- Open Access
Adaptive evolution of Moniliophthora PR-1 proteins towards its pathogenic lifestyle
BMC Ecology and Evolution volume 21, Article number: 84 (2021)
Plant pathogenesis related-1 (PR-1) proteins belong to the CAP superfamily and have been characterized as markers of induced defense against pathogens. Moniliophthora perniciosa and Moniliophthora roreri are hemibiotrophic fungi that respectively cause the witches’ broom disease and frosty pod rot in Theobroma cacao. Interestingly, a large number of plant PR-1-like genes are present in the genomes of both species and many are up-regulated during the biotrophic interaction. In this study, we investigated the evolution of PR-1 proteins from 22 genomes of Moniliophthora isolates and 16 other Agaricales species, performing genomic investigation, phylogenetic reconstruction, positive selection search and gene expression analysis.
Phylogenetic analysis revealed conserved PR-1 genes (PR-1a, b, d, j), shared by many Agaricales saprotrophic species, that have diversified in new PR-1 genes putatively related to pathogenicity in Moniliophthora (PR-1f, g, h, i), as well as in recent specialization cases within M. perniciosa biotypes (PR-1c, k, l) and M. roreri (PR-1n). PR-1 families in Moniliophthora with higher evolutionary rates exhibit induced expression in the biotrophic interaction and positive selection clues, supporting the hypothesis that these proteins accumulated adaptive changes in response to host–pathogen arms race. Furthermore, although previous work showed that MpPR-1 can detoxify plant antifungal compounds in yeast, we found that in the presence of eugenol M. perniciosa differentially expresses only MpPR-1e, k, d, of which two are not linked to pathogenicity, suggesting that detoxification might not be the main function of most MpPR-1.
Based on analyses of genomic and expression data, we provided evidence that the evolution of PR-1 in Moniliophthora was adaptive and potentially related to the emergence of the parasitic lifestyle in this genus. Additionally, we also discuss how fungal PR-1 proteins could have adapted from basal conserved functions to possible roles in fungal pathogenesis.
Pathogenesis related-1 (PR-1) proteins are part of the CAP (cysteine-rich secretory proteins, antigen 5, and pathogenesis-related 1) superfamily, also known as SCP/TAPS proteins (sperm-coating protein/Tpx-1/Ag5/PR-1/Sc7), and are present throughout the eukaryotic kingdom [1, 2]. In plants, PR-1 proteins are regarded as markers of induced defense responses against pathogens . These proteins have also been ascribed roles in different biological processes in mammals, insects, nematodes and fungi, including reproduction, cellular defense, virulence and evasion of the host immune system [4,5,6,7,8,9,10,11,12]. In Saccharomyces cerevisiae, Pry proteins (Pathogen related in yeast) bind and export sterols and fatty acids to the extracellular medium, an activity that has also been demonstrated for other proteins of the CAP superfamily through functional complementation assays [13,14,15,16,17].
The basidiomycete fungi Moniliophthora perniciosa and Moniliophthora roreri are hemibiotrophic phytopathogens that cause, respectively, the Witches’ Broom disease (WBD) and Frosty Pod Rot of cacao (Theobroma cacao). Currently, three biotypes are recognized for M. perniciosa based on the hosts that each one is able to infect. The C-biotype infects species of Theobroma and Herrania (Malvaceae); the S-biotype infects plants of the genus Solanum (e.g., tomato) and Capsicum (pepper); and the L-biotype is associated with species of lianas (Bignoniaceae), without promoting visible disease symptoms [18,19,20].
With the genome and transcriptome sequencing of the C-biotype, 11 PR-1-like genes, named MpPR-1a to k, were identified in M. perniciosa . Interestingly, many of these genes are upregulated during the biotrophic interaction of M. perniciosa and T. cacao, which constitutes a strong indication of the importance of these proteins in the disease process [21, 22]. In this context, efforts have been made to elucidate the role of these molecules during the interaction of M. perniciosa with cacao, such as the determination of the tridimensional structure of MpPR-1i  and the functional complementation of MpPR-1 genes in yeast Pry mutants . These studies revealed that seven MpPR-1 proteins display sterol or fatty acid binding and export activity, suggesting that they could function as detoxifying agents against plant lipidic toxins .
Despite these advances, studies with a deeper evolutionary perspective have not yet been performed for MpPR-1 proteins. Evolutionary analysis can be an important tool for the inference of gene function and the identification of mechanisms of evolution of specific traits, such as pathogenicity. Genes that are evolving under negative selection pressures are likely to play a crucial role in basal metabolism . On the other hand, genes that are evolving under positive selection may have changed to adjust their function to a relatively new environmental pressure . Thus, it can be hypothesized that Moniliophthora PR-1 might have accumulated adaptive substitutions in response to selective pressures related to a pathogenic lifestyle, and the analysis of these substitutions may reveal protein targets and specific codons that are potentially important for the pathogenicity in Moniliophthora.
