Genome assembly, comparative genomics, and identification of genes/pathways underlying plant growth-promoting traits of an actinobacterial strain, Amycolatopsis sp. (BCA-696)
The draft genome sequence of an agriculturally important actinobacterial species Amycolatopsis sp. BCA-696 was developed and characterized in this study. Amycolatopsis BCA-696 is known for its biocontrol properties against charcoal rot and also for plant growth-promotion (PGP) in several crop specie...
| Autores principales: | , , , , , , , , , |
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| Formato: | Journal Article |
| Lenguaje: | Inglés |
| Publicado: |
Nature Publishing Group
2024
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| Materias: | |
| Acceso en línea: | https://hdl.handle.net/10568/162551 |
| _version_ | 1855540346106150912 |
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| author | Gandham, Prasad Vadla, Nandini Saji, Angeo Srinivas, Vadlamudi Ruperao, Pradeep Selvanayagam, Sivasubramani Saxena, Rachit K. Rathore, Abhishek Gopalakrishnan, Subramaniam Thakur, Vivek |
| author_browse | Gandham, Prasad Gopalakrishnan, Subramaniam Rathore, Abhishek Ruperao, Pradeep Saji, Angeo Saxena, Rachit K. Selvanayagam, Sivasubramani Srinivas, Vadlamudi Thakur, Vivek Vadla, Nandini |
| author_facet | Gandham, Prasad Vadla, Nandini Saji, Angeo Srinivas, Vadlamudi Ruperao, Pradeep Selvanayagam, Sivasubramani Saxena, Rachit K. Rathore, Abhishek Gopalakrishnan, Subramaniam Thakur, Vivek |
| author_sort | Gandham, Prasad |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | The draft genome sequence of an agriculturally important actinobacterial species Amycolatopsis sp. BCA-696 was developed and characterized in this study. Amycolatopsis BCA-696 is known for its biocontrol properties against charcoal rot and also for plant growth-promotion (PGP) in several crop species. The next-generation sequencing (NGS)-based draft genome of Amycolatopsis sp. BCA-696 comprised of similar to 9.05 Mb linear chromosome with 68.75% GC content. In total, 8716 protein-coding sequences and 61 RNA-coding sequences were predicted in the genome. This newly developed genome sequence has been also characterized for biosynthetic gene clusters (BGCs) and biosynthetic pathways. Furthermore, we have also reported that the Amycolatopsis sp. BCA-696 produces the glycopeptide antibiotic vancomycin that inhibits the growth of pathogenic gram-positive bacteria. A comparative analysis of the BCA-696 genome with publicly available closely related genomes of 14 strains of Amycolatopsis has also been conducted. The comparative analysis has identified a total of 4733 core and 466 unique orthologous genes present in the BCA-696 genome The unique genes present in BCA-696 was enriched with antibiotic biosynthesis and resistance functions. Genome assembly of the BCA-696 has also provided genes involved in key pathways related to PGP and biocontrol traits such as siderophores, chitinase, and cellulase production. |
| format | Journal Article |
| id | CGSpace162551 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2024 |
| publishDateRange | 2024 |
| publishDateSort | 2024 |
| publisher | Nature Publishing Group |
| publisherStr | Nature Publishing Group |
| record_format | dspace |
| spelling | CGSpace1625512025-12-08T09:54:28Z Genome assembly, comparative genomics, and identification of genes/pathways underlying plant growth-promoting traits of an actinobacterial strain, Amycolatopsis sp. (BCA-696) Gandham, Prasad Vadla, Nandini Saji, Angeo Srinivas, Vadlamudi Ruperao, Pradeep Selvanayagam, Sivasubramani Saxena, Rachit K. Rathore, Abhishek Gopalakrishnan, Subramaniam Thakur, Vivek fungicides bacterial genomes immunity rhizobacteria symbiosis The draft genome sequence of an agriculturally important actinobacterial species Amycolatopsis sp. BCA-696 was developed and characterized in this study. Amycolatopsis BCA-696 is known for its biocontrol properties against charcoal rot and also for plant growth-promotion (PGP) in several crop species. The next-generation sequencing (NGS)-based draft genome of Amycolatopsis sp. BCA-696 comprised of similar to 9.05 Mb linear chromosome with 68.75% GC content. In total, 8716 protein-coding sequences and 61 RNA-coding sequences were predicted in the genome. This newly developed genome sequence has been also characterized for biosynthetic gene clusters (BGCs) and biosynthetic pathways. Furthermore, we have also reported that the Amycolatopsis sp. BCA-696 produces the glycopeptide antibiotic vancomycin that inhibits the growth of pathogenic gram-positive bacteria. A comparative analysis of the BCA-696 genome with publicly available closely related genomes of 14 strains of Amycolatopsis has also been conducted. The comparative analysis has identified a total of 4733 core and 466 unique orthologous genes present in the BCA-696 genome The unique genes present in BCA-696 was enriched with antibiotic biosynthesis and resistance functions. Genome assembly of the BCA-696 has also provided genes involved in key pathways related to PGP and biocontrol traits such as siderophores, chitinase, and cellulase production. 2024-07-10 2024-11-21T16:36:50Z 2024-11-21T16:36:50Z Journal Article https://hdl.handle.net/10568/162551 en Open Access application/pdf Nature Publishing Group Gandham, P., Vadla, N., Saji, A., Srinivas, V., Ruperao, P., Selvanayagam, S., Saxena, R. K., Rathore, A., Gopalakrishnan, S., & Thakur, V. (2024). Genome assembly, comparative genomics, and identification of genes/pathways underlying plant growth-promoting traits of an actinobacterial strain, Amycolatopsis sp. (BCA-696). Scientific Reports, 14(1), 15934. https://doi.org/10.1038/s41598-024-66835-y |
| spellingShingle | fungicides bacterial genomes immunity rhizobacteria symbiosis Gandham, Prasad Vadla, Nandini Saji, Angeo Srinivas, Vadlamudi Ruperao, Pradeep Selvanayagam, Sivasubramani Saxena, Rachit K. Rathore, Abhishek Gopalakrishnan, Subramaniam Thakur, Vivek Genome assembly, comparative genomics, and identification of genes/pathways underlying plant growth-promoting traits of an actinobacterial strain, Amycolatopsis sp. (BCA-696) |
| title | Genome assembly, comparative genomics, and identification of genes/pathways underlying plant growth-promoting traits of an actinobacterial strain, Amycolatopsis sp. (BCA-696) |
| title_full | Genome assembly, comparative genomics, and identification of genes/pathways underlying plant growth-promoting traits of an actinobacterial strain, Amycolatopsis sp. (BCA-696) |
| title_fullStr | Genome assembly, comparative genomics, and identification of genes/pathways underlying plant growth-promoting traits of an actinobacterial strain, Amycolatopsis sp. (BCA-696) |
| title_full_unstemmed | Genome assembly, comparative genomics, and identification of genes/pathways underlying plant growth-promoting traits of an actinobacterial strain, Amycolatopsis sp. (BCA-696) |
| title_short | Genome assembly, comparative genomics, and identification of genes/pathways underlying plant growth-promoting traits of an actinobacterial strain, Amycolatopsis sp. (BCA-696) |
| title_sort | genome assembly comparative genomics and identification of genes pathways underlying plant growth promoting traits of an actinobacterial strain amycolatopsis sp bca 696 |
| topic | fungicides bacterial genomes immunity rhizobacteria symbiosis |
| url | https://hdl.handle.net/10568/162551 |
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