Pathogenicity, Internal Transcribed Spacer-rDNA Variation, and Human Dispersal of Ceratocystis fimbriata on the Family Araceae

An expanded concept of Ceratocystis manginecans and five new species in the Latin American clade of Ceratocystis

The genus Ceratocystis contains a number of emerging plant pathogens, mostly members of the Latin American Clade (LAC), in which there are several unresolved taxonomic controversies. Among the most important are Brazilian pathogens in the C. fimbriata complex, C. manginecans and C. eucalypticola. Representatives of C. manginecans and C. eucalypticola from India and China, respectively, were shown to be fully interfertile in laboratory matings, and hybrids between the putative species were identified on Punica in India. An Indian tester strain was sexually compatible with representatives of what has been considered C. fimbriata on numerous hosts across Brazil. In this revision of the LAC, the name C. fimbriata is restricted to the widely dispersed Ipomoea strain, and C. manginecans is recognized as a Brazilian species that is important on Mangifera, Eucalyptus, and many other crops. C. mangivora and C. mangicola are also considered synonyms of C. manginecans. Based on phylogenetics and mating studies, two other Brazilian species are recognized: C. atlantica, sp. nov., and C. alfenasii, sp. nov., each with wide host ranges. Three new Caribbean species are recognized based on phylogenetics and earlier inoculation studies: C. costaricensis, sp. nov., on Coffea, C. cubensis, sp. nov., on Spathodea, and C. xanthosomatis, sp. nov., on the vegetatively propagated aroids Xanthosoma and Syngonium. Some of the other Ceratocystis species were based primarily on unique internal transcribed spacer (ITS) rDNA sequences, but the unreliability of rDNA sequences was demonstrated when intraspecific crossing of isolates with differing ITS sequences generated single-ascospore progeny with intragenomic variation in ITS sequences and others with new ITS sequences. Species recognition in Ceratocystis should use phenotype, including intersterility tests, to help identify which lineages are species. Although some species remain under-studied, we recognize 16 species in the LAC, all believed to be native to Latin America, the Caribbean region, or eastern USA.

Thermal Tolerance Data and Molecular Identification Are Useful for the Diagnosis, Control and Modeling of Diseases Caused by Thielaviopsis paradoxa

Several economically important diseases of forest trees and agricultural crops in many parts of the world have been linked to the ascomycete fungal pathogen Thielaviopsis paradoxa. This study compared the growth rate of 41 isolates of T. paradoxa sourced from different hosts and two countries (Nigeria and Papua New Guinea (PNG)) under six temperature levels (22 °C, 25 °C, 30 °C, 32 °C, 34 °C and 35 °C). Phylogenetic relationships were obtained from the analysis of their nuclear ribosomal DNA internal transcribed sequence (ITS) data. While all the isolates from PNG and few from Nigeria grew optimally between 22 °C and 32 °C, the majority had their highest growth rate (2.9 cm/day) between 25 °C and 32 °C. Growth performances were generally low between 34 °C and 35 °C; no isolate from the sugar cane grew at these high temperatures. The oil palm isolate DA029 was the most resilient, with the highest growth rate (0.97 cm/day) at 35 °C. Phylogenetic analysis delineated five clusters: a very large clade which accommodates the majority (30 Nigerian and 3 PNG oil palm isolates) and four small clades containing two members each. To a large extent, the clustering pattern failed to address the temperature-isolate relationship observed. However, only the four small clades represent isolates with similar temperature tolerances. It is most likely that wider and robust analyses with more diverse isolates and genetic markers will provide better insight on thermal resilience of T. paradoxa. Additionally, future research to establish relationships between vegetative growth at different temperatures and of different pathogenicity and disease epidemiology merits being explored. The results might provide useful information for the formulation of effective management and control strategies against the pathogen, especially in this era of climate change.

Uncovering a Complex Virome Associated with the Cacao Pathogens Ceratocystis cacaofunesta and Ceratocystis fimbriata

Theobroma cacao is one of the main crops of economic importance in the world as the source of raw material for producing chocolate and derivatives. The crop is the main source of income for thousands of small farmers, who produce more than 80% of the world's cocoa supply. However, the emergence, re-emergence and proliferation of pathogens, such as Ceratocystis spp., the causative agent of Ceratocystis wilt disease and canker disease, have been affecting the sustainability of many crops. Fungal control is laborious, often depending on fungicides that are expensive and/or toxic to humans, prompting researchers to look for new solutions to counteract the proliferation of these pathogens, including the use of biological agents such as mycoviruses. In this study, we investigated the diversity of microorganisms associated with the T. cacao pathogens Ceratocystis cacaofunesta and Ceratocystis fimbriata with a focus on the virome using RNA sequencing data available in public databases. We used a comprehensive bioinformatics pipeline containing several steps for viral sequence enrichment and took advantage of an integrated assembly step composed of different assemblers followed by sequence similarity searches using NCBI nonredundant databases. Our strategy was able to identify four putative C. cacaofunesta viruses (hypovirus, sclerotimonavirus, alphapartitivirus and narnavirus) and six C. fimbriata viruses (three alphaendornaviruses, one victorivirus and two mitoviruses). All the viral sequences identified showed similarity to viral genomes in public databases only at the amino acid level, likely representing new viral species. Of note, we present the first report of viruses associated with the cacao pathogens C. cacaofunesta and C. fimbriata and the second report of viral species infecting members of the Ceratocystidaceae family. Our findings highlight the need for further prospective studies to uncover the real diversity of fungus-infecting viruses that can contribute to the development of new management strategies.

