Of mushrooms and chocolate trees: aetiology and phylogeny of witches' broom and frosty pod diseases of cacao

The troubled history of the two major diseases of the chocolate tree (Theobroma cacao) in South America, witches' broom and frosty pod, is reviewed, concentrating on critical aspects of the aetiology as well as the phylogeny of the causal agents. Both diseases are caused by sister species within the genus Moniliophthora, belonging to the Marasmiaceae family of mushrooms. The witches' broom pathogen, Moniliophthora perniciosa, evolved on the Amazonian side of the Andes and induces brooms not only in cacao and its relatives in the genera Theobroma and Herrania (Malvaceae), but also in species in the plant families Bignoniaceae, Malpighiaceae and Solanaceae, on which the mushrooms (basidiomata) are produced. Moniliophthora roreri, the type species of the genus, evolved as a pod pathogen on endemic Theobroma species on the western side of the northern Andean Cordillera. Because Moniliophthora was described originally as the asexual form of an unknown basidiomycete, the generic diagnosis is amended here to accommodate species with agaricoid basidiomata. In addition, the new variety M. roreri var. gileri is designated for the morphotype occurring on Theobroma gileri, in northwest Ecuador. Cytology studies indicate that the supposed conidia of M. roreri are, in fact, sexual spores (meiospores) and it is posited that the fruiting structure represents a much‐modified mushroom. Finally, based on preliminary data from pathogenicity testing, it is hypothesized that the true causal agent of both diseases is an as yet unidentified infectious agent vectored into the host by the fungus.     

Analysis of resistance to witches’ broom disease (Moniliophthora perniciosa) in flower cushions of Theobroma cacao in a segregating population

This study evaluates resistance to witches’ broom disease in flower cushions of Theobroma cacao under field conditions. The aim was to determine optimal inoculation methods to evaluate the disease incidence using flower cushions in the field. A segregating mapping population of 580 trees (cultivar TSH 1188 × CCN 51) was analysed under two field conditions: high and low inoculum levels (in different years), corresponding respectively to trees with or without dried witches’ brooms hanging on the trees and producing basidiocarps. The number of newly formed cushion brooms in each tree was counted by the conventional method, and also the healthy and infected flower cushions in three 30 cm‐long regions along the trunk and the two main branches. The field inoculation methods discriminated between genotypes, with a 26% increase in disease incidence by Moniliophthora perniciosa at high inoculum. Two different segregation patterns were also observed: 27:27:9:1 under low, and 27:9:9:9:3:3:3:1 under high inoculum potential. It was also determined that at least 20 flower cushions were needed to accurately determine the percentage of infection. These methodologies allowed identification of the extreme phenotypes in this mapping population, and can therefore facilitate the detection of sources of resistance to witches’ broom disease.     

Induced resistance to foliar diseases by soil solarization and Trichoderma harzianum

The effect of soil solarization and Trichoderma harzianum on induced resistance to grey mould (Botrytis cinerea) and powdery mildew (Podosphaera xanthii) was studied. Plants were grown in soils pretreated by solarization, T. harzianum T39 amendment or both, and then their leaves were inoculated with the pathogens. There was a significant reduction in grey mould in cucumber, strawberry, bean and tomato, and of powdery mildew in cucumber, with a stronger reduction when treatments were combined. Bacillus, pseudomonad and actinobacterial communities in the strawberry rhizosphere were affected by the treatments, as revealed by denaturing gradient gel electrophoresis fingerprinting. In tomato, treatments affected the expression of salicylic acid (SA)‐, ethylene (ET)‐ and jasmonic acid (JA)‐responsive genes. With both soil treatments, genes related to SA and ET – PR1a, GluB, CHI9 and Erf1 – were downregulated whereas the JA marker PI2 was upregulated. Following soil treatments and B. cinerea infection, SA‐, ET‐, and JA‐related genes were globally upregulated, except for the LOX genes which were downregulated. Upregulation of the PR genes PR1a, GluB and CHI9 in plants grown in solarized soil revealed a priming effect of this treatment on these genes' expression. The present study demonstrates the capacity of solarization and T. harzianum to systemically induce resistance to foliar diseases in various plants. This may be due to either a direct effect on the plant or an indirect one, via stimulation of beneficial microorganisms in the rhizosphere.     

