search for




 

Draft genome sequences of Sabulilitoribacter multivorans KCTC 32326T and Sabulilitoribacter arenilitoris KCTC 52401T
Korean J. Microbiol. 2022;58(3):205-207
Published online September 30, 2022
© 2022 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 22, 2022; Revised September 1, 2022; Accepted September 1, 2022.
Abstract
The draft genome sequences of Sabulilitoribacter multivorans KCTC 32326T and Sabulilitoribacter arenilitoris KCTC 52401T were determined using Illumuna Hiseq X-ten platform. The assembled genome of Sabulilitoribacter multivorans KCTC 32326T was composed of 13 contigs with a total length of 3,278,864 bp and G + C content was 32.7%. The assembled genome of Sabulilitoribacter arenilitoris KCTC 52401T comprises 41 contigs with a total length of 3,491,608 bp and the genomic DNA G + C content was 32.0%. Two genomes showed differences in carotenoid biosynthesis, nitrogen metabolism and carbohydrate-active enzymes. These genome information of type strains will be expected to be helpful for classification of other isolated Sabulilitoribacter strains.
Keywords : Sabulilitoribacter multivorans KCTC 32326T, Sabulilitoribacter arenilitoris KCTC 52401T, draft genome sequence
Body

The genus Sabulilitoribacter, belong to the family Flavobacteriaceae, was first proposed by Park et al. (2013) and currently comprises 2 recognized species, including Sabulilitoribacter multivorans and S. arenilitoris. The members of the genus Sabulilitoribacter were isolated from sand of seashore, and were characterized by Gram-stain-negative, aerobic, catalase- and oxidase-positive, non-motile, rod shaped. Herein, we report the draft genome sequences and annotations of S. multivorans KCTC 32326T and S. arenilitoris KCTC 52401T.

Sabulilitoribacter multivorans KCTC 32326T and S. arenilitoris KCTC 52401T were obtained from the Korean Collection for Type Cultures (KCTC) and revival and routinely cultured on marine agar 2216 (Difco) at 30°C for 3 days. Genomic DNA was extracted using MagAttract® HMW DNA kit (Qiagen) according to the manufacturer’s instructions. The draft genome sequencing 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) (Bankevich et al., 2012) or Platanus-allee (version 2.2.2) (Kajitani et al., 2019). Orthologous average nucleotide identity (OrthoANI) and 16S rRNA gene sequence similarity were calculated using the Orthologous Average Nucleotide Identity Tool (http://www.ezbiocloud.net/tools/orthoani) and the online pairwise sequence alignment tool for the taxonomy (http://www.ezbiocloud.net/tools/pairAlign), respectively (Yoon et al., 2017). 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) and EggNOG 5.0 (Huerta-Cepas et al., 2018). The dbCAN2 meta server was used for carbohydrate-active enzyme (CAZyme) annotation (Zhang et al., 2018). A Bacterial Pan Genome Analysis pipeline (BPGA) was used to find the number of core gene (Chaudhari et al., 2016).

The genome features of S. multivorans KCTC 32326T and S. arenilitoris KCTC 52401T are shown in Table 1. The draft genome of S. multivorans KCTC 32326T contained 11 scaffolds with a total length of 3,278,864 bp (N50 value, 766,194 bp). The G + C content was 32.7%, and 2,886 protein-coding genes, 4 rRNA genes, 38 tRNA genes, 4 non-coding RNA genes and 8 pseudo genes were predicted. The draft genome of S. arenilitoris KCTC 52401T was composed of 37 scaffolds with a total length of 3,491,608 bp (N50 value, 204,683 bp). The G + C content was 32.0%, and 2,945 protein-coding genes, 3 rRNA genes, 34 tRNA genes, 4 non-coding RNA genes and 56 pseudo genes were predicted. Average nucleotide identity (ANI) value and 16S rRNA gene sequence similarity value between S. multivorans KCTC 32326T and S. arenilitoris KCTC 52401T were 79.3% and 96.9%, respectively. The number of core genes in both strains was 1,863 and a unique gene of each strain accounted for about one-third.

Genomic features of <italic>Sabulilitoribacter multivorans</italic> KCTC 32326<sup>T</sup> and <italic>Sabulilitoribacter arenilitoris</italic> KCTC 52401<sup>T</sup>
Property Value
S. multivorans KCTC 32326T S. arenilitoris KCTC 52401T
Genome assembly
Assemble method SPAdes (version 3.15.0) Paltanus-allee (version 2.2.2)
Genome coverage 147.9X 149.3X
Sequencing technology Illumina Hiseq X-ten Illumina Hiseq X-ten
Genome features
Genome size (bp) 3,278,864 3,491,608
Number of scaffolds 11 37
Number of contigs 13 41
G + C content (%) 32.7 32.0
Protein-coding genes (CDSs) 2,886 2,945
rRNA genes (5S, 16S, 23S) 1, 2, 1 1, 1, 1
tRNA genes 38 34
ncRNA genes 4 4
Pseudogenes 8 56
Accession number (GenBank) JAKKDV000000000 JAKKDU000000000