First Report of a New Postharvest Disease of Pear Fruit Caused by Ceratocystis fimbriata in Kunming, China

Pear (Pyrus pyrifolia (Burm.f.) Nakai) is widely planted in China and plays a key role in economy. In the autumn of 2016, five pear fruits showing symptoms of brown rot (Fig. 1A) were found in a Suancun farmer market in Kunming, Yunnan Province, China (25°02' N; 102°42' E). The incidence of this disease in postharvest pear fruits ranged from 2 % to 5 % in this city. Three fruit samples were taken to run further tests. The decayed area of the fruit was soft, brown, slightly sunken, and circular. Carrot baiting was used to isolate the pathogen from symptomatic tissue (Moller et al. 1968). Primary isolates were made by transferring ascospore drops from the tips of the perithecia formed on the carrot discs onto PDA plates. Single ascospore cultures were generated by transferring single ascospores to potatoe dextrose agar (PDA) plates. Cultures were incubated 7 days at 25°C with a 12-h light/12-h dark cycle. In culture, mycelium was initially white, turned to a shallow celadon and gradually to grey-greenish later. Measurements were made 10 days after the formation of perithecia. Six pure cultures (lik-1~lik-6) were stored at -80 °C in 15% glycerol and stored at the State Key Laboratory for Conservation and Utilization of Bio-Resources of Yunnan Agricultural University. Four isolates (lik-1~lik-4) produced ascomatal bases that were submerged in the agar. Bases (Fig. 1E) were globose, black, 192.15 to 250.81 µm wide, 192.94 to 251.31 µm long, and had straight necks terminating in ostiolar hyphae (Fig. 1F) that were divergent, hyaline, and 74.19 to 116.33 µm long. Asci were not observed. Ascospores (Fig. 1I) were ovoid, hat-shaped (dimensions 3.2 to 5.1 × 2.3 to 4.6 µm). Conidiogenous cells were with enteroblastic conidium ontogeny, flask-shaped or tubular, 65.3 to 130.6 μm long, and produced cylindrical, straight aseptate conidia (8.5 to 18 × 2.5 to 3.5 µm) (Fig.1 G). All isolates produced dark brown, 10.07 to 13.08 ×8.51 to 11.64 µm aleurioconidia (Fig. 1H). Two (lik-1, lik-3) of six isolates were used for molecular identification and genomic DNA was extracted using the CTAB method (Lee & Taylor 1990). The primers ITS1 and ITS4, EF1F and EF2R were used to amplify and sequence the rDNA-ITS and TEF-1α regions (Thorpe et al. 2005; Jacobs et al. 2004). The sequences of rDNA-ITS of the isolates lik-1 and lik-3 (GenBank Accession Nos: MF153994, MF153993) showed 99.49% similarity to AF395679 (C. fimbriata isolate CMW2219). Additionally, the TEF-1α sequences of isolates lik-1 and lik-3 (GenBank Accession Nos: KY708912, KY708915) showed 100% identify to MF347676 (C. fimbriata isolate CM18). Based on symptoms, morphological characteristics, rDNA-ITS and TEF1-α sequence analysis and pathogenicity, this fungus was identified as C. fimbriata. Pathogenicity tests were conducted using 2 isolates (lik-1, lik-3) and repeated three times. Three fresh pear fruits were disinfected with 75% alcohol, then they were wounded with a 2 mm hole punch and inoculated with 200 μL conidia suspension of the fungus (approximately 2.0 × 106 conidia / mL) on the fruit surface. After inoculation pear fruits were incubated in boxes at 25°C with a relative humidity of 80% and a 12-h light / 12-h dark cycle. Three pear fruits that served as controls were wounded by punching a 2 mm hole into the skin and inoculated with 200 μL sterile distilled water. Symptoms of rot were observed one week after inoculation (Fig.1 B). The diameter of the external lesion varied from 1.5 to 2.5 cm, on average 1.9 cm. When pears were cut, the white pulp had turned black and was rotting (Fig.1 C, D). The pathogen re-isolated from all inoculated symptomatic tissue was identical to the isolates originally obtained from the pear fruits at the market by morphology and ITS analysis. No symptoms developed on the control. The pathogenicity assay showed that C. fimbriata was pathogenic on pears. To our knowledge, this is the first report of C. fimbriata on pear in China. The spread of this disease may pose a threat to pear quality in China and further studies could be performed to determine effective disease management strategies.

Recent and Ongoing Horizontal Transfer of Mitochondrial Introns Between Two Fungal Tree Pathogens

Two recently introduced fungal plant pathogens (Ceratocystis lukuohia and Ceratocystis huliohia) are responsible for Rapid ‘ōhi‘a Death (ROD) in Hawai‘i. Despite being sexually incompatible, the two pathogens often co-occur in diseased ‘ōhi‘a sapwood, where genetic interaction is possible. We sequenced and annotated 33 mitochondrial genomes of the two pathogens and related species, and investigated 35 total Ceratocystis mitogenomes. Ten mtDNA regions [one group I intron, seven group II introns, and two autonomous homing endonuclease (HE) genes] were heterogeneously present in C. lukuohia mitogenomes, which were otherwise identical. Molecular surveys with specific primers showed that the 10 regions had uneven geographic distribution amongst populations of C. lukuohia. Conversely, identical orthologs of each region were present in every studied isolate of C. huliohia regardless of geographical origin. Close relatives of C. lukuohia lacked or, rarely, had few and dissimilar orthologs of the 10 regions, whereas most relatives of C. huliohia had identical or nearly identical orthologs. Each region included or worked in tandem with HE genes or reverse transcriptase/maturases that could facilitate interspecific horizontal transfers from intron-minus to intron-plus alleles. These results suggest that the 10 regions originated in C. huliohia and are actively moving to populations of C. lukuohia, perhaps through transient cytoplasmic contact of hyphal tips (anastomosis) in the wound surface of ‘ōhi‘a trees. Such contact would allow for the transfer of mitochondria followed by mitochondrial fusion or cytoplasmic exchange of intron intermediaries, which suggests that further genomic interaction may also exist between the two pathogens.