Phytophthora pachypleura sp. nov., a new species causing root rot of Aucuba japonica and other ornamentals in the United Kingdom

Isolates of an unknown Phytophthora species from the ‘Phytophthora citricola complex’ have been found associated with mortality of Aucuba japonica in the UK. Based on morphological characteristics, growth–temperature relationships, sequences of five DNA regions and pathogenicity assays, the proposed novel species is described as Phytophthora pachypleura. Being homothallic with paragynous antheridia and semipapillate sporangia, P. pachypleura resembles other species in the ‘P. citricola complex’ but can be discriminated by its distinctively thick‐walled oospores with an oospore wall index of 0·71. In the phylogenetic analysis based on three nuclear (ITS, β‐tubulin, EF‐1α) and two mitochondrial (cox1, nadh1) DNA regions, P. pachypleura formed a distinct clade within the ‘P. citricola complex’ with P. citricola s. str., P. citricola E and P. acerina as its closest relatives. Phytophthora pachypleura is more aggressive to A. japonica than P. plurivora and P. multivora and has the potential to affect other ornamental species.     

PCR‐based identification of cacao black pod causal agents and identification of biological factors possibly contributing to Phytophthora megakarya's field dominance in West Africa

Among the Phytophthora species that cause black pod of cacao, P. megakarya is the most virulent, posing a serious threat to cacao production in Africa. Correct identification of the species causing the black pod and understanding the virulence factors involved are important for developing sustainable disease management strategies. A simple PCR‐based species identification method was developed using the species‐specific sequences in the ITS regions of the rRNA gene. A phylogenetic tree generated for 119 Phytophthora isolates, based on the 60S ribosomal protein L10 gene and rDNA sequence, verified the PCR‐based identification assay and showed high interspecific variation among the species causing black pod. Phytophthora megakarya isolates were uniformly virulent in an assay using susceptible cacao pod husks inoculated with zoospores, while the P. palmivora isolates showed greater divergence in virulence. The virulence of P. megakarya was associated with earlier production of sporangia and an accelerated induction of necrosis. While zoospore germ tubes of both species penetrated pods through stomata, only P. megakarya produced significant numbers of appressoria. A hypersensitive‐like response was observed when attached SCA‐6 pods were inoculated with P. palmivora. SCA‐6 pods became vulnerable to P. palmivora when wounded prior to zoospore inoculation. Phytophthora megakarya was more aggressive than P. palmivora on attached SCA‐6 pods, causing expanding necrotic lesions with or without wounding. Phytophthora megakarya is predominant in the Volta region of Ghana and it remains to be seen whether it can displace P. palmivora from cacao plantations of Ghana as it has in Nigeria and Cameroon.     

The influence of flavonoids in maize pericarp on fusarium ear rot symptoms and fumonisin accumulation under field conditions

Breeding efforts have been undertaken to increase resistance of maize to fusarium ear rot (FER) and to fumonisin accumulation. Flavonoids in the pericarp of the kernels are considered particularly able to reduce the fumonisin accumulation. The aim of this 2‐year field study was to assess the effect of flavonoids on FER symptoms and fumonisin contamination in maize kernels using two isogenic hybrids, one providing pigmentation in the pericarp (P1‐rr) and the other without it (P1‐wr). FER incidence (FERi), FER severity (FERs), the incidence of infections caused by Fusarium spp. in symptomless kernels (FF) and fumonisin contamination (FUM) were assessed in both hybrids. Significant differences between the two hybrids were detected mainly in 2012 trials where P1‐rr showed lower FERi (P < 0·01), FF (P < 0·05) and FUM (P < 0·1) than P1‐wr. Site, characterized by local temperature and precipitation, played a relevant role in modelling all the measured variables, as its effect was highly significant in both years, whether they were considered individually or altogether. The interaction of hybrid with location was a significant (P < 0·001) source of variation only for FF. FF, together with FERi, was also significantly (P < 0·001) influenced by the interaction of hybrid with year. In general, FUM was more influenced by year and location parameters, such as temperatures during late ripening, than by flavonoid presence in kernel pericarp. The results indicate that flavonoid pigments alone may not be an important component in the resistance of maize to fumonisin accumulation.     

