Comparative Genomic Analysis of Agarolytic <i>Flavobacterium faecale</i> WV33<sup>T</sup>
<i>Flavobacteria</i> are widely dispersed in a variety of environments and produce various polysaccharide-degrading enzymes. Here, we report the complete genome of <i>Flavobacterium faecale</i> WV33<sup>T</sup>, an agar-degrading bacterium isolated from the stools...
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MDPI AG
2022-09-01
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| Series: | International Journal of Molecular Sciences |
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| Online Access: | https://www.mdpi.com/1422-0067/23/18/10884 |
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| author | Jun Ho Lee Seong-Rae Lee Sejong Han Pyung Cheon Lee |
| author_facet | Jun Ho Lee Seong-Rae Lee Sejong Han Pyung Cheon Lee |
| author_sort | Jun Ho Lee |
| collection | DOAJ |
| description | <i>Flavobacteria</i> are widely dispersed in a variety of environments and produce various polysaccharide-degrading enzymes. Here, we report the complete genome of <i>Flavobacterium faecale</i> WV33<sup>T</sup>, an agar-degrading bacterium isolated from the stools of Antarctic penguins. The sequenced genome of <i>F. faecale</i> WV33<sup>T</sup> represents a single circular chromosome (4,621,116 bp, 35.2% G + C content), containing 3984 coding DNA sequences and 85 RNA-coding genes. The genome of <i>F. faecale</i> WV33<sup>T</sup> contains 154 genes that encode carbohydrate-active enzymes (CAZymes). Among the CAZymes, seven putative genes encoding agarases have been identified in the genome. Transcriptional analysis revealed that the expression of these putative agarases was significantly enhanced by the presence of agar in the culture medium, suggesting that these proteins are involved in agar hydrolysis. Pangenome analysis revealed that the genomes of the 27 <i>Flavobacterium</i> type strains, including <i>F. faecale</i> WV33<sup>T</sup>, tend to be very plastic, and <i>Flavobacterium</i> strains are unique species with a tiny core genome and a large non-core region. The average nucleotide identity and phylogenomic analysis of the 27 <i>Flavobacterium</i>-type strains showed that <i>F. faecale</i> WV33<sup>T</sup> was positioned in a unique clade in the evolutionary tree. |
| first_indexed | 2024-03-09T23:42:11Z |
| format | Article |
| id | doaj.art-b1c2837cc779408381d78331cca163d8 |
| institution | Directory Open Access Journal |
| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-09T23:42:11Z |
| publishDate | 2022-09-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | International Journal of Molecular Sciences |
| spelling | doaj.art-b1c2837cc779408381d78331cca163d82023-11-23T16:49:53ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672022-09-0123181088410.3390/ijms231810884Comparative Genomic Analysis of Agarolytic <i>Flavobacterium faecale</i> WV33<sup>T</sup>Jun Ho Lee0Seong-Rae Lee1Sejong Han2Pyung Cheon Lee3Department of Molecular Science and Technology, Ajou University, Suwon 16499, KoreaDepartment of Molecular Science and Technology, Ajou University, Suwon 16499, KoreaDepartment of Polar Sciences, University of Science and Technology, Incheon 21990, KoreaDepartment of Molecular Science and Technology, Ajou University, Suwon 16499, Korea<i>Flavobacteria</i> are widely dispersed in a variety of environments and produce various polysaccharide-degrading enzymes. Here, we report the complete genome of <i>Flavobacterium faecale</i> WV33<sup>T</sup>, an agar-degrading bacterium isolated from the stools of Antarctic penguins. The sequenced genome of <i>F. faecale</i> WV33<sup>T</sup> represents a single circular chromosome (4,621,116 bp, 35.2% G + C content), containing 3984 coding DNA sequences and 85 RNA-coding genes. The genome of <i>F. faecale</i> WV33<sup>T</sup> contains 154 genes that encode carbohydrate-active enzymes (CAZymes). Among the CAZymes, seven putative genes encoding agarases have been identified in the genome. Transcriptional analysis revealed that the expression of these putative agarases was significantly enhanced by the presence of agar in the culture medium, suggesting that these proteins are involved in agar hydrolysis. Pangenome analysis revealed that the genomes of the 27 <i>Flavobacterium</i> type strains, including <i>F. faecale</i> WV33<sup>T</sup>, tend to be very plastic, and <i>Flavobacterium</i> strains are unique species with a tiny core genome and a large non-core region. The average nucleotide identity and phylogenomic analysis of the 27 <i>Flavobacterium</i>-type strains showed that <i>F. faecale</i> WV33<sup>T</sup> was positioned in a unique clade in the evolutionary tree.https://www.mdpi.com/1422-0067/23/18/10884agaraseCAZymes<i>Flavobacterium faecale</i>comparative genomics |
| spellingShingle | Jun Ho Lee Seong-Rae Lee Sejong Han Pyung Cheon Lee Comparative Genomic Analysis of Agarolytic <i>Flavobacterium faecale</i> WV33<sup>T</sup> International Journal of Molecular Sciences agarase CAZymes <i>Flavobacterium faecale</i> comparative genomics |
| title | Comparative Genomic Analysis of Agarolytic <i>Flavobacterium faecale</i> WV33<sup>T</sup> |
| title_full | Comparative Genomic Analysis of Agarolytic <i>Flavobacterium faecale</i> WV33<sup>T</sup> |
| title_fullStr | Comparative Genomic Analysis of Agarolytic <i>Flavobacterium faecale</i> WV33<sup>T</sup> |
| title_full_unstemmed | Comparative Genomic Analysis of Agarolytic <i>Flavobacterium faecale</i> WV33<sup>T</sup> |
| title_short | Comparative Genomic Analysis of Agarolytic <i>Flavobacterium faecale</i> WV33<sup>T</sup> |
| title_sort | comparative genomic analysis of agarolytic i flavobacterium faecale i wv33 sup t sup |
| topic | agarase CAZymes <i>Flavobacterium faecale</i> comparative genomics |
| url | https://www.mdpi.com/1422-0067/23/18/10884 |
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