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Complete genome sequence of Rossellomorea oryzaecorticis strain KS-H15a isolated from tidal flat
Korean J. Microbiol. 2023;59(1):39-41
Published online March 31, 2023
© 2023 The Microbiological Society of Korea.

Jae-Young Park1, Gyung Jin Bahk2, and Hyo Jung Lee1*

1Department of Biological Science, Kunsan National University, Gunsan 54150, Republic of Korea
2Department of Food and Nutrition, Kunsan National University, Gunsan 54150, Republic of Korea
Correspondence to: *E-mail: hjlee@kunsan.ac.kr; Tel.: +82-63-469-4584; Fax: +82-63-469-7412
Received January 25, 2023; Revised February 25, 2023; Accepted March 7, 2023.
Abstract
Rossellomorea oryzaecorticis is Gram-stain-positive, aerobic, endospore-forming and moderately halophilic rod. Rossellomorea oryzaecorticis KS-H15a (= KACC 22746) was isolated from tidal flat sediment at Shinan-gun, South Korea. The complete genome sequence of R. oryzaecorticis KS-H15a contained 4,409,168 bp length chromosomal DNA and G + C content of 44.0%. The complete genome possesses 4,347 CDSs, 110 transfer RNAs (tRNAs), and 33 ribosomal RNAs (rRNAs).
Keywords : Rossellomorea oryzaecorticis, complete genome, tidal flat
Body

The genus Rossellomorea, belonging to the family Bacillaceae, has been recent proposed by Gupta and distinguished from all other Bacillaceae species by the presence of exclusively shared conserved signature indels (Gupta et al., 2020). Type species of Rosellomorea, Rossellomorea aquimaris, was isolated from tidal flat (Yoon et al., 2003). At the time of writing, the genus comprises up to five validly named species, including R. aquimaris. Rossellomorea marisflavi from sea water of a tidal flat of the Yellow Sea in Korea (Gupta et al., 2020), R. arthrocnemi from roots of plant (Navarro-Torre et al., 2021), and R. vietnamensis from Vietnamese fish sauce (Noguchi et al., 2004). Rossellomorea oryzaecorticis was previously isolated as a moderately halophilic bacterium species from the rice husks (Hong et al., 2014). Here, we report the complete genome sequence of Rossellomorea oryzaecorticis KS-H15a.

Strain KS-H15a (KACC 22746) was isolated from tidal flat sediments in Shinan-gun (34.747742 N 125.932485 E), South Korea. Cultures of strain KS-H15a was obtained on Marine Agar (MA, BD) at 37°C. Genomic DNA was extracted from plate culture, grown on 37°C for 3 days in MA, using Wizard Genomic DNA Purification Kit (Promega) according to the manufacturer’s instructions. The genome of Rossellomorea oryzaecorticis KS-H15a was sequenced by NovaSeqTM 6000 (Illumina) and the PacBio sequel (Pacific Bioscience) system at Macrogen for short and long reads, respectively. The total of 939,371,378 bp with 108,678 reads (N50, 10,493 bp) were produced by the PacBio sequel platform and de novo assembly was performed by Canu v1.7 (Koren et al., 2017). An assembled contig was corrected using filtered short reads from illumina (total of 702,803,790 bp with 4,656,762 reads) and then annotations were performed by Pilon v1.21 (Walker et al., 2014) and Prokka v1.1.0 (Seemann, 2014) software, respectively. Aragon (v1.2.36) was used to predict tRNAs, and Barrnap software (v0.6) was used to predict rRNAs (5S rRNAs, 16S rRNAs, and 23S rRNAs) (Lagesen et al., 2007). The resulting circular genome has a length of 4,409,168 bp (190-fold coverage), with a GC content of 44.0%. Clustering of functional genes derived from the genome of R. oryzaecorticis KS-H15a was performed using the USEARCH program against the COG database within BPGA (Edgar, 2010). and the portions of genes assigned to each COG category were expressed as relative percentages. Default parameters were used for all software unless otherwise specified.

Genome features of Rossellomorea oryzaecorticis strain KS-H15a are presented in Table 1. Genome annotation was performed using NCBI Prokaryotic Genome Annotation Pipeline software. The complete genome sequence of R. oryzaecorticis KS-H15a has 148 RNAs (110 tRNAs, 33 rRNAs, and 5 non-coding RNAs), 4,347 protein coding genes, and 31 pseudogenes. Approximately 70% of the protein coding genes of strain KS-H15a were assigned to COGs. Functional genes belonging to COG categories involved in housekeeping processes including general function prediction only (R, 13%), amino acid transport and metabolism (E, 9.2%), and transcription (K, 8.8%) were enriched in the genome of R. oryzaecorticis KS-H15a. The genome contained oxidative stress response resistance related genes such as inorganic pyrophosphatase (M1J35_00550), thioredoxin (M1J35_18625), thiol peroxidase (M1J35_20375), glutaredoxin (M1J35_22265). A cluster of heat shock proteins: HtpX (M1J35_08105), molecular chaperone DnaJ (M1J35_17730), DnaK (M1J35_17735), GrpE (M1J35_17740), chaperonin GroEL (M1J35_04205) and GroES (M1J35_04200) was detected in the genome. In addition, L-lactate dehydrogenase (M1J35_09460) was found which means it is candidate lactic acid bacteria.

