http://mfuir.mfu.ac.th:80/xmlui/handle/123456789/400 Sun, 19 Apr 2026 15:36:20 GMT 2026-04-19T15:36:20Z http://mfuir.mfu.ac.th:80/xmlui/handle/123456789/1596 Molecular phylogeny and taxonomy of plant pathogenic genera diaporthe (Phomopsis) and colletotrichum Dhanushka Udayanga Hyde,Kevin David The genus Diaporthe (Phomopsis) is an important genus of phytopathogenic fungi with a worldwide distribution. Cryptic diversification, phenotypic plasticity and extensive host associations have complicated accurate species identification in the genus. In this study, the phylogenetic species recognition of Diaporthe is re-evaluated with worldwide collections with special reference to the significant phytopathogens on crops, ornamentals and forest trees and species complexes. The Genealogical Concordance Phylogenetic Species Recognition (GCPSR) was applied to resolve the species limits with four gene phylogenetic analysis of ITS (nuclear ribosomal internal transcribed spacer), EF1-α (translation elongation factor 1-α), TUB (β tubulin) and CAL (calmodulin). The four gene combined phylogeny was used to define novel taxa from Thailand including D. ptercarpicola, D. siamensis and D. thunbergii. The species of Diaporthe associated with melanose and stem end rot of Citrus were re-defined, implementing the combined analysis of ITS, EF1-α, TUB, CAL and ACT (actin) genes and Genealogical Sorting Index methods. (6) Diaporthe citri, D. cytosporella, D. foeniculina and D. rudis, are epitypified with clarification of nomenclature and taxonomy. The Diaporthe sojae species complex associated with soybean, cucurbits, and other herbaceous hosts were resolved based on five gene analysis including ITS, EF1- α, TUB, CAL and HIS (histone-3) genes. The seed decay pathogen D. longicolla was distinguished from the pod and stem blight pathogen Diaporthe sojae. The Lima bean pathogen D. phaseolorum, other herbaceous crop pathogens including D. arctii, D. batatas and D. cucurbitae were resolved with epitypes designated with the introduction of a new species D. ueckerae from cucurbits in USA. The generic type species Diaporthe eres was redefined with the strict application of genealogical concordance and non-discordance criteria in conjunction with morphology with the epitypification of six phylogenetic species within the complex. Eight molecular markers including ACT, Apn2 (DNA-lyase), CAL, EF1-α, Fg1093 (ribosomal protein L37), HIS, ITS and TUB were used in the phylogenetic analyses and testing the informativeness. The caution is warranted using the ITS sequence data within the cryptic species complexes, and EF1-α is proved to be the best single marker to resolve the species. The utility of EF1-α, Apn2, HIS and ACT genes are found to be superior to the other genes used with reference to the phylogenetic informativeness. New primers were designed and made available for the amplification of Apn2, ACT and CAL genes within Diaporthe. Guidelines for the identification and description of new species are provided with the discussions on insights in to the evolution and the pattern of speciation within the genus. A molecular phylogenetic analysis of anthracnose pathogens of tropical fruits was performed, with fresh collection of economic and wild fruits in northern Thailand. The species within Colletotrichum gloesporioides species complex were found to be the dominant among anthracnose pathogens. A six gene combined phylogeny of ITS, ACT, TUB, CAL, GPDH (glyceraldehyde-3-phosphate (7) dehydrogenase), GS (glutamine synthetase) was used to resolve the C. gloesporioides species complex with the description of the new species, C. syzygicola. In general, this thesis provides a comprehensive account in terms of utility of molecular data to resolve plant pathogenic species complexes in fungi. A number of economically important species of common plant pathogenic genera, Diaporthe and Colletotrichum were re-defined with accurate phylogenetic placement, morphology and insights in to the speciation and evolution. Dissertation (Ph.D.) -- Biotechnology, School of Science. Mae Fah Luang University, 2014 Wed, 01 Jan 2014 00:00:00 GMT http://mfuir.mfu.ac.th:80/xmlui/handle/123456789/1596 2014-01-01T00:00:00Z http://mfuir.mfu.ac.th:80/xmlui/handle/123456789/1594 Molecular phylogeny and taxonomy of plant pathogenic complex of bipolaris, cochliobolus, curvularia and endophytic colletotrichum Dimuthu Sandarenu Manamgoda Hyde,Kevin David The plant pathogenic generic complex Bipolaris - Cochliobolus - Curvularia comprises many destructive plant pathogens that cause severe cereal crop losses worldwide. The taxonomy of this complex is confused as frequent nomenclatural changes occurred over the past 50 years. The Bipolaris - Cochliobolus - Curvularia complex is investigated based on a set of ex-type cultures and collections from northern Thailand and elsewhere. Combined gene analysis of ITS (nuclear ribosomal internal transcribed spacer), GPDH (glyceraldehyde 3-phosphate dehydrogenase), LSU (large subunit) and TEF (translation elongation factor 1-α) revealed the segregation of this generic complex into major 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 of Curvularia. The initial generic resolution was fundamental to the comprehensive assessments of taxonomy and phylogeny. The nomenclatural conflict in this complex is resolved giving priority to the more commonly used established generic names (6) Bipolaris and Curvularia, therefore the Cochliobolus names were recognised as synonyms. The genus Bipolaris is revisited with all available type materials