Ekachai Chukeatirote

Families of Dothideomycetes

Dothideomycetes comprise a highly diverse range of fungi characterized mainly by asci with two wall layers (bitunicate asci) and often with fissitunicate dehiscence. Many species are saprobes, with many asexual states comprising important plant pathogens. They are also endophytes, epiphytes, fungicolous, lichenized, or lichenicolous fungi. They occur in terrestrial, freshwater and marine habitats in almost every part of the world. We accept 105 families in Dothideomycetes with the new families Anteagloniaceae, Bambusicolaceae, Biatriosporaceae, Lichenoconiaceae, Muyocopronaceae, Paranectriellaceae, Roussoellaceae, Salsugineaceae, Seynesiopeltidaceae and Thyridariaceae introduced in this paper. Each family is provided with a description and notes, including asexual and asexual states, and if more than one genus is included, the type genus is also characterized. Each family is provided with at least one figure-plate, usually illustrating the type genus, a list of accepted genera, including asexual genera, and a key to these genera. A phylogenetic tree based on four gene combined analysis add support for 64 of the families and 22 orders, including the novel orders, Dyfrolomycetales, Lichenoconiales, Lichenotheliales, Monoblastiales, Natipusillales, Phaeotrichales and Strigulales. The paper is expected to provide a working document on Dothideomycetes which can be modified as new data comes to light. It is hoped that by illustrating types we provide stimulation and interest so that more work is carried out in this remarkable group of fungi.

The genus Phomopsis: biology, applications, species concepts and names of common phytopathogens

The genus Phomopsis (teleomorph Diaporthe) comprises phytopathologically important microfungi with diverse host associations and a worldwide distribution. Species concepts in Phomopsis have been based historically on morphology, cultural characteristics and host affiliation. This paper serves to provide an overview of the current status of the taxonomy in Phomopsis with special reference to biology, applications of various species, species concepts, future research perspectives and names of common pathogens, the latter being given taxonomic reappraisal. Accurate species identification is critical to understanding disease epidemiology and in developing effective control measures for plant diseases. Difficulties in accurate species identification using morphology have led to the application of alternative approaches to differentiate species, including virulence and pathogenicity, biochemistry, metabolites, physiology, antagonism, molecular phylogenetics and mating experiments. Redefinition of Phomopsis/Diaporthe species has been ongoing, and some species have been redefined based on a combination of molecular, morphological, cultural, phytopathological and mating type data. Rapid progress in molecular identification has in particular revolutionized taxonomic studies, providing persuasive genetic evidence to define the species boundaries. A backbone ITS based phylogenetic tree is here in generated using the sequences derived from 46 type, epitype cultures, and vouchers and is presented as a rough and quick identification guide for species of Phomopsis. The need for epitypification of taxonomic entities and the need to use multiple loci in phylogenies that better reflect species limits are suggested. The account of names of phytopathogens currently in use are listed alphabetically and annotated with a taxonomic entry, teleomorph, associated hosts and disease symptoms, including brief summaries of taxonomic and phylogenetic research. Available type culture information and details of gene sequences derived from type cultures are also summarized and tabulated.

Colletotrichum gloeosporioides is not a common pathogen on tropical fruits

Colletotrichum gloeosporioides has been reported as one of the most important pathogens worldwide that infect at least 1000 plant species. Fruit rots (anthracnose) are often attributed to C. gloeosporioides and, to a lesser extent, to C. acutatum. These previous findings were, however, based on morphological identification or, if gene sequence data were used, comparisons were often made with wrongly applied names. Colletotrichum gloeosporioides was recently epitypified so that living cultures and sequence data are, for first time available for comparison with fresh collections. Analysis of sequence data of 25 isolates from eight tropical fruits are compared with the C. gloeosporioides epitype. Contrary to previous understanding, none of the 25 Colletotrichum isolates from tropical fruits was C. gloeosporioides. The five gene regions used in this study resolved Colletotrichum asianum, C fructicola, C. horii, C. kahawae and C. gloeosporioides in the ‘gloeosporioides’ complex as distinct phylogenetic lineages with high statistical support. Some other likely novel species in the “gloeosporioides” complex and C. siamense, however, received only moderate or low support and further studies are needed to clarify their phylogenetic affinities and taxonomic placements. Cultural, conidial and appressorial characters can be used to differentiate taxa into species complexes, but cannot separate species within a complex. This discovery will have significant impacts on many aspects of plant pathology, pathogen diagnosis, quarantine decisions, plant breeding, and plant disease management and control and these are discussed.

