Mycoparasitism illuminated by genome sequencing and digital gene expression profiling of Coniothyrium minitans, an important biocontrol fungus of the plant pathogen Sclerotinia sclerotiorum

Background Coniothyrium minitans is a mycoparasite of the notorious plant pathogen Sclerotinia sclerotiorum. To further understand the parasitism of C. minitans, here, we assembled and analyzed its genome by combining transcriptome data. The genome of C. minitans strain ZS-1 was 39.77 Mb in 350 scaffolds. A total of 11437 predicted genes and proteins were annotated, and 30.8% of blast hits matched proteins encoded by Paraphaeosphaeria sporulosa, a worldwide soil fungus. The transcriptome of strain ZS-1 during the early interaction at 0 h, 4 h and 12 h with its host was analyzed. The detected expressed genes were involved in response to host defenses, including cell wall-degrading enzymes, transporters, secretory proteins and secondary metabolites. The fungal cell wall-degrading enzymes belonged to the GH16, GH18, and GH72 classes in CAZymes, and some were significantly up-regulated during mycoparasitism. Most of the monocarboxylate transporter genes of the major facilitator superfamily and all the detected ABC transporters, especially the heavy metal transporters, were significantly up-regulated. Approximately 8% of the 11437 proteins in C. minitans were predicted to be secretory proteins, with catalytic activity, hydrolase activity, peptidase activity and serine hydrolase activity enriched in molecular function. Most genes involved in serine hydrolase activity were significantly up-regulated during mycoparasitism. This assemble genome and genome-wide expression study demonstrate that the mycoparasitism process of C. minitans is complex and a series of genes or proteins would be deployed by C. minitans to invade successfully the host. Our study provides insights into the mechanisms of the mycoparasitism between C. minitans and S. sclerotiorum and clues to excavate active secondary metabolites from C. minitans. the pathogenic fungi, respectively. Twenty-four orthologous groups were specific to C. minitans and Trichoderma spp. and absent in pathogenic fungi. The 45 unique proteins in C. minitans were annotated, and the results showed a PR–1-like protein (CMZSB_08830), an Acyl-CoA N-acyltransferase (CMZSB_04745), an amino acid transporter (CMZSB_05748), a protein with the DUF605 multi-domain (CMZSB_00858), and a FAD/NAD(P)-binding domain-containing protein (CMZSB_06166); 40 proteins were unknown proteins or hypothetical proteins with no specific functions reported.

production of AFS is regulated by the ambient pH, which is extremely affected by the oxalic acid secreted by S. sclerotiorum. C. minitans could synthesizeantibacterial substances (ABS) to inhibit the growth of bacteria in Clavibacter and Xanthomonas [43,44]. These ABS may break the balance of the microflora on the plant surface and help C. minitans colonize [45].
Although C. minitans has been developed as a successful biocontrol agent commercially, its mycoparasitism still needs further investigation to enhance biological control efficiency and to uncover novel genes and active secondary substances; thus, we sequenced the whole genome of C. minitans and combined the transcriptome data derived from RNA samples from the early stage of interaction with its host, S. sclerotiorum. Based on this analysis, the possible mechanism of mycoparasitism, the potential active secondary substances (antifungal or antibacterial substances) and gene resources for resistance breeding against fungal diseases were discussed.

Results
General features of the C. minitans genome The DNA of C. minitans strain ZS-1 was sequenced on the Illumina and PacBio platforms at BGI Technological Company. The 500-bp-long and 6-Kbp-long mate-pair libraries were sequenced using the Illumina platform, and the 20-Kbp-long library was sequenced using the PacBio RS II. The genome sequence was assembled based on the 6-Kbp-long library data with SOAPdenovo2 [46], the gaps were filled and sequences were extended with the 20 Kbp-long library, and the sequence was corrected using the data from a 500-bp-long library. In all, the data provided an average of 80-fold sequence coverage of the genome (Additional file 1: Table S1). The resulting assembly length was 38.72 Mb across 2,575 contigs, and the N50 length was 64,002 bps. The contigs were assembled into 350 scaffolds that were longer than 1 kb with a total length of 39.77 Mb (including gaps between contigs) using SSPACE [47], and the final N50 length was 653,176 bps ( Table 1).

