Complete genome sequence of a novel Prescottella sp. R16 isolate from deep-sea sediments in the western Pacific
Prescottella, a distinct genus separate from Rhodococcus, has garnered attention for its adaptability and ecological versatility. In this study, a Gram-stain positive and ovoid-rod shaped the actinobacterium strain R16 was isolated from deep-sea sediment (with a depth of 6,310 m) in the Western Paci...
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Frontiers Media S.A.
2024-03-01
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| Series: | Frontiers in Genetics |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fgene.2024.1356956/full |
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| author | Lingqi Ma Lingqi Ma Lingqi Ma Yuqi Bai Weili Wang Shengxiang Pei Gaiyun Zhang |
| author_facet | Lingqi Ma Lingqi Ma Lingqi Ma Yuqi Bai Weili Wang Shengxiang Pei Gaiyun Zhang |
| author_sort | Lingqi Ma |
| collection | DOAJ |
| description | Prescottella, a distinct genus separate from Rhodococcus, has garnered attention for its adaptability and ecological versatility. In this study, a Gram-stain positive and ovoid-rod shaped the actinobacterium strain R16 was isolated from deep-sea sediment (with a depth of 6,310 m) in the Western Pacific. On the basis of 16S rRNA gene sequence analysis, average nucleotide identity and phylogenomic analysis, strain R16 clearly represents a novel species within the genus Prescottella. Genomic analyses indicate Prescottella sp. R16 contains a circular chromosome of 4,531,251 bp with an average GC content of 68.9%, 4,208 protein-coding genes, 51 tRNA genes, and 12 rRNA operons. Additionally, four CRISPRs and 24 genomic islands are also identified. The presence of rich categories related to catalytic activity, membrane part and metabolic process highlights their involvement in cellular component, biological process, and molecular function. The genome sequence of strain R16 also revealed the presence of 13 putative biosynthetic gene clusters for secondary metabolites, including those for ε-Poly-L-lysine, ectoine, heterobactin, isorenieratene and corynecin, suggesting its potential for antibiotic production and warranting further exploration. |
| first_indexed | 2024-04-25T00:07:30Z |
| format | Article |
| id | doaj.art-e1bda3b2fcf5420bb68506160fce4a31 |
| institution | Directory Open Access Journal |
| issn | 1664-8021 |
| language | English |
| last_indexed | 2024-04-25T00:07:30Z |
| publishDate | 2024-03-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Genetics |
| spelling | doaj.art-e1bda3b2fcf5420bb68506160fce4a312024-03-14T04:32:57ZengFrontiers Media S.A.Frontiers in Genetics1664-80212024-03-011510.3389/fgene.2024.13569561356956Complete genome sequence of a novel Prescottella sp. R16 isolate from deep-sea sediments in the western PacificLingqi Ma0Lingqi Ma1Lingqi Ma2Yuqi Bai3Weili Wang4Shengxiang Pei5Gaiyun Zhang6Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, Fujian, ChinaDepartment of Environmental Sciences, College of the Coast & Environment, Louisiana State University, Baton Rouge, LA, United StatesState Key Laboratory of Marine Environmental Science, College of the Ocean and Earth Science, Xiamen University, Xiamen, Fujian, ChinaState Key Laboratory of Marine Environmental Science, College of the Ocean and Earth Science, Xiamen University, Xiamen, Fujian, ChinaHainan Observation and Research Station of Ecological Environment and Fishery Resource in Yazhou Bay, Hainan Institute of Zhejiang University, Sanya, Hainan, ChinaKey Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, Fujian, ChinaKey Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, Fujian, ChinaPrescottella, a distinct genus separate from Rhodococcus, has garnered attention for its adaptability and ecological versatility. In this study, a Gram-stain positive and ovoid-rod shaped the actinobacterium strain R16 was isolated from deep-sea sediment (with a depth of 6,310 m) in the Western Pacific. On the basis of 16S rRNA gene sequence analysis, average nucleotide identity and phylogenomic analysis, strain R16 clearly represents a novel species within the genus Prescottella. Genomic analyses indicate Prescottella sp. R16 contains a circular chromosome of 4,531,251 bp with an average GC content of 68.9%, 4,208 protein-coding genes, 51 tRNA genes, and 12 rRNA operons. Additionally, four CRISPRs and 24 genomic islands are also identified. The presence of rich categories related to catalytic activity, membrane part and metabolic process highlights their involvement in cellular component, biological process, and molecular function. The genome sequence of strain R16 also revealed the presence of 13 putative biosynthetic gene clusters for secondary metabolites, including those for ε-Poly-L-lysine, ectoine, heterobactin, isorenieratene and corynecin, suggesting its potential for antibiotic production and warranting further exploration.https://www.frontiersin.org/articles/10.3389/fgene.2024.1356956/fullPrescottellawhole-genome sequencingphylogenetic analysisbiotechnological applicationsextreme environments |
| spellingShingle | Lingqi Ma Lingqi Ma Lingqi Ma Yuqi Bai Weili Wang Shengxiang Pei Gaiyun Zhang Complete genome sequence of a novel Prescottella sp. R16 isolate from deep-sea sediments in the western Pacific Frontiers in Genetics Prescottella whole-genome sequencing phylogenetic analysis biotechnological applications extreme environments |
| title | Complete genome sequence of a novel Prescottella sp. R16 isolate from deep-sea sediments in the western Pacific |
| title_full | Complete genome sequence of a novel Prescottella sp. R16 isolate from deep-sea sediments in the western Pacific |
| title_fullStr | Complete genome sequence of a novel Prescottella sp. R16 isolate from deep-sea sediments in the western Pacific |
| title_full_unstemmed | Complete genome sequence of a novel Prescottella sp. R16 isolate from deep-sea sediments in the western Pacific |
| title_short | Complete genome sequence of a novel Prescottella sp. R16 isolate from deep-sea sediments in the western Pacific |
| title_sort | complete genome sequence of a novel prescottella sp r16 isolate from deep sea sediments in the western pacific |
| topic | Prescottella whole-genome sequencing phylogenetic analysis biotechnological applications extreme environments |
| url | https://www.frontiersin.org/articles/10.3389/fgene.2024.1356956/full |
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