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Draft genomes of type strains of Flavivirga amylovorans, Flavivirga aquimarina, and Flavivirga jejuensis
Korean J. Microbiol. 2023;59(4):336-339
Published online December 31, 2023
© 2023 The Microbiological Society of Korea.

Hyun-Myung Oh*

Institute of Liberal Arts Education, Pukyong National University, Busan 48547, Republic of Korea
Correspondence to: *E-mail: marinebio@pknu.ac.kr; Tel.: +82-51-629-6869; Fax: +82-51-629-6949
Received September 20, 2023; Revised October 3, 2023; Accepted October 4, 2023.
Abstract
Here I report draft genome sequences of three type strains from Flavivirga species isolated from marine environments. Draft genome sequences of F. amylovorans KACC 14157T included 14 contigs of 4,858,098 bp with a G-C content of 32.35% including 4,025 CDS, 54 tRNAs, 6 rRNAs, and 4 noncoding RNAs. Draft genome sequences of F. aquimarina KCTC 52353T included 184 contigs of 5,291,796 bp with a G-C content of 32.32% with 4,371 CDSs, 37 tRNAs, 11 rRNAs and 4 noncoding RNAs. Draft genome sequences of F. jejuensis KACC 14158T included 33 contigs of 6,017,851 bp with a G-C content of 32.26% including 4,758 CDSs, 39 tRNAs, 4 rRNAs, and 4 noncoding RNAs. In this study, it was confirmed that the draft genomes of F. amylovorans KACC 14157T, F. aquimarina KCTC 52353T, and F. jejuensis KACC 14158T are genetic repertoire for the hydrolysis proteins for alginate and other polycarbohydrates.
Keywords : Flavivirga amylovorans, Flavivirga aquimarina, Flavivirga jejuensis, alginate lyase, cellulase
Body

The genus Flavivirga belongs to the family Flavobacteriaceae, which is one of the major phylogenetic lineages within the phylum Bacteroidota (Garrity and Holt, 2001). As marine Flavobacteria, members of the genus Flavivirga would play a pivotal role in the photometabolic system in the ocean (Fuhrman et al., 2008). The genus Flavivirga was proposed by Yi et al. (2012): Flavivirga jejuensis and Flavivirga amylovorans from sea water with the emendation of other members of Flavobacteriaceae. Flavivirga jejuensis was the type species of the genus (Yi et al., 2012). Flavivirga eckloniae and Flavivirga aquimarina were isolated from the seaweed Ecklonia cava collected from the South Sea of Korea (Lee et al., 2017). The type strains of F. eckloniae showed the degradation activity of polycarbohydrates including agar, alginate, carboxymethyl cellulose, and starch (Lee et al., 2017). The complete genome sequence was reported for Flavivirga eckloniae ECD14T (= KCTC 52352T) (Lee et al., 2018). Here I report draft genome sequences of three type strains from Flavivirga species isolated from marine environments: F. amylovorans KACC 14157T, F. aquimarina KCTC 52353T, and F. jejuensis KACC 14158T.

The whole genomes of the strains were sequenced using Illumina HiSeq at Macrogen Inc. The Illumina reads were assembled by SPAdes v. 3.15.0 (Nurk et al., 2017; Prjibelski et al., 2020), and the assembled sequences were functionally annotated using the NCBI Prokaryotic Genome Annotation Pipeline (PGAP) (Tatusova et al., 2016). The annotation method used by the process is “Best-placed reference protein set; GeneMarkS-2+, Revision 6.5”. The genomes of F. amylovorans KACC 14157T, F. aquimarina KCTC 52353T, and F. jejuensis KACC 14158T included 14,184, and 33 contigs with 149x, 151x, and 150x genome coverages, respectively (Table 1).