Pestalotiopsis—morphology, phylogeny, biochemistry and diversity

The genus Pestalotiopsis has received considerable attention in recent years, not only because of its role as a plant pathogen but also as a commonly isolated endophyte which has been shown to produce a wide range of chemically novel diverse metabolites. Classification in the genus has been previously based on morphology, with conidial characters being considered as important in distinguishing species and closely related genera. In this review, Pestalotia, Pestalotiopsis and some related genera are evaluated; it is concluded that the large number of described species has resulted from introductions based on host association. We suspect that many of these are probably not good biological species. Recent molecular data have shown that conidial characters can be used to distinguish taxa; however, host association and geographical location is less informative. The taxonomy of the genera complex remains confused. There are only a few type cultures and, therefore, it is impossible to use gene sequences in GenBank to clarify species names reliably. It has not even been established whether Pestalotia and Pestalotiopsis are distinct genera, as no isolates of the type species of Pestalotia have been sequenced, and they are morphologically somewhat similar. When selected GenBank ITS accessions of Pestalotiopsis clavispora, P. disseminata, P. microspora, P. neglecta, P. photiniae, P. theae, P. virgatula and P. vismiae are aligned, most species cluster throughout any phylogram generated. Since there appears to be no living type strain for any of these species, it is unwise to use GenBank sequences to represent any of these names. Type cultures and sequences are available for the recently described species P. hainanensis, P. jesteri, P. kunmingensis and P. pallidotheae. It is clear that the important species in Pestalotia and Pestalotiopsis need to be epitypified so that we can begin to understand the genus/genera. There are numerous reports in the literature that various species produce taxol, while others produce newly discovered compounds with medicinal potential and still others cause disease. The names assigned to these novel compound-producing taxa lack an accurate taxonomic basis, since the taxonomy of the genus is markedly confused. Until the important species have been epitypified with living strains that have been sequenced and deposited in public databases, researchers should refrain from providing the exact name of species.

A multi-locus phylogenetic evaluation of Diaporthe (Phomopsis)

The genus Diaporthe (Phomopsis) includes important plant pathogenic fungi with wide host ranges and geographic distributions. In the present study, phylogenetic species recognition in Diaporthe is re-evaluated using a multi-locus phylogeny based on a combined data matrix of rDNA ITS, and partial sequences from the translation elongation factor 1-α (EF 1-α), β tubulin (TUB) and calmodulin (CAL) molecular markers. DNA sequences of available ex-type cultures have been included, providing a multi-locus backbone tree for future studies on Diaporthe. Four utilizable loci were analyzed individually and in combination, and ITS, EF 1-α and multi-locus phylogenetic trees are presented. The phylogenetic tree inferred by combined analysis of four loci provided the best resolution for species as compared to single gene analysis. Notes are provided for nine species previously known in Phomopsis that are transferred to Diaporthe in the present study. The unraveling of cryptic species complexes of Diaporthe based on Genealogical Concordance Phylogenetic Species Recognition (GCPSR) is emphasized.

A phylogenetic and taxonomic re-evaluation of the Bipolaris - Cochliobolus - Curvularia Complex

Three genera, Cochliobolus, Bipolaris and Curvularia form a complex that contains many plant pathogens, mostly on grasses (Poaceae) with a worldwide distribution. The taxonomy of this complex is confusing as frequent nomenclatural changes and refinements have occurred. There is no clear morphological boundary between the asexual genera Bipolaris and Curvularia, and some species show intermediate morphology. We investigated this complex based on a set of ex-type cultures and collections from northern Thailand. Combined gene analysis of rDNA ITS (internal transcribed spacer), GPDH (glyceraldehyde 3-phosphate dehydrogenase), LSU (large subunit) and EF1-α (translation elongation factor 1-α) shows that this generic complex divides into two groups. Bipolaris and Cochliobolus species clustered in Group 1 along with their type species, whereas Curvularia species (including species named as Bipolaris, Cochliobolus and Curvularia) clustered in Group 2, with its generic type. The nomenclatural conflict in this complex is resolved giving priority to the more commonly used established generic names Bipolaris and Curvularia. Modern descriptions of the genera Bipolaris and Curvularia are provided and species resolved in this study are transferred to one of these genera based on their phylogeny.

A multi-locus backbone tree for Pestalotiopsis, with a polyphasic characterization of 14 new species