Pathogenicity of Fusarium graminearum and F. meridionale on soybean pod blight and trichothecene accumulation

Soybean (Glycine max) is the most important crop in Argentina. At present Fusarium graminearum is recognized as a primary pathogen of soybean in several countries in the Americas, mainly causing seed and root rot and pre‐ and post‐emergence damping off. However, no information about infections at later growth stages of soybean development and pathogenicity of F. graminearum species complex is available. Therefore, the objectives of this study were to compare the pathogenicity of F. graminearum and F. meridionale isolates towards soybean under field conditions and to evaluate the degree of pathogenicity and trichothecene production of these two phylogenetic species that express different chemotypes. Six isolates of F. graminearum and F. meridionale were evaluated during 2012/13 and 2013/14 soybean growing seasons for pod blight severity, percentage of seed infected in pods and kernel weight reduction. The results showed a higher aggressiveness of both F. graminearum and F. meridionale species during the 2013/14 season. However, the differences in pathogenicity observed between the seasons were not reflected in a distinct trichothecene concentration in soybean seeds at maturity. Fusarium meridionale isolates showed similar pathogenicity to F. graminearum isolates but they were not able to produce this toxin in planta during the two field trials.     

Spatial genetic structure and dispersal of the cacao pathogen Moniliophthora perniciosa in the Brazilian Amazon

Moniliophthora perniciosa is the causal agent of witches’ broom in Theobroma cacao (cacao). Three biotypes of M. perniciosa are recognized, differing in host specificity, with two causing symptoms on cacao or Solanaceae species (C‐ and S‐biotypes), and the third found growing endophytically on lianas (L‐biotype). The objectives of this study were to clarify the genetic relationship between the three biotypes, and to identify those regions in the Brazilian Amazon with the greatest genetic diversity for the C‐biotype. Phylogenetic reconstruction based on the rRNA ITS regions showed that the C‐ and S‐biotypes formed a well‐supported clade separated from the L‐biotype. Analysis of 131 isolates genotyped at 11 microsatellite loci found that S‐ and especially L‐biotypes showed a higher genetic diversity. A significant spatial genetic structure was detected for the C‐biotype populations in Amazonia for up to 137 km, suggesting ‘isolation by distance’ mode of dispersal. However, in regions containing extensive cacao plantings, C‐biotype populations were essentially ‘clonal’, as evidenced by high frequency of repeated multilocus genotypes. Among the Amazonian C‐biotype populations, Acre and West Amazon displayed the largest genotypic diversity and might be part of the centre of diversity of the fungus. The pathogen dispersal may have followed the direction of river flow downstream from Acre, Rondônia and West Amazon eastward to the rest of the Amazon valley, where cacao is not endemic. The Bahia population exhibited the lowest genotypic diversity, but high allele richness, suggesting multiple invasions, with origin assigned to Rondônia and West Amazon, possibly through isolates from the Lower Amazon population.     

Epidemiological analysis of the effects of biofumigation for biological control of root rot in sugar beet

The effects of biofumigation using a Brassica juncea (mustard) cover crop on the dynamics of rhizoctonia root rot of sugar beet were recorded in two field trials in 2007 and 2008, and analysed using epidemiological modelling. Differences between partial biofumigation, involving the pulling up of mustard plants, and complete biofumigation, involving the crushing and incorporation of mustard residues into the soil, were compared with bare soil treatment. An epidemiological model was used that includes rates of transmission of primary and secondary infection, pre‐emergence damping off, and expression of wilting symptoms (above‐ground disease) due to infected roots (below‐ground disease). The model indicated that biofumigation reduces the transmission of primary infections but affects secondary infections in a variable pattern between field trials. Likewise, the proportion of infected plants expressing wilting was significantly reduced, by 28%, in the partial and complete biofumigation treatments compared with bare soil in the trial of 2007 but not in 2008. It is suggested that the effects of biofumigation on secondary infection and the expression of disease are more variable than those on primary infection, and that this is probably due to an interplay between pathogen, antagonists, host, and environmental factors. These interactions may or may not offset the benefits afforded by a reduction in primary infection and account for the overall variable success of biofumigation to control disease.     

Frequency of brown rot fungi on blossoms and fruit in stone fruit orchards in Greece

