Genome assembly, comparative genomics, and identification of genes/pathways underlying plant growth‑promoting traits of an actinobacterial strain, Amycolatopsis sp. (BCA‑696)

    Gandham, P and Vadla, N and Saji, A and Srinivas, V and Ruperao, P and Selvanayagam, S and Saxena, R K and Rathore, A and Gopalakrishnan, S and 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 (TSI), 14. pp. 1-11. ISSN 2045-2322

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    Abstract

    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 ~ 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.

    Item Type: Article
    Divisions: Center of Excellence in Genomics and Systems Biology
    Global Research Program - Accelerated Crop Improvement
    Research Program : Asia
    CRP: UNSPECIFIED
    Uncontrolled Keywords: Antifungal agents, Bacterial genomics, Plant immunity, Rhizobial symbiosis
    Subjects: Others > Genetics and Genomics
    Depositing User: Mr Nagaraju T
    Date Deposited: 01 Aug 2024 04:15
    Last Modified: 01 Aug 2024 04:15
    URI: http://oar.icrisat.org/id/eprint/12776
    Official URL: https://www.nature.com/articles/s41598-024-66835-y
    Projects: UNSPECIFIED
    Funders: UNSPECIFIED
    Acknowledgement: This work was undertaken as part of the CGIAR Research Program on Grain Legumes and Dry Land Cereals (GLDC). ICRISAT is a member of the CGIAR Consortium. This study was also supported by DBT’s Ramalingaswami grant, and author Vivek Thakur is grateful for this. Author Angeo Saji is financially supported by Junior Research Fellowship from the Council of Scientific and Industrial Research (CSIR), Govt. of India. We also thank Mr. PVS Prasad for his technical assistance. We would also like to thank the anonymous reviewers whose critical comments helped in making it comprehensive and scientifically insightful.
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