A Glimpse of Panax ginseng Genome Structure Revealed from Ten BAC Clone Sequences Obtained by SMRT Sequencing Platform

( Woojong Jang ),( Nam-hoon Kim ),( Junki Lee ),( Nomar Espinosa Waminal ),( Sang-choon Lee ),( Murukarthick Jayakodi ),( Hong-il Choi ),( Jee Young Park ),( Jong-eun Lee ),( Tae-jin Yang ) 한국육종학회 2017 Plant Breeding and Biotechnology Vol.5 No.1

Korean ginseng (Panax ginseng) is a well-known valuable medicinal plant with excellent therapeutic effects, however its complex genome structure has not been elucidated yet. To understand its genome structure, we obtained ten ginseng bacterial artificial chromosome (BAC) clone sequences by single-molecule real-time (SMRT) sequencing platform using a pooled DNA of the BAC clones. Out of the ten BAC clones, nine were completely assembled without any gap and one remained a single gap. The total length of BAC clone sequences was 1,163,364 bp. Sophisticated sequence analysis revealed that the 89.7% of the sequences are high copy repeat regions and the remaining 10.3% are non-repeat regions. Eleven protein-coding genes were identified in the non-repeat regions. Most of the repeat regions show more than 1,000 copies and complex structure of various repetitive elements. Ty3/Gypsy family long terminal repeat retrotransposons (LTR-RTs) are predominant repeats occupying 46.9% of the 1,163-kbp sequence. We identified six novel LTR-RTs and their insertion time. Fluorescence in situ hybridization (FISH) analysis demonstrated that PgDel2 and PgDel5 elements had a subgenome-biased distribution. Collectively, our analysis reveals that ginseng genome has very complex genome structure with abundant repetitive elements and rare gene frequency.

Antarctic tundra soil metagenome as useful natural resources of cold-active lignocelluolytic enzymes

Han Na Oh,Doyoung Park,Hoon Je Seong,Dockyu Kim,Woo Jun Sul 한국미생물학회 2019 The journal of microbiology Vol.57 No.10

Lignocellulose composed of complex carbohydrates and aromatic heteropolymers is one of the principal materials for the production of renewable biofuels. Lignocellulose-degrading genes from cold-adapted bacteria have a potential to increase the productivity of biological treatment of lignocellulose biomass by providing a broad range of treatment temperatures. Antarctic soil metagenomes allow to access novel genes encoding for the cold-active lignocellulose-degrading enzymes, for biotechnological and industrial applications. Here, we investigated the metagenome targeting cold-adapted microbes in Antarctic organic matter-rich soil (KS 2-1) to mine lignolytic and celluloytic enzymes by performing single molecule, real-time metagenomic (SMRT) sequencing. In the assembled Antarctic metagenomic contigs with relative long reads, we found that 162 (1.42%) of total 11,436 genes were annotated as carbohydrate-active enzymes (CAZy). Actinobacteria, the dominant phylum in this soil’s metagenome, possessed most of candidates of lignocellulose catabolic genes like glycoside hydrolase families (GH13, GH26, and GH5) and auxiliary activity families (AA7 and AA3). The predicted lignocellulose degradation pathways in Antarctic soil metagenome showed synergistic role of various CAZyme harboring bacterial genera including Streptomyces, Streptosporangium, and Amycolatopsis. From phylogenetic relationships with cellular and environmental enzymes, several genes having potential for participating in overall lignocellulose degradation were also found. The results indicated the presence of lignocellulose-degrading bacteria in Antarctic tundra soil and the potential benefits of the lignocelluolytic enzymes as candidates for cold-active enzymes which will be used for the future biofuel-production industry.

Complete genome sequencing and analysis of endophytic <i>Sphingomonas</i> sp. LK11 and its potential in plant growth

Asaf, Sajjad,Khan, Abdul Latif,Khan, Muhammad Aaqil,Al-Harrasi, Ahmed,Lee, In-Jung Springer International Publishing 2018 3 Biotech Vol.8 No.9

