• 한국균학회소식:학술대회논문집
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• 2018.05a
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• pp.22-22
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• 2018

Fungal genome sequencing and assembly have been trivial in these days. Genome analysis relies on high quality of gene prediction and annotation. Automatic fungal genome annotation pipeline is essential for handling genomic sequence data accumulated exponentially. However, building an automatic annotation procedure for fungal genomes is not an easy task. FunGAP (Fungal Genome Annotation Pipeline) is developed for precise and accurate prediction of gene models from any fungal genome assembly. To make high-quality gene models, this pipeline employs multiple gene prediction programs encompassing ab initio, evidence-, and homology-based evaluation. FunGAP aims to evaluate all predicted genes by filtering gene models. To make a successful filtering guide for removal of false-positive genes, we used a scoring function that seeks for a consensus by estimating each gene model based on homology to the known proteins or domains. FunGAP is freely available for non-commercial users at the GitHub site (https://github.com/CompSynBioLab-KoreaUniv/FunGAP).

• Mycobiology
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• v.48 no.3
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• pp.240-244
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• 2020

Alternaria alternata JS-1623 is an endophytic fungus isolated from a stem tissue of Korean fir, Abies koreana. Ethyl acetate extracts of culture filtrates exhibited anti-inflammatory activity in LPS induced microglia BV-2 cell without cytotoxicity. Here we report a 33.67 Mb sized genome assembly of JS-1623 comprised of 13 scaffolds with N50 of 4.96 Mb, and 92.41% of BUSCO completeness. GC contents were 50.97%. Of the 11,197 genes annotated, gene families related to the biosynthesis of secondary metabolites or transcription factors were identified.

• Genomics & Informatics
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• v.4 no.4
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• pp.147-160
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• 2006

GATA transcription factors are widespread eukaryotic regulators whose DNA-binding domain is a class IV zinc finger motif in the form $CX_{2}CX_{17-20}CX_{2}C$followed by a basic region. In fungi, they act as transcriptional activators or repressors in several different processes, ranging from nitrogen source utilization to mating-type switching. Using an in-house bioinformatics portal system, we surveyed 50 fungal and 9 out-group genomes and identified 396 putative fungal GATA transcription factors. The proportion of GATA transcription factors within a genome varied among taxonomic lineages. Subsequent analyses of phylogenetic relationships among the fungal GATA transcription factors, as well as a study of their domain architecture and gene structure, demonstrated high degrees of conservation in type IVa and type IVb zinc finger motifs and the existence of distinctive clusters at least at the level of subphylum. The SFH1 subgroup with a 20-residue loop was newly identified, in addition to six well-defined subgroups in the subphylum Pezizomycotina. Furthermore, a novel GATA motif with a 2f-residue loop ($CX_{2}CX_{21}CX_{2}C$, designated 'zinc finger type IVc') was discovered within the phylum Basidiomycota. Our results suggest that fungal GATA factors might have undergone multiple distinct modes of evolution resulting in diversified cellular modulation in fungi.

• Mycobiology
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• v.49 no.3
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• pp.294-296
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• 2021

An endolichenic fungus, Xylaria grammica strain EL000614, showed strong nematicidal effects against plant pathogenic nematode, Meloidogyne incognita by producing grammicin. We report genome assembly of X. grammica EL000614 comprised of 25 scaffolds with a total length of 54.73 Mb, N50 of 4.60 Mb, and 99.8% of BUSCO completeness. GC contents of this genome were 44.02%. Gene families associated with biosynthesis of secondary metabolites or regulatory proteins were identified out of 13,730 gene models predicted.

• Mycobiology
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• v.42 no.3
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• pp.241-248
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• 2014

NADPH oxidases (Noxes), transmembrane proteins found in most eukaryotic species, generate reactive oxygen species and are thereby involved in essential biological processes. However, the fact that genes encoding ferric reductases and ferric-chelate reductases share high sequence similarities and domains with Nox genes represents a challenge for bioinformatic approaches used to identify Nox-encoding genes. Further, most studies on fungal Nox genes have focused mainly on functionality, rather than sequence properties, and consequently clear differentiation among the various Nox isoforms has not been achieved. We conducted an extensive sequence analysis to identify putative Nox genes among 34 eukaryotes, including 28 fungal genomes and one Oomycota genome. Analyses were performed with respect to phylogeny, transmembrane helices, di-histidine distance and glycosylation. Our analyses indicate that the sequence properties of fungal Nox genes are different from those of human and plant Nox genes, thus providing novel insight that will enable more accurate identification and characterization of fungal Nox genes.