Pestalotiopsis is a taxonomically confused, pathogenic and chemically creative genus requiring a critical re-examination using a multi-gene phylogeny based on ex-type and ex-epitype cultures. In this study 40 isolates of Pestalotiopsis, comprised of 28 strains collected from living and dead plant material of various host plants from China were studied by means of morphology and analysis of ITS, β–tubulin and tef1 gene sequence data. Based on molecular and morphological data we describe 14 new species (Pestalotiopsis asiatica, P. chinensis, P. chrysea, P. clavata, P. diversiseta, P. ellipsospora, P. inflexa, P. intermedia, P. linearis, P. rosea, P. saprophyta, P. umberspora, P. unicolor and P. verruculosa) and three species are epitypified (P. adusta, P. clavispora and P. foedans). Of the 10 gene regions (ACT, β-tubulin, CAL, GPDH, GS, ITS, LSU, RPB 1, SSU and tef1) utilized to resolve cryptic Pestalotiopsis species, ITS, β–tubulin and tef1 proved to be the better markers. The other gene regions were less useful due to poor success in PCR amplification and/or in their ability to resolve species boundaries. As a single gene tef1 met the requirements for an ideal candidate and functions well for species delimitation due to its better species resolution and PCR success. Although β-tubulin showed fairly good differences among species, a combination of ITS, β-tubulin and tef1 gene data gave the best resolution as compared to single gene analysis. This work provides a backbone tree for 22 ex-type/epitypified species of Pestalotiopsis and can be used in future studies of the genus.

Astrosphaeriella is polyphyletic, with species in Fissuroma gen. nov., and Neoastrosphaeriella gen. nov.

Collections of fungi from bamboo and palm plants in Thailand resulted in the identification of several species of Astrosphaeriella, including the type species A. fusispora, which is a synonym of A. stellata. Species of Astrosphaeriella have been previously circumscribed on the basis of morphology and, to a lesser extent, on host affiliation. In order to obtain a phylogenetic understanding of the genus, eleven strains of Astrosphaeriella sensu lato were sequenced in this study. Molecular analyses based on a combined dataset of 18S and 28S nrDNA sequences were carried out to infer the phylogenetic placement of these strains in the Pleosporales. The phylogenetic analyses showed that Astrosphaeriella is polyphyletic, with Astrosphaeriella species clustering in four clades, two clades, including species with slit-like ostioles, clustered in Aigialaceae; the clade that includes the generic type clustered together with Delitschia; and A. Africana, which has striate ascospores, deviated from these three clades and had a basal position in the Pleosporales. A new combination in Fissuroma gen. nov. and new genus Neoastrosphaeriella are introduced in Aigialaceae to include the species with slit-like ascomata.

Insights into the genus Diaporthe: phylogenetic species delimitation in the D. eres species complex

The genus Diaporthe comprises pathogenic, endophytic and saprobic species with both temperate and tropical distributions. Cryptic diversification, phenotypic plasticity and extensive host associations have long complicated accurate identifications of species in this genus. The delimitation of the generic type species Diaporthe eres has been uncertain due to the lack of ex-type cultures. Species limits of D. eres and closely related species were evaluated using molecular phylogenetic analysis of eight genes including nuclear ribosomal internal transcribed spacer (ITS), partial sequences of actin (ACT), DNA-lyase (Apn2), translation elongation factor 1- α (EF1-α), beta-tubulin (TUB), calmodulin (CAL), 60s ribosomal protein L37 (FG1093) and histone-3 (HIS). The occurrence of sequence heterogeneity of ITS within D. eres is observed, which complicates the analysis and may lead to overestimation of the species diversity. The strict criteria of Genealogical Concordance Phylogenetic Species Recognition (GCPSR) were applied to resolve species boundaries based on individual and combined analyses of other seven genes except the ITS. We accept nine distinct phylogenetic species including Diaporthe alleghaniensis, D. alnea, D. bicincta, D. celastrina, D. eres, D. helicis, D. neilliae, D. pulla and D. vaccinii. Epitypes are designated for D. alnea, D. bicincta, D. celastrina, D. eres, D. helicis and D. pulla. Modern descriptions and illustrations are provided for these species. Newly designed primers are introduced to amplify and sequence the Apn2 (DNA- lyase) gene in Diaporthe. Based on phylogenetic informativeness profiles, EF1-α, Apn2 and HIS genes are recognised as the best markers for defining species in the D. eres complex.

Phyllosticta—an overview of current status of species recognition

Phyllosticta is an important coelomycetous plant pathogenic genus known to cause leaf spots and various fruit diseases worldwide on a large range of hosts. Species recognition in Phyllosticta has historically been based on morphology, culture characters and host association. Although there have been several taxonomic revisions and enumerations of species, there is still considerable confusion when identifying taxa. Recent studies based on molecular data have resolved some cryptic species and some novel taxa have been discovered. However, compared to the wide species diversity and taxonomic records, there is a lack of molecular studies to resolve current names in the genus. A phylogenetic tree is here generated by combined gene analysis (ITS, partial actin and partial elongation factor 1α) using a selected set of taxa including type-derived sequences available in GenBank. Life modes, modal lifecycle and applications of the genus in biocontrol and metabolite production are also discussed. We present a selected set of taxa as an example of resolved and newly described species in the genus and these are annotated with host range, distribution, disease symptoms and notes of additional information with comments where future work is needed.