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

Abstract

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.