• Journal of Microbiology and Biotechnology
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• v.14 no.1
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• pp.74-80
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• 2004

Aspergillus fumigatus is one of the most common fungi in the human environment, both in-doors and out-doors. It is the main causative agent of invasive aspergillosis, a life-threatening mycosis among immunocompromised patients. The genome has been sequenced by an international consortium, including the Wellcome Trust Sanger Institute (U.K.) and The Institute for Genomic Research (TIGR, U.S.A.), and a ten times whole genome shotgun sequence assembly has been made publicly available. In this study, we identified tricarboxylic acid (TCA) cycle enzymes of A. fumigatus by comparative analysis with four other fungal species. The open reading frames showed high amino acid sequence similarity with the other fungal citric acid enzymes and well-conserved functional domains. All genes present in Saccharomyces cerevisiae, Schizosaccharomyces pombe, Candida albicans, and Neurospora crassa were also found in A. fumigatus. In addition, we identified four A. fumigatus genes coding for enzymes in the glyoxylate shunt, which may be required for fungal virulence. The architecture of multi-gene encoded enzymes, such as isocitrate dehydrogenase, 2-ketoglutarate, succinyl-CoA synthetase, and succinate dehydrogenase was well conserved in A. fumigatus. Furthermore, our results show that genes of A. fumigatus can be detected reliably using GlimmerM.

• Mycobiology
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• v.44 no.2
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• pp.105-111
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• 2016

Paclitaxel (taxol) has long been used as a potent anticancer agent for the treatment of many cancers. Ever since the fungal species Taxomyces andreanae was first shown to produce taxol in 1993, many endophytic fungal species have been recognized as taxol accumulators. In this study, we analyzed the taxol-producing capacity of different Colletotrichum spp. to determine the distribution of a taxol biosynthetic gene within this genus. Distribution of the taxadiene synthase (TS) gene, which cyclizes geranylgeranyl diphosphate to produce taxadiene, was analyzed in 12 Colletotrichum spp., of which 8 were found to contain the unique skeletal core structure of paclitaxel. However, distribution of the gene was not limited to closely related species. The production of taxol by Colletotrichum dematium, which causes pepper anthracnose, depended on the method in which the fungus was stored, with the highest production being in samples stored under mineral oil. Based on its distribution among Colletotrichum spp., the TS gene was either integrated into or deleted from the bacterial genome in a species-specific manner. In addition to their taxol-producing capacity, the simple genome structure and easy gene manipulation of these endophytic fungal species make them valuable resources for identifying genes in the taxol biosynthetic pathway.

• Korean Journal of Microbiology
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• v.53 no.3
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• pp.216-218
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• 2017

We here provide the complete genome sequence of Bacillus thuringiensis C25, the strain showing antagonistic effects on fungal phytopathogens. The genome comprised of 5,308,062 bp with 35.32% G+C content of a circular chromosome and a plasmid containing 308,946 bp with 32.23% G+C content. The chromosome and plasmid genome included 5,683 protein coding DNA sequences, 107 tRNA and 42 rRNA genes.

• 한국균학회소식:학술대회논문집
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• 2015.05a
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• pp.20-20
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• 2015

Endophytic fungi are microorganisms inhabiting living plant tissues without causing apparent harm to the host. They are drawing increasing attention due to their ability to produce various bioactive compounds as well as their effects on host growth and resistance to biotic and abiotic stresses. As a first step to assess biodiversity of plant associated fungi in Korea and the following evaluation on diverse biological activities, we are collecting endophytic fungi from plant in wild followed by systematic long-term storage in liquid nitrogen. Molecular identification using ITS sequences was also incorporated for pure culture by hyphal tip isolation. As of April 2015, about 1,400 fungal strains had been isolated from about 170 plant taxa. Fungal isolates belonging to Pleosporales, Diaporthales, Glomerellales, Hypocreales, and Xylariales were the most abundant. These collections are being used for several complementary researches, including screening of isolates with novel bioactive compounds or conferring drought stress resistance, phylogenetic and genomic study. Genome sequencing was performed for 3 isolates, one Xylaria sp. strain JS573 producing griseofulvin, an antifungal compound, and two Fusarium spp. strains JS626 and JS1030, which are assumed to be new species found in Korea. More detailed analysis on these genomes will be presented. These collections and genome informations will serve as invaluable resources for identifying novel bioactive materials in addition to expand our knowledge on fungal biodiversity.

• Genomics & Informatics
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• v.11 no.1
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• pp.52-54
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• 2013

Proteins in DNAJ/K families are ubiquitous, from prokaryotes to eukaryotes, and function as molecular chaperones. For systematic phylogenomics of the DNAJ/K families, we developed the Eukaryotic DNAJ/K Database (EDD). A total of 12,908 DNAJs and 4,886 DNAKs were identified from 339 eukaryotic genomes in the EDD. Kingdom-wide comparison of DNAJ/K families provides new insights on the evolutionary relationship within these families. Empowered by 'class', 'cluster', and 'taxonomy' browsers and the 'favorite' function, the EDD provides a versatile platform for comparative genomic analyses of DNAJ/K families.