Genome assembly and annotation data of type strains from Flavivirga species
Flavivirga amylovorans KACC 14157T Flavivirga aquimarina KCTC 52353T Flavivirga jejuensis KACC 14158T
Genome Coverage 149x 151x 150x
Contigs 14 184 33
Total length 4,858,098 bp 5,291,796 bp 6,017,851 bp
%G+C ratio 32.35 32.35 32.26
Annotated Features Genes (total) 4,114 4,465 4,805
CDSs (total) 4,050 4,413 4,758
CDSs (with protein) 4,025 4,371 4,722
Pseudo Genes (CDS) 25 42 36
Genes (RNA) 64 52 47
rRNAs 1, 3, 2 (5S, 16S, 23S) 4, 4, 3 (5S, 16S, 23S) 1, 1, 2 (5S, 16S, 23S)
complete rRNAs 1 (5S) 2, 1, 1 (5S, 16S, 23S) 1, 1, 1 (5S, 16S, 23S)
partial rRNAs 3, 2 (16S, 23S) 2, 3, 2 (5S, 16S, 23S) 1 (23S)
tRNAs 54 37 39
ncRNAs 4 4 4
CRISPR Arrays 1 0 3
CAZymes predicted by 3 Annotation programsa 155 175 183
2 Annotation programs 36 47 41
1 Annotaion program 99 99 118

a 3 annotation programs: HMMER, dbCAN_sub, DIAMOND (Zheng et al., 2023).



Draft genome sequences of F. amylovorans KACC 14157T included 14 contigs of 4,858,098 bp with a G-C content of 32.35% and there were 4,025 predicted coding sequences (CDSs), 54 transfer RNAs (tRNA), 6 ribosomal RNA (rRNA), and 4 noncoding RNA (ncRNA) (Table 1). Draft genome sequences of F. aquimarina KCTC 52353T included 184 contigs of 5,291,796 bp with a G-C content of 32.32% and contains 4,371 predicted coding sequences (CDSs), 37 transfer RNAs (tRNA), 11 ribosomal RNA (rRNA) and 4 noncoding RNA (ncRNA) (Table 1). Draft genome sequences of F. jejuensis KACC 14158T included 33 contigs of 6,017,851 bp with a G-C content of 32.26% and contains 4,758 predicted coding sequences (CDSs), 39 transfer RNAs (tRNA), 4 ribosomal RNA (rRNA), and 4 noncoding RNA (ncRNA) (Table 1).

To search for CAZymes I installed run_dbCAN4 (https://github.com/linnabrown/run_dbcan), and all three annotation programs found less than 200 carbohydrate enzymes in number from each genome in this study (Table 1) when compared to those from Flavivirga eckloniae ECD14T (209 enzymes) and Flavivirga algicola Y03 (200 enzymes).

Lee et al. (2018) argued that there were 6 β-glucosidases and 2 alginate lyases on the genome of F. eckloniae KCTC 52352T for hydrolysis of carboxymethyl cellulose and alginic acid. This supported hydrolysis tests for F. eckloniae KCTC 52352T and F. aquimarina KCTC 52353T (Lee et al., 2017). Hydrolysis of alginate was positive for F. eckloniae KCTC 52352T and F. amylovorans KACC 14157T (Lee et al., 2017), but F. amylovorans KACC 14157T was not capable of hydrolyzing alginate as in F. jejuensis KACC 14158T (Yi et al., 2012). Hydrolysis of carboxymethyl cellulose which was negative in F. jejuensis KACC 14158T (Yi et al., 2012), which became positive as in F. eckloniae KCTC 52352T (Lee et al., 2017) (Table 2).

Hydrolysis tests of Flavivirga type strains in this study. Adapted from Table 1 from Lee et al. (2017) and test results reported by Yi et al. (2012). Older data by Yi et al. (2012) were in parentheses
Flavivirga eckloniae KCTC 52352T Flavivirga aquimarina KCTC 52353T Flavivirga amylovorans KACC 14157T Flavivirga jejuensis KACC 14158T
Hydrolysis of:
Agar + - +(-) -(-)
Alginate + - +(-) -(-)
CM-cellulose + - -(-) +(-)
Starch + - +(+) -(-)


To investigate cellulase and alginate lyase in F. amylovorans KACC 14157T, F. aquimarina KCTC 52353T, and F. jejuensis KACC 14158T, PSI-BLAST searching was done using 6 β-glucosidases and 2 alginate lyases of F. eckloniae KCTC 52352T. Glucosidases of GH1 or GH5 family is responsible for the cellulase functions, but there were none on the draft genomes of this study. The β-glucosidase from F. eckloniae KCTC 52352T had GH1 family gene (GenBank Acc. AUP80948.1), and five other β-glucosidases may be regarded as glucoamylases or bglX genes that could be found on the genomes of F. amylovorans KACC 14157T, F. aquimarina KCTC 52353T, and F. jejuensis KACC 14158T regardless of starch hydrolytic activities (Table 2).

