Browsing by Author "Nur Syamimi Yusoff"
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Publication Deciphering The Pan-Genome Of Ganoderma sp. To Depict Potential Genomic Components That Contribute To Ganoderma Boninense Pathogenicity(Malaysian Society of Applied Biology, 2018) ;Suhaila Sulaiman ;Nur Syamimi Yusoff ;Tan Joon SheongLee Yang PingThe soil-borne fungus, Ganoderma boninense is notorious as the cause of basal stem rot (BSR) disease in oil palm that results in severe economic losses. Due to insufficient functional information of its genome, mechanism underlying the infection is still enigmatic. Despite the constraint, here we report the pan-genome of eight draft genomes of Ganoderma sp. that delineated into 35,121 orthologous genes (OGs), consisting 4,898 genes in core genome and 30,223 genes in accessory genome, whilst the latter encompasses of 1,905 species-specific genes. Further genome-wide comparative analysis discovers 607 genes in pathogenic fungi G. boninense but not in its related non-pathogenic Ganoderma sp., suggesting their potential role in G. boninense pathogenicity towards its host. By implementing various bioinformatics tools and public databases, the incorporated functional enrichment of the candidate genes leads to inference of their role during host-pathogen interaction. This enables us to narrow down the entire gene catalogue in Ganoderma sp. for experimental verification in the laboratory. It is undeniable that the harnessing of Ganoderma sp. pan-genome data will conform to a more structured downstream analysis in understanding the role of G. boninense as the key agent of BSR in oil palm. - Some of the metrics are blocked by yourconsent settings
Publication Genome-wide Comparative Analysis In Discovering Potential Evolved Hypothetical Genes In Infected Oil Palm(Malaysian Society of Applied Biology, 2018) ;Suhaila Sulaiman ;Nur Syamimi YusoffLee Yang PingBased on the genome annotation, oil palm genes can have either known or unknown functions. Hypothetical genes or unknown genes constitute averagely 24.40% from three gene model versions of oil palm (Elaeis guineensis Jacq.). The conventional method to prove their existence is labourious and limited, thus by bioinformatics analysis of genomic and transcriptomicdata, the potential role of hypothetical genes can be scrutinised comprehensively. In this study, the annotated hypotheticalgenes are reanalysed using sequence-based and transcriptomic data analysis to investigate their presence, differential expression and potential horizontal gene transfer (HGT) event with distantly related organisms in infected oil palm. In total 610 sequences still remain as hypothetical whilst others showed similarities with known genes which are not considered as hypothetical anymore. From the 610 genes, 92 are conserved in model plants and non-Plantae and eight genes are potential candidates of HGT events in oil palm with changes of expression during Ganoderma boninense infection. A transferred gene usually possess critical function, thus the presence of true hypothetical genes should not be ignored since it can be served as potential biomarkers of desired traits in oil palm.