In this study, we performed a two-level evolutionary analysis of Moniliophthora PR-1 genes: (i) their macroevolution in the order Agaricales, which consists mainly of saprotrophic fungi, being the Moniliophthora species one of the few exceptions; (ii) and their microevolution within M. roreri and M. perniciosa and its biotypes that differ in host-specificity. By characterizing PR-1 proteins encoded by 22 Moniliophthora genomes, reconstructing their phylogenetic history, searching for evidence of positive selection and analyzing expression data, we identified an increased diversification in these proteins in Moniliophthora that is potentially adaptive and related to its pathogenic lifestyle.
Characterization of PR-1 gene families in Moniliophthora
Previous work had already reported the identification of 11 PR-1-like genes in the genome of M. perniciosa isolate CP02 (C-biotype), which were named MpPR-1a to MpPR-1k . Likewise, 12 PR-1-like genes were identified in the genome of M. roreri (MCA2977) . With the sequencing and assembly of 18 additional genomes of M. perniciosa isolates and other four genomes of M. roreri isolates, it was possible to characterize the PR-1 gene families in the different biotypes of M. perniciosa and in its sister species M. roreri in order to identify differences at the species and biotype levels. Figure 1a shows the number of genes identified as PR-1 per isolate.
The examination of orthogroups containing PR-1-like hits revealed that the PR-1i orthogroup has the highest number of duplications with two copies in M. roreri and in L-biotype. Moreover, a new PR-1-like orthogroup with seven candidates that are more similar to MpPR-1i (67% identity) was found. This newly identified gene was named “MpPR-1l” and was not found in M. roreri. It has the same number and structure of introns and exons as the MpPR-1i gene and they are closely located in the same scaffold, which is evidence of a duplication event within M. perniciosa. Interestingly, the sequences corresponding to MpPR-1l in the five S-biotype isolates from Minas Gerais were found in another orthogroup, in which MpPR-1l was fused to the adjacent gene in the genome (a putative endo-polygalacturonase gene containing the IPR011050 domain: Pectin lyase fold) with no start codon found between the two domains. Furthermore, we found that the MpPR-1i gene and, consequently, its predicted protein is truncated in almost all S-biotype isolates from MG (except for S-MG2) (Fig. 4).
Examining these gene families to look for other putatively species-specific PR-1 in Moniliophthora, we observed that the MpPR-1k and MpPR-1c genes are not found in the M. roreri genomes analyzed in this work, while MrPR-1n constitutes an exclusive family in this species. The MrPR-1o gene previously identified by Meinhardt et al.  was not predicted in any genome as a gene in this work. The protein sequence of MrPR-1o has higher identity with MrPR-1j (70%), MpPR-1j (66%) and MpPR-1c (56%), but it is shorter than all 3 protein sequences and does not have a signal peptide like other PR-1 proteins, which suggested that MrPR-1o is a pseudogenized paralog of MrPR-1j.
The absence of MpPR-1c in all S-biotype genomes suggested that this gene could be biotype-specific within M. perniciosa, however, it was predicted in the L-biotype genome L-EC2. Therefore, we sought to confirm the presence or absence of this gene in different M. perniciosa by PCR amplification and synteny analysis. The absence of MpPR-1c in the S-biotype isolates and in the L-biotype L-EC1 was confirmed, as well as its presence in L-EC2 (Fig. 1b). We also amplified the MpPR-1d gene, which was predicted in all genomes, in almost all tested isolates, except for S-MG3 because of a mismatch in the annealing regions of both primers. Even though our PCR results indicated that MpPR-1c is not present in the S-biotype, synteny analysis of the genome region where MpPR-1j-c-d are found in tandem  revealed that, in fact, MpPR-1c is partially present in these S-biotype genomes (Fig. 1c), suggesting again that the duplication event of PR-1j occured in the ancestral of Moniliophthora but this paralog was also pseudogenized in the evolution of the S-biotype.
PR-1 genes evolution along the Agaricales order
To study the macroevolution of PR-1 proteins, we identified orthologous sequences of genes encoding PR-1-like proteins in 16 genomes of species from the Agaricales order, including three selected M. perniciosa genomes (one of each biotype) and 1 M. roreri genome for comparisons. The phylogenetic reconstruction of Agaricales PR-1 proteins revealed a basal separation of two major clades, hereafter called clade1 and clade2 (Fig. 2a).
The first PR-1 clade includes most Agaricales species outside Moniliophthora showing PR-1 genes that diverged early in the phylogeny, before the appearance of PR-1a-l-n orthologues. From this first clade including the early diverged PR-1 proteins, subsequently diverged PR-1d and PR1-j. The separation between PR-1d and j proposed for Moniliophthora only occurs in Volvariella volvacea, while for all other species, paralogous of PR-1d diverged early. In Moniliophthora, PR-1j and PR-1d have more recent common ancestors, and the only paralogous of these Moniliophthora PR-1s originates from a possible duplication of MpPR-1j in the C-biotype of M. perniciosa, which was previously named MpPR-1c, therefore exclusive to this species and biotype.
