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Draft genome sequence of a ‘Aurantibacter crassamenti’ KCTC 52207 belonging to the family Flavobacteriaceae
Korean J. Microbiol. 2021;57(3):229-231
Published online September 30, 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 August 19, 2021; Revised September 8, 2021; Accepted September 9, 2021.
Abstract
Here we report draft genome sequence of ‘Aurantibacter crassamenti’ KCTC 52207, belonging to the family Flavobacteriaceae. Its draft genome sequence was determined using Illumuna Hiseq X-ten platform. The assembled genome of ‘A. crassamenti’ KCTC 52207 consisted of two contigs with a total length of 4,519,628 bp and the genomic DNA G + C content was 34.3 mol%. The draft genome encoded 3,739 protein-coding genes, 6 rRNA genes, 38 tRNA genes, 4 non-coding RNA genes, and 8 pseudo genes. The genome contained the genes related to the decomposition of carbohydrates and xenobiotics biodegradation in the marine environments, a characteristic of the family Flavobacteriaceae.
Keywords : Aurantibacter crassamenti KCTC 52207, draft genome sequence, family Flavobacteriaceae
Body

Aurantibacter crassamenti’ KCTC 52207, belonging to the family Flavobacteriaceae, was isolated from marine sediment in Japan. It was described as a novel genus by Yoon and Kasai (2017) to accommodate Gram-stain-negative, catalase-positive, oxidase-negative, non-motile, rod shaped and orange pigment producing bacteria. The strain contained manaquinone-6 (MK-6) and iso-C15:1 G, iso-C15:0, and iso-C17:0 3-OH as major respiratory quinone and cellular fatty acids, respectively. In this report, we describe the draft genome sequence and annotation of ‘Aurantibacter crassamenti’ KCTC 52207.

Aurantibacter crassamenti’ KCTC 52207 was obtained from the Korean Collection for Type Cultures (KCTC) and was revived. After reviving, the strain was routinely cultured on marine agar 2216 (Difco) at 30°C for 3 days. The genomic DNA was extracted using MagAttract® HMW DNA kit (Qiagen) according to the manufacturer’s instructions, and the sequencing of the draft genome was performed on the Illumina Hiseq X-ten platform with TruSeq Nano DNA (350 bp insert size) library by Macrogen. Trimming of adapters and quality checking of sequencing data were performed by Trimmomatic (version 0.36) and FastQC (version 0.11.5), respectively. As a result, 4,476,752 pair-end reads were selected for the assembly. The de novo assembly of qualified reads was performed by SPAdes (version 3.13.0). The final assembly consisted of 2 contigs with a total length of 4,519,628 bp (N50 value, 3,031,408 bp). The sequencing depth of coverage was 149.1× and the genomic DNA G + C content was 34.3 mol% (Table 1). Genome completeness and contamination were verified with CheckM (Version 1.0.18) (Parks et al., 2015). The results of CheckM estimation indicated that genome completeness was 99.01% with 0.61% contamination and 0% strain heterogeneity. The genome annotation was performed using NCBI Prokaryotic Genome Annotation Pipeline (PGAP) (Tatusova et al., 2016). A total of 3,739 protein-coding genes, 6 rRNA genes (two 5S, 16S, and 23S, respectively), 38 tRNA genes, 4 non-coding RNA genes and 8 pseudo genes were predicted. Additional function of the predicted genes was conducted by EggNOG 5.0 (Huerta-Cepas et al., 2018), BlastKOALA with KEGG database (Kanehisa et al., 2016) and RAST server with SEED database (Aziz et al., 2008). AntiSMASH 6.0 (https://antismash.secondarymetabolites.org/) (Blin et al., 2021) were used to predict the secondary metabolite gene cluster.