Prediction of the coding proteins and function analysis of C. minitans
Based on the analysis using bioinformatics software and RNA-seq, a total of 11,437 protein-coding genes (11,146 longer than 100 amino acids) were predicted, and all the proteins shared an average length of 481 amino acids (Table 1) InterPro, Swiss-Prot, GO-Slim, KEGG and KOG databases, respectively (Additional file 2: Figure S1).
A total of 10884 (94.97%) of the predicted proteins matched the local Nr database (updated on 20180717) with an e-value cutoff of 1e-10, and 32364 blast hits were returned with no more than 3 hits mapped for each protein. The distributions of blast hits in the Nr annotation were determined, and the similarity distribution indicated that 61.11% of all predicted genes of C. minitans had over 80% similarity to proteins of other fungal species (Fig. 1a). A total of 30.8% of the protein blast hits mapped to protein sequences from Paraphaeosphaeria sporulosa AP3s5-JAC2a, which is saprophytic on wood and has biocontrol ability by nutrition competition and niche occupation [48,49]; 11.98% of the blast hits mapped to proteins from Periconia macrospinosa, a "dark septate endophytic" fungus [50], and 11.51% of the hits matched the proteins of Corynespora cassiicola, an endophyte, saprobe or necrotrophic plant pathogen [51]; 5.00% of the blast hits were identified as proteins of Clohesyomyces aquaticus, a saprotrophic fungus originally isolated from submerged wood [52]; 4.53% of the blast hits were similar to sequences of Pyrenochaeta sp. DS3sAY3a, which plays a role in the bioremediation of metal polluted environments due to the oxidation of manganese (Mn) compounds [48]; 4.26% of the blast hits matched proteins of Alternaria alternata, a worldwide plant pathogen known to perform lignocellulose degradation and Mn(II) oxidation [48]; an additional 185 species also matched 5 or more blast hits ( Fig. 1b and Additional file 3: Table S2).

Carbohydrate-active enzymes (CAZymes) in C. minitans
The complement of each predicted family was conserved in the analyzed fungal genomes from the same order or with similar nutrition type. The CAZyme families predicted in C. minitans, along with other fungal genomes from Pleosporales, were classed into a group cluster using principal component analysis (PCA), and the fungi from Hypocreales, Helotiales and Erysiphales were also classified into corresponding groups (Fig. 2a). Magnaporthe grisea, Fusarium graminearum and Aspergillus nidulans from different orders were grouped into a cluster. Not considering the number of carbohydratebinding modules (CBMs), C. minitans encodes 434 catalytic protein modules in CAZymes, which is moderate compared with the other 39 tested species in our analysis (Additional file 4: Table S3). The number of modules was lower than those in the two phylogenetically nearest fungi, P. sporulosa (556) and Karstenula rhodostoma (507) and higher than the average level (380) of the three species in Trichoderma and two species in Sclerotinia. GO analysis showed that the CAZyme protein-coding genes were annotated with functions of catalytic activity (GO: 0003824), carbohydrate binding of (GO: 0030246), transferase activity (GO: 0016757 and GO: 0016758), hydrolase activity (GO: 0016787) (p ≤ 0.05), cell wall biosynthesis (GO: 0071554) (p ≤ 0.05) and metabolic process (GO: 0008152) (p ≤ 0.05) (Additional file 5: Table S4).
The cell wall-degrading enzymes were divided into 2 classes, the plant cell wall-degrading enzymes lyases were specifically present in C. minitans, while 13 and 46 unique orthologous groups were present in Trichoderma spp. and plant fungal pathogens, respectively. A total of 54 unique orthologous groups (including 58 proteins of C. minitans) were shared by C. minitans and the other pathogenic fungi analyzed. One orthologous group protein encoding endo-1,4-beta-xylanase (in the GH43 family) was identified in only C. minitans and Trichoderma spp., while 13 specific orthologous groups were commonly present in Trichoderma spp. and the other pathogens (Fig. 2b). These results suggest that C. minitans also has the potential to break down the complex composition of plant cell walls. with those of the selected pathogenic fungi (7 fungi) and Trichoderma spp. (3 species), most orthologous groups of C. minitans were shared with either Trichoderma spp. or pathogenic fungi, while 4 unique orthologous groups (4 proteins) were found only in C. minitans. These 4 orthologous groups encode glycoside hydrolase family 16 protein (GH16), concanavalin A-like lectin/glucanase (GH16), GPI-anchored cell wall beta-1,3-endoglucanase (GH17) and glycoside hydrolase (GH20).
To investigate the potential CAZyme functions of C. minitans during the early stage of interaction with S. sclerotiorum, the expression of FCWDEs was examined. The results showed that out of 64 FCWDEs, 45 encoding genes were expressed, and 17 genes were significantly regulated at 4 hpi (hour post inoculation) and 12 hpi; most GH families encoding genes were up-regulated (Fig. 3), while only one GH18 gene (CMZSB_08720), which was distributed in all the fungi tested, was significantly downregulated. However, the expression of the 4 unique FCWDEs and 3 Trichoderma-shared FCWDEs was not significantly altered. Interestingly, PCWDE expression in C. minitans was also significantly changed (Additional file 6: Figure S2). These results suggest that cell wall-degrading enzymes may play important roles during the early interaction of C. minitans and its host.