Brown rot is a devastating disease of stone fruits caused by Monilinia spp. This study was conducted to investigate the disease aetiology on blossoms and fruit in peach, apricot, sweet cherry and plum orchards, in Greece. In total, 1433 isolates obtained from orchards located in the main stone fruit production regions of Greece were identified to species based on the presence/size of a cyt b intron. Monilinia laxa and M. fructicola were detected at frequencies of 59 and 41%, respectively, while M. fructigena was absent. Monilinia fructicola was more common on fruit whereas M. laxa occurred in similar frequency on blossoms and fruit. Monilinia laxa was replaced by M. fructicola in fruit infections of peach in both regions investigated and in fruit infections of plum in the Imathia region. Assessments of aggressiveness of 30 isolates of both species on the petals and fruits of the hosts showed that M. fructicola isolates were more aggressive. This suggests that the predominance of M. laxa on the blossoms cannot be explained by higher aggressiveness. Measurements of the effect of temperature on mycelial growth showed that M. laxa isolates had a higher growth rate than M. fructicola at the lowest temperature tested of 5°C, whereas M. fructicola isolates showed higher growth rates at higher temperatures. The observed high frequency of M. fructicola in Greece represents a major threat for stone fruit production. Furthermore, the information obtained about delineation of species and plant organ preference could be useful for the implementation of disease management strategies.     

Effect of environmental factors and Sclerotium cepivorum isolate on sclerotial degradation and biological control of white rot by Trichoderma

Laboratory assays demonstrated that two isolates of Trichoderma viride and one isolate of Trichoderma pseudokoningii degraded up to 80% of sclerotia of four isolates of Sclerotium cepivorum in a silty clay soil, and also degraded up to 60% of sclerotia in three other soil types. Relationships were defined between the degree of sclerotial degradation by the two T. viride isolates in the silty clay soil and both temperature and soil water potential. Sclerotia were degraded between 10 and 25°C at −0·00012 MPa, but there was little activity of T. viride at 5°C or at −4 MPa. Degradation of S. cepivorum sclerotia also occurred in the absence of Trichoderma at soil water potentials approaching saturation . Experiments using onion seedling bioassays showed that the efficacy of Trichoderma isolates for the control of white rot using the same selection of soils and S. cepivorum isolates was variable, but that there was significant disease control overall. The importance of environmental factors and pathogen isolate in relation to effective biological control of white rot is discussed.     

The control of sclerotinia stem rot on oilseed rape (Brassica napus): current practices and future opportunities

Sclerotinia stem rot (SSR) caused by the phytopathogenic fungus Sclerotinia sclerotiorum is a major disease of oilseed rape (Brassica napus). During infection, large, white/grey lesions form on the stems of the host plant, perturbing seed development and decreasing yield. Due to its ability to produce long‐term storage structures called sclerotia, S. sclerotiorum inoculum can persist for long periods in the soil. Current SSR control relies heavily on cultural practices and fungicide treatments. Cultural control practices aim to reduce the number of sclerotia in the soil or create conditions that are unfavourable for disease development. These methods of control are under increased pressure in some regions, as rotations tighten and inoculum levels increase. Despite their ability to efficiently kill S. sclerotiorum, preventative fungicides remain an expensive gamble for SSR control, as their effectiveness is highly dependent on the ability to predict the establishment of microscopic infections in the crop. Failure to correctly time fungicide applications can result in a substantial cost to the grower. This review describes the scientific literature pertaining to current SSR control practices. Furthermore, it details recent advances in alternative SSR control methods including the generation of resistant varieties through genetic modification and traditional breeding, and biocontrol. The review concludes with a future directive for SSR control on oilseed rape.     

Diversity and pathogenicity of Fusarium graminearum species complex from maize stalk and ear rot strains in northeast China

The Fusarium graminearum species complex (FGSC) is an important group of pathogens distributed in maize‐producing areas worldwide. This study investigated the genetic diversity and pathogenicity of 40 FGSC isolates obtained from stalk rot and ear rot samples collected from 42 locations in northeastern China during 2013 and 2014. A phylogenetic tree of translation elongation factor (EF‐la) sequences designated the 40 isolates as F. graminearum sensu stricto (67.5%) and F. boothii (32.5%). By using inter‐simple sequence repeat analysis (ISSR), it was shown that the isolates were divided into two clades, which corresponded to the species identity of the isolates. However, the isolates from the two different diseases could not be distinguished in pathogenicity. The disease severity index of seedlings inoculated with stalk isolates was slightly higher than that of seedlings inoculated with isolates from infected ears, whereas the pathogenicity of the stalk and ear isolates were identical.     

