Identifying pathogenicity genes in the rubber tree anthracnose fungus Colletotrichum gloeosporioides through random insertional mutagenesis

Characterization of Colletotrichum Causing Anthracnose on Rubber Trees in Yunnan: Two New Records and Two New Species from China

Among the most damaging diseases of rubber trees is anthracnose caused by the genus Colletotrichum, which leads to significant economic losses. Nonetheless, the specific Colletotrichum spp. that infect rubber trees in Yunnan Province, an important natural rubber base in China, have not been extensively investigated. Here, we isolated 118 Colletotrichum strains from rubber tree leaves exhibiting anthracnose symptoms in multiple plantations in Yunnan. Based on comparisons of their phenotypic characteristics and internal transcribed spacer ribosomal DNA sequences, 80 representative strains were chosen for additional phylogenetic analysis based on eight loci (act, ApMat, cal, CHS-1, GAPDH, GS, his3, and tub2), and nine species were identified. Colletotrichum fructicola, C. siamense, and C. wanningense were found to be the dominant pathogens causing rubber tree anthracnose in Yunnan. C. karstii was common, whereas C. bannaense, C. brevisporum, C. jinpingense, C. mengdingense, and C. plurivorum were rare. Among these nine species, C. brevisporum and C. plurivorum are reported for the first time in China, and two species are new to the world: C. mengdingense sp. nov. in the C. acutatum species complex and C. jinpingense sp. nov. in the C. gloeosporioides species complex. Their pathogenicity was confirmed with Koch's postulates by inoculating each species in vivo on rubber tree leaves. This study clarifies the geographic distribution of Colletotrichum spp. associated with anthracnose on rubber trees in representative locations of Yunnan, which is crucial for the implementation of quarantine measures.

Genomic analysis of Colletotrichum camelliae responsible for tea brown blight disease

BACKGROUND

Colletotrichum camelliae, one of the most important phytopathogenic fungi infecting tea plants (Camellia sinensis), causes brown blight disease resulting in significant economic losses in yield of some sensitive cultivated tea varieties. To better understand its phytopathogenic mechanism, the genetic information is worth being resolved.

RESULTS

Here, a high-quality genomic sequence of C. camelliae (strain LT-3-1) was sequenced using PacBio RSII sequencing platform, one of the most advanced Three-generation sequencing platforms and assembled. The result showed that the fungal genomic sequence is 67.74 Mb in size (with the N50 contig 5.6 Mb in size) containing 14,849 putative genes, of which about 95.27% were annotated. The data revealed a large class of genomic clusters potentially related to fungal pathogenicity. Based on the Pathogen Host Interactions database, a total of 1698 genes (11.44% of the total ones) were annotated, containing 541 genes related to plant cell wall hydrolases which is remarkably higher than those of most species of Colletotrichum and others considered to be hemibiotrophic and necrotrophic fungi. It's likely that the increase in cell wall-degrading enzymes reflects a crucial adaptive characteristic for infecting tea plants.

CONCLUSION

Considering that C. camelliae has a specific host range and unique morphological and biological traits that distinguish it from other species of the genus Colletotrichum, characterization of the fungal genome will improve our understanding of the fungus and its phytopathogenic mechanism as well.

Identifying pathogenicity-related genes in the pathogen Colletotrichum magnum causing watermelon anthracnose disease via T-DNA insertion mutagenesis