The second clade includes all other PR-1 families and other Agaricales PR-1s that do not have a common ancestor with a single PR-1 from Moniliophthora. Clade2 is divided into two subclasses in its base, one of them composed of the PR-1b clade, which is distributed among 14 species. In the second subgroup, PR-1a shows a common ancestor in a total of 16 species, being the most common PR-1 here. The great diversification of a PR-1a-like ancestor in Moniliophthora resulted in the formation of at least 4 new and exclusive PR-1 genes (k, g, i, l) with high evolutionary rates reflected on the branch lengths (Fig. 2b). PR-1n showed a putative ortholog in Armillaria mellea, the only other plant pathogen in the Agaricales dataset, however, this connection has low branch support.
Recent diversification of PR-1 genes in Moniliophthora
Through the investigation of the phylogenetic history of PR-1 proteins within 22 Moniliophthora isolates (Fig. 3), we found that the previous classification of MpPR-1a to k and MrPR-1n represents monophyletic clades in the tree, except for MpPR-1c which is a recent paralogous of MpPR-1j. The evolution of Moniliophthora PR-1 also reflected the basal divergence between two large clades as observed in the Agaricales PR-1 tree (Fig. 2). The only incongruence between the two phylogenetic trees is the relative position of PR-1k, which appeared after the divergence of PR-1a in Agaricales and before it in Moniliophthora. This incongruence may be due to the extreme differentiation of PR-1k, with longer branch lengths in Moniliophthora, being its position on the Agaricales tree more reliable.
Among the PR-1 families, the proteins with the greatest number of changes in the tree are PR-1g, i, and k, which are exclusive PR-1s in the genus Moniliophthora, as pointed out by the previous phylogenetic analysis. In addition, PR-1h also showed a greater branch length than the others, being a family of PR-1s only shared between Moniliophthora and Marasmius in the Agaricales PR-1 tree (Fig. 2). PR-1c also presented a large number of changes in relation to its ancestor PR-1j. This greater number of changes in these MpPR-1s, and their exclusive presence in comparison to the other Agaricales, indicate a recent potential adaptive process of diversification of these proteins in Moniliophthora.
Positive selection shaping PR-1 families in Moniliophthora
Based on the observations of high diversification of PR-1 families within Moniliophthora, we hypothesized that positive selection could be shaping these proteins either in the C-biotype or in the S-biotype. To test this hypothesis, we tested the branch-sites evolutionary model for each PR-1 family. None of these tests brought evidence of positive selection in any PR-1 family for the C-biotype branches. For the S-biotype branches, a signal of positive selection was detected for PR-1g on one site of the protein sequence.
Considering that the existence of M. perniciosa biotypes are very recent in the evolutionary timescale and that C-biotype itself has almost no genetic variation among its sequences, which makes it very difficult to apply separate dN/dS tests, we tested both C- and S-biotypes together. We tested the hypothesis that there was a single selective pressure shaping PR-1 families throughout the M. perniciosa and M. roreri evolution regardless of the biotype, using the site model test. In these tests, sites with positive selection signs were detected in five families (PR-1f, g, h, i, l) (Table 1). The PR-1n family was not included in these tests because all sequences were identical.
PR-1g stands out for having the highest omega and for being one of the most expressed genes during the green broom stage . Three of the codons under positive selection are part of the ‘keke’ domain, which is possibly involved in the interaction with divalent ions or proteins . Among the sites detected under positive selection for PR-1i, one is found in the caveolin binding motif (CBM), an important region for binding to sterols, and another site is in the α-helix 1, which together with α-helix 4 form the cavity for ligation to palmitate  (Fig. 4).
Although the two exclusive PR-1 families of M. perniciosa, PR-1c and PR-1k, do not present evidence of positive selection, both revealed processes of diversification in the PR-1 phylogenies. It is possible that these families have also undergone selective pressures in their evolution, but the short time of evolution of M. perniciosa in relation to the genus has reduced the accuracy of the dN/dS tests in these exclusive families.
Adaptive evolution of PR-1 is reflected on expression data
It has already been shown that MpPR-1 genes of the C-biotype have distinct expression profiles in several different conditions of the WBD Transcriptome Atlas, which were also confirmed by quantitative RT-PCR [21, 22]. MpPR-1a, b, d, e are ubiquitously expressed during the necrotrophic mycelial stage, while MpPR-1j is mainly expressed in primordia and basidiomata. Six MpPR-1s are highly and almost exclusively expressed during the biotrophic stage of WBD: MpPR-1c, f, g, h, i, k . However, in contrast to MpPR-1i, the newly discovered MpPR-1l is not expressed in any of the conditions analyzed, suggesting that this gene may not be functional in the C-biotype.
