Taxonomy and phylogeny of microfungi with emphasis on Vitis species

Name: Jayawardena, Ruvishika S.

Organization : Mae Fah Luang University

keyword: Microfungi

LCSH: Microfungi

Classification :.LCCS: QK603.2

LCSH: Fungi

LCSH: Elsinoe

LCSH: Colletotrichum

Abstract: Vitis is an economically important fruit crop worldwide. China is one of the worlds’ main grape production countries. Microfungi associated with this crop include pathogens, saprotrophs and endophytes. These fungi cause many diseases and curtail productivity, yet only a few groups of microfungi have received attention in China. There are many problems with identification and classification of the microfungi associated with grapevine in China and worldwide. This study aimed to examine the taxonomy and phylogeny of several important plant pathogens of Vitis species as well as the saprotrophic communities associated with this crop in Chinese vineyards. The data generated in this study are intended to provide an insight into the classification of microfungi associated with Vitis species. Colletotrichum is one of the most important pathogens worldwide. Three species were identified in this study to be responsible for grape ripe rot disease in China and 13 species were identified as associated with grape ripe rot worldwide, using multigene analyses. Disease symptoms, infection strategies and control measures are provided for grape ripe rot disease. A backbone phylogenetic tree with notes on host and geographical distribution of all the accepted Colletotrichum species is also provided. Notes and phylogenetic analysis of each and every Colletotrichum species complex is also given. The taxonomy, classification and new data of all accepted Colletotrichum species are provided. Pestalotiod fungi are another group that have received a less attention in Chinese vineyards. One Neopestalotiopsis species and one Pestalotiopsis species were identified in Chinese vineyards causing fruit rot, leaf spot and stem die back. Eight Pestalotiopsis species and four Neopestalotiopsis species were identified to be associated with the pestalotiod fungal diseases worldwide. The type herbarium specimens of Elsinoe and Moleriella were studied. Descriptions and notes are provided in order to resolve their classification. The genera in the family Elsinoaceae were revised using morphological characters. A phylogenetic analysis was conducted in order to establish the familial position of Elsinoaceae within class Dothideomycetes. Seven genera that were earlier belonged to the family Elsinoaceae was excluded and placed in other families. An overview of the grapevine anthracnose caused by Elsinoe around the world is given. Elsinoe ampelina appears to be the sole causal agent of this disease. A survey of vineyards in four provinces of China was carried out to identify the causal agent of pseudocercospora leaf spot. A phylogenetic analysis based on combined LSU, ITS and ACT loci, coupled with morphology, showed that Pseudocercospora vitis is the sole causal agent of this leaf spot disease in China. Botrytis cinerea is the main causal agent of the Botrytis bunch rot and blight in China. An overview of the above two diseases with symptoms, infection strategy and control methods are given. Specimens obtained from Italy, Russia, Thailand and China were morphologically and phylogenetically analyzed. We have provided notes on various fungal taxa. In this set of notes we deal with species found on the grape genus Vitis. We provide notes of 49 taxa of fungi, including an asexual report of Alfaria cyperi-esculenti and 34 new host records or distribution records. Vitis is one of the most important economically important crops grown worldwide. The taxonomic placement of most taxa discussed in this study is based on a modern taxonomic framework based on analysis of multi-gene sequence data. Of the recorded saprotrophic species, Alternaria alternata, Colletotrichum siamense, Diplodia seriata, Dothiorella sarmentorum, Fusarium oxysporum and Neofussicoccum parvum are known to be major pathogens. Saprotrophs are among the key players in decomposition and play a major role in nutrient recycling. However, saprotroph communities associated with Vitis vinifera have received a less attention. Using both culture dependent and culture independent techniques, identification of saprotroph communities of table grape (Red Globe) and wine grape (Carbanate Gernischet) in China was investigated. Single spore isolation combined with phylogenetic analysis was carried out for the culture dependent approach, while for the culture independent approach mycobiome internal transcribed spacer (ITS1) region was sequenced for the two cultivars. Culture dependent and culture independent approaches for characterisation of the saprotrophic fungal communities associated with V. vinifera were compared in this thesis. A comparison of the potential effect of grape cultivars on fungal saprotrophic community composition and richness is also provided. Potential plant pathogens and endophytes within the saprotrophic fungal community associated with Vitis vinifera were also investigated. The culture dependent approach revealed 46 taxa. The two approaches showed that the saprotrophic fungal communities on the two cultivars are relatively distinct. Red Globe variety showed a higher species richness than the Carbanate Gernischet. However the diversity indices do not appear to have a significant difference between the two communities. In the culture independent approach we detected a total of 226 fungal OTUs with 176 and 189 belonging to the cultivars Carbanate Gernischet and Red Globe, respectively. There were 139 fungal OTUs shared between the two V. vinifera cultivars and 37 and 50 OTUs were specific to Carbanate Gernischet and Red Globe cultivars. The NMDS ordination plot and SIMPER analysis revealed distinct fungal communities in the two cultivars. In Carbanate Gernischet, members of Ascomycota accounted for 77% and in Red Globe, almost all sequences were Ascomycota. We identified several main grapevine pathogens as saprotrophs in both studies which leads us to the conclusion that dead plant matters in a grape orchard are the potential primary inocula for plant pathogens. A worldwide checklist of fungi on Vitis species, based on the present and previous research, which includes their modes and distribution for 890 taxa is provided. Camellia sinensis is another important crop cultivated in China. Botryosphaeriaceous taxa associated with leaf necrosis of this crop are reported. Botryosphaeria dothidea, Lasiodiplodia pseudotheobromae and L. theobromae were identified as the causal agents of this disease based on morphology, phylogeny and pathogenicity tests. In all, twelve publications (nine first author and three co-first author) were published during this study, and these are appended in the thesis. Conclusions drawn and future possible works relevant to this study are given at the end of the thesis. An exhaustive list of references and materials used are also provided.

Mae Fah Luang University

Address: CHIANG RAI

Email: library@mfu.ac.th

Name: Kevin David Hyde

Role: Advisor

Name: Somrudee Nilthong

Role: Co-Advisor

Created: 2017

Issued: 2561

Modified: 2020-01-21

Issued: 2018-09-11

วิทยานิพนธ์/Thesis

application/pdf

CallNumber: Thesis QK603.2 J426t 2017

eng

DegreeName: Dotor of Philosophy

Level: Doctoral Degree

Descipline: Biosciences

Grantor: Mae Fah Luang University

©copyrights Mae Fah Luang University

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