Fruit rot caused by Colletotrichum magnum is a crucial watermelon disease threatening the production and quality. To understand the pathogenic mechanism of C. magnum, we optimized the Agrobacterium tumefaciens-mediated transformation system (ATMT) for genetic transformation of C. magnum. The transformation efficiency of ATMT was an average of around 245 transformants per 100 million conidia. Southern blot analysis indicated that approximately 75% of the mutants contained a single copy of T-DNA. Pathogenicity test revealed that three mutants completely lost pathogenicity. The T-DNA integration sites (TISs) of three mutants were Identified. In mutant Cm699, the TISs were found in the intron region of the gene, which encoded a protein containing AP-2 complex subunit σ, and simultaneous gene deletions were observed. Two deleted genes encoded the transcription initiation protein SPT3 and a hypothetical protein, respectively. In mutant Cm854, the TISs were found in the 5'-flanking regions of a gene that was similar to the MYO5 encoding Myosin I of Pyricularia oryzae (78%). In mutant Cm1078, the T-DNA was integrated into the exon regions of two adjacent genes. One was 5'-3' exoribonuclease 1 encoding gene while the other encoded a WD-repeat protein retinoblastoma binding protein 4, the homolog of the MSl1 of Saccharomyces cerevisiae.

T-DNA insertion mutagenesis in Penicillium brocae results in identification of an enolase gene mutant impaired in secretion of organic acids and phosphate solubilization

Penicillium brocae strain P6 is a phosphate-solubilizing fungus isolated from farmland in Guangdong Province, China. To gain better insights into the phosphate solubilization mechanisms of strain P6, a T-DNA insertion population containing approximately 4500 transformants was generated by Agrobacterium tumefaciens-mediated transformation. The transformation procedure was optimized by using a Hybond N membrane for co-cultivation of A. tumefaciens and P. brocae. A mutant impaired in phosphate solubilization (named MT27) was obtained from the T-DNA insertion population. Thermal asymmetric interlaced PCR was then used to identify the nucleotide sequences flanking the T-DNA insertion site. The T-DNA in MT27 was inserted into the fourth exon of an enolase gene, which shows 90.8 % nucleotide identity with enolase mRNA from Aspergillus neoniger. Amino acid sequence homology analysis indicated that the enolase is well conserved among filamentous fungi and Saccharomyces cerevisiae. Complementation tests with the MT27 mutant confirmed that the enolase gene is involved in phosphate solubilization. Analysis of organic acids in culture supernatants indicated reduced levels of oxalic acid and lactic acid for the MT27 mutant compared to the parent strain P6 or the complementation strain. In conclusion, we suggest that the identified enolase gene of P. brocae is involved in production of specific organic acids, which, when secreted, act as phosphate solubilizing agents.

Comparative Transcriptome Analyses Reveal Conserved and Distinct Mechanisms of the SDHI Fungicide Benzovindiflupyr Inhibiting Colletotrichum

Colletotrichum leaf disease (CLD) is an annual production concern for commercial growers worldwide. The succinate dehydrogenase inhibitor (SDHI) fungicide benzovindiflupyr shows higher bioactivity against CLD than other SDHIs. However, the mechanism underlying such difference remains unclear. In this study, benzovindiflupyr exhibits good inhibitory activity against Colletotrichum siamense and C. nymphaeae in vitro and in vivo. To reveal its mechanism for inhibiting Colletotrichum, we compared transcriptomes of C. siamense and C. nymphaeae under treatment with benzovindiflupyr and boscalid. Benzovindiflupyr exhibited higher inhibitory activity against SDH enzyme than boscalid, resulting in a greater reduction in the ATP content of Colletotrichum isolates. Most of the metabolic pathways induced in these fungicide-treated isolates were similar, indicating that benzovindiflupyr exhibited a conserved mechanism of SDHIs inhibiting Colletotrichum. At the same level of suppressive SDH activity, benzovindiflupyr activated more than three times greater gene numbers of Colletotrichum than boscalid, suggesting that benzovindiflupyr could activate distinct mechanisms against Colletotrichum. Membrane-related gene ontology terms, mainly including intrinsic components of membrane, were highly abundant for the benzovindiflupyr-treated isolates rather than boscalid-treated isolates. Only benzovindiflupyr increased the relative conductivities of hyphae, indicating that it could damage the cell membrane and increase mycelial electrolyte leakage. Thus, we proposed that the high bioactivity of benzovindiflupyr against Colletotrichum occurred by inhibiting SDH activity and damaging the cell membrane at the same time. The research improves our understanding the mode of action of SDHI fungicides against Colletotrichum.

