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Colletotrichum acutatum sensu lato : from diversity study to genome analysis
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Baroncelli, Riccardo (2012) Colletotrichum acutatum sensu lato : from diversity study to genome analysis. PhD thesis, University of Warwick.
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Official URL: http://webcat.warwick.ac.uk/record=b2680945~S1
Abstract
Colletotrichum acutatum sensu lato includes a number of important pathogens that cause
economically significant losses of various crops. The C. acutatum species complex has a
wide host range in both domesticated and wild plant species, and its capability to infect
different types of hosts such as insects has also been described. Members belonging to this
complex are able to develop three different types of interaction with plant hosts including
biotrophic, necrotrophic and hemibiotrophic infections and are also capable of surviving on
weeds and non-hosts without causing visible symptoms. They are mainly asexual, but some
have a teleomorphic state called Glomerella and can be either homothallic or heterothallic.
The sexual behaviour in Glomerella is more complicated than in most ascomycetes, and
strains within the same species do not show a typical MAT1-1/2 system.
The overall aim of this study was to gain an improved understanding of the relationships
between the genetic diversity of global populations, host association patterns, geographic
distribution and biological and pathological attributes. A database (CaITSdb) containing
more than 800 rRNA sequences deposited in GenBank was created along with key
biogeographic information, and the data have been analysed in order to investigate genetic
diversity and distribution of sub-populations and their evolutionary relationships. The
combined evidence was used to assemble a core collection of 120 isolates that are
representative of the diversity in host preference, geographic origin, mating behaviour and
molecular genetic variation. A multi-locus sequencing approach (based on four neutral loci)
has been used to evaluate phylogenetic relationships amongst the isolates in the core
collection. A strong relationship was observed between various genetic groups distinguished
and their mating behaviour, geographic distribution and host association patterns.
Oceania
has been identified as a likely geographic origin of this pathogen, as the highest level of
variability and groups related to a hypothetical ancestral population are mainly distributed in
these countries. All homothallic isolates capable of producing perithecia belonged to the
same genetic group A7; whereas all self-sterile heterothallic isolates were classified as either
A3 or A5. Isolates derived from the same host tend to cluster together into genetic groups or
sub-populations. This evidence is generally in agreement with recent published work on
taxonomic re-assessment of Colletotrichum acutatum sensu lato, which indicates at least
fifteen new species. This study has provided the evidence for the occurrence of three distinct
genetic groups on strawberry in the UK corresponding to three species reported in the
literature namely, C. nymphaeae, C. fioriniae and C. godetiae. Isolates belonging to the
genetic groups that correspond to C. nymphaeae and C. fioriniae appeared to be the most
aggressive on strawberry, followed by C. godetiae, and C. simmondsii (not found in the UK).
Representative isolates of other species were less aggressive.
The first whole genome sequence an isolate (A9 = C. simmondsii) from the C. acutatum
sensu species complex was assembled and analysed using a range of bioinformatics
algorithms. An isolate of C. simmondsii was chosen based on its wide host range including
strawberry and the phylogeographic position. Genome analyses enabled prediction and
annotation of the whole gene set at 13549 including 6 % unique to this species. The data also
suggested an interesting expansion of several gene families, such as those encoding
carbohydrate-active enzymes, secondary metabolites pathways and effectors which could be
associated with the wide host range. The new knowledge and resources developed with the
genome analyses along with the results of the population level diversity studies provide a
platform for future comparative and functional genomics investigations to advance this
research.
Item Type: | Thesis (PhD) | ||||
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Subjects: | Q Science > QH Natural history > QH426 Genetics Q Science > QK Botany |
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Library of Congress Subject Headings (LCSH): | Genomics, Colletotrichum, Phytopathogenic microorganisms, Variation (Biology) | ||||
Official Date: | October 2012 | ||||
Dates: |
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Institution: | University of Warwick | ||||
Theses Department: | School of Life Sciences | ||||
Thesis Type: | PhD | ||||
Publication Status: | Unpublished | ||||
Supervisor(s)/Advisor: | Sreenivasaprasad, Surapareddy; Holub, E. B.; Barbaba, Dez; Peterson, J. (Jeff); Lane, Charles R. | ||||
Extent: | 1 volume (various pagings) : illustrations, charts. | ||||
Language: | eng |
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