Precision Agriculture Digital Technologies for Sustainable Fungal Disease Management of Ornamental Plants

Ornamental plant production constitutes an important sector of the horticultural industry worldwide and fungal infections, that dramatically affect the aesthetic quality of plants, can cause serious economic and crop losses. The need to reduce the use of pesticides for controlling fungal outbreaks requires the development of new sustainable strategies for pathogen control. In particular, early and accurate large-scale detection of occurring symptoms is critical to face the ambitious challenge of an effective, energy-saving, and precise disease management. Here, the new trends in digital-based detection and available tools to treat fungal infections are presented in comparison with conventional practices. Recent advances in molecular biology tools, spectroscopic and imaging technologies and fungal risk models based on microclimate trends are examined. The revised spectroscopic and imaging technologies were tested through a case study on rose plants showing important fungal diseases (i.e., spot spectroscopy, hyperspectral, multispectral, and thermal imaging, fluorescence sensors). The final aim was the examination of conventional practices and current e-tools to gain the early detection of plant diseases, the identification of timing and spacing for their proper management, reduction in crop losses through environmentally friendly and sustainable production systems. Moreover, future perspectives for enhancing the integration of all these approaches are discussed.

Ginger wilt and rot disease caused by Ceratocystis fimbriata in China

Ginger (Zingiber officinale Rosc.) is an herb that has been grown in China for more than 2500 years. It can be used as both a spice and a therapeutic drug. In July 2013, ginger plants were found to have wilting symptoms and yellowing leaves with netrotics leaf tips in a farm in Kunming city of Yunnan province (25. 02 N; 102.42 E), southwest China, and we also found gray-black lesion on the surface of the harvest gingers in a market in Kunming. Initial symptoms on harvest gingers appeared as gray-black mycelia growth on the surface of the harvested ginger, which enlarged and extended internally. Carrot baiting was used to isolate the pathogen from rotted gingers and diseased ginger leaves (Moller and Devay. 1968). After two weeks, spores developing from perithecia on the carrot pieces were transferred to malt extract agar (MEA) and incubate at 25°C constant-temperature incubator. Six single-spore isolates (ZOR-1 to ZOR-6) were obtained, the isolates were stored in 15% glycerol at -80°C refrigerator in State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan Agricultural University. Cultures varied in color from white to brownish green to brown. N = 50 for all measurements. Blackish brown, globose perithecia (131.9 to 186.0 μm × 138.5 to 188.3 μm) with a long black neck (400.2 to 644.7 μm) were immersed, partially embedded or superficial on the substrate. Ascospores were globose or had a "hat-like" morphology typical of Ceratocystis fimbriata, and were 4.0 to 5.3 μm × 4.8 to 6.2 μm. Endoconidia were cylindrical and clavate (2.9 to 7.4 μm × 7.5 to 32.8 μm), conidia were barrel-shaped (4.4 to 10.4 μm× 6.2 to 12.9 μm), and chlamydospores were smooth, blackish brown, ovoid or obpyriform (8.42 to 12.21 μm × 10.47 to 17.65 μm) (Webster and Butler. 1967; Engelbrecht and Harrington. 2005). Genomic DNA was extracted from two isolates (ZOR-1, ZOR-2) using the CTAB method (Lee and Taylor 1990). The internal transcribed spacers (ITS) region of rDNA was amplified using primers ITS1F/ITS4 (Thorpe et al. 2005). The nucleotide sequences of ZOR-1 and ZOR-2 (GenBank accessions KJ511490 and KJ511491) were 100% homologous to those of the isolates of C. fimbriata from diseased Cucumis sativus L. and Punica granatum L. in China (GenBank accessions MH535909 and KT963159). Thus, the pathogen was identified as C. fimbriata. Pathogenicity tests were made on fresh ginger rhizomes in laboratory, the pathogen was cultured for 14 days on MEA (ZOR-1, ZOR-2), which were washed with sterilized water and the resulting spore suspensions diluted to 1.0 × 106 spores/ml . Wounds (0.5 × 0.5 cm) were made on the surface of healthy mature ginger rhizomes by scraping with a sterile scalpel, then treated with a 100 ul spore suspension. Control ginger rhizomes were coated sterile water. Ginger rhizomes were stored at room temperature. Each treatment was performed in triplicate. After 5 days, grey-black mycelia developed on the rhizome surface, becoming a visible black mould after 1 week. We reisolated the pathogen from infected tissues, but not from the controls. In the greenhouse, 20ml of 1.0 × 106 spores/ml suspensions from isolates ZOR-1 and ZOR-2, or sterile water were injected into two-month- old ginger seedlings in triplicate. The inoculated site on the stem turned black in 5 days. 6 weeks after inoculation, the inoculated plants developed yellowing leaves and wilting symptoms. The same fungus was re-isolated from inoculated plants, but not from the controls. According to Koch's Postulation, the inoculated strains of ZOR-1 and ZOR-2 were the pathogens causing ginger wilt and rot disease. To the best of our knowledge, ginger is a new host plant of Ceratocystis fimbriata from China. In recent years, we have found that this disease incidence was approxmiatelt 5 to 10% of the farmland and 5 to 15% of the stored condition respectively in Yunnan Province. If not prevented ginger production in China will be affected.

