Computational approach to identify novel genomic features conferring high fitness in Bacillus atrophaeus CNY01 and Bacillus velezensis AK-0 associated with plant growth promotion (PGP) in apple
Abstract A comparative genomic analysis approach provides valuable information about genetic variations and evolutionary relationships among microorganisms, aiding not only in the identification of functional genes responsible for traits such as pathogenicity, antibiotic resistance, and metabolic ca...
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| Format: | Article |
| Language: | English |
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BMC
2024-11-01
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| Series: | BMC Plant Biology |
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| Online Access: | https://doi.org/10.1186/s12870-024-05795-x |
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| author | Vandana Apurva Das Budhayash Gautam Pramod Kumar Yadav Pritish Kumar Varadwaj Gulshan Wadhwa Satendra Singh |
| author_facet | Vandana Apurva Das Budhayash Gautam Pramod Kumar Yadav Pritish Kumar Varadwaj Gulshan Wadhwa Satendra Singh |
| author_sort | Vandana Apurva Das |
| collection | DOAJ |
| description | Abstract A comparative genomic analysis approach provides valuable information about genetic variations and evolutionary relationships among microorganisms, aiding not only in the identification of functional genes responsible for traits such as pathogenicity, antibiotic resistance, and metabolic capabilities but also in enhancing our understanding of microbial genomic diversity and their ecological roles, such as supporting plant growth promotion, thereby enabling the development of sustainable strategies for agriculture. We used two strains from different Bacillus species, Bacillus velezensis AK-0 and Bacillus atrophaeus CNY01, which have previously been reported to have PGP activity in apple, and performed comparative genomic analysis to understand their evolutionary process and obtain a mechanistic understanding of their plant growth-promoting activity. We identified genomic features such as mobile genetic elements (MGEs) that encode key proteins involved in the survival, adaptation and growth of these bacterial strains. The presence of genomic islands and intact prophage DNA in Bacillus atrophaeus CNY01 and Bacillus velezensis AK-0 suggests that horizontal gene transfer has contributed to their diversification and acquisition of adaptive traits, enhancing their evolutionary advantage. We also identified novel DNA motifs that are associated with key physiological processes and metabolic pathways. |
| format | Article |
| id | doaj-art-8cd03df2fc934a969ac027665c015cc7 |
| institution | OA Journals |
| issn | 1471-2229 |
| language | English |
| publishDate | 2024-11-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Plant Biology |
| spelling | doaj-art-8cd03df2fc934a969ac027665c015cc72025-08-20T02:08:24ZengBMCBMC Plant Biology1471-22292024-11-0124111310.1186/s12870-024-05795-xComputational approach to identify novel genomic features conferring high fitness in Bacillus atrophaeus CNY01 and Bacillus velezensis AK-0 associated with plant growth promotion (PGP) in appleVandana Apurva Das0Budhayash Gautam1Pramod Kumar Yadav2Pritish Kumar Varadwaj3Gulshan Wadhwa4Satendra Singh5Department of Computational Biology and Bioinformatics, JIBB, Sam Higginbottom University of Agriculture Technology and SciencesDepartment of Computational Biology and Bioinformatics, JIBB, Sam Higginbottom University of Agriculture Technology and SciencesDepartment of Computational Biology and Bioinformatics, JIBB, Sam Higginbottom University of Agriculture Technology and SciencesBioinformatics Centre, Indian Institute of Information Technology-AllahabadDepartment of Biotechnology, Ministry of Science and TechnologyDepartment of Computational Biology and Bioinformatics, JIBB, Sam Higginbottom University of Agriculture Technology and SciencesAbstract A comparative genomic analysis approach provides valuable information about genetic variations and evolutionary relationships among microorganisms, aiding not only in the identification of functional genes responsible for traits such as pathogenicity, antibiotic resistance, and metabolic capabilities but also in enhancing our understanding of microbial genomic diversity and their ecological roles, such as supporting plant growth promotion, thereby enabling the development of sustainable strategies for agriculture. We used two strains from different Bacillus species, Bacillus velezensis AK-0 and Bacillus atrophaeus CNY01, which have previously been reported to have PGP activity in apple, and performed comparative genomic analysis to understand their evolutionary process and obtain a mechanistic understanding of their plant growth-promoting activity. We identified genomic features such as mobile genetic elements (MGEs) that encode key proteins involved in the survival, adaptation and growth of these bacterial strains. The presence of genomic islands and intact prophage DNA in Bacillus atrophaeus CNY01 and Bacillus velezensis AK-0 suggests that horizontal gene transfer has contributed to their diversification and acquisition of adaptive traits, enhancing their evolutionary advantage. We also identified novel DNA motifs that are associated with key physiological processes and metabolic pathways.https://doi.org/10.1186/s12870-024-05795-xPlant growth promotion (PGP)Comparative genomic analysisGenomic island (GI)Horizontal gene transfer (HGT)ProphageDNA motif |
| spellingShingle | Vandana Apurva Das Budhayash Gautam Pramod Kumar Yadav Pritish Kumar Varadwaj Gulshan Wadhwa Satendra Singh Computational approach to identify novel genomic features conferring high fitness in Bacillus atrophaeus CNY01 and Bacillus velezensis AK-0 associated with plant growth promotion (PGP) in apple BMC Plant Biology Plant growth promotion (PGP) Comparative genomic analysis Genomic island (GI) Horizontal gene transfer (HGT) Prophage DNA motif |
| title | Computational approach to identify novel genomic features conferring high fitness in Bacillus atrophaeus CNY01 and Bacillus velezensis AK-0 associated with plant growth promotion (PGP) in apple |
| title_full | Computational approach to identify novel genomic features conferring high fitness in Bacillus atrophaeus CNY01 and Bacillus velezensis AK-0 associated with plant growth promotion (PGP) in apple |
| title_fullStr | Computational approach to identify novel genomic features conferring high fitness in Bacillus atrophaeus CNY01 and Bacillus velezensis AK-0 associated with plant growth promotion (PGP) in apple |
| title_full_unstemmed | Computational approach to identify novel genomic features conferring high fitness in Bacillus atrophaeus CNY01 and Bacillus velezensis AK-0 associated with plant growth promotion (PGP) in apple |
| title_short | Computational approach to identify novel genomic features conferring high fitness in Bacillus atrophaeus CNY01 and Bacillus velezensis AK-0 associated with plant growth promotion (PGP) in apple |
| title_sort | computational approach to identify novel genomic features conferring high fitness in bacillus atrophaeus cny01 and bacillus velezensis ak 0 associated with plant growth promotion pgp in apple |
| topic | Plant growth promotion (PGP) Comparative genomic analysis Genomic island (GI) Horizontal gene transfer (HGT) Prophage DNA motif |
| url | https://doi.org/10.1186/s12870-024-05795-x |
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