The G-protein alpha subunit CgGa1 mediates growth, sporulation, penetration and pathogenicity in Colletotrichum gloeosporioides

Colletotrichum gloeosporioides is the main pathogen causing rubber anthracnose, which brings huge economic loss to the natural rubber industry. Heterotrimeric G proteins play a vital role in signal transduction in filamentous fungi, and G alpha subunits are the major component of G proteins. In this study, we characterize a group I Gα subunit CgGa1 in C. gloeosporioides as a homolog of MagB in Pyricularia oryzae. CgGa1 encodes a 353-amino acid protein and has a G_alpha domain. Deletion of CgGa1 results in reduced vegetative growth and conidia yield, and the mutant cannot produce a fruiting body. The CgGa1 deletion mutant also exhibits decreased conidial germination and appressorium formation significantly. Moreover, the mutant has an obvious deficiency in penetration and loses its virulence completely. Transcriptome analysis showed that CgGa1 could affect the expression of many genes related to carbohydrate metabolism, amino acid metabolism and signal transduction, etc. In conclusion, CgGa1 regulates growth, asexual and sexual sporulation, appressorium formation, penetration and pathogenicity of C. gloeosporioides.

Melatonin Mitigates the Infection of Colletotrichum gloeosporioides via Modulation of the Chitinase Gene and Antioxidant Activity in Capsicum annuum L

Anthracnose, caused by Colletotrichum gloeosporioides, is one of the most damaging pepper (Capsicum annum L.) disease. Melatonin induces transcription of defense-related genes that enhance resistance to pathogens and mediate physiological activities in plants. To study whether the melatonin-mediated pathogen resistance is associated with chitinase gene (CaChiIII2), pepper plants and Arabidopsis seeds were treated with melatonin, then CaChiIII2 activation, hydrogen peroxide (H₂O₂) levels, and antioxidant enzymes activity during plant–pathogen interactions were investigated. Melatonin pretreatment uncoupled the knockdown of CaChiIII2 and transiently activated its expression level in both control and CaChiIII2-silenced pepper plants and enhanced plant resistance. Suppression of CaChiIII2 in pepper plants showed a significant decreased in the induction of defense-related genes and resistance to pathogens compared with control plants. Moreover, melatonin efficiently enabled plants to maintain intracellular H₂O₂ concentrations at steady-state levels and enhanced the activities of antioxidant enzymes, which possibly improved disease resistance. The activation of the chitinase gene CaChiIII2 in transgenic Arabidopsis lines was elevated under C. gloeosporioides infection and exhibited resistance through decreasing H₂O₂ biosynthesis and maintaining H₂O₂ at a steady-state level. Whereas melatonin primed CaChiIII2-overexpressed (OE) and wild-type (WT) Arabidopsis seedlings displayed a remarkable increase in root-length compared to the unprimed WT plants. Using an array of CaChiIII2 knockdown and OE, we found that melatonin efficiently induced CaChiIII2 and other pathogenesis-related genes expressions, responsible for the innate immunity response of pepper against anthracnose disease.

Deciphering the Infectious Process of Colletotrichum lupini in Lupin through Transcriptomic and Proteomic Analysis

The fungal phytopathogen Colletotrichum lupini is responsible for lupin anthracnose, resulting in significant yield losses worldwide. The molecular mechanisms underlying this infectious process are yet to be elucidated. This study proposes to evaluate C. lupini gene expression and protein synthesis during lupin infection, using, respectively, an RNAseq-based transcriptomic approach and a mass spectrometry-based proteomic approach. Patterns of differentially-expressed genes in planta were evaluated from 24 to 84 hours post-inoculation, and compared to in vitro cultures. A total of 897 differentially-expressed genes were identified from C. lupini during interaction with white lupin, of which 520 genes were predicted to have a putative function, including carbohydrate active enzyme, effector, protease or transporter-encoding genes, commonly described as pathogenicity factors for other Colletotrichum species during plant infection, and 377 hypothetical proteins. Simultaneously, a total of 304 proteins produced during the interaction were identified and quantified by mass spectrometry. Taken together, the results highlight that the dynamics of symptoms, gene expression and protein synthesis shared similarities to those of hemibiotrophic pathogens. In addition, a few genes with unknown or poorly-described functions were found to be specifically associated with the early or late stages of infection, suggesting that they may be of importance for pathogenicity. This study, conducted for the first time on a species belonging to the Colletotrichum acutatum species complex, presents an opportunity to deepen functional analyses of the genes involved in the pathogenicity of Colletotrichum spp. during the onset of plant infection.

