Whole genome sequencing of actinobacterial strain Amycolatopsis sp. (BCA-696) identifies the underlying plant growth-promoting genes

Abstract The complete genome sequence of one rare actinobacteria Amycolatopsis sp. BCA−696 was characterized in this study. BCA−696 was previously reported as a biocontrol agent against charcoal rot in sorghum and a plant growth-promoting agent in sorghum and chickpea. The next-generation sequencing based whole draft genome of BCA−696 comprises of ~ 9.05Mb circular chromosome with 68.75% GC content. In total, 8,716 protein-coding sequences and 61 RNA-coding sequences were predicted, and the species-specific genomic features of Amycolatopsis sp. BCA−696 was analysed. Here we also report the Amycolatopsis sp. BCA−696 produces the glycopeptide antibiotic vancomycin that inhibits the growth of pathogenic gram-positive bacteria. Moreover, BCA−696 possesses 23 biosynthetic gene clusters (BGCs) that may be of biological importance. The comparative genomic analysis of BCA−696 and fourteen other strains of Amycolatopsis revealed a total of 3,627 core and 1,423 unique orthologous genes present in the genome. The number of unique genes ranged from 654 to 2557 across 15 strains of Amycolatopsis . Genome assembly of the BCA−696 also provided genes involved in key pathways related to plant growth promotion (PGP) and biocontrol traits such as siderophores, chitinase, and cellulase.