Expression data of MpPR-1 genes from the S-biotype during a time course of the biotrophic interaction with MT tomato revealed that MpPR-1f, g, h, l, and k are highly expressed during 10–30 days after infection (d.a.i.) (Fig. 3). These results are similar to the expression profile verified for the C-biotype during the biotrophic interaction with T. cacao, with the exceptions that MpPR-1c is absent in the S-biotype and, instead of MpPR-1i, MpPR-1l is expressed during tomato infection. S-biotype MpPR-1s are highly expressed starting at 10 d.a.i., which is usually when the first symptoms of stem swelling are visible in MT tomato . MpPR-1a and b appear to have ubiquitous expression profiles since they show similar expression levels in almost all conditions. MpPR-1j, d, e, and i did not show significant expression in these libraries. Because MpPR-1i is truncated in the S-MG1 genome, quantification of expression was also done with S-MG2 as a reference, since it has a complete MpPR-1i gene. However, we still obtained the same expression profiles as S-MG1 for all MpPR-1. This could suggest that MpPR-1l is expressed in S-biotype even with a fusion to the adjacent gene. In the C-biotype, this adjacent gene is only expressed during the biotrophic interaction.
In M. roreri, it has been previously reported that MrPR-1n, MrPR-1g and MrPR-1i2 were upregulated in samples from the biotrophic phase (30 days post infection of pods), MrPR-1d was upregulated in the necrotrophic phase (60 days post infection of pods) and five other MrPR-1 were constitutively expressed under these conditions . The heatmap in Fig. 3 shows that similar to M. perniciosa’s PR-1 expression profile, MrPR-1g is the most expressed PR-1 gene during the biotrophic stage. Moreover, while MrPR-1h and MrPR-1f were not differentially expressed when comparing the biotrophic and necrotrophic stages, they also showed higher expression when compared to other MrPR-1s that belong to the conserved families.
Expression of recently diversified MpPR-1 was not induced by plant antifungal compounds
It has been previously demonstrated that CAP proteins of M. perniciosa bind to a variety of small hydrophobic ligands with different specificities. Thus, it has been suggested that the MpPR-1 genes induced in the biotrophic interaction could function in the detoxification of hydrophobic molecules produced by the host as a defense strategy . In this context, we investigated if MpPR-1 genes, especially the ones induced in WBD (c, f, h, i, k, g), are differentially expressed by the presence of the plant antifungal compounds eugenol or α-tomatin, which are similar to sterol and fatty acids, respectively. However, when the necrotrophic mycelia of M. perniciosa was treated with eugenol, only MpPR-1e, k, d were up-regulated, while MpPR-1f was down-regulated in α-tomatin-treated samples (Fig. 5). In all samples, among all MpPR-1 genes, MpPR-1a and MpPR-1b had the highest expression levels, while MpPR-1c, i, g, j have the lowest (TPM ≤ 2).
The evolution of PR-1 and the emergence of pathogenicity among saprotrophs
The plant pathogen M. perniciosa has at least 11 genes encoding PR-1-like secreted proteins, which were previously identified and characterized in the genome of the C-biotype CP02 isolate . Many of these genes were shown to be highly expressed during the biotrophic interaction of M. perniciosa and cacao, suggesting that MpPR-1 proteins have important roles during this stage of WBD. M. perniciosa has two other known biotypes (S and L) that differ in host specificity and virulence, the closest related species M. roreri that also is a T. cacao pathogen, and other nine Moniliophthora species: one described as a non-pathogenic grass endophyte , three of biotrophic/parasitic habit , and five species of unascertained lifestyle, found in dead or decaying vegetal substrates [31,32,33]. Because the majority of Moniliophthora related fungi in the Agaricales order are saprotrophs, the occurrence of parasitic Moniliophthora species raises the question about the emergence of biotrophic/parasitic lifestyle in this lineage of Marasmiaceae [30, 34]. The evolutionary scenario of host–pathogen arms race that emerges through the diversification of the Moniliophthora genus in the Agaricales order and of host-specific biotypes in M. perniciosa isolates, is especially suitable for the study of adaptive evolution in pathogenicity-related genes. Besides, the knowledge on putative adaptations gained through pathogen evolution are also specially interesting for further development of strategies against the pathogen. Based on our findings, Fig. 6 presents a model for the adaptive evolution of PR-1 proteins in Moniliophthora.
Through the characterization of the evolution of PR-1 proteins in Agaricales, we observe that at least one copy of PR-1 is present in all the sampled fungi, with most of the Agaricales species encoding between 1 and 7 PR-1 proteins. This is in contrast with Moniliophthora genomes, which encode among 10–12 proteins. Moniliophthora PR-1 proteins are derived independently from both ancient clades in the Agaricales gene tree. The longer branch-lengths in PR-1 families exclusive to Moniliophthora along with the evidence of evolution under positive selection identified in independently diverged clades suggest that the diversification of PR-1 in the genus was adaptive and related to its pathogenic lifestyle. The accentuated adaptive evolution of PR-1 in Moniliophthora is not only reflected in the genomic evolution of these genes, but also in their expression context. PR-1c, f, g, h, i, k, l, n are upregulated during the biotrophic interaction, while PR-1s that are also conserved in other Agaricales species are mainly expressed in mycelial stages of M. perniciosa (MpPR-1a, b, d, e). Most Agaricales species are not plant pathogens, which is also an evidence that PR-1 in Moniliophthora diverged from a few ancestral PR-1s that are related to basal metabolism in fungi and have been evolving under positive selective pressure possibly because of a benefit for the biotrophic/pathogenic lifestyle.