MFS and ABC transporters in C. minitans
The ATP-binding Cassette (ABC) primary transporter superfamily and the Major Facilitator Superfamily (MFS) are the most ubiquitous transporters in fungi and other organisms [53]. Based on the transporter classification databases (TCDB), the transporters of the MFS superfamily and ABC superfamily were identified in C. minitans and 11 other fungal genomes. Among these 9 genes, 4 were significantly up-regulated, and one was down-regulated. The results suggest the involvement of MCT in the biocontrol event.
Fifty-one ABC transporters in 13 subfamilies were predicted in C. minitans, which is similar to those in P. sporulosa (52), S. sclerotiorum (49) Table S6). There were no orthologous ABC transporters identified between C. minitans and Trichoderma spp., while 23 transporters were present in all the fungi detected (Fig. 5a).
This suggests that C. minitans, Trichoderma spp. and the plant pathogenic fungi analyzed share a similar transporter distribution of the ABC superfamily, or the function of ABC transporters is conserved in different fungi. C. minitans has 7 HMTs (heavy metal transporters), which is almost twice as many as the other 11 fungi analyzed. Group 2983 (TC# 3.A. 1 were specific to C. minitans. Thirty-six of the 51 ABC transporter genes predicted were up-regulated during the early stages of mycoparasitism in C. minitans, and 23 were significantly altered (Fig. 5b). Five of the 7 HMT coding genes, including CMZSB_03503 (orthologous groups 12899) and CMZSB_09545 (specific to C. minitans),, were significantly up-regulated at the primary stage of infection (Fig. 5b), and all 7 genes were mapped to the iron-binding (GO: 0005506) molecular function based on GO.

Secretory proteins enriched in the mycoparasitism process in C. minitans
A total of 908 secretory proteins were predicted in C. minitans, accounting for 8.29% of the total proteins. The proportion of secretory proteins was 5.50% in Sclerotinia spp., 6.52% in Botrytis spp., 6.66% in Trichoderma spp., and 9.36% in P. sporulosa. Taking no account of CAZymes, the 695 predicted secretory proteins were classified into 675 orthologous groups, and 45 were unique to C. minitans without orthologs in Trichoderma spp. or the 7 selected plant pathogens in our analysis. In addition, 307, 499 and 1041 specific orthologs were predicted in C. minitans, Trichoderma spp. and the pathogenic fungi, respectively. Twenty-four orthologous groups were specific to C. minitans and During the early stages of mycoparasitism in C. minitans, 53 DEGs were identified among the genes detected in the PKS and NRPS biosynthesis gene clusters. Of these, 31 were up-regulated at 4 hpi, while 40 were up-regulated and 7 were down-regulated at 12 hpi. At the later mycoparasitism stage (12 h versus 4 h), 13 genes were up-regulated, and 8 were down-regulated (Fig. 7). Most core biosynthetic genes of NRPS involved in mycoparasitism were up-regulated, with the NRPS-3-related core gene CMZSB_06212 and the NRPS-6-related gene CMZSB_10567 down-regulated significantly.
The expression of all the core biosynthetic genes of t1PKS, t3PKS and hybrid t1PKS-NRPS were significantly induced when in contact with S. sclerotiorum. The t1PKS encoding gene CmPKS1 (CMZSB_04445) was proven to be associated with the mycoparasitism of C. minitans [54].
Nine genes in five clusters related to gliotoxin were annotated in C. minitans: GliA (gliotoxin A) (CMZSB_03977 and CMZSB_08616), 2 GliC (gliotoxin C) (CMZSB_03976 and CMZSB_03979), 1 GliT (gliotoxin T) (CMZSB_03988) and 1 GliP (gliotoxin P) (CMZSB_03975) involved in gliotoxin biosynthesis. The expression of these genes could not be detected at 4 hpi, and only 2 were expressed at 12 hpi. One or more of these genes may play important roles in the mycoparasitism of C. minitans on S. sclerotiorum. Three of the gliotoxin-related genes were mapped to the function of oxidoreductase activity (GO: 0016491), and three steps related to oxidation in gliotoxin biosynthesis were predicted from the only known intermediate compounds cyclo-L-phenylalanyl-L-serine (Gardiner and Howlett, 2005). The CMZSB_02816 was annotated into MFS gliotoxin efflux transporter and was similar to the protein GliA reported from Aspergillus fumigatus, which plays a significant role in tolerance to gliotoxin and protection from extracellular gliotoxin [55].

