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Complete genome sequence of Arachidicoccus ginsenosidivorans Gsoil 809T , a ginsenoside-converting bacterium, isolated from ginseng cultivating soil
Korean J. Microbiol. 2019;55(4):454-455
Published online December 31, 2019
© 2019 The Microbiological Society of Korea.

Ji Eun Lee1, Byoung Hee Lee2, Ki-Eun Lee2, Myung-Suk Kang2, and Wan-Taek Im1,3*

1Department of Biotechnology, Hankyong National University, Gyeonggi-do 17579, Republic of Korea
2Microorganism Resources Division, National Institute of Biological Resources, Incheon 22689, Republic of Korea
3AceEMzyme Co., Ltd., Academic Industry Cooperation, Gyeonggi-do 17579, Republic of Korea
Correspondence to: *E-mail: wandra@hknu.ac.kr;
Tel.: +82-31-670-5335; Fax: +82-31-670-5339
Received October 30, 2019; Revised December 6, 2019; Accepted December 7, 2019.
Abstract

A Gram-stain-negative, aerobic, non-motile, non-spore-forming, and rod-shaped bacterium, designated Arachidicoccus ginsenosidivorans Gsoil 809T, was isolated from soil of a ginseng field. Arachidicoccus ginsenosidivorans Gsoil 809T showed the ability to transform major ginsenoside Rg1 to minor ginsenoside Rh1, and its whole genome was sequenced. The whole genome of Arachidicoccus ginsenosidivorans Gsoil 809T consists of a single circular chromosome of 5,773,153 bp, with 41.1% G + C content. Based on the complete genome sequence of strain Gsoil 809T, we found several glycoside hydrolase- encoding genes and polysaccharide lyases.

Keywords : Arachidicoccus ginsenosidivorans, complete genome, glycoside hydrolase, PacBio RS II, soil of ginseng field
Body

The genus Arachidicoccus was recently described by Madhaiyan et al. (2015). Species of this genus were Gram-stain-negative, non-motile, non-sporeforming, coccoid rods and formed non-pigmented colonies. The DNA G + C content ranges between 43.1 and 44.3%. Currently, the genus comprises of 2 recognized species with published names (LPSN, http://www.bacterio.net/niabella.html), which are commonly isolated from rhizosphere soils.

A Gram-stain-negative bacterium, Arachidicoccusginsenosidivorans Gsoil 809T, was isolated from ginseng cultivating soil, in the Republic of Korea. A. ginsenosidivorans Gsoil 809T was light yellow coloured, non-spore-forming, non-motile, and rod-shaped bacterium. Based on the production of minor ginsenoside Rh1 from major ginsenoside Rg1 (Siddiqi et al., 2017), Gsoil 809T was selected for a whole genome study to identify the target functional genes. Whole genome sequence analysis showed many glycoside hydrolases that may be involved in the conversion of ginsenosides. This strain is available from the host institute and from two culture collections (= KCTC 22820T = JCM30984T).

Genomic DNA of A. ginsenosidivorans Gsoil 809T was extracted using a MagAttract HMW DNA kit (Qiagen) and was purified using the chloroform wash method (shared protocol; Pacific Biosciences). Genome sequencing was performed using a Pacific Biosciences RSII sequencing platform, with a 20 kb SMRTbellTM template library, at DNA Link, Inc. Sequences were assembled using the HGAP3 protocol (Pacific Biosciences) and the sequencing depth was 60.58 ×. The genome sequence was annotated using the NCBI Prokaryotic Genome Automatic Annotation Pipeline (http://www.ncbi.nlm.nih.gov/books/NBK174280/). rRNAs and tRNAs were predicted using rRNAmmer and tRNAscan-SE, respectively (Anthony and Kin, 2015).

The complete genome of A. ginsenosidivorans Gsoil 809T consist of one circular chromosome of 5,773,153 bp, with 41.1% G + C content. Of the 4,628 predicted genes, 4,073 were protein-coding genes (CDS), and 59 were RNA genes. Moreover, 496 pseudogenes were also identified. The majority of the protein-coding genes (89.14%) were assigned a putative function. The genome statistics are presented in Table 1. Whole genome sequence analysis showed more than 96 hydrolase-encoding genes, including 18 β-glucosidases, 21 α-glucosidases, 41 β-xylosidases, 7 α-L-rhamnosidases, and 3 β-galactosidases which may be responsible for its ability to convert ginsenosides. In addition, genome annotation revealed other genes of interest, including polysaccharide lyases such as α-amylase and cellulase, antibiotic bleomycin resistance, nitrite reductase, photosynthetic reaction center cytochrome c subunit gene which may synthesize organic matter on its own, photolyase which may repair the DNA caused by exposure to ultraviolet light (Junpei et al., 2017). The being of these genes show the significance for the cycling of organic and inorganic elements.

General features of Arachidicoccus ginsenosidivorans Gsoil 809T

FeaturesChromosome
Genome size (bp)5,773,153
G + C content (%)41.1%
Total genes4,628
Pseudo genes496
Coding sequences (CDSs)4,073
Number of rRNA genes (5S, 16S, 23S)9 (3, 3, 3)
Number of tRNA genes47

Nucleotide sequence accession number

The complete genome sequence of Arachidicoccus ginsenosidivorans Gsoil 809T has been deposited in NCBI GenBank under accession number CP042434.

적 요

인삼토양으로부터 분리한 Arachidicoccus ginsenosidivorans Gsoil 809T 균주의 유전체서열을 분석하였다. 균주 Gsoil 809T의 유전체는 G + C 비율이 41.1%이며 4,628개의 유전자와 4,073개의 단백질 코딩 유전자, 496개의 위유전자 그리고 59개의 RNA 유전자를 포함한 단일 원형 염색체로 구성되었으며 그 크기는 5,773,153 bp였다. Gsoil 809T는 주요 진세노사이드 Rg1을 마이너 진세노사이드 Rh1로 변환하는 능력을 보여주었다. Gsoil 809T 는 인삼사포닌의 당 분해에 관여하는 여러 타입의 글라이코시다제 유전자, 고분자 분해 유전자를 가지고 있었다.

Acknowledgements

This work was supported by grants from the National Institute of Biological Resources, funded by the Ministry of Environment (No. NIBR201801106).

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