Whole-genome sequence of Pseudomonas sp. strain HOU2 isolated from dangshen (Codonopsis javanica) roots
Abstract Objectives This study aims to generate a de novo complete whole-genome assembly of Pseudomonas sp. strain HOU2, which is an endophytic bacterium isolated from dangshen roots that shows to improve the growth of in vitro dangshen plants. Further investigation of the whole genome of Pseudomona...
Saved in:
| Main Authors: | , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
BMC
2024-12-01
|
| Series: | BMC Genomic Data |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12863-024-01291-1 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1846100849768529920 |
|---|---|
| author | Van Hong Thi Dao Loan To Nguyen Khanh Phuong Do Vinh The Nguyen Hieu Van Nguyen Khanh Ngoc Pham Truong Xuan Nguyen Son Truong Dinh |
| author_facet | Van Hong Thi Dao Loan To Nguyen Khanh Phuong Do Vinh The Nguyen Hieu Van Nguyen Khanh Ngoc Pham Truong Xuan Nguyen Son Truong Dinh |
| author_sort | Van Hong Thi Dao |
| collection | DOAJ |
| description | Abstract Objectives This study aims to generate a de novo complete whole-genome assembly of Pseudomonas sp. strain HOU2, which is an endophytic bacterium isolated from dangshen roots that shows to improve the growth of in vitro dangshen plants. Further investigation of the whole genome of Pseudomonas sp. strain HOU2 will help identify potential genes or pathways that could be involved in the plant growth-promoting effects on in vitro dangshen plants, providing valuable information for future applications. Data description The genomic DNA of Pseudomonas sp. strain HOU2 was sequenced using Oxford Nanopore’s PromethION sequencer with an R10.4.1 flow cell (Table 1, Data file 1). The assembly of the Pseudomonas sp. strain HOU2 genome was conducted using Flye version 2.9, resulting in a single circular chromosome of 6,047,544 bp with a mean coverage of 488 (Table 1, Data file 2). The annotation of genes, proteins, and features of the HOU2 genome were performed by the RAST server (Rapid Annotation using Subsystem Technology) ( https://rast.nmpdr.org/ ) (Table 1, Data file 3, 4, 5) [6, 7]. The Pseudomonas sp. strain HOU2 genome was determined to be most similar to that of Pseudomonas koreensis using the Type Strain Genome Server ( https://tygs.dsmz.de/ , version v391) [8]. |
| format | Article |
| id | doaj-art-a88e90df647b48de8a2c00de78b1b9b6 |
| institution | Kabale University |
| issn | 2730-6844 |
| language | English |
| publishDate | 2024-12-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomic Data |
| spelling | doaj-art-a88e90df647b48de8a2c00de78b1b9b62024-12-29T12:49:37ZengBMCBMC Genomic Data2730-68442024-12-012511310.1186/s12863-024-01291-1Whole-genome sequence of Pseudomonas sp. strain HOU2 isolated from dangshen (Codonopsis javanica) rootsVan Hong Thi Dao0Loan To Nguyen1Khanh Phuong Do2Vinh The Nguyen3Hieu Van Nguyen4Khanh Ngoc Pham5Truong Xuan Nguyen6Son Truong Dinh7Hanoi Open UniversityCentre for Animal Science, Queensland Alliance for Agriculture and Food Innovation, The University of QueenslandHanoi Open UniversityHanoi Open UniversityInstitute of Biotechnology, Vietnam Academy of Science and TechnologyNational Institute of Medicinal MaterialsInstitute of Agrobiology, Vietnam National University of AgricultureInstitute of Agrobiology, Vietnam National University of AgricultureAbstract Objectives This study aims to generate a de novo complete whole-genome assembly of Pseudomonas sp. strain HOU2, which is an endophytic bacterium isolated from dangshen roots that shows to improve the growth of in vitro dangshen plants. Further investigation of the whole genome of Pseudomonas sp. strain HOU2 will help identify potential genes or pathways that could be involved in the plant growth-promoting effects on in vitro dangshen plants, providing valuable information for future applications. Data description The genomic DNA of Pseudomonas sp. strain HOU2 was sequenced using Oxford Nanopore’s PromethION sequencer with an R10.4.1 flow cell (Table 1, Data file 1). The assembly of the Pseudomonas sp. strain HOU2 genome was conducted using Flye version 2.9, resulting in a single circular chromosome of 6,047,544 bp with a mean coverage of 488 (Table 1, Data file 2). The annotation of genes, proteins, and features of the HOU2 genome were performed by the RAST server (Rapid Annotation using Subsystem Technology) ( https://rast.nmpdr.org/ ) (Table 1, Data file 3, 4, 5) [6, 7]. The Pseudomonas sp. strain HOU2 genome was determined to be most similar to that of Pseudomonas koreensis using the Type Strain Genome Server ( https://tygs.dsmz.de/ , version v391) [8].https://doi.org/10.1186/s12863-024-01291-1Endophytic bacteriumPromethIONPseudomonas sp. strain HOU2Whole-genome sequencing |
| spellingShingle | Van Hong Thi Dao Loan To Nguyen Khanh Phuong Do Vinh The Nguyen Hieu Van Nguyen Khanh Ngoc Pham Truong Xuan Nguyen Son Truong Dinh Whole-genome sequence of Pseudomonas sp. strain HOU2 isolated from dangshen (Codonopsis javanica) roots BMC Genomic Data Endophytic bacterium PromethION Pseudomonas sp. strain HOU2 Whole-genome sequencing |
| title | Whole-genome sequence of Pseudomonas sp. strain HOU2 isolated from dangshen (Codonopsis javanica) roots |
| title_full | Whole-genome sequence of Pseudomonas sp. strain HOU2 isolated from dangshen (Codonopsis javanica) roots |
| title_fullStr | Whole-genome sequence of Pseudomonas sp. strain HOU2 isolated from dangshen (Codonopsis javanica) roots |
| title_full_unstemmed | Whole-genome sequence of Pseudomonas sp. strain HOU2 isolated from dangshen (Codonopsis javanica) roots |
| title_short | Whole-genome sequence of Pseudomonas sp. strain HOU2 isolated from dangshen (Codonopsis javanica) roots |
| title_sort | whole genome sequence of pseudomonas sp strain hou2 isolated from dangshen codonopsis javanica roots |
| topic | Endophytic bacterium PromethION Pseudomonas sp. strain HOU2 Whole-genome sequencing |
| url | https://doi.org/10.1186/s12863-024-01291-1 |
| work_keys_str_mv | AT vanhongthidao wholegenomesequenceofpseudomonasspstrainhou2isolatedfromdangshencodonopsisjavanicaroots AT loantonguyen wholegenomesequenceofpseudomonasspstrainhou2isolatedfromdangshencodonopsisjavanicaroots AT khanhphuongdo wholegenomesequenceofpseudomonasspstrainhou2isolatedfromdangshencodonopsisjavanicaroots AT vinhthenguyen wholegenomesequenceofpseudomonasspstrainhou2isolatedfromdangshencodonopsisjavanicaroots AT hieuvannguyen wholegenomesequenceofpseudomonasspstrainhou2isolatedfromdangshencodonopsisjavanicaroots AT khanhngocpham wholegenomesequenceofpseudomonasspstrainhou2isolatedfromdangshencodonopsisjavanicaroots AT truongxuannguyen wholegenomesequenceofpseudomonasspstrainhou2isolatedfromdangshencodonopsisjavanicaroots AT sontruongdinh wholegenomesequenceofpseudomonasspstrainhou2isolatedfromdangshencodonopsisjavanicaroots |