Fusarium species and chemotypes associated with fusarium head blight and fusarium root rot on wheat in Sardinia

Environmental conditions in Sardinia (Tyrrhenian Islands) are conducive to fusarium root rot (FRR) and fusarium head blight (FHB). A monitoring survey on wheat was carried out from 2001 to 2013, investigating relations among these diseases and their causal agents. FHB was more frequently encountered in the most recent years while FRR was constantly present throughout the monitored period. By assessing the population composition of the causal agents as well as their genetic chemotypes and EF‐1α polymorphisms, the study examined whether the two diseases could be differentially associated to a species or a population. Fusarium culmorum chemotypes caused both diseases and were detected at different abundances (88% 3‐ADON, 12% NIV). Fusarium graminearum (15‐ADON genetic chemotype) appeared only recently (2013) and in few areas as the causal agent of FHB. In F. culmorum, two haplotypes were identified based on an SNP mutation located 34 bp after the first exon of the EF‐1α partial sequence (60% adenine, 40% thymine); the two populations did not segregate with the chemotype but the A‐haplotype was significantly associated with FRR in the Sardinian data set (P = 0·001), suggesting a possible fitness advantage of the A‐haplotype in the establishment of FRR that was neither dependent on the sampling location nor the sampling year. The SNP determining the Sardinian haplotype is distributed worldwide. The question whether the A‐haplotype segregates with characters facilitating FRR establishment will require further validation on a specifically sampled international data set.     

Fusarium species associated with stalk rot and head blight of grain sorghum in Queensland and New South Wales,Australia

Historical records report Fusarium moniliforme sensu lato as the pathogen responsible for Fusarium diseases of sorghum; however, recent phylogenetic analysis has separated this complex into more than 25 species. During this study, surveys were undertaken in three major sorghum‐producing regions in eastern Australia to assess the diversity and frequency of Fusarium species associated with stalk rot‐ and head blight‐infected plants. A total of 523 isolates were collected from northern New South Wales, southern Queensland and central Queensland. Nine Fusarium species were isolated from diseased plants. Pathogenicity tests confirmed F. andiyazi and F. thapsinum were the dominant stalk rot pathogens, whilst F. thapsinum and species within the F. incarnatum–F. equiseti species complex were most frequently associated with head blight.     

Severity of phytophthora root rot and pre‐emergence damping‐off in subterranean clover influenced by moisture,temperature, nutrition,soil type,cultivar and their interactions

Studies were carried out in controlled environment rooms reflecting field situations. In the presence of the devastating soilborne pathogen Phytophthora clandestina, subterranean clover (Trifolium subterraneum) seedling emergence was significantly affected by moisture, soil type, temperature and cultivar. The level of rotting of tap and lateral roots was significantly affected by nutrition, soil type, temperature and cultivar. There were significant interactions involving temperature, moisture, soil type and cultivar; cultivar resistance, high moisture, high or medium temperature, high nutrition and sand soil all contributed towards less pre‐emergence damping‐off and tap and lateral root disease and to greater clover productivity. Host resistance of subterranean clover cultivars was critical for reducing disease severity and increasing productivity, even when favourable environmental conditions for severe disease occurred. In the presence of P. clandestina, the most resistant cultivar, Seaton Park, performed best under a high temperature, high nutrition and high moisture combination, but showed lower productivity under conditions of low nutrition or lower temperature, even when moisture level was high. In contrast, less resistant cultivars Riverina and Meteora had less disease and greater productivity under low moisture conditions. Findings reflect field observations that pre‐emergence damping‐off and root disease from P. clandestina in subterranean clover is particularly severe under colder conditions and in nutritionally impoverished sandy soils, and demonstrate how variations in soil type, nutrition, moisture, temperature and cultivar have profound effects on the expression and severity of phytophthora pre‐emergence damping‐off and root disease and the productivity of subterranean clover forages.     

The impact of management on weeds and aquatic plant communities in Hungarian rice crops

This study assessed the cultural and weed management factors influencing the weed communities of Hungarian rice fields. Hungary is situated at the northern limit of rice production with a history of about 300 years of rice culture. We surveyed the weed flora and 25 background variables in 100 active rice fields. Using a minimal adequate model containing 11 terms, 48.5% of the total variation in weed species data could be explained. The net effects of nine variables on species composition were significant. Crop cover was found to be the most important explanatory variable, which was followed by the herbicides penoxsulam and azimsulfuron, tillage depth, phosphorous and potassium fertilisers, years after last rotation, water depth in May, sowing type, pendimethalin and water conductivity. Filamentous algae, as the most abundant group of weeds, were positively associated with deep tillage, deep water and surface sowing. Echinochloa crus‐galli, one of the most troublesome grass weeds, was associated with low rice cover, shallow water and later years after crop rotation, while weedy rice favoured high crop cover, deep water and soil sowing. These findings can be used to design improved weed management strategies. The occurrence of red list species and charophytes in diverse micro‐mosaic patterns deserves attention from a conservation perspective, as well. The maintenance of these unique charophyte communities can be facilitated by shallow tillage without soil inversion.     