First Report of Ceratocystis changhui Causing Postharvest Fruit Rot of Peach in Kunming, China

The peach (Prunus persica (L) Batsch) is a predominant commercially grown stone fruit in China (Lee et al. 1990). Ceratocystis changhui is an aggressive pathogen causing typical black rot symptoms on corms of taro (Colocasia esculenta) (Liu et al. 2018), it has not been reported on other hosts. During the summer and autumn of 2013, a postharvest fruit rot disease was observed on several peaches at a farmer's market (N 25°02'; E 102°42') in Kunming City, Yunnan Province, China. The incidence of the disease varied from 5 to 20%. Necrotic spots were first observed on the infected peach fruit (Prunus persica cv. shuimitao). The spots enlarged gradually and developed into a brown, water-soaked and rotted lesion. Eventually, the whole fruit became soft, rotted and covered with a gray-brown mycelium (Fig. 1 A, B). The isolates were obtained from the symptomatic tissues incubated on slices of fresh carrot root (Moller et al. 1968). After 5 to 10 days of incubation, perithecia and mycelium were observed growing on carrot slices. Spore masses were removed from the apices of perithecia, transferred to potato dextrose agar medium (PDA) and incubated at 25°C for 5 to 10 days, followed by single-spore isolation. All eight single-spore isolates from peach fruits obtained in this study were deposited in the State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, China. In culture, mycelium was initially white, gradually turned to greyish-green or brown (Fig. 1E, F). Measurements were made 7 days after the formation of perithecia. Perithecia (Fig. 1G) were black, globose, 185.71 to 305.56 μm × 142.86 to 264.29 µm and showed a long black neck, 600 to 957.14 µm (Fig. 1H). Ascospores (Fig. 1I) were helmet-hat shaped and 2.86 to 6.67 µm ×3.81 to 4.76 µm. Cylindrical conidia (Fig. 1J) 6.67 to 38. 95 µm × 2.86 to7.62 µm were observed. Chlamydospore (Fig. 1K), 8.57 to 13.33 μm × 5.71 to 9.52 μm, were ovoid or obpyriform, smooth. To further verify pathogen identity the internal transcribed spacer (ITS) region of rDNA was amplified using primers ITS1F and ITS4 (Thorpe et al. 2005), and the total genomic DNA from the mycelia of five isolates was extracted using a CTAB method (Lee &Taylor 1990). The nucleotide sequences have been blasted and deposited in the GenBank database. Analysis of the ITS sequences from the isolates T1-1yp, T1-2yp, T2-1yp (GenBank accession no. KY580895-KY580897) showed 99% to 100% similarity with isolates C. changhui CMW43272 (KY643886), CMW43281 (KY643884), CMW46112 (KY643891) and CMW46113 (KY643892) from taro in China. Phylogenetic trees based on the maximum-likelihood (ML) method were constructed using MEGA 7. ITS sequences of other Ceratocystis spp. were attained from NCBI for comparative analysis (Liu et al. 2018), and Davidsoniella virescens (CMW11164) served as outgroup. The robustness of ML tree was evaluated with 1,000 bootstrap (BS) values. The pathogen was identified as C. changhui based on the phylogenetic analysis (Fig. 2). Three isolates (T1-1yp, T1-2yp, T2-1yp) were used for pathogenicity. Nine Prunus persica cv. yingzuitao fruits at early maturity (8 points out of 10) were wound inoculated with 200μL conidia suspension of the fungus (approximately 2.0 × 106 conidia / mL). Degreasing cotton dipped in sterile water was used to raise the humidity in preservation boxes. Boxes were incubated for 10 days at 25°C. Three peaches as controls were treated only with sterile distilled water in the same way. Symptoms of sunken lesions and fruit rot were observed two days after inoculation, and measured at 1.8 to 3.2 cm from the inoculation point within 5 days (Fig. 1C: right, D). The same pathogen was re-isolated from them confirming Koch's postulates. Control peaches remained symptomless. This fungus was morphologically and phylogenetically identified as C. changhui. To our knowledge, this is the first report of C. changhui on postharvest peach in Yunnan, China. The disease will affect quality and taste of peach, so it is critical to deploy appropriate management strategies to limit the fungus spread.

First Report of Wilt of Rubber Tree Caused by Chalaropsis thielavioides in China

Rubber tree (Hevea brasiliensis (Willd. ex Adr. Juss) Müll. Arg.) is used for the extraction of natural rubber and is an economically and socially important estate crop commodity in many Asian countries such as Indonesia, Malaysia, Thailand, India, Sri Lanka, China and several countries in Africa (Pu et al, 2007). Xishuangbanna City and Wenshan City are the main rubber cultivation areas in Yunnan Province, China. In November 2012, rubber tree showing typical wilt symptoms (Fig. 1 A) and vascular stains (Fig. 1 B) were found in Mengla County, Xishuangbanna City. This disease was destructive in these trees and plant wilt death rate reached 5%. The diseased wood pieces (0.5cm long) from trunk of rubber was surface disinfected with 75% ethanol for 30s and 0.1% mercuric chloride (HgCl2) for 2min, rinsed three times with sterile distilled water, plated onto malt extract agar medium (MEA), and incubated at 28℃. After 7 days, fungal-like filaments were growing from the diseased trunk. Six cultures from 6 rubber trunk were obtained and incubated on MEA at 28℃, after 7 days to observe the cultural features. The mycelium of each culture was white initially on MEA, and then became dark green. Cylindrical endoconidia apices rounded, non-septate, smooth, single or borne in chains (8.9 to 23.6 × 3.81 to 6.3μm) (Fig. 1 C). Chlamydospores (Fig. 1 D) were abundant, thick walled, smooth, forming singly or in chains (11.1 to 19.2 × 9.4 to 12.0μm). The mould fungus was identifed as Chalaropsis based on morphology (Paulin-Mahady et al. 2002). PCR amplification was carried out for 3 isolates, using rDNA internal transcribed spacer (ITS) primer pairs ITS1F and ITS4 (Thorpe et al. 2005). The nucleotide sequences were deposited in the GenBank data base and used in a Blast search of GenBank. Blast analysis of sequenced isolates XJm8-2-6, XJm8-2 and XJm10-2-6 (accessions KJ511486, KJ511487, KJ511489 respectively) had 99% identity to Ch. thielavioides strains hy (KF356186) and C1630 (AF275491). Thus the pathogen was identified as Ch. thielavioides based on morphological characteristics and rDNA-ITS sequence analysis. Pathogenicity test of the isolate (XJm8-2) was conducted on five 1-year-old rubber seedlings. The soil of 5 rubber seedlings was inoculated by drenching with 40 ml spore suspension (106 spores / ml). Five control seedlings were inoculated with 40 ml of sterile distilled water. All the seedlings were maintained in a controlled greenhouse at 25°C and watered weekly. After inoculated 6 weeks, all the seedlings with spore suspension produced wilt symptoms, as disease progressed, inoculated leaves withered (Fig. 1 E) and vascular stains (Fig. 1 F) by 4 months. While control seedlings inoculated with sterile distilled water remained healthy. The pathogen re-isolated from all inoculated symptomatic trunk was identical to the isolates by morphology and ITS analysis. But no pathogen was isolated from the control seedlings. The pathogenicity assay showed that Ch. thielavioides was pathogenic to rubber trees. Blight caused on rubber tree by Ceratocystis fimbriata previously in Brazil (Valdetaro et al. 2015), and wilt by Ch. thielavioides was not reported. The asexual states of most species in Ceratocystis are "chalara" or "thielaviopsis" (de Beer et al. 2014). To our knowledge, this is the first report of this fungus causing wilt of rubber in China. The spread of this disease may pose a threat to rubber production in China.