Discussion
In this study, the genome of C. minitans was sequenced, assembled and annotated, and the potential mechanism of parasitism was analyzed based on the RNA-seq data. The size of the genome of C.
minitans is approximately 39.77 Mb, which is moderate among ascomycetes. C. minitans has a large number of genes encoding enzymes for both plant and fungal cell wall degradation; it also has many genes for MFS and ABC transporters, PKS and NRPS; a high proportion of genes coding for secretory proteins were also predicted.
Plant and fungal cell wall degrading enzymes in C. minitans C. minitans has 434 putative catalytic protein modules in CAZymes, and this number is moderate compared with the other 39 fungal species in our study; many of these proteins were predicted to be enzymes for degrading either plant cell walls or fungal cell walls. The number of genes coding for PCWDEs is not smaller than those of plant necrotrophic pathogenic fungi, such as M. oryzae, B.
cinerea and its host, S. sclerotiorum, and it is significantly larger than those of biotrophic fungal pathogens. Compared to pathogenic fungi, C. minitans has 17 unique PCWDEs (distributed in 15 orthologous proteins). These genes may enable C. minitans to live on dead plants. Interestingly, in this study, we found that the expression of many PCWDE genes was highly induced at the early stage of C. minitans contact with S. sclerotiorum, suggesting that these PCWDEs may also play some role in parasitizing S. sclerotiorum; further experiments are needed to confirm this hypothesis.
FCWDEs may play essential roles in fungal development [56][57][58]; thus, no fungi without FCWDEs could survive in nature. As a mycoparasite, C. minitans might reasonably have a powerful fungal cell wall-degrading enzyme system to attack S. sclerotiorum. However, the number of FCWDE genes in C. minitans is not significantly different from that in plant pathogenic fungi; furthermore, C. minitans shared 47 orthologous FCWDEs with the pathogenic fungi tested. Interestingly, the mycoparasitic Trichoderma spp. have many more FCWDEs than C. minitans, and the GH18 family is considered to play an important role during mycoparasitization [59][60][61][62]. Only three orthologs in GH18were shared by C. minitans and Trichoderma spp., but they were not detected during the early stage of interaction between C. minitans and S. sclerotiorum. The chitinase gene (CMZSB_00640) and β-1,3-endoglucanase (CMZS_02526) of C. minitans are usually used as two marker genes for mycoparasitism [63], while their orthologs can also be identified in pathogenic fungi. Furthermore, these two genes and CMZSB_02023 (encoding chitinase) were also up-regulated significantly (log2 ratio > 2.5, FDR ≤ 0.001) at conidiationdata not shown). This evidence suggests that the FCWDEs of C. minitans may play a role not only in parasitizing S. sclerotiorum but also in shaping the cell walls of C. minitans,asinplant pathogens [64].

