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Draft genome sequence of a Sneathiella sp. HT1-7, isolated from coastal seawater
Korean J. Microbiol. 2021;57(4):292-294
Published online December 31, 2021
© 2021 The Microbiological Society of Korea.

Ji-Sung Oh and Dong-Hyun Roh*

Department of Biological Sciences and Biotechnology, Chungbuk National University, Cheongju 28644, Republic of Korea
Correspondence to: E-mail: dhroh@chungbuk.ac.kr;
Tel.: +82-43-261-3368;Fax: +82-43-264-9600
Received November 25, 2021; Revised December 15, 2021; Accepted December 16, 2021.
Abstract
The draft genome sequence of strain HT1-7, isolated from seawater, was determined using Illumina Hiseq X-ten platform. The assembled genome comprises 11 contigs with a total length of 3,830,890 bp and the genomic DNA G + C content was 51.9%. The draft genome encoded 3,629 protein-coding genes, 3 rRNA genes, 47 tRNA genes, 3 non-coding RNA genes and 29 pseudo genes. Various aromatic compounds degradation related genes were present in the genome, and these are expecting to help for understanding of the bacterial degradation of xenobiotics in marine environments.
Keywords : Sneathiella sp. HT1-7, draft genome sequence, polycyclic aromatic hydrocarbon
Body

The genus Sneathiella was first described as a novel genus by Jordan et al. (2007). Thereafter, it was reclassified to the family Sneathiellaceae, the order Sneathiellales in the class Alphaproteobacteria based on the 16S rRNA gene analysis (Kurahashi et al., 2008). The genus Sneathiella had following characteristics; Gram-stain-negative, catalase- and oxidase-positive, motile, rod shaped containing C18:1 ω7c, C16:0, and C19:0 cyclo ω8c as major cellular fatty acids, Q-10 as major isoprenoid quinone, phosphatidylethanolamine, phosphatidylglycerol and an unidentified aminophospholipid as major polar lipids, and the range of 54.9–57.1 mol% G + C content (Jordan et al., 2007; Siamphan et al., 2014; Lee, 2019). Currently, the genus Sneathiella comprises 5 recognized species, S. chienesis from a sediment sample from an aquaculture (Jordan et al., 2007), S. glossodoripedis from the foot epidermis of a nudibranch (Glossodoris cincta; Mollusca) collected in the sea (Kurahashi et al., 2008), S. chungangensis from marine sand (Siamphan et al., 2014), S. limimaris from a tidal mudflat (Lee, 2019) and S. aquimaris from aquaculture seawater (Li et al., 2020). Ecologically, there has been reported that this genus Sneathiella decomposes low-molecular polycyclic aromatic hydrocarbons in oil-contaminated seawater (Kappel et al., 2014; Sauret et al., 2014). The genus also existed on the plastic surfaces (Dussud et al., 2018) and intestines of salmon (Gupta et al., 2019), and was enriched when treating coral (the Porites) exudates (Nelson et al., 2013). In this paper, we describe the draft genome sequence and annotation of a strain Sneathiella sp. HT1-7 isolated from seawater.

Strain HT1-7 was isolated from coastal seawater, South Sea of Korea, using a standard dilution plating method on marine agar 2216 (Difco). The isolate was routinely cultured on MA at 30°C for 5 days. Based on the 16S rRNA gene sequence analysis, strain HT1-7 showed that most closely related to Sneathiella chungangensis CAU 1294T (97.8% sequence identity), followed by S. aquimaris 216LB-ZA1-12T (96.6%), S. glossodoripedis JCM 23214T (96.0%), S. limimaris GH1-24T (95.9%) and S. chinensis LMG 23452T (95.4%).

For the extraction of genomic DNA, strain HT1-7 was incubated in marine broth 2216 (Difco) at 30°C for 3 days, and the genomic DNA was extracted using MagAttract® HMW DNA kit (Qiagen) according to the manufacturer’s instructions. The draft genome sequencing of strain HT1-7 was performed on the Illumina Hiseq X-ten platform with TruSeq Nano DNA (350 bp insert size) library by Macrogen Inc. Raw reads were qualified by FastQC (version 0.11.5) and were assembled by SPAdes (version 3.13.0). Genome completeness and contamination were analyzed with CheckM (Version 1.0.18) (Parks et al., 2015). The genome annotation was conducted using NCBI Prokaryotic Genome Annotation Pipeline (PGAP) (Tatusova et al., 2016), and additional function of the predicted genes were conducted by BlastKOALA with KEGG database (Kanehisa et al., 2016), RAST server with SEED database (Aziz et al., 2008) and PathoSystems Resource Integration Center server (Davis et al., 2020).