The emergence of SCP/TAPs proteins as pathogenicity factors has been reported in other organisms, such as the yeast Candida albicans and the filamentous fungus Fusarium oxysporum [10, 35]. Even though their specific function and mode of action may be different and remains to be characterized in plant pathogens, the recent evolution of these proteins towards their pathogenic role in the Moniliophthora genus could have contributed for the transition from a saprotrophic to parasitic lifestyle. Accelerated adaptive evolution evidenced by positive selection signs has also been observed in other virulence-associated genes of pathogenic fungi, such as the genes PabaA, fos-1, pes1, and pksP of Aspergillus fumigatus, which are involved in nutrient acquisition and oxidative stress response , and several gene families in C. albicans, including cell surface protein genes enriched in the most pathogenic Candida species .
Adaptive evolution of PR-1 within Moniliophthora species and its biotypes
The high diversification of PR-1 families observed within Moniliophthora was reinforced by our findings of positive selection in families that have also augmented expressions during infection: PR-1f, g, h, i, l. Among these five families, PR-1g and PR-1i are two of the most diversified families in Moniliophthora and have a more recent common ancestor with PR-1f than with the other PR-1s, placing this monophyletic clade of PR-1f, g, i as the key one to diversification and adaptive evolution of these proteins in the genus. Many sites that potentially evolved under selective pressure were also found in PR1-h, indicating that a parallel process of adaptive evolution occurred in this family.
Within the diversification of PR-1 in Moniliophthora, four cases of putative species-specific evolution of PR-1 families were found: PR-1c, PR-1k and PR-1l in M. perniciosa and PR-1n in M. roreri. Although vestigial sequences indicate that PR-1c probably emerged as a paralog of PR-1j in the ancestral of both species, it was only kept in the evolution of C-biotype, in which a change in expression profile occurred, thus placing MpPR-1c as a case of PR-1 diversification within M. perniciosa biotypes and a potential candidate for host specificity. Another candidate for biotype-specific diversification is PR-1l, which diverged from a duplication of PR-1i. Even though PR-1l was found in all three M. perniciosa biotypes, it was expressed only in the S-biotype during the biotrophic interaction, instead of PR-1i, which is expressed in M. roreri and in the C-biotype. This suggests that the divergence of PR-1i can be host-specific, but further experiments are necessary to clarify if they are either a cause or consequence of M. perniciosa pathogenicity.
Even though almost all PR-1 families are present in the genomes of L-biotype isolates, this biotype has an endophytic lifestyle and does not cause visible disease symptoms in their hosts [18, 38]. There is no available expression data for the L-biotype, so it is unknown whether their PR-1 genes could have any role related to their lifestyle or these genes are not pseudogenized yet due to a small evolutionary time. Evans  reported that the L-biotype can induce weak symptoms in seedlings of the Catongo variety of T. cacao. Therefore, it could be possible that host susceptibility is an important factor for the manifestation of WBD symptoms.
From basal metabolism to key roles in disease: how PR-1 proteins could have functionally adapted for pathogenicity?
It was previously shown that Pry proteins detoxify and protect yeast cells against eugenol  and that MpPR-1 proteins can bind to hydrophobic compounds secreted by plants, indicating that they could antagonize the host defense response . When the necrotrophic mycelia of M. perniciosa was cultivated with eugenol, expression of MpPR-1d and MpPR-1k was up-regulated, which is in agreement with the ability of these two proteins to bind to plant and fungal sterol compounds . MpPR-1e expression was also highly induced by eugenol, even though it was previously shown to bind only to fatty acids, but not sterols. Additionally, MpPR-1f, which is up-regulated during the biotrophic interaction like MpPR-1k, was down-regulated by α-tomatin. Given the above, it appears that M. perniciosa does not rely on MpPR-1 for cellular detoxification or this function is not transcriptionally regulated by plant hydrophobic compounds in the necrotrophic mycelia, or even, they could have different roles other than detoxification.
Considering that some PR-1 proteins are not associated with infection and are conserved in other saprotrophic fungi, here we hypothesize that the primary function of PR-1 in fungi can be related to the export of sterols from basal metabolism, such as ergosterol, the most abundant sterol in fungal cell membrane [39, 40]. PRY of S. cerevisiae transports acetylated ergosterol to the plasma membrane  and MpPR-1d, which belongs to a relatively conserved PR-1 family in Agaricales, can also efficiently bind to ergosterol . Furthermore, ergosterol acts as a PAMP molecule (pathogen‐associated molecular pattern) in plants , resulting in the activation of defense‐related secondary metabolites and genes, including plant PR-1s [3, 42,43,44], which are likely to have a role in sequestering sterols from the membranes of microbes  and stress signaling [45, 46]. Additionally, PR-1 receptor-like kinases (PR-1-RLK) from T. cacao are also upregulated on WBD and could be binding to the same ligand of PR-1 . Given that, it is possible that MpPR-1 could have evolved different adaptive roles through neofunctionalization. Besides export of hydrophobic compounds of basal metabolism, they could be acting in the protection of the cell membrane against the disruption caused by antifungal compounds, in the detoxification of hydrophobic compounds like phytoalexins secreted by the host, or it could even be possible that those MpPR-1s expressed during infection are sequestering the membrane sterols of the fungus itself in order to prevent detection by a possible ergosterol recognition complex from the host , thus compromising the elicitation of plant immunity in a similar fashion of MpChi, a chitinase-like effector that is highly expressed by M. perniciosa during the biotrophic stage of WDB .