Secondary metabolites and their functions in C. minitans
Fungi are known to produce a large number of secondary metabolites, and genes for secondary metabolites are often distributed in clusters on genomes. Many biocontrol agents can produce antagonistic secondary metabolites to suppress the growth of pathogens or to occupy advantageous niches [65][66][67]. Early experiments found that C. minitans could produce both antifungal substances and antibacterial substances [13,43], among which macrosphelide A has antimicrobial activity against some ascomycetes, such as Sclerotinia spp., basidiomycetes, oomycetes and Gram-positive bacteria [41,68]. Macrosphelide A, benzenediol and 5-aminopentanoate were the three most accumulated compounds when C. minitans was co-cultured with S. sclerotiorum for 2 days [40].
PKS) and NRPS are the main synthases of polyketides and peptides. As in S. sclerotiorum, B. cinerea, secondary metabolism, including 7 NRPS clusters, 6 t1PKS clusters, 1 t3PKS cluster, and 1 hybrid t1PKS-NRPS gene cluster. The number of related genes was counted within each cluster, and no significant difference was found with the comparison of all the tested fungal genomes among genes related to the t1PKS clusters. Previously, we identified a type I PKS gene (CmPKS1) and found that disruption of CmPKS1 led to an absence of melanin but could not significantly affect the mycoparasitism of S. sclerotiorum [54]. Disruption of CmMR1, a transcription factor gene, blocked the production of melanin but could not affect the mycoparasitism of C. minitans [31].
Gliotoxin is a secondary metabolite produced by many fungi. It can suppress immunity, promote apoptosis of mammalian cells [69] and inhibit the growth of microorganisms by disrupting NAPDH oxidase activity [70]. The non-ribosomal peptide synthetase GliP in A. fumigatus catalyzes the first biosynthetic step in the synthesis of gliotoxin and was reported as the determinant of host-specific virulence [71]. When gliP was disrupted, T. virens lost the ability to produce gliotoxin and parasitize S. sclerotiorum [72]; T. virens and T. harzianum have 6 [69,73] and 9 NRPS-encoding genes, respectively, but non-mycoparasitic Trichoderma reesei has 9 genes in the biosynthetic cluster.
Although gliotoxin has not yet been identified, a NRPS cluster with 9 genes related to gliotoxin synthesis was predicted on Scaffold 12 and annotated in C. minitans. The homologous gene clusterof gliotoxin biosynthesis in C. minitans displays a similarity of 47% with that of T. reesei and much lower with that of the biocontrol Trichoderma species. We speculate that C. minitans encodes a type of gliotoxin biosynthetic gene cluster different from those in biocontrol Trichoderma spp. but similar to that in T. reesei. Two of the annotated gliotoxin-related genes were up-regulated at 12 hpi with S.
sclerotiorum. This evidence suggests that gliotoxin or gliotoxin-like substances may be synthesized and contribute to the parasitism of C. minitans.

MFS and ABC transporters in C. minitans
The MFS transporter superfamily and ABC transporter superfamily are the most ubiquitous transporters in fungi and other organisms [53]. MFS transporters and ABC transporters play very important roles in resistance against drug and plant toxic components for pathogens and are also very important for beneficial microorganisms [74][75][76][77]. The expression of MFS transporters and ABC transporters was induced in C. minitans during interaction with S. sclerotiorum, suggesting that these two classes of transporters may play important roles in the mycoparasitism process.
Siderophores are responsible for the storage of iron and the protection of cells from oxidative stress [78,79]. In T. virens, deletion of TvTex10, an intracellular siderophore biosynthesis-related gene, increased the fungal growth rate and sensitivity to oxidative stress and simultaneously decreased conidia and gliotoxin production [80]. Fifty-four ABC transporters in 14 subfamilies were predicted in

Effector-like proteins in C. minitans
Typical effectors are small cysteine-rich secretory proteins (usually less than 150 aa) and are released by pathogens into host cells to disrupt the host's resistance system. Cerato-platanin proteins are effectors for many pathogenic fungi [81] and were also identified in Trichoderma spp.,which could induce plant defense against pathogens [82]. SM1, an elicitor of induced systemic resistance (ISR), was identified as an effector-like protein involved in the colonization of maize roots by T. virens [83].
In Trichoderma spp., 233 effector-like proteins have been annotated, and a Class II hydrophobin family gene tvhyiil, could help T. virens colonize plant roots and participate in antagonistic activity against Rhizoctonia solani [84]. In this study, 80 genes encoding effector-like proteins were identified in C. minitans,and 50 of them were expressed during the early stage of interaction between C. minitans and S. sclerotiorum. We further found that some of these effector-like protein genes could induce a hypersensitive reaction when transiently expressed in the leaves of Nicotiana benthamiana, and four other effector-like protein genes led to a decrease in hyphal growth when expressed in S. sclerotiorum, suggesting that some of these effector-like proteins may potentially function in plants, and some may function in the parasitism of C. minitans. It may not be surprising that Trichoderma spp. release effector-like proteins into plant cells, because they can live endophytically in plant roots.
However, C. minitans is a soil-borne fungus and has not been found to live in plants. Considering that C. minitans can parasitize only fungi in the genus Sclerotinia, we hypothesize that some effector-like