While both genomes contained carotenoid biosynthesis related genes such as 15-cis-phytoene synthase CrtB, phytoene desaturase CrtI and β-carotene 3-hydroxylase CrtZ, lycopene β-cyclase CrtY, β-carotene/zeaxanthin 4-ketolase CrtW and zeaxanthin glucosyltransferase CrtX were found only in S. arenilitoris KCTC 52401T. In the nitrogen metabolism, both genomes commonly contained nitrous-oxide reductase NosZ, but ferredoxin-nitrate reductase NarB and nitrite reductase (NADH) large subunit NirB were found only in S. multivorans KCTC 32326T. As a result of CAZyme annotation, S. multivorans KCTC 32326T involved 138 CAZymes (4 auxiliary activities, 3 carbohydrate-binding modules, 11 carbohydrate esterases, 55 glycoside hydrolases, 49 glycosyl transferases and 16 polysaccharide lyases), and S. arenilitoris KCTC 52401T involved 149 CAZymes (1 auxiliary activity, 2 carbohydrate-binding modules, 8 carbohydrate esterases, 84 glycoside hydrolases, 53 glycosyl transferases and 1 polysaccharide lyases). Both genomes common encoded biopolymeric degradation related genes such as exodeoxyribonuclease III XthA, β-glucosidase BglX, α-glucosidase MalZ, β-galactosidase LacZ, xylose isomerase XylA and xylose kinase XylB. α-Amylase AmyA, pullanase PulA and xylan 1,4-β-xylosidase XynB were only found in S. multivorans KCTC 32326T, and chitinase was only found in S. arenilitoris KCTC 52401T. These genomic data might be useful for the genetic classification of the genus Sabulilitoribacter, and for study the ecological status and organic material circulation of the marine Flavobacteriaceae.

Nucleotide sequence accession numbers

The draft genome sequence of Sabulilitoribacter multivorans KCTC 32326T and Sabulilitoribacter arenilitoris KCTC 52401T has been deposited to GenBank under the accession number JAKKDV000000000 and JAKKDU000000000, respectively. The version described in this paper are JAKKDV010000000 and JAKKDU010000000.

적 요

Sabulilitoribacter multivorans KCTC 32326TSabulilitoribacter arenilitoris KCTC 52401T의 유전체 초안을 Illumina Hiseq X-ten platform을 사용하여 결정하였다. Sabulilitoribacter multivorans KCTC 32326T의 조립된 유전체는 전체 길이 3,278,864 bp의 13개 contig로 구성되었고 G + C 함량은 32.7% 이었다. Sabulilitoribacter arenilitoris KCTC 52401T의 조립된 유전체는 전체 길이 3,491,608 bp의 41개 contig로 구성되었고 G + C 함량은 32.0% 이었다. 이들 유전체는 carotenoid 생합성, 질소 대사 및 탄수화물 활성 효소 들에서 차이를 보였다. 이러한 type 균주의 유전 정보는 다른 분리된 Subulilitoribacter 균의 분류에 도움이 될 것으로 기대된다.

Acknowledgments

This research was supported by Chungbuk National University Korea National University Development Project (2021).

Conflict of Interest

The authors have no conflict of interest to report.

References
  1. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, and Prjibelski ADPrjibelski AD, et al. 2012. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J. Comput. Biol. 19, 455-477.
    Pubmed KoreaMed CrossRef
  2. Chaudhari NM, Gupta VK, and Dutta C. 2016. BPGA-an ultra-fast pan-genome analysis pipeline. Sci. Rep. 6, 24373.
    Pubmed KoreaMed CrossRef
  3. Huerta-Cepas J, Szklarczyk D, Heller D, Hernández-Plaza A, Forslund SK, Cook H, Mende DR, Letunic I, Rattei T, and Jensen LJJensen LJ, et al. 2018. eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses. Nucleic Acids Res. 47, D309-D314.
    Pubmed KoreaMed CrossRef
  4. Kajitani R, Yoshimura D, Okuno M, Minakuchi Y, Kagoshima H, Fujiyama A, Kubokawa K, Kohara Y, Toyoda A, and Itoh T. 2019. Platanus-allee is a de novo haplotype assembler enabling a comprehensive access to divergent heterozygous regions. Nat. Commun. 10, 1702.
    Pubmed KoreaMed CrossRef
  5. Kanehisa M, Sato Y, and Morishima K. 2016. BlastKOALA and GhostKOALA: KEGG tools for functional characterization of genome and metagenome sequences. J. Mol. Biol. 428, 726-731.
    Pubmed CrossRef
  6. Park S, Jung YT, Lee JS, Lee KC, and Yoon JH. 2013. Sabulilitoribacter multivorans gen. nov., sp. nov., a polysaccharide-degrading bacterium of the family Flavobacteriaceae isolated from seashore sand. Antonie van Leeuwenhoek 104, 973-981.
    Pubmed CrossRef
  7. Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki EP, Zaslavsky L, Lomsadze A, Pruitt KD, Borodovsky M, and Ostell J. 2016. NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res. 44, 6614-6624.
    Pubmed KoreaMed CrossRef
  8. Yoon SH, Ha SM, Kwon S, Lim J, Kim Y, Seo H, and Chun J. 2017. Introducing EzBioCloud: a taxonomically united database of 16S rRNA and whole genome assemblies. Int. J. Syst. Evol. Microbiol. 67, 1613-1617.
    Pubmed KoreaMed CrossRef
  9. Zhang H, Yohe T, Huang L, Entwistle S, Wu P, Yang Z, Busk PK, Xu Y, and Yin Y. 2018. dbCAN2: a meta server for automated carbohydrate-active enzyme annotation. Nucleic Acids Res. 46, W95-W101.
    Pubmed KoreaMed CrossRef


September 2022, 58 (3)
Full Text(PDF) Free

Social Network Service
Services

Author ORCID Information