It has been shown that the ability of MpPR-1 proteins to bind to sterols can be altered by a point mutation in the caveolin binding motif , highlighting the significance of understanding those sites under positive selection that are detected in important regions of the proteins, such as the candidate sites found in the CBM and alpha-helix 1 of PR-1i. These findings are central to learn how changes in the nucleotide or protein sequences could impact binding affinity and function. Even though this is speculative, as the specific role of PR-1 remains unknown, these results can guide further validation experiments and maybe demonstrate another case of adaptive evolution of fungal effectors.
Based on genomic and transcriptomic data, we presented evidence of adaptive evolution of PR-1 proteins in processes underlying the pathogenic lifestyle in Moniliophthora. These results reinforce the power of evolutionary analysis to reveal key proteins in the genomes of pathogenic fungi and contribute to the understanding of the evolution of pathogenesis. Our results indicate a set of PR-1 families that are putatively related to pathogenicity in the genus (PR-1f, g, h, i) and specialization within M. perniciosa biotypes (PR-1c, k and l) and M. roreri (PR-1n). The positive selection analysis also indicates protein sites that are putatively related to those adaptations. PR-1 genes and sites with evidence of adaptations are strong candidates for further study and should be evaluated in order to understand how changes in these sites can affect structure, binding affinity and function of these proteins.
Identification of PR-1-like gene families
In this study, we used a dataset of families of genes predicted in 22 genomes of Moniliophthora (unpublished) and 16 genomes of other fungal species of the order Agaricales, which were obtained from the Joint Genome Institute (JGI) Mycocosm database . The Moniliophthora genomes included are 7 isolates of the S-biotype (collected at the states of Amazonas and Minas Gerais, in Brazil), 9 isolates of the C-biotype (collected at the states of Amazonas, Pará, and Acre, in Brazil), 2 isolates of the L-biotype (from Colombia) and 4 samples of M. roreri (from Colombia). Additional file 1 contains the list of species and isolates, their genome identification and source (collection location or reference publication).
To identify candidate PR-1 gene families, we performed a search for genes encoding the CAP/SCP/PR1-like domain (CDD: cd05381, Pfam PF00188) using the HMMER software . The assignment of protein sequences to families of homologues (orthogroups) was done using Orthofinder (v. 1.1.2) . In addition, we searched all gene families for families containing PR-1 candidate genes with Blastp  using the known 11 MpPR-1 sequences  as baits, in order to search for possible candidates that were not previously identified and/or that have been wrongly assigned to other orthogroups due to incorrect gene prediction. To verify the presence of the SCP PR1-like/CAP domain (InterPro entry IPR014044) in the sequence, the InterProscan platform  was used. All Moniliophthora PR-1 candidate sequences identified in this study are deposited in GenBank under Accession numbers MW659198–MW659445.
Sequence alignment and phylogenetic reconstruction
For the inference of the phylogenetic history of the gene, the protein sequences of the PR-1 homologue families identified in the 22 Moniliophthora isolates were aligned with the PRY1 sequence of S. cerevisiae (GenBank ID CAA89372.1), which was used as outgroup. Multiple sequence alignments were performed with Mafft (v. 7.407)  using the iterative refinement method that incorporates local alignment information in pairs (L-INS-i), with 1000 iterations performed. Then, the alignments were used for phylogenetic reconstruction using the maximum likelihood method with IQ-Tree (v. 1.6.6) , which performs the selection of the best replacement model automatically, with 1000 bootstraps for branch support. Bootstraps were recalculated with BOOSTER (v. 0.1.2) for better support of branches in large phylogenies . Likewise, the phylogenetic inference for PR-1 of the Agaricales group of species was performed with the alignment of the homologous proteins identified in the 16 species obtained from Mycocosm, 3 isolates of M. perniciosa (C-BA3, S-MG3, L-EC1, one representing each biotype), an isolate of M. roreri (R-CO1), and PRY1 of S. cerevisiae as the outgroup. To improve alignment quality, trimAl package  was used. For dN/dS analysis, considering each gene family independently, the phylogenetic reconstruction was performed using IQ-Tree (v. 1.6.6)  with the multiple local alignment of the protein sequences obtained with Mafft (v. 7.407) , and the codon-based alignment of the nucleotide sequences was performed with Macse (v. 2.01) .
Detection of positive selection signals
To search for genes and regions that are potentially under positive selection in each of the PR-1 families of the 22 isolates, the CodeML program of the PAML 4.7 package  was used with the ETEToolkit tool . CodeML implements a modification of the model proposed by  to calculate the omega (rate of non-synonymous mutations (dN)/rate of synonymous mutations (dS)) of a coding gene from the multiple alignment sequences and phylogenetic relationships that have been previously inferred.
