol. 2:e384. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, et al. 2011. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol. 29:644–652. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Grigoriev IV, Cullen D, Goodwin SB, Hibbett D, Jeffries TW, et al. 2011. Fueling the future with fungal genomics. Mycology. 2:192–209. [Google Scholar]
  27. Grigoriev IV, Nikitin R, Haridas S, Kuo A, Ohm R, et al. 2014. MycoCosm portal: gearing up for 1000 fungal genomes. Nucleic Acids Res. 42:D699–D704. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Han YW, Kajitani R, Morimoto H, Palihati M, Kurokawa Y, et al. 2020. Draft genome sequence of Naganishia liquefaciens strain N6, isolated from the Japan Trench. Microbiol Resour Announc. 9:e00827-20. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Huelsenbeck JP, Ronquist F.. 2001. Bayesian inference of phylogeny. Bioinformatics. 17:754–755. [DOI] [PubMed] [Google Scholar]
  30. Huerta-Cepas J, Szklarczyk D, Heller D, Hernández-Plaza A, Forslund SK, et al. 2019. eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses. Nucleic Acids Res. 47:D309–D314. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Kameshwar AKS, Qin W.. 2018. Comparative study of genome-wide plant biomass-degrading CAZymes in white rot, brown rot and soft rot fungi. Mycology. 9:93–105. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Kämper J, Friedrich MW, Kahmann R.. 2020. Creating novel specificities in a fungal nonself recognition system by single step homologous recombination events. New Phytol. 228:1001–1010. [DOI] [PubMed] [Google Scholar]
  33. Kämper J, Reichmann M, Romeis R, Bölker M, Kahmann R.. 1995. Multiallelic recognition: nonself-dependent dimerization of the bE and bW homeodomain proteins in Ustilago maydis. Cell. 81:73–83. [DOI] [PubMed] [Google Scholar]
  34. Katoh K, Standley DM.. 2013. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 30:772–780. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Kourist R, Bracharz F, Lorenzen J, Kracht ON, Chovatia M, et al. 2015. Genomics and transcriptomics of the oil-accumulating basidiomycete yeast Trichosporon oleaginosus: insights into substrate utilization and alternative evolutionary trajectories of fungal mating systems. mBio. 6:e00918. [DOI] [PMC free article] [PubMed] [Google Scholar]
  36. Kües U, James TY, Heitman J.. 2011. Mating type in basidiomycetes: unipolar, bipolar, and tetrapolar patterns of sexuality. In:Pöggeler S, Wöstemeyer J, editors. The Mycota XIV. Evolution of Fungi and Fungal-Like Organisms. Berlin, Heidelberg: Springer. p. 97–160. [Google Scholar]
  37. Kurtz S, Phillippy A, Delcher AL, Smoot M, Shumway M, et al. 2004. Versatile and open software for comparing large genomes. Genome Biol. 5:R12. [DOI] [PMC free article] [PubMed] [Google Scholar]
  38. Kwon-Chung KJ. 2011. Filobasidium Olive, 1968. In: Kurtzman CP, Fell JW, Boekhout T, editors. The Yeasts.. Amsterdam: Elsevier. p. 1457–1465. [Google Scholar]
  39. Lam KK, Labutti K, Khalak A, Tse D.. 2015. FinisherSC: a repeat-aware tool for upgrading de novo assembly using long reads. Bioinformatics. 31:3207–3209. [DOI] [PubMed] [Google Scholar]
  40. Langmead B, Salzberg SL.. 2012. Fast gapped-read alignment with Bowtie 2. Nat Methods. 9:357–359. [DOI] [PMC free article] [PubMed] [Google Scholar]
  41. Lengeler KB, Fox DS, Fraser JA, Allen A, Forrester K, et al. 2002. Mating-type locus of Cryptococcus neoformans: a step in the evolution of sex chromosomes. Eukaryot Cell. 1:704–718. [DOI] [PMC free article] [PubMed] [Google Scholar]
  42. Lengeler KB, Wang P, Cox GM, Perfect JR, Heitman J.. 2000. Identification of the MATa mating-type locus of Cryptococcus neoformans reveals a serotype A MATa strain thought to have been extinct. Proc Natl Acad Sci USA. 97:14455–14460. [DOI] [PMC free article] [PubMed] [Google Scholar]
  43. Liu XZ, Wang QM, Göker M, Groenewald M, Kachalkin AV, et al. 2015a. Towards an integrated phylogenetic classification of the Tremellomycetes. Stud Mycol. 81:85–147. [DOI] [PMC free article] [PubMed] [Google Scholar]
  44. Liu XZ, Wang QM, Theelen B, Groenewald M, Bai FY, et al. 2015b. Phylogeny of tremellomycetous yeasts and related dimorphic and filamentous basidiomycetes reconstructed from multiple gene sequence analyses. Stud Mycol. 81:1–26. [DOI] [PMC free article] [PubMed] [Google Scholar]
  45. Loftus BJ, Fung E, Roncaglia P, Rowley D, Amedeo P, et al. 2005. The genome of the basidiomycetous yeast and human pathogen Cryptococcus neoformans. Science. 307:1321–1324. [DOI] [PMC free article] [PubMed] [Google Scholar]
  46. Mäkelä MR, Donofrio N, De Vries RP.. 2014. Plant biomass degradation by fungi. Fungal Genet Biol. 72:2–9. [DOI] [PubMed] [Google Scholar]
  47. Manni M, Berkeley MR, Seppey M, Simão FA, Zdobnov EM.. 2021. BUSCO update: novel and streamlined workflows along with broader and deeper phylogenetic coverage for scoring of eukaryotic, prokaryotic, and viral genomes. Mol Biol Evol. 38:4647–4654. doi: 10.1093/molbev/msab1199. [DOI] [PMC free article] [PubMed] [Google Scholar]