Control of the rubber anthracnose fungus Colletotrichum gloeosporioides using culture filtrate extract from Streptomyces deccanensis QY-3

Colletotrichum gloeosporioides is a main cause of rubber anthracnose, which results in a huge loss for the natural rubber industry. In this study, an actinomycete strain QY-3 was isolated and had good antagonistic activity against C. gloeosporioides with an inhibition rate of 86.6%. Strain QY-3 was identified as Streptomyces deccanensis preliminarily. Millet medium was selected as the optimal fermentation broth for antifungal metabolites production by S. deccanensis QY-3. The culture filtrate extract (CFE) from the millet broth of S. deccanensis QY-3 exhibits broad-spectrum antifungal activity against plant pathogenic fungi, and its EC₅₀ inhibiting the mycelial growth of C. gloeosporioides is 6.3 μg/mL. The CFE has good thermal and pH stabilities, and it can break the hyphae and inhibit the conidial germination of C. gloeosporioides. 100 μg/mL of CFE had an obvious control effect on rubber anthracnose, and the control efficacy was 63.7% on 5 days after inoculation. Two compounds with inhibitory effects on C. gloeosporioides, anthranilic acid and sangivamycin, were isolated from the CFE. The MICs of both compounds against C. gloeosporioides were 29.3 and 23.0 μg/mL respectively. In conclusion, the CFE from S. deccanensis QY-3 has great potential to be a promising fungicide for rubber anthracnose.

Dinactin from a new producer, Streptomyces badius gz-8, and its antifungal activity against the rubber anthracnose fungus Colletotrichum gloeosporioides

Colletotrichum gloeosporioides is a main cause of rubber anthracnose, which results in very large losses for the natural rubber industry. In this study, an actinomycete strain gz-8 was isolated and had strong antagonistic activity against C. gloeosporioides, with an inhibition rate of 72.5 %. Strain gz-8 was identified as Streptomyces badius. Three active compounds were separated from S. badius gz-8 and identified as feigrisolide B, feigrisolide C and dinactin according to the mass spectrometry and NMR-spectra results. In the three compounds, dinactin exhibited the best antifungal activity against C. gloeosporioides, with an EC₅₀ value of 2.55 μg/mL, and its minimum inhibitory concentration was 44 μg/mL. Dinactin had broad inhibitory activities against nine other pathogenic fungi, and it also had an obvious control effect on rubber anthracnose comparable to that of chlorothalonil. Dinactin could inhibit the conidiogenesis and spore germination of C. gloeosporioides. This report will contribute to understanding the antifungal activity of dinactin against C. gloeosporioides.

Revealing the dominant long noncoding RNAs responding to the infection with Colletotrichum gloeosporioides in Hevea brasiliensis

Background

Rubber tree (Hevea brasiliensis) acts as an important tropic economic crop and rubber tree anthracnose, mainly caused by Colletotrichum gloeosporioides, is one of the most common fungal disease, which leads to serious loss of rubber production. Therefore, the investigation on disease resistance is of great worldwide significance. In the past decades, substantial progress has been made on coding gene families related with plant disease resistance. However, in rubber tree, whether the disease resistance mechanism involves noncoding RNAs, especially long noncoding RNAs (lncRNAs), still remains poorly understood.