In order to detect positive selection signals in isolates or specific positions in the sequences, we performed tests with the “branch-site” model, which compares a null model (bsA1) in which the branch under consideration is evolving without restrictions (dN/dS = 1) against a model in which the same branch has sites evolving under positive selection (bsA) (dN/dS > 1) . In these tests, those branches that were tested for significantly different evolving rates from the others (foreground branches ωfrg) are marked in the phylogenetic trees—in this case, the branches corresponding to the isolates of the C-biotype or S-biotype. To detect signs of positive selection at specific sites throughout the sequences, regardless of the isolate, we used the “sites” model (M2 and M1, NSsites 0 1 2) to test all branches of the phylogenetic trees.
In both tests, the models are executed several times with different initial omegas (0.2, 0.7, 1.2), and the models with the highest probability are selected for the hypothesis test, in which a comparison between the alternative model and the null model is made through a likelihood ratio test. If the alternative model is the most likely one (p-value < 0.05), then the possibility of positive selection (ω > 1) can be accepted, and sites with evidence of selection (probability > 0.95) are reported by Bayes Empirical Bayes analysis (BEB) .
Gene amplification and synteny analysis of PR-1c
In order to confirm the presence or absence of MpPR-1c and MpPR-1d genes in the genomes of M. perniciosa isolates, these genes were amplified by polymerase chain reaction (PCR) from isolates C-AC1, C-BA1a, C-BA3, S-AM1, S-MG3, S-MG4, L-EC1 and L-EC2. The necrotrophic mycelia of these isolates was cultivated in 1.7% MYEA media (15 g/L agar; 5 g/L yeast extract, 17 g/L malt extract) at 28 °C for 14 days, then harvested and ground in liquid nitrogen for total DNA isolation with the phenol–chloroform method . PCRs were performed with primers designed for MpPR-1c (F: 5ʹ-GGATCCCGACTTGACAACTCCATCTCG-3ʹ, R: 5ʹ-GAGCTCTCACTCAAACTCCCCGTCATAAT-3ʹ) and MpPR-1d (F: 5ʹ-GGATCCCCCTCGCAATGGGTTTTC-3ʹ, R: 5ʹ-GTCGACTCAGTCAAGATCAGCCTGGAGA-3ʹ) and amplifications cycles consisting of an initial stage of 94 °C for 3 min, 35 cycles of 95 °C for 30 s, 60 °C for 50 s and 72 °C for 1 min, and final extension at 72 °C for 10 min.
For synteny analysis, the positions of PR-1j, PR-1c and PR-1d genes were searched in the scaffolds of genomes C-BA3, S-MG2, R-CO2, L-EC1 and L-EC2 by blastn. The scaffolds were then excised 5000 bp upstream and 5000 bp downstream from the starting position of PR-1j in the scaffolds. The resulting 10,000 bp excised scaffolds were used for synteny analysis with Mummer (v. 4.0.0beta2) , using the C-BA3 sequence as the reference.
MpPR-1 expression data
MpPR-1 expression data in RPKM (Reads Per Kilobase per Million mapped reads) values from the C-biotype of M. perniciosa in seven biological conditions (dikaryotic mycelium 14 days, basidiomata, germinating spores, green broom, initial necrosis, advanced necrosis, dry broom) were downloaded from the Witches’ Broom Disease Transcriptome Atlas (v. 1.1) (http://bioinfo08.ibi.unicamp.br/atlas/).
MpPR-1 expression data of M. perniciosa treated with plant antifungal compounds were obtained from RNA-seq data (unpublished). The C-BA1a isolate’s necrotrophic mycelia was initially inoculated in 100 mL of liquid MYEA media and cultivated for 5 days under agitation of 150 rpm at 30 °C, then 5 mL of this initial cultivation were transferred to 50 mL of fresh MYEA liquid media containing eugenol (500 µM), α-tomatin (80 µM) or DMSO (250 µL, solvent control) and cultivated again under agitation of 150 rpm at 30 °C for 7 days. The total RNA was extracted using the Rneasy® Plant Mini Kit (Quiagen, USA) and quantified on a fluorimeter (Qubit, Invitrogen). cDNA libraries were prepared in five biological replicates for each treatment, plus biological control. The cDNA libraries were built from 1000 ng of total RNA using Illumina’s TruSeq RNA Sample Prep kit, as recommended by the manufacturer. The libraries were prepared according to Illumina’s standard procedure and sequenced on Illumina’s HiSeq 2500 sequencer. The quality of raw sequences was assessed with FastQC (v.0.11.7) . Read quantification was performed by mapping the generated reads against 16,084 gene models of the C-BA1a genome using Salmon (v.0.14.1) in mapping-based mode . Read counts were normalized to Transcripts Per Million (TPM) values for plotting. Differential expression analysis was performed with the DESeq2 (v.1.22.2) package using Wald test and Log fold change shrinkage by the apeglm method (IfcThreshold = 0.1, s-value < 0.005) . TPM values and DESeq2 results for MpPR-1 genes in these experimental conditions are available at Additional file 2.