Pathogenicity, Symptom Development, and Colonization of Metrosideros polymorpha by Ceratocystis lukuohia

Extensive mortality of Metrosideros polymorpha (`ōhi`a) trees has been associated with Ceratocystis spp. on Hawai`i Island and was named rapid `ōhi`a death (ROD). Both C. lukuohia and C. huliohia have been associated with ROD, although C. lukuohia appears to be the more important pathogen. Crown observations and dissections of forest trees either wound-inoculated with, or naturally infected by, C. lukuohia were conducted to confirm pathogenicity and document patterns of host colonization. In pathogenicity trials, one of three and two of three trees inoculated with the fungus in February and August, respectively, exhibited crown wilt symptoms at 92 and 69 days after inoculation. Extensive, radial, black staining of the sapwood was found in main stems, while no crown wilt or xylem staining was found in control trees. Xylem staining, necrotic phloem, and fungus presence was noted in six trees inoculated in May to June and harvested 37 to 42 days later, and these observations were compared with those in two naturally infected trees felled in early August. Contiguous xylem staining was found in the main stems and into crowns of all diseased trees, while discontinuous streaks of xylem staining extended into the main forks and side branches. Necrotic phloem associated with xylem staining occurred on the lower stems of inoculated trees. Aside from the necrotic phloem and radial staining of the sapwood, symptom development in `ōhi`a infected with C. lukuohia is similar to other systemic wilt diseases on hardwood trees. We propose Ceratocystis wilt of `ōhi`a as the official name of the disease.

Phylogenomic incongruence in Ceratocystis: a clue to speciation?

Background

The taxonomic history of Ceratocystis, a genus in the Ceratocystidaceae, has been beset with questions and debate. This is due to many of the commonly used species recognition concepts (e.g., morphological and biological species concepts) providing different bases for interpretation of taxonomic boundaries. Species delineation in Ceratocystis primarily relied on genealogical concordance phylogenetic species recognition (GCPSR) using multiple standard molecular markers.

Results

Questions have arisen regarding the utility of these markers e.g., ITS, BT and TEF1-α due to evidence of intragenomic variation in the ITS, as well as genealogical incongruence, especially for isolates residing in a group referred to as the Latin-American clade (LAC) of the species. This study applied a phylogenomics approach to investigate the extent of phylogenetic incongruence in Ceratocystis. Phylogenomic analyses of a total of 1121 shared BUSCO genes revealed widespread incongruence within Ceratocystis, particularly within the LAC, which was typified by three equally represented topologies. Comparative analyses of the individual gene trees revealed evolutionary patterns indicative of hybridization. The maximum likelihood phylogenetic tree generated from the concatenated dataset comprised of 1069 shared BUSCO genes provided improved phylogenetic resolution suggesting the need for multiple gene markers in the phylogeny of Ceratocystis.

Conclusion

The incongruence observed among single gene phylogenies in this study call into question the utility of single or a few molecular markers for species delineation. Although this study provides evidence of interspecific hybridization, the role of hybridization as the source of discordance will require further research because the results could also be explained by high levels of shared ancestral polymorphism in this recently diverged lineage. This study also highlights the utility of BUSCO genes as a set of multiple orthologous genes for phylogenomic studies.

Taxonomic revision and multi-locus phylogeny of the North American clade of Ceratocystis

The North American clade (NAC) of Ceratocystis includes pathogenic species that infect a wide range of woody hosts. Previous phylogenetic analyses have suggested that this clade includes cryptic species and a paraphyletic C. variospora. In this study, we used morphological data and phylogenetic analyses to characterize NAC taxa, including Ceratocystis isolates causing a serious disease of almond trees in California. Phylogenetic analyses based on six gene regions supported two new species of Ceratocystis. Ceratocystis destructans is introduced as the species causing severe damage to almond trees in California, and it has also been isolated from wounds on Populus and Quercus in Iowa. It is morphologically similar to C. tiliae, a pathogen on Tilia and the most recently characterized species in the NAC. Ceratocystis betulina collected from Betula platyphylla in Japan is also newly described and is the sister taxon to C. variospora. Our six-locus phylogenetic analyses and morphological characterization resolved several cryptic species in the NAC.