Conclusions
Given that our study assembled the genome of the important mycoparasite of the plant pathogen S. sclerotiorum firstly, and analyzed the orthologous proteins between the biocontrol fungi and other two group fungi (biocontrol group of Trichoderma and plant pathogens group of 7 selected pathogens in our study) to develop the possible mycoparasitism mechanism. Combining with the RNA-seq of mycoparasitism process, the genes expression related mycoparasitism was detected to elucidate the process of mycoparasitism in C. minitans with its host S. sclerotiorum. Our analysis sheds light on the mycoparasitism of C. minitans and provides clues to excavate active secondary metabolites from C.

minitans.
Tables Table 1 The  Genome assembly genome assembler with the 6 Kbp mate-pair library data. The best preassembly of a longer N50 contig size and a lower number of the contigs was assembled as the initial assembly (Version1.0). The GapCloser v1.12 (GapCloser, RRID: SCR 015026) was used to fill gaps into Version1.0; then, the contigs were linked to assemble genome scaffolds using the software SSPACE (SSPACE, RRID: SCR_005056) with the PacBio library data [47,86]. The scaffolds of the initial assembly were against to the NCBI NT database (08/17/2016) (ftp://ftp.ncbi.nlm.nih.gov/blast/db/) testing for removing the contamination by bacteria or other organisms. With removing the length under 1 Kbp of the initial assembly scaffolds, the other kept scaffolds were the final assembled genome sequences of C.

Genome annotation
Gene predictions on the masked genome were performed using both transcript mapping-based and ab initio methods. Transcript mapping-based methods: Transcripts were generated by first mapping the RNA-seq reads to the assembled genome using Hisat2 (Hisat2, RRID: SCR_015530) [87,88], and SAMtools (Samtools, RRID: SCR_002105) [89] was used to convert the sam files to bam files. A set of transcripts was generated by Cufflinks (Cufflinks, RRID: SCR_014597) with the mapping data [90,91].

Functional annotation
Nr annotation, Gene Ontology (GO) and InterPro identification were performed using Blast2GO [101].
The gene clusters of PKS and NRPS were investigated based on the prediction results.

Secretome prediction
Protein sequences with extracellular secretary signals were predicted using SignalP 4.1 (SignalP, RRID: SCR_015644) [116,117] with the default settings for eukaryotic organisms. Proteins were considered to be secreted if the signal peptide probability was greater than or equal to 0.90 and a cleavage site was within the first approximately 25 amino acids. These predictions were further refined using TargetP v1.1 with a non-plant program and default cutoff parameters [118,119], and candidate secreted proteins predicted to target the mitochondria were discarded. Subsequently, these candidate secreted proteins were checked for transmembrane domains using TMHMM v.2.0 [113,120]. Finally, the candidate secreted proteins were compared by WoLF PSORT (WoLF PSORT, RRID: SCR_002472) [121] with the weighted k-nearest neighbor classifier no less than 15. Putative small secreted proteins (SSPs), which were also considered effectors, were predicted as no more than 300 amino acids and cysteine content with no less than 4%.

Analysis of differentially expressed genes (DEGs) at different interaction time points
The raw RNA data from the three libraries were sequenced via Illumina HiSeq 2000. Adaptors, reads with more than 10% unknown bases and low-quality reads (quality value ≤ 5 of a read) were removed from the raw reads to obtain the clean reads. The clean reads were mapped tothe C. minitans genome using SOAP aligner/soap2 [122]. Mismatches of no more than 2 bases were allowed in the alignment. The gene expression level was calculated using the RPKM method (reads per kb per million reads) [123].
A method described in "The significance of digital gene expression profiles" [124] was used to screen the DEGs. We used FDR (False Discovery Rate) ≤ 0.001 and the absolute value of log 2 ratio ≥ 1.5 as the threshold to judge the significance of gene expression differences. Three

Competing interests
Additional file 3: Table S2. Species distribution of the 11437 proteins in Coniothyrium minitans ZS-1 based on the Non-redundant (NR) annotation.
Additional file 4: Table S3. Distribution of CAZymes in Coniothyrium minitans ZS-1 and other detected genomes in our analyses.