Alginate is polysaccharides in which β-D-mannuronate and α-L-guluronate are covalently linked (Kim et al., 2011), and two alginate lyases from of F. eckloniae KCTC 52352T are alginate enzyme from polysaccharide lyase family 6. One (GenBank Acc. AUP78684.1) was similar to AlyF from Vibrio splendidus OU02 (Lyu et al., 2019) and the other (GenBank Acc. AUP81569.1) was similar to the marine bacterial AlyGC from Paraglaciecola chathamensis (Xu et al., 2017). Using AlyF (AUP78684.1) and AlyGC (AUP81569.1) from F. eckloniae KCTC 52352T as query psi-blast resulted in sequences annotated as chondroitinase-B domain-containing proteins in F. amylovorans KACC 14157T, F. aquimarina KCTC 52353T, and F. jejuensis KACC 14158T. In this regard, AlyF and AlyGC could be found on the three draft genomes in this study. AlyF proteins included accessions MDO5987758.1 (F. amylovorans KACC 14157T), MDO5969023.1 (F. aquimarina KCTC 52353T), and MDO5973396.1 (F. jejuensis KACC 14158T). AlyGC proteins included MDO5989213.1 (F. amylovorans KACC 14157T), MDO5970340.1 (F. aquimarina KCTC 52353T), and MDO5973429.1 (F. jejuensis KACC 14158T). When it comes to agarolytic test (Table 2), I used two β-agarase sequences from Flavivirga algicola strain Y03 (GenBank Acc. NMH88854.1 and NMH85987.1), but there were no agarase or “family 16 glycosylhydrolases” hits on the genomes in this study.

Draft genomes of F. amylovorans KACC 14157T, F. aquimarina KCTC 52353T, and F. jejuensis KACC 14158T included genes that have potential for the hydrolysis of alginate, carboxymethyl cellulose, and starch. The genotypic features of the genomes of the type strains of Flavivirga in this study conforms to the roles Flavobacteria play in the carbon cycles in marine environments (Fuhrman et al., 2008)

Nucleotide sequence accession numbers

Genome sequences for F. amylovorans KACC 14157T, F. aquimarina KCTC 52353T, and F. jejuensis KACC 14158T were deposited in GenBank/DDBJ/EMBL with accession numbers of JAUOEM00000000, JAUOEK00000000, and JAUOEL00000000, respectively.

적 요

해양 환경에서 분리된 Flavivirga 종으로부터 얻은 세가지 표준 균주의 초안 유전체의 서열분석을 실시하였다. Flavivirga amylovorans KACC 14157T의 유전체 서열은 총 4,858,098 bp 길이의 14개의 콘티그(contig)로 이루어진 32.35%의 G-C 함량을 포함하며, 이 중에 4,025개의 CDS, 54개의 tRNA, 6개의 rRNA 및 4개의 ncRNA가 포함되었다. F. aquimarina KCTC 52353T의 유전체 서열은 5,291,796 bp 길이의 184개의 콘티그와 32.32%의 G-C 함량을 가지며, 이 중에 4,371개의 CDS, 37개의 tRNA, 11개의 rRNA 및 4개의 ncRNA가 포함되었다. F. jejuensis KACC 14158T의 유전체 서열은 총 6,017,851 bp의 33개의 콘티그가 32.26%의 G-C 함량을 가지며, 4,758개의 CDS, 39개의 tRNA, 4개의 rRNA 및 4개의 ncRNA가 포함되었다. F. amylovorans KACC 14157T, F. aquimarina KCTC 52353TF. jejuensis KACC 14158T의 유전체가 알긴산과 다른 다당류의 가수분해 단백질 유전자의 자원임을 확인할 수 있었다.

Acknowledgments

This work was supported by Pukyong National University Research Fund (2022).

Conflict of Interest

Hyun-Myung Oh is Editor of KJM. He was not involved in the review process of this article. Also, author have no conflict of interest to report.

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