• Animal Systematics, Evolution and Diversity
• /
• v.26 no.3
• /
• pp.197-201
• /
• 2010

We sequenced the whole mitochondrial genome of Dendronephthya gigantea (Anthozoa: Octocorallia: Nephteidae), the first mitochondrial genome sequence report in the Family Nephtheidae. The mitochondrial genome of D. gigantea was 18,842 bp in length, and contained 14 protein coding genes (atp6 and 8, cox1-3, cytb, nd1-6 and 4L, and msh1), two ribosomal RNAs, and only one transfer RNA. The gene content and gene order is identical to other octocorals sequenced to date. The portion of the noncoding regions is slightly larger than the other octocorals (5.08% compared to average 3.98%). We expect that the information of gene content, gene order, codon usage, noncoding region and protein coding gene sequence could be used in the further analysis of anthozoan phylogeny.

• Journal of Microbiology and Biotechnology
• /
• v.22 no.5
• /
• pp.649-653
• /
• 2012

A temperate phage was isolated from emetic Bacillus cereus NCTC 11143 by mitomycin C and characterized by transmission electron microscopy and DNA and protein analyses. Whole genome sequencing of Bacillus phage 11143 was performed by GS-FLX. The phage has a dsDNA genome of 39,077 bp and a 35% G+C content. Bioinformatic analysis of the phage genome revealed 49 putative ORFs involved in replication, morphogenesis, DNA packaging, lysogeny, and host lysis. Bacillus phage 11143 could be classified as a member of the Siphoviridae family by morphology and genome structure. Genomic comparisons at the DNA and protein levels revealed homologous genetic modules with patterns and morphogenesis proteins similar to those of other Bacillus phages. Thus, Bacillus phages might have a mosaic genetic relationship.

• Journal of Dairy Science and Biotechnology
• /
• v.38 no.3
• /
• pp.142-145
• /
• 2020

Enterococcus faecalis CAUM157, isolated from raw cow's milk, is a Gram-positive, facultatively anaerobic, and non-spore-forming bacterium capable of inhabiting a wide range of environmental niches. E. faecalis CAUM157 was observed to produce a two-peptide bacteriocin that had a wide range of activity against several pathogens, including Listeria monocytogenes, Staphylococcus aureus, and periodontitis-causing bacteria. The whole genome of E. faecalis CAUM157 was sequenced using the PacBio RS II platform, revealing a genome size of 2,972,812 bp with a G+C ratio of 37.44%, assembled into two contigs. Annotation analysis revealed 2,830 coding sequences, 12 rRNAs, and 61 tRNAs. Further, in silico analysis of the genome identified a single bacteriocin gene cluster.

• Journal of Animal Science and Technology
• /
• v.62 no.3
• /
• pp.420-422
• /
• 2020

Streptococcus hyointestinalis B19 was isolated from chicken feces collected from local farm in Anseong, Korea. S. hyointestinalis B19 was shown to produce bacteriocin-like compounds exhibiting inhibitory activities against several pathogens including strains of Clostridium perfringens and Listeria monocytogenes. The whole genome of S. hyointestinalis B19 strain was sequenced using PacBio RS II platform. The genome comprised four contigs with a size of 2,217,061 bp. The DNA G + C content was found to be 42.95 mol%. Annotation results revealed 2,266 coding sequences (CDSs), 18 rRNAs, and 61 tRNA genes. Based on genome analysis, we found that the strain B19 possessed various genes associated with bacteriocin synthesis, modification, and transport.

• Journal of Animal Science and Technology
• /
• v.63 no.6
• /
• pp.1464-1467
• /
• 2021

Bacillus coagulans CACC 834 was isolated from canine feces, and its potential probiotic properties were characterized by functional genome analysis. Whole-genome sequencing of B. coagulans CACC 834 was performed using the PacBio RSII platforms. The complete genome assembly consisted of one circular chromosome (3.1 Mb) with guanine (G) + cytosine (C) content of 47.1%. Annotation revealed 3,181 protein-coding sequences (CDSs), 30 rRNAs, and 83 tRNAs. Gene associated 11% of the genes were involved in replication, recombination, and repair. We also annotated various stress-related, acid resistance, bile salt resistance and adhesion-related domains in this strain, which likely provide support in exerting probiotic action by survival under gastrointestinal tract. These results add to our comprehensive understanding of B. coagulans and suggest potential mammal-related industrial applications.

