Ranjita Subramaniam (2014) De novo whole genome sequencing of a wood-degrading basidiomycetes, Tinctoporellus epimiltinus RS1. Masters thesis, Universiti Malaysia Sabah.
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Abstract
Members of the genus Tinctoporellus which belong to the wood-degrading basidiomycetes, possess the ability to synthesize an array of industrially potent enzymes and metabolites. In spite of its importance, members of this genus are poorly investigated. As such, the aim of this project is to perform whole genome sequencing (WGS) of Tinctopore//us epimiltinus RSl which was isolated from a culture plate that was originally thought to be Trichoderma. The identification of this fungal species was carried out through macroscopic and microscopic analysis which indicated the identification of the species as Tinctoporellus epimiltinus. Further testing by DNA sequencing of the partial 185-ITS1-5.85-ITS2-partial28S region was performed to verify the identity of the species. Next, WGS was performed using the Illumina Miseq Sequencer. The Nextera DNA sample preparation kit was used to produce the sequencing-ready libraries with an average fragment size of 468 bp. Sequencing was done with a paired-end 2x1so bp protocol. The sequencing process generated 29.22 million paired-end reads with a total output of 4.0 Gb. De novo assembly was carried out using the CLC Genomic Workbench version 6.5.1 resulted in 2,004 contigs with an NS0 of 58,556. The selftraining GeneMark-ES software predicted 13,795 protein coding sequences which were then screened for ligninolytic enzyme coding sequences. The results indicate that the genome of Tinctoporellus epimiltinus RSl possess 10 putative manganese peroxidases (MnPs), 12 laccases, 4 undetermined genes, which were suspected to encode for versatile peroxidases (VPs), and 1 putative dye-decolourizing type protein. Interestingly, lignin peroxidases were not detected. The exon length conservation diagrams were plotted based upon reference gene models. At the same time, neighbour joining trees with Kimura 2-parameter model were plotted for MnP and laccase encoding genes with 1,000 bootstrap replicates. An insight into the predicted gene models and phylogenetic analysis suggests that the presence of high number of isoforms of MnPs and laccases might be driven by gene duplication events. As such, Tinctoporellus epimiltinus RSl is potentially a reservoir of MnPs and laccases and other ligninolytic enzymes.
| Item Type: | Thesis (Masters) |
|---|---|
| Keyword: | Tinctoporellus epimiltinus, Whole genome sequencing, Ligninolytic enzymes, Manganese peroxidase, Laccase |
| Subjects: | Q Science > QK Botany > QK1-989 Botany > QK504-(638) Cryptogams |
| Department: | INSTITUTE > Biotechnology Research Institute (BRI) |
| Depositing User: | DG MASNIAH AHMAD - |
| Date Deposited: | 19 Jun 2025 15:42 |
| Last Modified: | 19 Jun 2025 15:42 |
| URI: | https://eprints.ums.edu.my/id/eprint/44193 |
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