Results

Here, we modeled the development of H. brasiliensis leaf samples inoculated with C. gloeosporioides at divergent stages, explored to identify the expressed ncRNAs by RNA-seq, and investigated the dominant lncRNAs responding to the infection, through constructing a co-expressed network systematically. On the dominant lncRNAs, we explored the potential functional role of lncRNA11254 recruiting the transcription factor, and that lncRNA11041 and lncRNA11205 probably stimulate the accumulation of corresponding disease responsive miRNAs, and further modulate the expressions of target genes, accompanying with experimental examination.

Conclusions

Take together, computational analyses in silico and experimental evidences in our research collectively revealed the responsive roles of dominant lncRNAs to the pathogen. The results will provide new perspectives to unveil the plant disease resistance mechanisms, and will presumably provide a new theoretical basis and candidate prognostic markers for the optimization and innovation of genetic breeding for rubber tree.

Reviewers

This article was reviewed by Ryan McGinty and Roland Huber.

Electronic supplementary material

The online version of this article (10.1186/s13062-019-0235-z) contains supplementary material, which is available to authorized users.

Alternaria yunnanensis sp. nov., a New Alternaria Species Causing Foliage Spot of Rubber Tree in China

A new species of Alternaria causing leaf spots on the rubber tree (Hevea brasiliensis) in Yunnan, China, was isolated, examined, and illustrated. Morphologically, it belongs to the section Porri of Alternaria, which produces relatively large conidia and a simple or branched, filamentous long beak. It is, however, characterized by conidiophores gradually enlarging near the apex into a clavate conidiogenous cell and long ellipsoid to obclavate, smooth-walled conidia with a long filamentous beak. Molecular phylogenetic analyses based on ITS rDNA, GAPDH, and TEF1-alpha sequences demonstrate that the phytopathogen falls in the clade of the section Porri, being most closely related to A. sidae, A. sennae, A. deseriticola, A. cyamopsidis, A. rostellata, A. nitrimali, A. crassa, and A. thunbergiae.

Coryneumheveanum sp. nov. (Coryneaceae, Diaporthales) on twigs of Para rubber in Thailand

During studies of microfungi on para rubber in Thailand, we collected a new Coryneum species on twigs which we introduce herein as C.heveanum with support from phylogenetic analyses of LSU, ITS and TEF1 sequence data and morphological characters. Coryneumheveanum is distinct from other known taxa by its conidial measurements, number of pseudosepta and lack of a hyaline tip to the apical cell.

Dicer-like Proteins Regulate the Growth, Conidiation, and Pathogenicity of Colletotrichum gloeosporioides from Hevea brasiliensis

Colletotrichum gloeosporioides from Hevea brasiliensis is the hemibiotrophic fungi which could cause anthracnose in rubber trees. Dicer like proteins (DCL) were the core enzymes for generation of small RNAs. In the present study, the knocking-out mutants of two dicer like proteins encoding genes of C. gloeosporioides were constructed; and functions of two proteins were investigated. The results showed that DCL play important roles in regulating the growth, conidiation and pathogenicity of C. gloeosporioides; and there is a functional redundancy between DCL1 and DCL2. Microscopy analysis and DAB staining revealed that loss of penetration ability into the host cells, instead of the decreased growth rate, was the main cause for the impaired pathogenicity of the ΔDcl1ΔDcl2 double mutant. Proteomics analysis suggested that DCL proteins affected the expression of functional proteins to regulating multiple biological processes of C. gloeosporioides. These data lead to a better understanding of the functions of DCL proteins in regulating the development and pathogenesis of C. gloeosporioides.

