Comparative Whole-Genome Sequence Analyses of Fusarium Wilt Pathogen (Foc R1, STR4 and TR4) Infecting Cavendish (AAA) Bananas in India, with a Special Emphasis on Pathogenicity Mechanisms

Abstract

Fusarium wilt is caused by the fungus Fusarium oxysporum f. sp. cubense (Foc) and is the most serious disease affecting bananas (Musa spp.). The fungus is classified into Foc race 1 (R1), Foc race 2, and Foc race 4 based on host specificity. As the rate of spread and the ranges of the devastation of the Foc races exceed the centre of the banana’s origin, even in non-targeted cultivars, there is a possibility of variation in virulence-associated genes. Therefore, the present study investigates the genome assembly of Foc races that infect the Cavendish (AAA) banana group in India, specifically those of the vegetative compatibility group (VCG) 0124 (race 1), 0120 (subtropical race 4), and 01213/16 (tropical race 4). While comparing the general features of the genome sequences (e.g., RNAs, GO, SNPs, and InDels), the study also looked at transposable elements, phylogenetic relationships, and virulence-associated effector genes, and sought insights into race-specific molecular mechanisms of infection based on the presence of unique genes. The results of the analyses revealed variations in the organisation of genome assembly and virulence-associated genes, specifically secreted in xylem (SIX) genes, when compared to their respective reference genomes. The findings contributed to a better understanding of Indian Foc genomes, which will aid in the development of effective Fusarium wilt management techniques for various Foc VCGs in India and beyond.

Development of PCR-Based Race-Specific Markers for Differentiation of Indian Fusarium oxysporum f. sp. cubense, the Causal Agent of Fusarium Wilt in Banana

“…Molecular methods based on Foc race identification have been extensively investigated by several researchers such as Lin et al [21], Fourie et al [50], Dita et al [19], Carvalhais et al [40], and Magdama [51]. However, the present study used molecular markers that were already available as a positive check [19,40,44], which failed to amplify the Indian Foc isolates due to genome variations [42]. There are no race-specific markers specifically available for detecting any of the Indian Foc races.…”

“…The purpose of this study was to develop PCR-based molecular markers that can be used to accurately identify Indian Foc R1 and R4 which differ in genome size and SIX organization [42] with other reference Foc of the same races. Molecular methods based on Foc race identification have been extensively investigated by several researchers such as Lin et al [21], Fourie et al [50], Dita et al [19], Carvalhais et al [40], and Magdama [51].…”

“…Although just a few Foc specific primers are currently available, the simultaneous use of these primers will ensure not only the accuracy, but also false-positive or negative results do not occur [41] in diagnosing and detecting Indian Foc isolates which have variations in whole-genome sequences. Therefore, the study aimed to: (1) identify virulence-associated genes with putative roles in Fusarium wilt from whole-genome sequences published by Thangavelu et al [42]; (2) find a unique variable region that could be used to design markers for different races (Foc R1, R4, TR4, and STR4) for specific detection; and (3) determine the specificity and sensitivity of the newly developed primers in identifying highly virulent Indian Foc isolates amongst characterized and uncharacterized Fo populations collected from various locations of India.…”

Assembly, Annotation, and Comparative Whole Genome Sequence of Fusarium verticillioides Isolated from Stored Maize Grains

“…To the best of our knowledge, only six F. verticillioides WGS are available at NCBI. However, there has been no detailed research on the F. verticillioides genome reported from an Indian origin [ 10 , 34 ]. This reveals a scientific chasm that may lead to significant plant and animal diseases.…”

“…spp. cubense is the most severe tropical race 4 (TR4) that infects the Cavendish (AAA) group of bananas from the subtropical region of India [ 34 ]. Further, detailed phylogenetic relationships, virulence-associated effector genes, and race-specific molecular mechanisms of infection based on the presence of unique genes were studied [ 35 ].…”