• Genomics & Informatics
• /
• v.21 no.3
• /
• pp.35.1-35.12
• /
• 2023

The Bacillus cereus group, also known as B. cereus sensu lato (B. cereus s.l.), is composed of various Bacillus species, some of which can cause diarrheal or emetic food poisoning. Several emerging highly heat-resistant Bacillus species have been identified, these include B. thermoamylovorans, B. sporothermodurans, and B. cytotoxicus NVH 391-98. Herein, we performed whole genome analysis of two thermotolerant Bacillus sp. isolates, Bacillus sp. B48 and Bacillus sp. B140, from an omelet with acacia leaves and fried rice, respectively. Phylogenomic analysis suggested that Bacillus sp. B48 and Bacillus sp. B140 are closely related to B. cereus and B. thuringiensis, respectively. Whole genome alignment of Bacillus sp. B48, Bacillus sp. B140, mesophilic strain B. cereus ATCC14579, and thermophilic strain B. cytotoxicus NVH 391-98 using the Mauve program revealed the presence of numerous homologous regions including genes responsible for heat shock in the dnaK gene cluster. However, the presence of a DUF4253 domain-containing protein was observed only in the genome of B. cereus ATCC14579 while the intracellular protease PfpI family was present only in the chromosome of B. cytotoxicus NVH 391-98. In addition, prophage Clp protease-like proteins were found in the genomes of both Bacillus sp. B48 and Bacillus sp. B140 but not in the genome of B. cereus ATCC14579. The genomic profiles of Bacillus sp. isolates were identified by using whole genome analysis especially those relating to heat-responsive gene clusters. The findings presented in this study lay the foundations for subsequent studies to reveal further insights into the molecular mechanisms of Bacillus species in terms of heat resistance mechanisms.

• Proceedings of the Plant Resources Society of Korea Conference
• /
• 2018.04a
• /
• pp.43-43
• /
• 2018

Dumortiera hirsuta (Sw.) Nees (Dumortieraceae) is a thallose liverwort distributed in tropics and subtropics. It is the only species in family Dumortieraceae, which is the second basal family in order Marchantiales. D. hirsuta is characterized by hairy receptacles and lacking air chamber. The complete chloroplast genome of D. hirsuta was successfully rescued from raw reads generated by HiSeq4000. Its total length is 122,050 bp consisting of four regions: large single copy (LSC) region (81,697 bp), small single copy (SSC) region (20,061 bp), and two inverted repeats (IRs; 10,146 bp per each). It contained 129 genes (84 coding DNA sequence (CDS), eight rRNAs, and 37 tRNAs); 18 genes including four rRNAs, and five tRNAs are duplicated in the IR regions. The overall GC content of D. hirsuta is 28.7%, which is almost same to that of Marchantia paleacea. Phylogenetic tree based on all genes from whole chloroplast genomes will provides phylogenetic position of D. hirstua. This sequence will be an fundamental resources for further researches of order Marchantiales.

• Genomics & Informatics
• /
• v.20 no.3
• /
• pp.35.1-35.9
• /
• 2022

Microsatellites or simple sequence repeats are motifs of 1 to 6 nucleotides in length present in both coding and non-coding regions of DNA. These are found widely distributed in the whole genome of prokaryotes, eukaryotes, bacteria, and viruses and are used as molecular markers in studying DNA variations, gene regulation, genetic diversity and evolutionary studies, etc. However, in vitro microsatellite identification proves to be time-consuming and expensive. Therefore, the present research has been focused on using an in-house built java pipeline to identify, analyse, design primers and find related statistics of perfect and compound microsatellites in the seven complete genome sequences of coronavirus, including the genome of coronavirus disease 2019, where the host is Homo sapiens. Based on search criteria among seven genomic sequences, it was revealed that the total number of perfect simple sequence repeats (SSRs) found to be in the range of 76 to 118 and compound SSRs from 01 to10, thus reflecting the low conversion of perfect simple sequence to compound repeats. Furthermore, the incidence of SSRs was insignificant but positively correlated with genome size (R² = 0.45, p > 0.05), with simple sequence repeats relative abundance (R² = 0.18, p > 0.05) and relative density (R² = 0.23, p > 0.05). Dinucleotide repeats were the most abundant in the coding region of the genome, followed by tri, mono, and tetra. This comparative study would help us understand the evolutionary relationship, genetic diversity, and hypervariability in minimal time and cost.

• Journal of Animal Science and Technology
• /
• v.63 no.1
• /
• pp.191-193
• /
• 2021

Lactococcus lactis is a fermentative lactic acid bacterium that is used extensively in food fermentations. The L. lactis strain K_LL005 was isolated from the grasshopper (Oxya chinensis sinuosa) gut in Korea. In this study, we reported the complete genome sequence of Lactococcus lactis K_LL005. The final complete genome assembly consist of one circular chromosome (2,375,093 bp) with an overall guanine + cytosine (G + C) content of 35.0%. Annotation results revealed 2,281 protein-coding sequences (CDSs), 19 rRNAs, and 68 tRNA genes. Lactococcus lactis K_LL005 has a gene encoding xylose metabolism such as xylR, xylA, and xylB (xylRAB).

• Mycobiology
• /
• v.49 no.1
• /
• pp.86-88
• /
• 2021

The monokaryotic strain, Schizophyllum commune strain IUM1114-SS01, was generated from a basidiospore of dikaryotic parental strain IUM1114. It even showed the decolorizing activities for several textile dyes much better than its parental strain. Based on the results of a single-molecule real-time sequencing technology, we present the draft genome of S. commune IUM1114-SS01, comprising 41.1 Mb with GC contents of the genome were 57.44%. Among 13,380 protein-coding genes, 534 genes are carbon hydrate-active enzyme coding genes.