Restriction enzyme-mediated insertional mutagenesis: an efficient method of Rosellinia necatrix transformation

Rosellinia necatrix: causing root rot disease is a very destructive pathogen of woody plants and is responsible for yield losses to a large number of fruit trees. The genetic analysis of this pathogen has not been picked up because of difficulty in generating mutations in Rosellinia necatrix for many reasons. A number of methods have been proposed for inducing mutations in Rosellinia necatrix but none of them proved worth because of very low transformation efficiencies. Here, we propose an efficient method for Rosellinia necatrix protoplast production, where protoplasts in the tune of 10⁷ per ml can be easily generated. We also propose a restriction enzyme-mediated integration (REMI)-based methods for efficient transformation of Rosellinia necatrix. In the present study, an approximate of 800 transformants was obtained from 5 μg of linearized plasmid. Out of 47 single spored transformants analyzed, only 33 showed hygromycin gene amplification using PCR and only 19 transformants showed single gene integration in southern hybridization, which accounted for single gene integration percentage of 42%, highest amongst all the previous reports on Rosellinia necatrix transformations. Some of the transformants studied for pathogenicity phenotype also showed a marked reduction in pathogenicity. Thus, in the present investigation, 42% single gene integrations among the transformed colonies can be considered as excellent transformation efficiency.

Functional analysis of a regulator of G-protein signaling CgRGS1 in the rubber tree anthracnose fungus Colletotrichum gloeosporioides

Colletotrichum gloeosporioides is the causal agent of rubber anthracnose, which is also one of the important biological factors threatening the development of natural rubber industry in the world. Regulators of G-protein signaling (RGS) are key negative regulators of G-proteins, which play important roles in growth, development and pathogenic processes of plant pathogens. In this study, a RGS gene CgRGS1 was functionally characterized in C. gloeosporioides. Compared to the wild type, the CgRGS1 deletion mutant had slow vegetative growth, reduced conidia with multi-end germination, low appressorium formation rate, high resistance to oxidative stress and SDS. Moreover, the mutant was sensitive to osmotic pressure and showed decreased virulence. In conclusion, CgRGS1 is involved in regulation of vegetative growth, conidiation, germination, appressorium formation, oxidative stress, osmotic pressure response and pathogenicity in C. gloeosporioides.

A silver bullet in a golden age of functional genomics: the impact of Agrobacterium-mediated transformation of fungi

The implementation of Agrobacterium tumefaciens as a transformation tool revolutionized approaches to discover and understand gene functions in a large number of fungal species. A. tumefaciens mediated transformation (AtMT) is one of the most transformative technologies for research on fungi developed in the last 20 years, a development arguably only surpassed by the impact of genomics. AtMT has been widely applied in forward genetics, whereby generation of strain libraries using random T-DNA insertional mutagenesis, combined with phenotypic screening, has enabled the genetic basis of many processes to be elucidated. Alternatively, AtMT has been fundamental for reverse genetics, where mutant isolates are generated with targeted gene deletions or disruptions, enabling gene functional roles to be determined. When combined with concomitant advances in genomics, both forward and reverse approaches using AtMT have enabled complex fungal phenotypes to be dissected at the molecular and genetic level. Additionally, in several cases AtMT has paved the way for the development of new species to act as models for specific areas of fungal biology, particularly in plant pathogenic ascomycetes and in a number of basidiomycete species. Despite its impact, the implementation of AtMT has been uneven in the fungi. This review provides insight into the dynamics of expansion of new research tools into a large research community and across multiple organisms. As such, AtMT in the fungi, beyond the demonstrated and continuing power for gene discovery and as a facile transformation tool, provides a model to understand how other technologies that are just being pioneered, e.g. CRISPR/Cas, may play roles in fungi and other eukaryotic species.

The function and transcriptome analysis of a bZIP transcription factor CgAP1 in Colletotrichum gloeosporioides

Colletotrichum gloeosporioides is an important pathogen of anthracnose, which is able to infect numerous crops in tropical and subtropical regions, causing great economic losses. To investigate the fungal response to host-generated reactive oxygen species (ROS), we cloned and characterized the CgAP1 gene of C. gloeosporioides. CgAP1 encoded a bZIP transcription factor which had a bZIP DNA-binding domain and two cysteine-rich domains structurally and functionally related to Saccharomyces cerevisiae YAP1. Deletion of CgAP1 in C. gloeosporioides resulted in increasing sensitivity to H₂O₂, changes in cell wall integrity and loss of pathogenicity. To understand the regulatory network of CgAP1, RNA sequencing was used to identify differentially expressed genes in the CgAP1 mutant. It was shown that several genes involved in ROS detoxification and cell wall integrity were affected by CgAP1. Moreover, CgAP1 was also involved in many biological processes especially ribosome, cellular transport and amino acid metabolism. In conclusion, CgAP1 is an important transcription factor involved in oxidative stress, cell wall integrity and pathogenicity in C. gloeosporioides.