Genomic features of ‘Aurantibacter crassamenti’ KCTC 52207

Features Value
Genome size (bp) 4,519,628
Number of contigs 2
Depth (×) 149.1
G + C content (%) 34.3
Protein-coding genes (CDSs) 3,739
rRNA genes 6
tRNA genes 38
ncRNA genes 4
Pseudogenes 8
Accession number (GenBank) JAFBGM000000000


Only 1669 genes comprised of 44.6% of the total genes were annotated in the KEGG database. The draft genome sequence of ‘A. crassamenti’ KCTC 52207 contained two carotenoid biosynthesis gene cluster, responsible for orange colony color (Yoon and Kasai, 2017); gene locus JQC67_01575 to JQC67_ 01625 (genes encoding 15-cis-phytoene synthase, pytoene desaturase, HAMP domain-containing histidine kinase and Gfo/Idh/MocA family oxidoreductase) and gene locus JQC67_ 12780 to JQC67_12845 (genes encoding aldo/keto reductase, phytoene desaturase, phytoene/squalene synthase family protein, phytoene desaturase, glycosyltransferase family 2 protein, RluA family pseudouridine synthase and YgiQ family radical SAM protein). Additionally, diapolycopene oxygenase and β-carotene 3-hydroxylase that were involved in the biosynthesis of carotenoid existed. Interestingly, according to the Yoon and Kasai (2017), the flexirubin pigment was not produced, but a gene cluster for flexirubin biosynthesis were found from gene locus JQC67-05060 to JQC67-05235.

Total 17 secretion system related genes consisting of bacterial type I, type II, type IX (Por), Sec and twin-arginine translocation (Tat) secretion system and extracellular nucleation-precipitation pathway system were annotated. A porP/sprF gene that found in most genome belonging to Flavobacteriaceae (McBride, 2014) was also found in genome.

Since most members of Flavobacteriaceae have genes for polysaccharides and xenobiotics degradation (McBride, 2014), these degradation-related genes were investigated. As result, genome contained various polysaccharides degradation-related genes encoding α-amylase, β-glucosidase, amidohydrolase family, glucosamine-6-phosphate isomerase, pullulanase and endo-1,4-β-xylanase. The genome also comprised benzoate degradation gene cluster (pcaHGBC-pobA-pcaJF; gene locus from JQC67_14290 to JQC67_14320) coding protocatechuate 3,4-dioxygenase beta subunit, protocatechuate 3,4-dioxygenase alpha subunit, 3-carboxy-cis, cis-muconate cycloisomerase, 4-carboxymuconolactone decarboxylase, 4-hydroxybenzoate 3-monooxygenase (JQC67_14300), 3-oxoacid CoA-transferase subunit B (JQC67_14295) and 3-oxoadipyl-CoA thiolase, respectively, which were enzymes contributing to the conversion of protocatechuate to succinyl-CoA. Among them, 4-hydroxybenzoate 3-monooxygenase catalyzed p-hydroxybenzoate to protocatechuate, a step before protocatechuate degradation. Besides, other benzoate degradation-related genes encoding 3-hydroxybutyryl-CoA dehydrogenase, glutaryl-CoA dehydrogenase, catechol 2,3-dioxygenase, ρ-hydroxybenzoate 3-monooxygenase, acetyl-CoA C-acetyltransferase, acetyl-CoA acyltransferase, catechol 2,3-dioxygenase and 3-hydroxylacyl-CoA dehydrogenase were found. This genome should be helpful in understanding biodegradation of polysaccharides and xenobiotics in the marine environments and application of bioorganic materials decomposition.

Nucleotide sequence accession numbers

The draft genome sequence of ‘A. crassamenti’ KCTC 52207 has been deposited to GenBank under the accession number JAFBGM000000000. The version described in this paper is version JAFBGM010000000.

적 요

본 연구에서 Flavobacteriaceae 과에 속하는 ‘Aurantibacter crassamenti’ KCTC 52207의 유전체를 분석하였다. 유전체 서열은 Illumina Hiseq X-ten platform을 사용하여 결정하였다. ‘A. crassamenti’ KCTC 52207의 조립된 유전체는 2개의 contig로 구성되었고, 총 길이는 4,519,628 bp이고, 34.3 mol%의 G + C 함량을 보유하였다. 유전체는 3,739개의 단백질 코딩 유전자, 6개의 rRNA 유전자, 38개의 tRNA 유전자, 4개의 non-coding RNA 유전자 및 8 위유전자 (pseudo gene)를 암호화하였다. 유전체에는 해양 환경에서 Flavobacteriaceae 과의 특징인 탄수화물과 xenobiotics 분해에 관련된 유전자를 포함하고 있었다.

Acknowledgments

This research was supported by Chungbuk National University Korea National University Development Project (2020).

Conflict of Interest

The authors have no conflict of interest to report.

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