Genome features of <italic>Rossellomorea oryzaecorticis</italic> KS-H15a
Genome features Value
Genome size (bp) 4,409,168
G + C content (%) 44.0
Total genes 4,526
Protein coding genes 4,347
No. of tRNAs 110
No. of rRNAs (5S, 16S, 23S) 11, 11, 11
No. of ncRNAs 5
Pseudo-genes 31
GenBank Accession No. CP096886


Nucleotide sequence accession number

The complete genome sequence and raw sequencing reads for strain KS-H15a were deposited under GenBank accession numbers CP096886. The associated BioProject and BioSample accession numbers are PRJNA832433 and SAMN27863079, respectively.

적 요

Rossellomorea oryzaecorticis는 그람 양성, 호기성, 내생포자를 형성하는 중호염성 막대균이다. 대한민국 신안군의 갯벌로부터 R. oryzaecorticis KS-H15a (= KACC 22746) 균주를 분리하였다. Rossellomorea oryzaecorticis KS-H15의 전장 유전체 염기서열은 4,409,168 bp 크기로 G + C 함량은 44.0%였다. 전장 유전체는 4,347개의 단백질을 암호화하는 유전자와 110개의 전달 RNA (tRNA) 및 리보솜 RNA (rRNA)를 보유하고 있다.

Acknowledgments

This work was supported by the National Research Foundation of Korea (NRF) grant funded by the Korea government (MSIT; [2021R1C1C1013796]).

Conflict of Interest

The authors have no conflict of interest to report.

References
  1. Edgar RC. 2010. Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26, 2460-2461.
    Pubmed CrossRef
  2. Gupta RS, Patel S, Saini N, and Chen S. 2020. Robust demarcation of 17 distinct Bacillus species clades, proposed as novel Bacillaceae genera, by phylogenomics and comparative genomic analyses: description of Robertmurraya kyonggiensis sp. nov. and proposal for an emended genus Bacillus limiting it only to the members of the Subtilis and Cereus clades of species. Int. J. Syst. Evol. Microbiol. 70, 5753-5798.
    CrossRef
  3. Hong SW, Kwon SW, Kim SJ, Kim SY, Kim JJ, Lee JS, Oh MH, Kim AJ, and Chung KS. 2014. Bacillus oryzaecorticis sp. nov., a moderately halophilic bacterium isolated from rice husks. Int. J. Syst. Evol. Microbiol. 64, 2786-2791.
    Pubmed CrossRef
  4. Koren S, Walenz BP, Berlin K, Miller JR, Bergman NH, and Phillippy AM. 2017. Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Genome Res. 5, 722-736.
    Pubmed KoreaMed CrossRef
  5. Lagesen K, Hallin P, Rødland EA, Staerfeldt HH, Rognes T, and Ussery DW. 2007. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res. 35, 3100-3108.
    Pubmed KoreaMed CrossRef
  6. Navarro-Torre S, Carro L, Igual JM, and Montero-Calasanz MDC. 2021. Rossellomorea arthrocnemi sp. nov., a novel plant growth-promoting bacterium used in heavy metal polluted soils as a phytoremediation tool. Int. J. Syst. Evol. Microbiol. 71, 005015.
    Pubmed KoreaMed CrossRef
  7. Noguchi H, Uchino M, Shida O, Takano K, Nakamura LK, and Komagata K. 2004. Bacillus vietnamensis sp. nov., a moderately halotolerant, aerobic, endospore-forming bacterium isolated from Vietnamese fish sauce. Int. J. Syst. Evol. Microbiol. 54, 2117-2120.
    Pubmed CrossRef
  8. Seemann T. 2014. Prokka: rapid prokaryotic genome annotation. Bioinformatics 30, 2068-2069.
    Pubmed CrossRef
  9. Walker BJ, Abeel T, Shea T, Priest M, Abouelliel A, Sakthikumar S, Cuomo CA, Zeng Q, Wortman J, and Young SKYoung SK, et al. 2014. Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS ONE 9, e112963.
    Pubmed KoreaMed CrossRef
  10. Yoon JH, Kim IG, Kang KH, Oh TK, and Park YH. 2003. Bacillus marisflavi sp. nov. and Bacillus aquimaris sp. nov., isolated from sea water of a tidal flat of the Yellow Sea in Korea. Int. J. Syst. Evol. Microbiol. 53, 1297-1303.
    Pubmed CrossRef


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