Diversity and pathogenicity of the Ceratocystidaceae associated with cacao agroforests in Cameroon

Knowledge of the diversity and ecology of plant pathogenic fungi in cacao agroforests and surrounding natural ecosystems can inform the development of sustainable management strategies for new cacao disease outbreaks. This study investigated the occurrence of fungi related to the Ceratocystidaceae and their nitidulid beetle vectors in cacao agroforests in Cameroon, under diverse agroecological conditions. The fungi and their vectors were collected from artificially induced stem wounds on cacao and associated shade trees. Collections were also made from abandoned cacao pod husks and other tree wounds within and around plantations. Fungal isolates were identified using DNA sequence‐based phylogenies and morphological comparisons, and two representatives of each species were evaluated for pathogenicity on cacao. Five species of Ceratocystidaceae were recovered, including Huntiella chlamydoformis sp. nov., H. pycnanthi sp. nov. and H. moniliformis, as well as Thielaviopsis cerberus and T. ethacetica. The incidence of these fungi appeared to be influenced by the prevailing agroecological conditions. Nitidulid beetles in the genus Brachypeplus were found to be their most common insect associates on cacao. Both T. ethacetica and H. pycnanthi produced extensive lesions after inoculation on branches of mature cacao trees, while T. ethacetica also caused pod rot. Although their impact remains unknown, fungi in the Ceratocystidaceae and their nitidulid beetle vectors are common and probably contribute to the parasitic pressure in Cameroonian cacao agrosystems.     

Testing and modelling the effects of climate on the incidence of the emergent nut rot agent of chestnut Gnomoniopsis castanea

Gnomoniopsis castanea is an emerging fungal pathogen causing nut rot of sweet chestnut, Castanea sativa. This study was aimed at testing and modelling the effects of climate on disease incidence. Up to 120 ripe nuts were collected in 2011 from trees in each of 12 sites located in the northwest of Italy. The incidence of G. castanea in each site was expressed as the number of infected nuts out of the total number of nuts sampled (%), determined by combining the results of morphological identification of isolates obtained from nuts, and their typing through a newly developed taxon‐specific molecular assay. Disease incidence ranged from 20 to 93%, depending on site. Geostatistical analyses revealed that, despite the clustering of sites (P < 0·05), disease incidence was not spatially autocorrelated (P > 0·05). This finding suggests that the disease is influenced by site‐dependent factors whose scale (c. 7·5–15·6 km) is consistent with the climate variability throughout the sampling region. Multivariate analyses on maximum, mean and minimum temperatures and on rainfall showed that warmer temperatures were associated with higher levels of disease incidence. The temperatures of months before nut harvesting were selected as predictors for partial least squares regression (PLSR) models (GnoMods) of G. castanea incidence. External validation on data collected either on sites or in years not used for model fitting showed the good predictive abilities of the GnoMods (Spearman's ρ_obs/pred > 0·72, P < 0·05). The above findings support a relationship between climate and incidence of G. castanea, providing statistical tools to forecast disease incidence at site level.     

Molecular and biological characterization of Cowpea mild mottle virus isolates infecting soybean in Brazil and evidence of recombination

The biological and molecular characterization of six isolates of a new Cowpea mild mottle virus strain (CPMMV; Carlavirus, Betaflexiviridae) are reported. Soybean plants with mosaic and stem necrosis were collected in Bahia, Goiás, Mato Grosso and Minas Gerais states, Brazil. Complete genomes of the CPMMV isolates are 8180–8198 nucleotides (nt) long, excluding the 3′‐polyadenylated tail, and have 67–68% nt sequence identity with a Ghana isolate of CPMMV, the only CPMMV isolate for which the genome has previously been sequenced. The replicase has only 60–61% nt sequence identity with the Ghana CPMMV isolate, and the coat protein (CP) is highly conserved (79% nt sequence identity and 95–96% amino acid sequence identity). The high CP identity and the phylogenetic analyses supported the classification of the Brazilian isolates as CPMMV. Biological and molecular differences with the Ghana CPMMV isolate were found and indicated that the six isolates represent a distinct CPMMV strain denominated as CPMMV‐BR. Furthermore, it is shown that recombination occurred mainly in the polymerase gene, and may occur less frequently in other regions of the CPMMV genome.