The draft genome of strain HT1-7 consists of 11 contigs with a total length of 3,830,890 bp (N50 value, 914,801 bp; Table 1). Genome coverage was 151.6 X and the G + C content was 51.9%. The results of CheckM estimation indicated that genome completeness was 100% with 1.52% contamination and 0% strain heterogeneity. The draft genome comprised 3,629 protein-coding genes, 3 rRNA genes, 47 tRNA genes, 3 non-coding RNA genes and 29 pseudo genes.

Genomic features of Sneathiella sp. HT1-7

Features Value
Genome size (bp) 3,830,890
Number of contigs 11
Depth (X) 151.6
G + C content (%) 51.9
Protein-coding genes (CDSs) 3,629
rRNA genes 3
tRNA genes 47
ncRNA genes 3
Pseudogenes 29
Accession number (GenBank) JAJFZN000000000


Some species of the genus Sneathiella known that played a key role in the degradation of polycyclic aromatic hydrocarbon (Kappell et al., 2014; Sauret et al., 2014). The draft genome of strain HT1-7 contained parts of naphthalene degradation coding genes such as 1-methylnaphthalene hydroxylase (EC 1.14.13.-), alcohol dehydrogenase (EC 1.1.1.1) and 1-naphthaldehyde dehydrogenase (EC 1.2.1.-), which convert 1- or 2-methylnahthalene to 1- or 2-naphthoate, respectively. The genome also contained the genes coding for the degradation of various aromatic compounds. Of these, strain HT1-7 had complete phthalate degradation related genes such as 4,5-dihydroxyphthalate decarboxylase (EC 4.1.1.55), phthalate 4,5-cis-dihydrodiol dehydrogenase (EC 1.3.1.64), phthalate 4,5-dioxygenase (EC 1.14.12.7) and phthalate 4,5-dioxygenase reductase component (EC 1.18.1.-), which convert phthalate to protocatechuate. Its draft genome also contained benzoate and aminobenzoate degradation related genes such as ρ-hydroxybenzoate 3-monooxygenase (EC 1.14.13.2), protocatechuate 4,5-dioxygenase alpha chain (EC 1.13.11.8), 2-hydroxy-4-carboxymuconate semialdehyde hemiacetal dehydrogenase (EC 1.1.1.312), 2-pyrone-4,6-dicarboxylate lactonase (EC 3.1.1.57), 4-oxalomesaconate tautomerase (EC 5.3.2.8), 4-oxalmesaconate hydratase (EC 4.2.1.83) and 4-hydroxy-4-methyl-2-oxoglutarate aldolase (EC 4.1.3.17), which convert 4-hydroxy-benzoate to pyruvate and oxaloacetate. In addition, it were absent only 2 genes such as styrene-oxide isomerase (EC 5.3.99.7) and maleylacetoacetate isomerase (EC 5.2.1.2) out of 8 genes involved in the decomposition of styrene to fumarate and acetoacetate in the genome.

Based on these genomic information, strain HT1-7 is expected to play a role in the degradation of aromatic compounds and xenobiotics in the marine environments.

Nucleotide sequence accession numbers

The draft genome sequence and strain Sneathiella sp. HT1-7 has been deposited to GenBank and the Korean Culture Center of Microorganisms under the accession number JAJFZN000000000 and KCCM 43344, respectively.

적 요

해수로부터 분리된 HT1-7 균주의 유전체 초안을 Illumina Hiseq X-ten platform을 사용하여 결정하였다. 조립된 유전자는 전체 길이 3,830,890 bp의 11개 contig로 구성되었고, 유전체의 G + C 함량은 51.9%이었다. 초안 유전체는 3,629개의 단백질 암호와 유전자, 3개의 rRNA 유전자, 47개의 tRNA 유전자, 3개의 non-coding RNA 유전자 및 29 위유전자(pseudo gene)를 암호화하였다. 이 유전체는 다양한 방향족 화합물 분해 관련 유전자가 존재하였으며, 이는 해양 환경에서의 세균성 xenobiotics 분해를 이해하는 데 도움이 될 것으로 기대된다.

Acknowledgments

This research was supported by Basic Science Research Program through the National Research Foundation of Korea (NRF) funded by the Ministry of Education (NRF-2017R1 D1A3B04033871).

Conflict of Interest

The authors have no conflict of interest to report.

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