and most of the additional materials selected from worldwide herbaria. A phylogenetic analysis of the genus provided with fresh collections and including the additional authenticated cultures. The generic type Bipolaris maydis is neo-typified with other ex, neo-types of B. chloridis, B. cynodontis, B.maydis, B. salviniae, B. victoriae, and B. yamadae. Lectotypes were designated for B. hadrotrichoides and B. stenospila. Modern descriptions and illustrations are provided for 46 species of Bipolaris, with a revision of synonyms, and notes on nomenclature, biology and ecology of the species. A taxonomic key is provided for the morphological identification of the species within the genus. The generic wide phylogenetic tree is provided for future studies within the genus. The genus Curvularia is revised in two consecutive phylogenetic assessments resulting 3 new species including C. asianensis, C. alcornii and C. boedjinii. Additionally the generic type C. lunats and C. kusanoi is neotypified, and the generic concepts were reassessed. Nineteen species previously thought to be Bipolaris are transferred to the genus Curvularia, broadening the species numbers within the genus based on phylogenetic and morphological deference. The endophytic Colletotrichum from several grass species were studied with ITS, ACT (actin), CAL (calmodulin) and GPDH phylogeny and morphology. A new species, C. endophytica is described with full descriptions and illustrations. This study revealed an unknown diversity of Colletotrichum species associated with tropical grass with perspectives for future studies. (7) In overall, this thesis serves as a complete account of graminicolous species complex Bipolaris-Curvularia, as well as endophytic Colletotrichum providing grounds for further study in plant pathology and fungal systematics. Dissertation (Ph.D.) -- Biotechnology, School of Science. Mae Fah Luang University, 2014 Wed, 01 Jan 2014 00:00:00 GMT http://mfuir.mfu.ac.th:80/xmlui/handle/123456789/1594 2014-01-01T00:00:00Z http://mfuir.mfu.ac.th:80/xmlui/handle/123456789/953 Taxonomy and phylogeny of phyllosticta Saowanee Wikee Hyde,Kevin David Dissertation (Ph.D.) -- Biotechnology, School of Science. Mae Fah Luang University, 2013 Tue, 01 Jan 2013 00:00:00 GMT http://mfuir.mfu.ac.th:80/xmlui/handle/123456789/953 2013-01-01T00:00:00Z http://mfuir.mfu.ac.th:80/xmlui/handle/123456789/540 Genetic diversity and biology of Sirindhornia H. AE. Pedersen & Suksathan (orchidaceae) Kanok-orn Srimuang Prapassorn D. Eungwanichayaphant The natural populations of Sirindhornia species were studied on their biology and genetic variation during 2006-2008 in Thailand. It was found that each species are self-compatible and depend on insects for the pollination. Sirindhornia mirabilis exhibited prolonged longevity of individual flowers and produced more flowers per inflorescence features that may have evolved in response to low visitation rates. In all three species, the female (and in S. mirabilis also the male) reproductive success decreased from the basal to the apical part of the inflorescence with differential fruit set in rewarding orchid species. Comparison of demographic and reproductive characteristics between the local endemics S. mirabilis and S. pulchella and the widespread S. monophylla found that the three species had similar demographic characteristics, but different reproductive attributes. The local endemics were more reproductively restricted than the widespread S. monophylla. Thus, the latter exhibited higher relative fruit set, higher seed production per inflorescence and more equal individual contributions of progeny. However, recruitment appeared to be more efficient in S. pulchella than the other two species. The observation of pollination biology in S. mirabilis was shown that the small carpenter bee in the genus Ceratina (Apidae, Xylocopinae) was very important pollinator, but visited infrequency. In the roots of all species of Sirindhornia found most of Rhizoctonia-like fungi. Seed germination in situ of S. mirabilis could develop into seedling stage with very low number, whereas, seeds of S. monophylla could germinate into protocorms stage, but no further development. Only mature seeds of S. monophylla germinated after 16 month of incubation in vitro, while, only immature seeds (5 weeks after pollination) of S. mirabilis germinated. Thus, seed germination requires different factors for each species. The study of genetic variation of the genus Sirindhornia revealed that they have moderate genetic diversity ranged from 0.11-0.15, a little lower than other allogamous orchid species, due to sharing male gamete from the same plant. They also have rather similar genetic diversity between populations, which can be explained by high gene flow (pollen-mediated and seed mediated) or by the history of populations, such as recent colonization or continue connection between population in the past as a large population. Finally, it was found that S. monophylla, wider distribution has genetic diversity higher than S. mirabilis and S. pulchella, endemic species. For conservation point of view, natural populations, individuals and seeds need to be conserved in order to keep genetic resource of these vulnerable species. Cross hand pollination may help to increase genetic variation in population, but it needs to be confirmed by further study. Dissertation (Ph.D.) -- Biotechnology, School of Science. Mae Fah Luang University, 2010 Thu, 01 Jan 2009 00:00:00 GMT http://mfuir.mfu.ac.th:80/xmlui/handle/123456789/540 2009-01-01T00:00:00Z