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Fulltext Dissecting the fungal biology of Bipolaris papendorfii: from phylogenetic to comparative genomic analysis

Kuan CS, Yew SM, Toh YF, Chan CL, Ngeow YF, Lee KW, et al.

DNA Res, 2015 Jun;22(3):219-32.
PMID: 25922537 DOI: 10.1093/dnares/dsv007

Bipolaris papendorfii has been reported as a fungal plant pathogen that rarely causes opportunistic infection in humans. Secondary metabolites isolated from this fungus possess medicinal and anticancer properties. However, its genetic fundamental and basic biology are largely unknown. In this study, we report the first draft genome sequence of B. papendorfii UM 226 isolated from the skin scraping of a patient. The assembled 33.4 Mb genome encodes 11,015 putative coding DNA sequences, of which, 2.49% are predicted transposable elements. Multilocus phylogenetic and phylogenomic analyses showed B. papendorfii UM 226 clustering with Curvularia species, apart from other plant pathogenic Bipolaris species. Its genomic features suggest that it is a heterothallic fungus with a putative unique gene encoding the LysM-containing protein which might be involved in fungal virulence on host plants, as well as a wide array of enzymes involved in carbohydrate metabolism, degradation of polysaccharides and lignin in the plant cell wall, secondary metabolite biosynthesis (including dimethylallyl tryptophan synthase, non-ribosomal peptide synthetase, polyketide synthase), the terpenoid pathway and the caffeine metabolism. This first genomic characterization of B. papendorfii provides the basis for further studies on its biology, pathogenicity and medicinal potential.
Fulltext Complete Genome Sequence of Pasteurella multocida Serotype A Strain PMTB2.1 Isolated from Buffaloes That Died of Septicemia in Malaysia

Jabeen S, Yong YH, Abdullah FJF, Zakaria Z, Mat Isa N, Tan YC, et al.

Genome Announc, 2017 Nov 02;5(44).
PMID: 29097462 DOI: 10.1128/genomeA.01190-17

Pasteurella multocida causes pneumonic pasteurellosis and hemorrhagic septicemia (HS) in large ruminants. In this study, we determined the complete genome sequence of P. multocida strain PMTB2.1 capsular serotype A isolated from buffaloes that died of septicemia.
Fulltext De novo transcriptome analyses of host-fungal interactions in oil palm (Elaeis guineensis Jacq.)

Ho CL, Tan YC, Yeoh KA, Ghazali AK, Yee WY, Hoh CC

BMC Genomics, 2016;17:66.
PMID: 26781612 DOI: 10.1186/s12864-016-2368-0

Basal stem rot (BSR) is a fungal disease in oil palm (Elaeis guineensis Jacq.) which is caused by hemibiotrophic white rot fungi belonging to the Ganoderma genus. Molecular responses of oil palm to these pathogens are not well known although this information is crucial to strategize effective measures to eradicate BSR. In order to elucidate the molecular interactions between oil palm and G. boninense and its biocontrol fungus Trichoderma harzianum, we compared the root transcriptomes of untreated oil palm seedlings with those inoculated with G. boninense and T. harzianum, respectively.
Bursal transcriptome profiling of different inbred chicken lines reveals key differentially expressed genes at 3 days post-infection with very virulent infectious bursal disease virus

Farhanah MI, Yasmin AR, Mat Isa N, Hair-Bejo M, Ideris A, Powers C, et al.

J Gen Virol, 2018 Jan;99(1):21-35.
PMID: 29058656 DOI: 10.1099/jgv.0.000956

Infectious bursal disease is a highly contagious disease in the poultry industry and causes immunosuppression in chickens. Genome-wide regulations of immune response genes of inbred chickens with different genetic backgrounds, following very virulent infectious bursal disease virus (vvIBDV) infection are poorly characterized. Therefore, this study aims to analyse the bursal tissue transcriptome of six inbred chicken lines 6, 7, 15, N, O and P following infection with vvIBDV strain UK661 using strand-specific next-generation sequencing, by highlighting important genes and pathways involved in the infected chicken during peak infection at 3 days post-infection. All infected chickens succumbed to the infection without major variations among the different lines. However, based on the viral loads and bursal lesion scoring, lines P and 6 can be considered as the most susceptible lines, while lines 15 and N were regarded as the least affected lines. Transcriptome profiling of the bursa identified 4588 genes to be differentially expressed, with 2985 upregulated and 1642 downregulated genes, in which these genes were commonly or uniquely detected in all or several infected lines. Genes that were upregulated are primarily pro-inflammatory cytokines, chemokines and IFN-related. Various genes that are associated with B-cell functions and genes related to apoptosis were downregulated, together with the genes involved in p53 signalling. In conclusion, bursal transcriptome profiles of different inbred lines showed differential expressions of pro-inflammatory cytokines and chemokines, Th1 cytokines, JAK-STAT signalling genes, MAPK signalling genes, and their related pathways following vvIBDV infection.
Fulltext Draft Genome Sequence of Ochroconis constricta UM 578, Isolated from Human Skin Scraping

Chan CL, Yew SM, Na SL, Tan YC, Lee KW, Yee WY, et al.

Genome Announc, 2014;2(2).
PMID: 24744321 DOI: 10.1128/genomeA.00074-14

Ochroconis constricta is a soilborne dematiaceous fungus that has never been reported to be associated with human infection. Here we report the first draft genome sequence of strain UM 578, isolated from human skin scraping. The genomic information revealed will contribute to a better understanding of this species.
Fulltext Genome analysis of Daldinia eschscholtzii strains UM 1400 and UM 1020, wood-decaying fungi isolated from human hosts

Chan CL, Yew SM, Ngeow YF, Na SL, Lee KW, Hoh CC, et al.

BMC Genomics, 2015 Nov 18;16:966.
PMID: 26581579 DOI: 10.1186/s12864-015-2200-2

BACKGROUND: Daldinia eschscholtzii is a wood-inhabiting fungus that causes wood decay under certain conditions. It has a broad host range and produces a large repertoire of potentially bioactive compounds. However, there is no extensive genome analysis on this fungal species.
RESULTS: Two fungal isolates (UM 1400 and UM 1020) from human specimens were identified as Daldinia eschscholtzii by morphological features and ITS-based phylogenetic analysis. Both genomes were similar in size with 10,822 predicted genes in UM 1400 (35.8 Mb) and 11,120 predicted genes in UM 1020 (35.5 Mb). A total of 751 gene families were shared among both UM isolates, including gene families associated with fungus-host interactions. In the CAZyme comparative analysis, both genomes were found to contain arrays of CAZyme related to plant cell wall degradation. Genes encoding secreted peptidases were found in the genomes, which encode for the peptidases involved in the degradation of structural proteins in plant cell wall. In addition, arrays of secondary metabolite backbone genes were identified in both genomes, indicating of their potential to produce bioactive secondary metabolites. Both genomes also contained an abundance of gene encoding signaling components, with three proposed MAPK cascades involved in cell wall integrity, osmoregulation, and mating/filamentation. Besides genomic evidence for degrading capability, both isolates also harbored an array of genes encoding stress response proteins that are potentially significant for adaptation to living in the hostile environments.
CONCLUSIONS: Our genomic studies provide further information for the biological understanding of the D. eschscholtzii and suggest that these wood-decaying fungi are also equipped for adaptation to adverse environments in the human host.