Kerry O'DOnnell

The current study was conducted to obtain the first detailed assessment of true morel (Morchella) species diversity in Pakistan. A collection of 179 morels was obtained by conducting field surveys in 13 districts during spring and autumn of 2014 through 2020. Species were identified phylogenetically by analyzing portions of two (RPB1, RPB2) or four (RPB1, RPB2, TEF1, ITS rDNA) marker loci together with authentic reference sequences of known species and by conducting BLASTn queries of National Center for Biotechnology Information (NCBI) GenBank. A retrospective analysis of morel sequences from Pakistani (N = 52) and Indian (N = 69) collections accessioned in GenBank was also conducted to expand and compare our knowledge of Morchella species diversity in both countries. Analyses of our 179-morel collection and the 52 Pakistani sequences deposited in GenBank indicated that at least 20 species are present in Pakistan, including five putatively novel taxa within the Elata subclade here informally distinguished as Morchella spp. (Mel-43 to Mel-47). Phylospecies Mel-45 and Mel-46 were described formally as M. pycnogranulata and M. waziristanica, respectively. By comparison, analyses of the 69 Indian sequences deposited in GenBank indicated that at least 12 species are extant in India. However, only 4/9 Pakistani and 3/12 Indian species were correctly identified in GenBank. Two collections of the steppe morel, M. steppicola (Mes-1), from Afghanistan were also included in the present study, which extends the southeasternmost range of this morphologically distinct species.

Guaraná is indigenous to the Brazilian Amazon where it has cultural and agroeconomic significance. However, its cultivation is constrained by a disease termed oversprouting of guaraná caused by Fusarium decemcellulare, with yield losses reaching as high as 100%. The disease can affect different parts of the plant, causing floral hypertrophy and hyperplasia, stem galls, and oversprouting of vegetative buds. To date, no study has been conducted characterizing the genetic diversity and population structure of this pathogen. Here, we report genetic diversity and genetic structure among 224 isolates from eight guaraná production areas of Amazonas State, Brazil, that were genotyped using a set of 10 inter-simple-sequence repeat (ISSR) markers. Despite moderate gene diversity (Hexp = 0.21 to 0.32), genotypic diversity was at or near maximum (223 multilocus genotypes among 224 isolates). Population genetic analysis of the 10 ISSR marker fragments with STRUCTURE software identified two populations designated C1 and C2 within the F. decemcellulare collection from the eight sites. Likewise, UPGMA hierarchical clustering and discriminant analysis of principal components of the strains from guaraná resolved these same two groups. Analysis of molecular variance demonstrated that 71% of genetic diversity occurred within the C1 and C2 populations. A pairwise comparison of sampling sites for both genetic populations revealed that 59 of 66 were differentiated from one another (P < 0.05), and high and significant gene flow was detected only between sampling sites assigned to the same genetic population. The presence of MAT1-1 and MAT1-2 strains, in conjunction with the high genotypic diversity and no significant linkage disequilibrium, suggests that each population of F. decemcellulare might be undergoing sexual reproduction. Isolation by distance was not observed (R² = 0.02885, P > 0.05), which suggests that human-mediated movement of seedlings may have played a role in shaping the F. decemcellulare genetic structure in Amazonas State, Brazil.

In this study, DNA sequence data were used to characterize 290 Fusarium strains isolated during a survey of root-colonizing endophytic fungi of agricultural and nonagricultural plants in northern Kazakhstan. The Fusarium collection was screened for species identity using partial translation elongation factor 1-α (TEF1) gene sequences. Altogether, 16 different Fusarium species were identified, including eight known and four novel species, as well as the discovery of the phylogenetically divergent F. steppicola lineage. Isolates of the four putatively novel fusaria were further analyzed phylogenetically with a multilocus data set comprising partial sequences of TEF1, RNA polymerase II largest (RPB1) and second-largest (RPB2) subunits, and calmodulin (CaM) to assess their genealogical exclusivity. Based on the molecular phylogenetic and comprehensive morphological analyses, four new species are formally described herein: F. campestre, F. kazakhstanicum, F. rhizicola, and F. steppicola.