A host specialized form of Ceratocystis fimbriata causes seed and seedling blight on native Carapa guianensis (andiroba) in Amazonian rainforests

Ceratocystis fimbriata Ellis & Halsted recently was recorded causing seed and seedling blight on Carapa guianensis Aubl. (andiroba), a tree species native to the Amazon Rainforest and prized for its valuable timber and medicinal seed oil. C. fimbriata more commonly causes wilt type diseases in woody hosts, especially on non-native host trees. However, on andiroba the disease occurs on seedlings and seeds, affecting the species regeneration. We studied 73 isolates of C. fimbriata on andiroba from three regions of the Amazon Basin to see if they represented natural or introduced populations. Analysis of ITS rDNA sequences and phylogenetic analysis of mating type genes revealed new haplotypes of C. fimbriata from the Latin American Clade that were closely related to other Brazilian populations of the fungus. In mating experiments, andiroba isolates were inter-fertile with tester strains of C. fimbriata from Brazil and elsewhere, confirming that they belong to a single biological species. Using microsatellite markers, 14 genotypes and populations with intermediate levels of genetic variability were found, suggesting that the fungus is indigenous to the Amazon Basin. Inoculation tests indicated that the andiroba isolates are host-specialized on andiroba, supporting the proposition of the special form C. fimbriata f. sp. carapa.

Real-Time PCR Assays to Detect and Distinguish the Rapid 'Ōhi'a Death Pathogens Ceratocystis lukuohia and C. huliohia

Ceratocystis lukuohia and C. huliohia are recently described fungal species that cause rapid 'ōhi'a death (ROD) of Metrosideros polymorpha, Hawaii's most abundant and ecologically important native species. Although the pathogens are now widespread on Hawai'i Island, a major effort is underway to study and manage affected forests, and particularly to prevent the disease from spreading to other islands in the State or throughout the Pacific. Rapid and accurate detection is critical. Molecular diagnostic real-time PCR protocols were developed to detect and distinguish the two pathogens, suitable for detection of fungal DNA from extracts of wood, soil, and insect frass. The assays detect as few as 2 to 4 or 16 spores of C. huliohia or C. lukuohia, respectively. These assays are valuable tools for monitoring disease spread and offer a significant advantage over culture-based methods for diagnostics, requiring <1 day to arrive at definitive results.

New Ceratocystis species associated with rapid death of Metrosideros polymorpha in Hawai'i

The native ‘ōhi’a lehua (Metrosideros polymorpha) has cultural, biological and ecological significance to Hawai’i, but it is seriously threatened by a disease commonly referred to as rapid ‘ōhi’a death (ROD). Preliminary investigations showed that a Ceratocystis species similar to C. fimbriata s.lat. was the cause of the disease. In this study, we used a combination of the phylogenetic, morphological and biological species concepts, as well as pathogenicity tests and microsatellite analyses, to characterise isolates collected from diseased ‘ōhi’a trees across Hawai’i Island. Two distinct lineages, representing new species of Ceratocystis, were evident based on multigene phylogenetic analyses. These are described here as C. lukuohia and C. huliohia. Ceratocystis lukuohia forms part of the Latin American clade (LAC) and was most closely associated with isolates from Syngonium and Xanthosoma from the Caribbean and elsewhere, including Hawai’i, and C. platani, which is native to eastern USA. Ceratocystis huliohia resides in the Asian-Australian clade (AAC) and is most closely related to C. uchidae, C. changhui and C. cercfabiensis, which are thought to be native to Asia. Morphology and interfertility tests support the delineation of these two new species and pathogenicity tests show that both species are aggressive pathogens on seedlings of M. polymorpha. Characterisation of isolates using microsatellite markers suggest that both species are clonal and likely represent recently-introduced strains. Intensive research is underway to develop rapid screening protocols for early detection of the pathogens and management strategies in an attempt to prevent the spread of the pathogens to the other islands of Hawai’i, which are currently disease free.

Genetic Diversity, Fungicide Sensitivity, and Host Resistance to Ceratocystis fimbriata Infecting Sweetpotato in North Carolina

Black rot of sweetpotato, caused by Ceratocystis fimbriata, has recently reemerged as a significant threat to sweetpotato production in North Carolina and other states across the United States. This disease has historically been controlled largely through cultural management strategies and, in some cases, fungicide application. The sudden and destructive reemergence of this disease in 2015 created the need for rapidly evaluating disease control strategies. Genetic diversity of current C. fimbriata isolates infecting sweetpotato in North Carolina was assessed using ITS, TEF, and MAT-2 sequences. All 50 tested isolates were confirmed to be of a single mating type, MAT-2, based on PCR amplification. Alignment of ITS, TEF, and MAT-2 sequences revealed all isolates were identical at each locus. Fourteen common sweetpotato cultivars and advanced breeding lines were screened for black rot resistance using two isolates. None of the cultivars were completely resistant to the disease and most were equally susceptible. 'Stokes Purple' and 'Covington' were the least susceptible, but significantly (P < 0.05) differed only from 'Bellevue', the most susceptible cultivar. Sensitivity of 50 C. fimbriata isolates to difenoconazole, fludioxonil, thiabendazole, dicloran, azoxystrobin, pyraclostrobin, fenamidone, and fluazinam was evaluated in vitro. Difenoconazole, thiabendazole, and fluazinam were most effective in reducing mycelia growth. Postharvest fungicide application on black rot-infected roots provided similar results. Low efficacy of dicloran, as well as a range of EC₅₀ values among isolates, suggests potential resistance to this commonly applied fungicide. Results obtained in this study provide current and useful information so that improved recommendations can be made to reduce losses in sweetpotato to black rot.

