Genomic insights into Agrobacteria inducing galls on raspberry

Raspberry (Rubus idaeus L.) is a crop with increasing commercial value due to its nutritional properties and demand in national and international markets. Throughout the growing process, there have been reports of the presence of galls on roots and stems, which reduce plant size and yields. The current study used phylogenetic reconstruction to identify bacteria associated with these symptoms in raspberry plantations in the Mexican states of Jalisco and Michoacán. A total of 69 representative strains selected according to their colony morphotype were identified based on partial sequencing of the 16S ribosomal gene. Forty-nine of them were tested for pathogenicity, including of which three strains induced gall symptoms in raspberry and tomato plants. A set of 28 strains identified within the Agrobacterium and Rhizobium genera were chosen for amplification of the atpD, glnA, gyrB, and rpoB genes. Strain CPO 2.419 was selected for whole genome sequencing, with a total length of 5,679,921 base pairs assembled into 46 contigs. This strain was identified as A. tumefaciens (GenBank JAVIYJ000000000.1) using phylogenetic reconstruction. According to the OrthoANIu and dDDH percentage values, the CPO 2.419 strain belongs to the A. tumefaciens complex, along with the closely related strains of A. tumefaciens LMG 232 (99.4, 89.1), A. tumefaciens CNPSo 675 (98.5, 84.8), and A. tumefaciens ATCC 4720^T (98.1, 78), respectively. This study contributes to the understanding of the genomic Agrobacterium diversity in raspberry-producing areas in Mexico and highlights the relevance of genomics for accurate bacterial identification, with important implications for agriculture.