Ji-Chuan Kang

ITS and β-tubulin phylogeny of Phaeoacremonium and Phaeomoniella species

Based on ITS and β-tubulin sequence data of 33 isolates, the newly introduced genus, Phaeomoniella was confirmed as being distinct from Phaeoacremonium (Pm.). Phylogeny inferred from DNA sequences and cultural characteristics also confirmed the species status of Pm. aleophilum and Pm. angustius , which were recently reduced to synonymy. Pm. aleophilum has an optimum growth rate at 30 °C and the ability to grow at 35°, whereas Pm. angustius has an optimum growth rate at 25 °C and does not grow at 35°. Furthermore, ITS and β-tubulin sequence data showed Pm. viticola to be indistinguishable from Pm. angustius , while a new species, Pm. mortoniae , could be distinguished from this complex.

Characterisation of Alternaria species-groups associated with core rot of apples in South Africa

Alternaria core rot of red apple cultivars is a serious post-harvest disease in South Africa. Thirty isolates of Alternaria spp. previously isolated from apple, together with reference isolates of A. alternata and A. infectoria, were characterised and grouped according to their sporulation patterns and conidial morphology. Isolates were identified as belonging to A. arborescens, A. infectoria and A. tenuissima species-groups. The isolates were also analysed for production of mycotoxins and other secondary metabolites and their cultural characteristics on DRYES medium were recorded. Apple fruit were artificially inoculated with the thirty-two Alternaria isolates and the resulting lesion types were recorded. A data matrix was constructed using all these characters and subjected to cluster analysis to show the similarity between different isolates. Isolates classified as A. infectoria species-group based on sporulation patterns, cultural and biochemical data could be easily differentiated from isolates classified as A. arborescens and A. tenuissima species-groups, which clustered close together. Isolates were further subjected to DNA sequence analysis of the internal transcribed spacers (ITS) 1 and 2 of the nuclear rRNA gene. A phylogeny estimated from the ITS data set delineated two clades, one being typified by the A. infectoria species-group, and the other representing both A. tenuissima and A. arborescens species-groups. The ITS data set clearly separated isolates of A. infectoria species-group from the other species-groups, as all isolates had a distinction of 35 base pair insertions and 6 base pair deletions in the ITS regions. The results obtained in the present study showed that the major pathogens associated with core rot disease of Top Red apples in South Africa belong to the A. tenuissima species-group.

Phylogenetic analysis of Alternaria spp. associated with apple core rot and citrus black rot in South Africa

Dry core rot of apple (DCR) and Alternaria black rot of citrus (ABR) have in the past respectively been ascribed to Alternaria alternata and A. citri. In recent years, however, it has been speculated that several other species of Alternaria could also be associated with these diseases. In an attempt to elucidate the identity of these taxa, 25 isolates associated with DCR, and 26 isolates associated with ABR were selected for molecular characterisation. Nucleotide sequences of 1116 sites including the histone gene section and the internal transcribed spacers (ITS 1 and 2) of the rRNA gene were determined for these isolates. The gene trees generated from the individual and combined data sets using maximum parsimony, maximum likelihood and neighbour-joining analysis methods distinguished five clades with strong bootstrap support, namely Alternaria sp., A. arborescens, A. infectoria, A. tenuissima, and a clade containing isolates variable in morphology, referred to as the Alternaria group. In the alignment of the combined ITS and histone data set, unique transition/transversion substitutions, as well as positional insertions and deletions were observed for each of the above clades. In addition, key sequences in the form of serial composing nucleotides in both the ITS and histone sections of the alignment were also discovered for the molecular identification of A. arborescens, A. infectoria and A. tenuissima. The final phylogeny also indicated that no host specificity existed among the species associated with these two post-harvest disease complexes. Contrary to the host specificity observed on leaf diseases of these hosts in the field, it appears that the post-harvest diseases are the result of adverse storage conditions and opportunism of different small-spored Alternaria spp.

Species concepts in the Cylindrocladium floridanum and Cy. Spathiphylli complexes ( Hypocreaceae ) based on multi-allelic sequence data, sexual compatibility and morphology.

Much attention has recently been devoted to the delimitation of species units in Cylindrocladium (Cy.). In this regard the present study focuses on the taxa within the unresolved Cy. floridanum and Cy. spathiphylli species complexes. Maximum parsimony analyses of DNA sequences of ITS, beta-tubulin and histone regions of rRNA genes, and mating experiments revealed a geographically isolated species of Cylindrocladium in the Cy. spathiphylli (teleomorph: Calonectria spathiphylli) species complex. Cy. pseudospathiphylli sp. nov. (teleomorph: Ca. pseudospathiphylli sp. nov.) is described as a new phylogenetic, biological and morphological species. It is distinguished from Cy. spathiphylli by being homothallic, having smaller macroconidia, and distinct DNA sequences of beta-tubulin and histone genes. Similarly, parsimony analysis of a combined data set also indicated several phylogenetic species to exist within Cy. floridanum (teleomorph: Ca. kyotensis). Based on differences in vesicle morphology and conidium dimensions, the Canadian population of Cy. floridanum, formerly known as Cy. floridanum Group 2, is described as Cy. canadense sp. nov., while a further collection from Hawaii is described as Cy. pacificum sp. nov.

Phylogenetic confirmation of Calonectria spathulata and Cylindrocladium leucothoes based on morphology, and sequence data of the β-tubulin and ITS rRNA genes

ACalonectria sp. forming aCylindrocladium anamorph was found to be commonly associated with leaf spot and cutting rot ofEucalyptus in Brazil, Colombia, Ecuador and Argentina. Based on morphology, isolates of this species resembledCal. hederae, Cal. reteaudii andCy. leucothoes, taxa that are commonly referred to as theCal. reteaudii-complex. Using DNA sequence data of the ITS1, 5.8S and ITS2 of the rRNA gene, as well as the β-tubulin gene, this species was shown to represent a previously described, but rather poorly known species,Cal. spathulata, for which an emended description is provided. Furthermore, the recently describedCy. perseae was also shown to be synonymous withCy. leucothoes, a species shown to be distinct fromCy. spathulatum. Based on vesicle and conidium morphology, as well as perithecial colour and ascospore morphology, it appears thatCal. hederae andCal. reteaudii should also be retained as separate species. Additional collections and cultures would be required, however, to suitably characterise the latter two species in future studies.