<P>Our study aimed to elucidate the plant growth-promoting characteristics and the structure and composition of <I>Sphingomonas</I> sp. LK11 genome using the single molecule real-time (SMRT) sequencing technology of Pacific Biosciences. The results revealed that LK11 produces different types of gibberellins (GAs) in pure culture and significantly improves soybean plant growth by influencing endogenous GAs compared with non-inoculated control plants. Detailed genomic analyses revealed that the <I>Sphingomonas</I> sp. LK11 genome consists of a circular chromosome (3.78 Mbp; 66.2% G+C content) and two circular plasmids (122,975 bps and 34,160 bps; 63 and 65% G+C content, respectively). Annotation showed that the LK11 genome consists of 3656 protein-coding genes, 59 tRNAs, and 4 complete rRNA operons. Functional analyses predicted that LK11 encodes genes for phosphate solubilization and nitrate/nitrite ammonification, which are beneficial for promoting plant growth. Genes for production of catalases, superoxide dismutase, and peroxidases that confer resistance to oxidative stress in plants were also identified in LK11. Moreover, genes for trehalose and glycine betaine biosynthesis were also found in LK11 genome. Similarly, <I>Sphingomonas</I> spp. analysis revealed an open pan-genome and a total of 8507 genes were identified in the <I>Sphingomonas</I> spp. pan-genome and about 1356 orthologous genes were found to comprise the core genome. However, the number of genomes analyzed was not enough to describe complete gene sets. Our findings indicated that the genetic makeup of <I>Sphingomonas</I> sp. LK11 can be utilized as an eco-friendly bioresource for cleaning contaminated sites and promoting growth of plants confronted with environmental perturbations.</P><P><B>Electronic supplementary material</B></P><P>The online version of this article (10.1007/s13205-018-1403-z) contains supplementary material, which is available to authorized users.</P>

Complete genome sequence of Celeribacter marinus IMCC12053^T, the host strain of marine bacteriophage P12053L

Yang, J.A.,Kang, I.,Moon, M.,Ryu, U.C.,Kwon, K.K.,Cho, J.C.,Oh, H.M. Elsevier Publishing Services 2016 MARINE GENOMICS Vol.26 No.-

<P>Isolated from coastal seawater from Yellow Sea of Korea, Celeribacter marinas IMCC12053 was used as the host bacterium for bacteriophage P12053L. Here we report the complete genome sequence of strain IMCC12053 for further study of the marine bacteriophage P12053L functional genes. Single molecule real-time technology (PacBio RSII) was used for the single circular chromosome that is 3,096,705 base pairs in length and the GC content is 56.24%. It contains 3155 ORFs with 45 tRNAs and 6 rRNAs genes. N-6-methyladenosine patterns were also investigated for 32 unmethylated genes and intergenic regions that covered many regulators and phage genes as well as ribosomal RNA genes and tRNA genes. Cryptic N-4-methylcytosine pattern was investigated to speculate GpC methylase activity throughout the genome. Comparative genomics with other Celeribacter genomes were carried out for polyaromatic hydrocarbon degradation, but there were no aromatic ring oxygenases in IMCC12053 when compared to Celeribacter indicus P73. (C) 2015 Elsevier B.V. All rights reserved.</P>

Draft genome sequence of lytic bacteriophage SA7 infecting Staphylococcus aureus isolates

김영주,이규민,한범구,김현일,안정근,김동혁,Kim, Youngju,Lee, Gyu Min,Taizhanova, Assiya,Han, Beom Ku,Kim, Hyunil,Ahn, Jeong Keun,Kim, Donghyuk The Microbiological Society of Korea 2018 미생물학회지 Vol.54 No.1

포도상구균(Staphylococcus aureus)은 그람양성이고 구형의 박테리아로 Firmicutes 문에 속하며, 피부나 호흡기 감염 그리고 식중독의 주요 감염원 중에 하나이다. 포도상구균을 감염시키는 박테리오파지는 포도상구균 감염에 효과적인 처방으로 쓰일 수 있다. 본 연구에서는 충청남도에 위치한 가축 농장의 오수에서 분리된 포도상구균 박테리오파지 SA7 균주의 유전체 초안을 분석하였다. 본 균주는 G + C 비율이 34.1%이며, 34,730 bp 로 구성된 dsDNA 를 지니고 있었다. 염색체에서 53 개의 단백질 코딩 유전자가 확인되었으며, 이 중 23 개의 유전자는 BLASTp 분석으로부터 기능을 가지고 있다고 추정되었다. 나머지는 가설 단백질 혹은 보존 단백질이었다. Staphylococcus aureus is a Gram-positive and a round-shaped bacterium of Firmicutes phylum, and is a common cause of skin infections, respiratory infections, and food poisoning. Bacteriophages infecting S. aureus can be an effective treatment for S. aureus infections. Here, the draft genomic sequence is announced for a lytic bacteriophage SA7 infecting S. aureus isolates. The bacteriophage SA7 was isolated from a sewage water sample near a livestock farm in Chungcheongnam-do, South Korea. SA7 has a genome of 34,730 bp and 34.1% G + C content. The genome has 53 protein-coding genes, 23 of which have predicted functions from BLASTp analysis, leaving the others conserved proteins with unknown function.