MpPR-1 expression data in TPM for the S-biotype was obtained from RNA-seq libraries of infected MicroTom tomato plants in seven different time points after inoculation (12 h, 24 h, 48 h, 5 days, 10 days, 20 days, 30 days) (unpublished). The quality of raw sequences was assessed with FastQC (v. 0.11.7) . Next, Trimmomatic (v.0.36)  was used to remove adaptor-containing and low-quality sequences. Quality-filtered reads were then aligned against the S-MG1 or S-MG2 reference genome using HISAT2 (v.2.1.0) with default parameters . Reads that mapped to coding sequences were counted with featureCounts (v.1.6.3) . TPM values for MpPR-1 genes in these experimental conditions are available at Additional file 3.
MrPR-1 expression data in TPM was obtained from RNA-Seq reads of M. roreri in the biotrophic (30 days after infection) and necrotrophic (60 days after infection) stages of frosty pod rot from . Reads were mapped and quantified with Salmon (v.0.14.1)  using 17,910 gene models of M. roreri MCA 2997 (GCA_000488995) available at Ensembl Fungi.
Availability of data and materials
The datasets supporting the conclusions of this article are included within the article and its additional files. All Moniliophthora PR-1 candidate sequences identified in this study are deposited in GenBank under Accession numbers MW659198–MW659445.
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We are thankful to Dr. Jorge M. Mondego for helping with the conceptualization of the experiments of M. perniciosa treated with antifungal compounds and M.sc. Bárbara A. Pires and Dr. Mario O. Barsottini for helping with the execution of these experiments. We thank M.sc. Leandro C. do Nascimento for performing the assembly of Moniliophthora genomes.
This work was supported by the São Paulo Research Foundation (FAPESP) Grants to M.F.C (#2013/08293-7), G.A.G.P. and A. F. (#2016/10498-4), and FAPESP fellowships to A.A.V (#2017/13015-7), A.P.C. (#2018/04240–0), P.J.P.L.T. (#2009/51018–1), G.L.F (#2011/23315-1, #2013/09878-9, #2014/06181-0), P.F.V.P. (#2013/05979-5, #2014/00802-2), J.L.C. (#2013/04309-6) and R.M.B (#2017/13319-6). The funders were not involved in the design of the study and collection, analysis, and interpretation of data and in writing the manuscript.
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List of fungal genomes and their source (collection site or reference publication. Excel file with table containing the species names and biotypes of the fungal genomes used for the identification of PR-1-like genes, the identification names we used for the genomes, and their source, which for M. perniciosa and M. roreri isolates corresponds to their collection site, and for the other Agaricales species corresponds to their reference publication.
MpPR-1 quantification data and differential expression results of M. perniciosa treated with eugenol or alpha-tomatin treatment. Excel file with three spreadsheets (three tabs). First spreadsheet contains a matrix of expression values in Transcripts Per Million (TPM) for MpPR-1 genes of the necrotrophic mycelia of M. perniciosa (C-biotype) treated with eugenol (500 µM), α-tomatin (80 µM) or DMSO (250 µL) (solvent control) for 7 days. Quantification was performed from RNA-Seq reads using the C-BA1a genome as reference. Second spreadsheet contains the results table for MpPR-1 genes in the differential expression analysis comparing the expression profiles between Eugenol vs Control treatments, while comparison between α-tomatin vs Control treatments is shown in the third spreadsheet.
MpPR-1 expression data in S-biotype infection in tomato. Excel file containing the matrix of expression values in Transcripts Per Million (TPM) for MpPR-1 genes of M. perniciosa S-biotype infection in MicroTom tomato in various time points of infection (12 h, 24 h, 48 h, 5 days, 10 days, 20 days, 30 days). Quantification was performed from RNA-Seq reads using the S-MG1 (data in first spreadsheet) or S-MG2 genome (data in second spreadsheet) as reference.
Phylogenetic reconstruction of PR-1 proteins in Moniliophthora isolates (version with non-collapsed branches). Figure of phylogenetic tree with non-collapsed branches of PR-1 proteins identified from genomes of 18 M. perniciosa and 4 M. roreri isolates, inferred by maximum likelihood and branch support obtained using 1000 bootstraps. The PRY1 protein of Saccharomyces cerevisiae was used as an outgroup.
Protein sequence alignment and omega (dN/dS) values of each PR-1i family of Moniliophthora genomes. PDF file containing figures of the protein sequence alignment for each PR-1 family from Moniliophthora isolates and a bar chart of omega (dN/dS) values calculated for each amino acid site along the alignment using the site model test of codeML. Sites with positive selection signs are indicated by red (p-value ≤ 0.01) or orange (p-value ≤ 0.05) bars in the bar chart of omega values below the alignment. Figures are organized by alphabetical order of the names of PR-1 families.
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Vasconcelos, A.A., José, J., Tokimatu, P.M. et al. Adaptive evolution of Moniliophthora PR-1 proteins towards its pathogenic lifestyle. BMC Ecol Evo 21, 84 (2021). https://doi.org/10.1186/s12862-021-01818-5
- Witches’ broom disease
- Gene evolution
- Positive selection