  48. Metin B, Findley K, Heitman J.. 2010. The mating type locus (MAT) and sexual reproduction of Cryptococcus heveanensis: insights into the evolution of sex and sex-determining chromosomal regions in fungi. PLoS Genet. 6:e1000961. [DOI] [PMC free article] [PubMed] [Google Scholar]
  49. Mistry J, Chuguransky S, Williams L, Qureshi M, Salazar GA, et al. 2021. Pfam: the protein families database in 2021. Nucleic Acids Res. 49:D412–D419. [DOI] [PMC free article] [PubMed] [Google Scholar]
  50. Nizovoy P, Bellora N, Haridas S, Sun H, Daum C, et al. 2021. Unique genomic traits for cold adaptation in Naganishia vishniacii, a polyextremophile yeast isolated from Antarctica. FEMS Yeast Res. 21:foaa056. [DOI] [PubMed] [Google Scholar]
  51. Prjibelski A, Antipov D, Meleshko D, Lapidus A, Korobeynikov A.. 2020. Using SPAdes de novo assembler. Curr Protoc Bioinformatics. 70:e102. [DOI] [PubMed] [Google Scholar]
  52. Rodrigues De Miranda L. 1972. Filobasidum capsuligenum nov. comb. Antonie Van Leeuwenhoek. 38:91–99. [DOI] [PubMed] [Google Scholar]
  53. Ronquist F, Huelsenbeck JP.. 2003. Bayesian phylogenetic inference under mixed models. Bioinformatics. 19:1572–1574. [DOI] [PubMed] [Google Scholar]
  54. Rytioja J, Hildén K, Yuzon J, Hatakka A, De Vries RP, et al. 2014. Plant-polysaccharide-degrading enzymes from basidiomycetes. Microbiol Mol Biol Rev. 78:614–649. [DOI] [PMC free article] [PubMed] [Google Scholar]
  55. Sharma R, Gassel S, Steiger S, Xia X, Bauer R, et al. 2015. The genome of the basal agaricomycete Xanthophyllomyces dendrorhous provides insights into the organization of its acetyl-CoA derived pathways and the evolution of Agaricomycotina. BMC Genomics. 16:233. [DOI] [PMC free article] [PubMed] [Google Scholar]
  56. Spatafora JW, Aime MC, Grigoriev IV, Martin F, Stajich JE, et al. 2017. The fungal tree of life: from molecular systematics to genome-scale phylogenies. Microbiol Spectr. 5. 10.1128/microbiolspec.FUNK-0053-2016. [DOI] [PMC free article] [PubMed] [Google Scholar]
  57. Sriswasdi S, Takashima M, Manabe R, Ohkuma M, Sugita T, et al. 2016. Global deceleration of gene evolution following recent genome hybridizations in fungi. Genome Res. 26:1081–1090. [DOI] [PMC free article] [PubMed] [Google Scholar]
  58. Stamatakis A. 2014. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics. 30:1312–1313. [DOI] [PMC free article] [PubMed] [Google Scholar]
  59. Stanke M, Diekhans M, Baertsch R, Haussler D.. 2008. Using native and syntenically mapped cDNA alignments to improve de novo gene finding. Bioinformatics. 24:637–644. [DOI] [PubMed] [Google Scholar]
  60. Sun S, Coelho MA, David-Palma M, Priest SJ, Heitman J.. 2019a. The evolution of sexual reproduction and the mating-type locus: links to pathogenesis of Cryptococcus human pathogenic fungi. Annu Rev Genet. 53:417–444. [DOI] [PMC free article] [PubMed] [Google Scholar]
  61. Sun S, Coelho MA, Heitman J, Nowrousian M.. 2019b. Convergent evolution of linked mating-type loci in basidiomycete fungi. PLoS Genet. 15:e1008365. [DOI] [PMC free article] [PubMed] [Google Scholar]
  62. Takashima M, Manabe R-I, Iwasaki W, Ohyama A, Ohkuma M, et al. 2015. Selection of orthologous genes for construction of a highly resolved phylogenetic tree and clarification of the phylogeny of Trichosporonales species. PLoS One. 10:e0131217. [DOI] [PMC free article] [PubMed] [Google Scholar]
  63. Takashima M, Sriswasdi S, Manabe RI, Ohkuma M, Sugita T, et al. 2018. A Trichosporonales genome tree based on 27 haploid and three evolutionary conserved ‘natural’ hybrid genomes. Yeast. 35:99–111. [DOI] [PubMed] [Google Scholar]
  64. Tanimura A, Takashima M, Sugita T, Endoh R, Kikukawa M, et al. 2014. Cryptococcus terricola is a promising oleaginous yeast for biodiesel production from starch through consolidated bioprocessing. Sci Rep. 4:4776. [DOI] [PMC free article] [PubMed] [Google Scholar]
  65. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG.. 1997. The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 25:4876–4882. [DOI] [PMC free article] [PubMed] [Google Scholar]
  66. Vajpeyi S, Chandran K.. 2016. Draft genome sequence of the oleaginous yeast Cryptococcus albidus var. albidus. Genome Announc. 4:e00390-16. [DOI] [PMC free article] [PubMed] [Google Scholar]
  67. Walker BJ, Abeel T, Shea T, Priest M, Abouelliel A, et al. 2014. Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS One. 9:e112963. [DOI] [PMC free article] [PubMed] [Google Scholar]
  68. Yong X, Yan Z, Xu L, Zhou J, Wu X, et al. 2016. Genome sequence of a microbial lipid producing fungus Cryptococcus albidus NT2002. J Biotechnol. 223:6–7. [DOI] [PubMed] [Google Scholar]
  69. Zhang H, Yohe T, Huang L, Entwistle S, Wu P, et al. 2018. dbCAN2: a meta server for automated carbohydrate-active enzyme annotation. Nucleic Acids Res. 46:W95–W101. [DOI] [PMC free article] [PubMed] [Google Scholar]
  70. Zhao Z, Liu H, Wang C, Xu JR.. 2013. Comparative analysis of fungal genomes reveals different plant cell wall degrading capacity in fungi. BMC Genomics. 14:274. [DOI] [PMC free article] [PubMed] [Google Scholar]