Genetic Bottlenecks for Two Populations of Ceratocystis fimbriata on Sweet Potato and Pomegranate in China

Chinese isolates of Ceratocystis fimbriata from sweet potato (Ipomoea batatas) and pomegranate (Punica granatum) were genetically compared with a worldwide collection of isolates from a variety of hosts. Isolates from black-rotted storage roots of sweet potato in China, Japan, Australasia, and the United States had identical internal transcribed spacer (ITS) ribosomal DNA (rDNA) sequences and only minor variation in microsatellite alleles. Sequences of their mating type genes were most similar to those of isolates from various hosts in Ecuador, a center of diversity for sweet potato. Isolates from Colocasia esculenta (taro) and pomegranate from Yunnan and Sichuan had only one ITS rDNA sequence (haplotype ITS5). This haplotype, sequences of mating type genes, and microsatellite alleles linked these isolates to isolates from Eucalyptus stumps in South China and diseased Eucalyptus trees in Brazil, supporting the hypothesis that the pomegranate population originated from Brazil via cuttings of Eucalyptus. Isolates from sweet potato and pomegranate in China were interfertile with tester strains of C. fimbriata, confirming that the causes of the two epidemics in China belong to a single biological species. However, other isolates from Eucalyptus stumps were intersterile with the tester strains and had ITS rDNA sequences typical of the Asian species, C. cercfabiensis.

Mapping Global Potential Risk of Mango Sudden Decline Disease Caused by Ceratocystis fimbriata

The Mango Sudden Decline (MSD), also referred to as Mango Wilt, is an important disease of mango in Brazil, Oman and Pakistan. This fungus is mainly disseminated by the mango bark beetle, Hypocryphalus mangiferae (Stebbing), by infected plant material, and the infested soils where it is able to survive for long periods. The best way to avoid losses due to MSD is to prevent its establishment in mango production areas. Our objectives in this study were to: (1) predict the global potential distribution of MSD, (2) identify the mango growing areas that are under potential risk of MSD establishment, and (3) identify climatic factors associated with MSD distribution. Occurrence records were collected from Brazil, Oman and Pakistan where the disease is currently known to occur in mango. We used the correlative maximum entropy based model (MaxEnt) algorithm to assess the global potential distribution of MSD. The MaxEnt model predicted suitable areas in countries where the disease does not already occur in mango, but where mango is grown. Among these areas are the largest mango producers in the world including India, China, Thailand, Indonesia, and Mexico. The mean annual temperature, precipitation of coldest quarter, precipitation seasonality, and precipitation of driest month variables contributed most to the potential distribution of MSD disease. The mango bark beetle vector is known to occur beyond the locations where MSD currently exists and where the model predicted suitable areas, thus showing a high likelihood for disease establishment in areas predicted by our model. Our study is the first to map the potential risk of MSD establishment on a global scale. This information can be used in designing strategies to prevent introduction and establishment of MSD disease, and in preparation of efficient pest risk assessments and monitoring programs.

Ceratocystis tiliae sp. nov., a wound pathogen on Tilia americana

Species in the North American clade (NAC) of the Ceratocystis fimbriata complex are mostly weak pathogens that infect native tree hosts through fresh wounds. Isolations from discolored tissue of wounded Tilia americana (basswood) in Iowa and Nebraska yielded a Ceratocystis species that was similar to but distinct from isolates of C. variospora from other hosts. Sequences of 28S rDNA showed that isolates from basswood did not differ from C. variospora, but there were minor differences in ITS rDNA sequences. The DNA sequences of a portion of the Cerato-platanin gene and TEF1α showed the basswood fungus to be a unique lineage. Cross inoculations in two experiments showed that the basswood isolates and C. variospora isolates from Quercus spp. were most aggressive to their respective hosts. Isolates from basswood grew slower and were less pigmented than C. variospora isolates from Quercus spp. The basswood fungus thus is distinguished from C. variospora based on phylogenetic analyses and phenotype and is herein described as C. tiliae sp. nov.

Genetic Analyses Trace the Yunnan, China Population of Ceratocystis fimbriata on Pomegranate and Taro to Populations on Eucalyptus in Brazil

Genotypes of the Latin American wilt pathogen Ceratocystis fimbriata have been moved around the world in vegetatively propagated material of various crop plants, including Ipomoea batatas (sweet potato), Colocasia esculenta (taro), and Eucalyptus spp. When compared to a worldwide collection of isolates of C. fimbriata, isolates from taro, Punica granatum (pomegranate), and Eriobotrya japonica (loquat) from Yunnan Province, China were found to have sequences of internal transcribed spacer (ITS) rDNA and mating type genes that were identical to isolates from Eucalyptus in Brazil. Analyses of 35 isolates with 14 microsatellite markers revealed that the Yunnan population was nearly uniform, consisting of only 19 alleles and seven closely related genotypes, suggesting that the population is not natural and is the result of an introduction. As in comparisons of sequences of ITS rDNA and mating type genes, the microsatellite alleles of the Yunnan isolates were most similar to those of Eucalyptus isolates from Minas Gerais and Bahia, Brazil, where C. fimbriata is native, soilborne, and commonly infects cuttings of Eucalyptus spp. used for rooting in nurseries. Thus, the Yunnan population, which is causing severe losses on pomegranate, may have been indirectly derived from introductions of C. fimbriata in contaminated Eucalyptus cuttings from Brazil.

Redefining Ceratocystis and allied genera

The genus Ceratocystis was established in 1890 and accommodates many important fungi. These include serious plant pathogens, significant insect symbionts and agents of timber degradation that result in substantial economic losses. Virtually since its type was described from sweet potatoes, the taxonomy of Ceratocystis has been confused and vigorously debated. In recent years, particulary during the last two decades, it has become very obvious that this genus includes a wide diversity of very different fungi. These have been roughly lumped together due to their similar morphological structures that have clearly evolved through convergent evolution linked to an insect-associated ecology. As has been true for many other groups of fungi, the emergence of DNA-based sequence data and associated phylogenetic inferences, have made it possible to robustly support very distinct boundaries defined by morphological characters and ecological differences. In this study, DNA-sequence data for three carefully selected gene regions (60S, LSU, MCM7) were generated for 79 species residing in the aggregate genus Ceratocystis sensu lato and these data were subjected to rigorous phylogenetic analyses. The results made it possible to distinguish seven major groups for which generic names have been chosen and descriptions either provided or emended. The emended genera included Ceratocystis sensu stricto, Chalaropsis, Endoconidiophora, Thielaviopsis, and Ambrosiella, while two new genera, Davidsoniella and Huntiella, were described. In total, 30 new combinations have been made. This major revision of the generic boundaries in the Ceratocystidaceae will simplify future treatments and work with an important group of fungi including distantly related species illogically aggregated under a single name.

