Genome sequencing and in silico characterisation of cladosporium sphaerospermum / Yew Su Mei
Dematiaceous fungi are a taxonomically diverse group of heterogeneous fungi that are present in the environment. Although rare, many species in this group are known to cause diseases in humans and animals. In this study, a collection of 75 fungal isolates were recovered from various clinical spec...
Saved in:
| Main Author: | |
|---|---|
| Format: | Thesis |
| Published: |
2017
|
| Subjects: | |
| Online Access: | http://studentsrepo.um.edu.my/11635/4/su_mei.pdf http://studentsrepo.um.edu.my/11635/ |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| Summary: | Dematiaceous fungi are a taxonomically diverse group of heterogeneous fungi that
are present in the environment. Although rare, many species in this group are known to
cause diseases in humans and animals. In this study, a collection of 75 fungal isolates
were recovered from various clinical specimens. They were identified through
morphology and molecular methods using the internal transcribed spacer (ITS)-based
phylogenetic analysis. The complementation of the molecular approach enables the
identification of 73 isolates at the species level. The most common species isolated were
Cladosporium, Cochliobolus, and Neoscytalidium. Also, 16 isolates from the seven
species identified have not been reported to cause human infections. Among the
Cladosporium species that were isolated, the species C. sphaerospermum was most
frequently isolated. This study was proceeded by whole genome analysis of the C.
sphaerospermum, using the strain UM 843 as a study model to explore genetic
information and its basic biology. C. sphaerospermum is a ubiquitous saprophytic
fungus that has been documented to cause allergy and other opportunistic diseases in
humans. Detail characterisation of this isolate has affirmed the identity of UM 843 and
its ability to survive in high salt medium (up to 20% NaCl). The genome of UM 843
was generated by combining 500-bp and 5-kb insert libraries, containing 9,652
predicted gene models in the 26.89 Mb genome. Functional annotation of the predicted
genes suggests this fungus has the capability to degrade carbohydrate and protein
complexes. The abundance of carbohydrate active enzymes (CAZymes) assists in the
degradation of hemicellulose and pectin, thus suggesting the precedence of this fungus
towards soft plant tissues. Putative genes encoding peptidases from family A01, S09,
and M36 that share similarity with Aspergillus peptidases responsible for lung tissue
hydrolysis were also identified. UM 843 was also found to carry 16 putative secondary
iv
metabolite backbone genes, three of these are predicted to be responsible for the
synthesis of melanin, siderophores, and cladosins. Besides siderophores, UM 843
contains gene encoding proteins that are involved in iron homeostasis via the reductive
iron assimilation (RIA) process. In response to salinity, UM 843 was identified to
encode 29 ion transporters and the synthesis of various compatible solutes. The analysis
of sexual reproduction suggests that UM 843 is a heterothallic fungus. The genome of
UM 843 revealed 28 putative genes associated with C. sphaerospermum allergy.
Orthologous gene analysis on UM 843 with 22 other Dothideomycetes showed 125
genes uniquely present in UM 843. Of these, four genes were predicted to encode class
1 hydrophobins which may be allergens specific to Cladosporium. Further analysis
showed that the mRNA of the four genes were detected by reverse transcriptionpolymerase chain reaction (RT-PCR). The genomic analysis of C. sphaerospermum UM
843, can significantly contribute to the knowledge of the biology and allergenicity of
this species which has not been studied previously |
|---|