Associated Data

This section collects any data citations, data availability statements, or supplementary materials included in this article.

Supplementary Materials

jkab398_Supplementary_Data
Click here for additional data file. (982.5KB, pdf)

Data Availability Statement

PacBio reads from CBS6241 (genome sequencing) were deposited in the NCBI SRA database under accession number SRP256613. Illumina reads from CBS6241 (RNA-seq) were deposited at the NCBI SRA database under accession number SRP256618. Illumina reads from CBS6242 (genome sequencing) were deposited in the NCBI SRA database under accession number SRP258233. The CBS6241 genome sequence (BioProject ID PRJNA621322) was deposited at DDBJ/ENA/GenBank under the accession JAIFAB000000000, and the CBS6242 genome sequence (BioProject ID PRJNA627804) under the accession JABELV000000000. Supplemental material (Supplementary Figures S1–S10, Tables S1–S3, Supplementary Texts S1–S2) is part of the manuscript submission. Supplementary Figure S1: Phylogenetic analysis of Tremellomycetes. Supplementary Figure S2: Multiple alignment of Ste3 homologs in the MAT loci of several Tremellomycetes. Supplementary Figure S3: Analysis of Sxi proteins from Tremellomycetes. Supplementary Figure S4: MAT loci of CBS6241 and CBS6242. Supplementary Figure S5: Overview of CAZyme category AA. Supplementary Figure S6: Overview of CAZyme category CBM. Supplementary Figure S7: Overview of CAZyme category CE. Supplementary Figure S8: Overview of CAZyme category GH. Supplementary Figure S9: Overview of CAZyme category GT. Supplementary Figure S10: Overview of CAZyme category PL. Supplementary Table S1: Genome assemblies that were used in this study. Supplementary Table S2: Analysis of putative telomeric repeats at contig ends of CBS6241. Supplementary Table S3: Analysis of unique orthogroups in F. floriforme. Supplementary Text S1: Perl script for searching for putative pheromone genes. Supplementary Text S2: Perl script for searching for putative telomeric repeats.

Supplementary material is available at G3 online.

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