Genetic variation and variation in aggressiveness to native and exotic hosts among Brazilian populations of Ceratocystis fimbriata

Ceratocystis fimbriata is a complex of many species that cause wilt and cankers on woody plants and rot of storage roots or corms of many economically important crops worldwide. In Brazil, C. fimbriata infects different cultivated crop plants that are not native to Brazil, including Gmelina arborea, Eucalyptus spp., Mangifera indica (mango), Ficus carica (fig), and Colocasia esculenta (inhame). Phylogenetic analyses and inoculation studies were performed to test the hypothesis that there are host-specialized lineages of C. fimbriata in Brazil. The internal transcribed spacer region ribosomal DNA sequences varied greatly but there was little resolution of lineages based on these sequences. A portion of the MAT1-2 mating type gene showed less variation, and this variation corresponded more closely with host of origin. However, mango isolates were found scattered throughout the tree. Inoculation experiments on the five exotic hosts showed substantial variation in aggressiveness within and among pathogen populations. Native hosts from the same families as the exotic hosts tended to be less susceptible than the cultivated hosts, but there was little correlation between aggressiveness to the cultivated and native hosts of the same family. Cultivation and vegetative propagation of exotic crops may select for strains that are particularly aggressive on those crops.

Development of a Nested Polymerase Chain Reaction Assay for Detection of Colletotrichum acutatum on Symptomless Strawberry Leaves

A nested polymerase chain reaction (PCR) assay was developed for detection of Colletotrichum acutatum on symptomless strawberry leaves. In pure culture, the assay detected as little as 1.0 fg of DNA extracted from mycelium and as few as 1.5 conidia ml^-1 when conidial suspensions were sonicated. On detached inoculated leaves, three alternative protocols to dislodge the pathogen were assessed: (i) immersion of whole leaves in 0.05% Tween 20 and manual agitation in plastic bags for 1 min (A); (ii) immersion in Tween 20, sonication for 30 min, then agitation for 1 min (SA); and (iii) freezing for 3 h, incubation for 2 days at 27°C, immersion in Tween 20, then sonication for 30 min and agitation for 1 min (FISA). Each method removed significantly (P ≤ 0.05) more conidia from leaves than the nontreated control; however, removal of appressoria did not vary among assays. In composite samples of noninoculated and inoculated (1.5 ×10³ conidia ml^-1) strawberry leaves, the nested PCR assay using the FISA protocol detected C. acutatum in as few as 1 infested leaf in 50 noninfested leaves. In a strawberry field, the assay detected the presence of C. acutatum in samples of asymptomatic strawberry leaves, showing potential as a powerful tool for reliable diagnosis of the pathogen in the field.

Annona squamosa, a new host of Ceratocystis fimbriata

Mango branch blight disease, caused by Ceratocystis fimbriata, is endemic to the municipality of São Fidelis in northern Rio de Janeiro State. In addition to mango, C. fimbriata was found associated with sugar apple trees (Annona squamosa) showing symptoms of branch blight in São Fidelis. Sugar apple and mango isolates from the same region had the same morphology and showed similar ITS-rDNA sequences. These sequences were also similar to other Brazilian isolates of C. fimbriata sensu stricto. Cross inoculation of such isolates obtained from diseased sugar apple and mango resulted in diseased symptoms on both plant species. This is the first record of A. squamosa as a host for C. fimbriata.

Intraspecific variability of Pythium myriotylum isolated from cocoyam and other host crops

Intraspecific variability within 51 isolates of Pythium myriotylum from cocoyam (Xanthosoma sagittifolium) and other host crops was analysed using optimum growth temperature, esterase banding patterns, AFLPs, rDNA-ITS sequencing, and virulence to cocoyam. P. myriotylum isolates virulent to cocoyam could easily be differentiated from other isolates of P. myriotylum by their optimum growth temperature. Isolates from cocoyam grew best at 28 degrees C with no growth at 37 degrees C, while P. myriotylum isolates from other host crops had their optimum growth temperature at 37 degrees C. Esterases produced consistent zymograms with 18 discrete esterase markers, but no monomorphic markers were produced for isolates virulent to cocoyam. Isozyme profiles based on esterase analysis showed that isolates that infect cocoyam plantlets formed a related group, irrespective of their geographic origin. P. myriotylum isolates from other host plants also grouped together, but could clearly be distinguished from the cocoyam cluster. AFLPs produced 189 scorable bands for the cocoyam isolates, of which 77% are monomorphic. Phenetic analysis of AFLP data grouped all isolates originating from cocoyam together except for the isolates C103-04, CMR17, CMR22, and CMR25. These isolates regrouped with isolates of Pythium myriotylum from other host crops or the outgroup and were found not to be pathogenic for cocoyam. ITS sequences of isolates of P. myriotylum from cocoyam were 99.1-99.7% identical to sequences deposited in GenBank. However, alignments of ITS sequences revealed a base transition at position 824 from adenine in typical isolates of P. myriotylum to guanine in isolates that could infect cocoyam plantlets. In a limited pathogenicity test, all isolates from cocoyam having guanine at position 824 were able to infect tissue culture derived cocoyam but not those exhibiting adenine. This study demonstrates for the first time, molecular evidence that isolates of P. myriotylum that infect cocoyam are distinct from P. myriotylum isolates from other crops and have developed a certain degree of host adaptation.