This study was conducted to elucidate evolutionary relationships and species diversity within the Fusarium buharicum species complex (FBSC). We also evaluate the potential of these species to produce mycotoxins and other bioactive secondary metabolites. Maximum likelihood and maximum parsimony analyses of sequences from portions of four marker loci (ITS rDNA, TEF1, RPB1, and RPB2) and the combined 4495 bp data set support recognition of seven genealogically exclusive species within the FBSC. Two of the three newly discovered species are formally described as F. abutilonis and F. guadeloupense based on concordance of gene genealogies and morphological data. Fusarium abutilonis induces leaf, stem, and root lesions on several weedy Malvaceae (Abution theophrasti, Anoda cristata, Sida spinosa) and a fabaceous host (Senna obtusifolia) in North America and also was recovered from soil in New Caledonia. Fusarium abutilonis, together with its unnamed sister, Fusarium sp. ex common marsh mallow (Hibiscus moscheutos) from Washington state, and F. buharicum pathogenic to cotton and kenaf in Russia and Iran, respectively, were strongly supported as a clade of malvaceous pathogens. The four other species of the FBSC are not known to be phytopathogenic; however, F. guadeloupense was isolated from human blood in Texas and soil in Guadeloupe. The former isolate is unique because it represents the only known case of a fusarial infection disseminated hematogenously by a species lacking microconidia and the only documented fusariosis caused by a member of the FBSC. Whole genome sequence data and extracts of cracked maize kernel cultures were analyzed to assess the potential of FBSC isolates to produce mycotoxins, pigments, and phytohormones.

Accurate species-level identification of an etiological agent is crucial for disease diagnosis and management because knowing the agent’s identity connects it with what is known about its host range, geographic distribution, and toxin production potential. This is particularly true in publishing peer-reviewed disease reports, where imprecise and/or incorrect identifications weaken the public knowledge base. This can be a daunting task for phytopathologists and other applied biologists that need to identify Fusarium in particular, because published and ongoing multilocus molecular systematic studies have highlighted several confounding issues. Paramount among these are: (i) this agriculturally and clinically important genus is currently estimated to comprise more than 400 phylogenetically distinct species (i.e., phylospecies), with more than 80% of these discovered within the past 25 years; (ii) approximately one-third of the phylospecies have not been formally described; (iii) morphology alone is inadequate to distinguish most of these species from one another; and (iv) the current rapid discovery of novel fusaria from pathogen surveys and accompanying impact on the taxonomic landscape is expected to continue well into the foreseeable future. To address the critical need for accurate pathogen identification, our research groups are focused on populating two web-accessible databases (FUSARIUM-ID v.3.0 and the nonredundant National Center for Biotechnology Information nucleotide collection that includes GenBank) with portions of three phylogenetically informative genes (i.e., TEF1, RPB1, and RPB2) that resolve at or near the species level in every Fusarium species. The objectives of this Special Report, and its companion in this issue ( Torres-Cruz et al. 2022 ), are to provide a progress report on our efforts to populate these databases and to outline a set of best practices for DNA sequence-based identification of fusaria.

Species within Fusarium are of global agricultural, medical, and food/feed safety concern and have been extensively characterized. However, accurate identification of species is challenging and usually requires DNA sequence data. FUSARIUM-ID ( http://isolate.fusariumdb.org/blast.php ) is a publicly available database designed to support the identification of Fusarium species using sequences of multiple phylogenetically informative loci, especially the highly informative ∼680-bp 5′ portion of the translation elongation factor 1-alpha (TEF1) gene that has been adopted as the primary barcoding locus in the genus. However, FUSARIUM-ID v.1.0 and 2.0 had several limitations, including inconsistent metadata annotation for the archived sequences and poor representation of some species complexes and marker loci. Here, we present FUSARIUM-ID v.3.0, which provides the following improvements: (i) additional and updated annotation of metadata for isolates associated with each sequence, (ii) expanded taxon representation in the TEF1 sequence database, (iii) availability of the sequence database as a downloadable file to enable local BLAST queries, and (iv) a tutorial file for users to perform local BLAST searches using either freely available software, such as SequenceServer, BLAST+ executable in the command line, and Galaxy, or the proprietary Geneious software. FUSARIUM-ID will be updated on a regular basis by archiving sequences of TEF1 and other loci from newly identified species and greater in-depth sampling of currently recognized species.

Mango malformation disease (MMD) caused by Fusarium spp. is an important limiting factor in most production areas worldwide. Fusarium mexicanum and F. pseudocircinatum have been reported as causing MMD in Mexico. These two pathogens also cause a similar disease in Swietenia macrophylla (big-leaf mahogany malformation disease) in central western Mexico, and F. pseudocircinatum was recently reported as causing malformation disease in Tabebuia rosea (rosy trumpet) in the same region. These studies suggest that additional plant species, including weeds, might be hosts of these pathogens. The role that weed hosts might have in the disease cycle is unknown. The objectives of this work were to recover Fusarium isolates from understory vegetation in mango orchards with MMD, identify the Fusarium isolates through DNA sequence data, and determine whether F. mexicanum is capable of inducing disease in the weedy legume Senna uniflora (oneleaf senna). Additional objectives in this work were to compare Fusarium isolates recovered from weeds and mango trees in the same orchards by characterizing their phylogenetic relationships, assessing in vitro production of mycotoxins, and identifying their mating type idiomorph. A total of 59 Fusarium isolates from five species complexes were recovered from apical and lateral buds from four weed species. Two of the species within the F. fujikuroi species complex are known to cause MMD in Mexico. Trichothecene production was detected in five isolates, including F. sulawense and F. irregulare in the F. incarnatum-equiseti species complex and F. boothii in the F. sambucinum species complex. Both mating types were present among mango and weed isolates. This is the first report of herbaceous hosts harboring Fusarium species that cause mango malformation in Mexico. The information provided should prove valuable for further study of the epidemiological role of weeds in MMD and help manage the disease.