Use of Random T-DNA Mutagenesis in Identification of Gene UvPRO1, A Regulator of Conidiation, Stress Response, and Virulence in Ustilaginoidea virens

False smut of rice, caused by Ustilaginoidea virens (Cooke) Takahashi (teleomorph: Villosiclava virens), is one of the most important diseases affecting rice worldwide. Agrobacterium tumefaciens-mediated transformation was used to identify functional genes in U. virens. In this study, we selected a single-copy insertion mutant T133 with deficiency in producing conidia by screening the T-DNA insertion mutant library of U. virens. The UvPRO1-deletion mutant was successfully obtained after cloning the targeted gene by analysis of the T-DNA insert site of mutant T133. Further research showed that the UvPRO1 mutant was reduced in growth rate and could not produce conidia in PSB medium, while sensitivities to sodium dodecyl sulfate, Congo red, and hyperosmotic stress increased. Moreover, the UvPRO1 deletion mutant hyphae could extend along the surface of spikelets at 1-3 dpi, but mycelia became shriveled and completely lost the ability to infect spikelets at 4 dpi. The relative expression level of UvPRO1 at 8 dpi was more than twice as high as that at 1-2 dpi. These results suggest that UvPRO1 plays a critical role in hyphal growth and conidiation, as well as in stress response and pathogenesis. These findings provide a novel mode of action for the PRO1 protein in fungi and improve the understanding of the function of UvPRO1 in the life cycle of U. virens.

Development of Microsatellite Markers and Analysis of Genetic Diversity and Population Structure of Colletotrichum gloeosporioides from Ethiopia

Twenty three polymorphic microsatellite markers were developed for citrus plant pathogenic fungus, Colletotrichum gloeosporioides, and were used to analyze genetic diversity and population structure of 163 isolates from four different geographical regions of Ethiopia. These loci produced a total of 118 alleles with an average of 5.13 alleles per microsatellite marker. The polymorphic information content values ranged from 0.104 to 0.597 with an average of 0.371. The average observed heterozygosity across all loci varied from 0.046 to 0.058. The gene diversity among the loci ranged from 0.106 to 0.664. Unweighted Neighbor-joining and population structure analysis grouped these 163 isolates into three major groups. The clusters were not according to the geographic origin of the isolates. Analysis of molecular variance showed 85% of the total variation within populations and only 5% among populations. There was low genetic differentiation in the total populations (FST = 0.049) as evidenced by high level of gene flow estimate (Nm = 4.8 per generation) among populations. The results show that Ethiopian C. gloeosporioides populations are generally characterized by a low level of genetic diversity. The newly developed microsatellite markers were useful in analyzing the genetic diversity and population structure of the C. gloeosporioides populations. Information obtained from this study could be useful as a base to design strategies for better management of leaf and fruit spot disease of citrus in Ethiopia.

Physcomitrella patens Activates Defense Responses against the Pathogen Colletotrichum gloeosporioides

The moss Physcomitrella patens is a suitable model plant to analyze the activation of defense mechanisms after pathogen assault. In this study, we show that Colletotrichum gloeosporioides isolated from symptomatic citrus fruit infects P. patens and cause disease symptoms evidenced by browning and maceration of tissues. After C. gloeosporioides infection, P. patens reinforces the cell wall by the incorporation of phenolic compounds and induces the expression of a Dirigent-protein-like encoding gene that could lead to the formation of lignin-like polymers. C. gloeosporioides-inoculated protonemal cells show cytoplasmic collapse, browning of chloroplasts and modifications of the cell wall. Chloroplasts relocate in cells of infected tissues toward the initially infected C. gloeosporioides cells. P. patens also induces the expression of the defense genes PAL and CHS after fungal colonization. P. patens reporter lines harboring the auxin-inducible promoter from soybean (GmGH3) fused to β-glucuronidase revealed an auxin response in protonemal tissues, cauloids and leaves of C. gloeosporioides-infected moss tissues, indicating the activation of auxin signaling. Thus, P. patens is an interesting plant to gain insight into defense mechanisms that have evolved in primitive land plants to cope with microbial pathogens.

The Pathogen-Host Interactions database (PHI-base): additions and future developments

Rapidly evolving pathogens cause a diverse array of diseases and epidemics that threaten crop yield, food security as well as human, animal and ecosystem health. To combat infection greater comparative knowledge is required on the pathogenic process in multiple species. The Pathogen-Host Interactions database (PHI-base) catalogues experimentally verified pathogenicity, virulence and effector genes from bacterial, fungal and protist pathogens. Mutant phenotypes are associated with gene information. The included pathogens infect a wide range of hosts including humans, animals, plants, insects, fish and other fungi. The current version, PHI-base 3.6, available at http://www.phi-base.org, stores information on 2875 genes, 4102 interactions, 110 host species, 160 pathogenic species (103 plant, 3 fungal and 54 animal infecting species) and 181 diseases drawn from 1243 references. Phenotypic and gene function information has been obtained by manual curation of the peer-reviewed literature. A controlled vocabulary consisting of nine high-level phenotype terms permits comparisons and data analysis across the taxonomic space. PHI-base phenotypes were mapped via their associated gene information to reference genomes available in Ensembl Genomes. Virulence genes and hotspots can be visualized directly in genome browsers. Future plans for PHI-base include development of tools facilitating community-led curation and inclusion of the corresponding host target(s).

Cloning of insertion site flanking sequence and construction of transfer DNA insert mutant library in Stylosanthes colletotrichum

Stylosanthes sp. is the most important forage legume in tropical areas worldwide. Stylosanthes anthracnose, which is mainly caused by Colletotrichum gloeosporioides, is a globally severe disease in stylo production. Little progress has been made in anthracnose molecular pathogenesis research. In this study, Agrobacterium tumefaciens-mediated transformation was used to transform Stylosanthes colletotrichum strain CH008. The major factors of the genetic transformation system of S. colletotrichum were optimized as follows: A. tumefaciens' AGL-1 concentration (OD(600)), 0.8; concentration of Colletotrichum conidium, 1 × 10(6) conidia/mL; acetosyringone concentration, 100 mmol/L; induction time, 6 h; co-culture temperature, 25 °C; and co-culture time, 3 d. Thus, the transformation efficiency was increased to 300-400 transformants per 106 conidia. Based on the optimized system, a mutant library containing 4616 mutants was constructed, from which some mutants were randomly selected for analysis. Results show that the mutants were single copies that could be stably inherited. The growth rate, spore amount, spore germination rate, and appressorium formation rate in some mutants were significantly different from those in the wild-type strain. We then selected the most appropriate method for the preliminary screening and re-screening of each mutant's pathogenic defects. We selected 1230 transformants, and obtained 23 strains with pathogenic defects, namely, 18 strains with reduced pathogenicity and five strains with lost pathogenicity. Thermal asymmetric interlaced PCR was used to identify the transfer DNA (T-DNA) integration site in the mutant that was coded 2430, and a sequence of 476 bp was obtained. The flanking sequence of T-DNA was compared with the Colletotrichum genome by BLAST, and a sequence of 401 bp was found in Contig464 of the Colletotrichum genome. By predicting the function of the flanking sequence, we discovered that T-DNA insertion in the promoter region of the putative gene had 79% homology with the aspartate aminotransferase gene in Magnaporthe oryzae (XP_003719674.1).