Fusarium ranks as the most important group of plant pathogens, responsible for a wide range of economically destructive diseases, including vascular wilts and root, crown, and stem rots. In addition, head blight and ear rot diseases are associated with the accumulation of mycotoxins in cereals. With over 300 phylogenetically distinct species, and a dearth of phenotypical characteristics, DNA sequence data in most instances is the only reliable means for obtaining an accurate species identification. Here we describe how to obtain single-spored pure cultures from symptomatic host tissue and a molecular identification by querying publicly accessible DNA sequence databases using a portion of translation elongation factor 1-α (TEF1), the largest subunit of RNA polymerase (RPB1), and/or the second largest subunit of RNA polymerase (RPB2).

Tabebuia rosea (rosy trumpet) is an economically important neotropical tree in Mexico that is highly valued for the quality of its wood, which is used for furniture, crafts, and packing, and for its use as an ornamental and shade tree in parks and gardens. During surveys conducted in the lower Balsas River Basin region in the states of Guerrero and Michoacán, symptoms of floral malformation were detected in T. rosea trees. The main objectives of this study were to describe this new disease, to determine its causal agent, and to identify it using DNA sequence data. A second set of objectives was to analyze the phylogenetic relationship of the causal agent to Fusarium spp. associated with Swietenia macrophylla trees with malformation surveyed in the same region and to compare mycotoxin production and the mating type idiomorphs of fusaria recovered from T. rosea and S. macrophylla. Tabebuia rosea showed malformed inflorescences with multiple tightly curled shoots and shortened internodes. A total of 31 Fusarium isolates recovered from symptomatic T. rosea (n = 20) and S. macrophylla (n = 11) trees were identified by molecular analysis as Fusarium pseudocircinatum. Pathogenicity tests showed that isolates of F. pseudocircinatum recovered from T. rosea induced malformation in inoculated T. rosea seedlings. Eighteen F. pseudocircinatum isolates were tested for their ability to produce mycotoxins and other secondary metabolites. Moniliformin, fusaric acid, bikaverin, beauvericin, aurofusarin. and 8-O-methylbostrycoidin were produced by at least one strain of the 18 isolates tested. A multiplex PCR assay for mating type idiomorph revealed that 22 F. pseudocircinatum isolates were MAT1-1 and that 9 were MAT1-2. Here, we report a new disease of T. rosea in Mexico caused by F. pseudocircinatum.

The Ambrosia Fusarium Clade (AFC) is a monophyletic lineage within clade 3 of the Fusarium solani species complex (FSSC) that currently comprises 19 genealogically exclusive species. These fungi are known or predicted to be farmed by adult female Euwallacea ambrosia beetles as a nutritional mutualism (Coleoptera: Scolytinae; Xyleborini). To date, only eight of the 19 AFC species have been described formally with Latin binomials. We describe three AFC species, previously known as AF-8, AF-10, and AF-11, based on molecular phylogenetic analysis of multilocus DNA sequence data and comparative morphological/phenotypic studies. Fusarium duplospermum (AF-8) farmed by E. perbrevis on avocado in Florida, USA, is distinguished by forming two morphologically different types of multiseptate conidia and brownish orange colonies on potato dextrose agar (PDA). Fusarium drepaniforme (AF-10), isolated from an unknown woody host in Singapore and deposited as Herb IMI 351954 in the Royal Botanic Gardens, Kew, UK, under the name F. bugnicourtii, is diagnosed by frequent production of multiseptate sickle-shaped conidia. Fusarium papillatum (AF-11), isolated from mycangia of E. perbrevis infesting tea in Kandy, Sri Lanka, forms multiseptate clavate conidia that possess a papillate apical cell protruding toward the ventral side. Lastly, we prepared an augmented description of F. kuroshium (AF-12), previously isolated from the heads or galleries of E. kuroshio in a California sycamore tree, El Cajon, California, USA, and recently validated nomenclaturally as Fusarium. Conidia formed by F. kuroshium vary widely in size and shape, suggesting a close morphological relationship with F. floridanum, compared with all other AFC species. Maximum likelihood and maximum parsimony analyses of a multilocus data set resolve these three novel AFC species, and F. kuroshium, as phylogenetically distinct based on genealogical concordance. Given the promiscuous nature of several Euwallacea species, and the overlapping geographic range of several AFC species and Euwallacea ambrosia beetles, the potential for symbiont switching among sympatric species is discussed.