Dataset from transcriptome profiling of Musa resistant and susceptible cultivars in response to Fusarium oxysporum f.sp. cubense race1 and TR4 challenges using Illumina NovaSeq.

In this investigation, the study focused on the RNAseq data generated in response to Fusarium oxysporum f.sp. cubense (Foc) race1 (Cavendish infecting strain VCG 0124), targeting both resistant (cv. Rose, AA) and susceptible cultivars (Namarai, AA), and Tropical Race 4 (TR4, strain VCG 01213/16), involving resistant (cv. Rose, AA) and susceptible cultivars (Matti, AA). The respective contrasting cultivars were independently challenged with Foc race1 and TR4, and the root and corm samples were collected in two replications at varying time intervals [0th (control), 2nd, 4th, 6th, and 8th days] in duplicates. The RNA samples underwent stringent quality checks, with all 80 samples meeting the primary parameters, including a satisfactory RNA integrity number (>7). Subsequent library preparation and secondary quality control steps were executed successfully for all samples, paving the way for the sequencing phase. Sequencing generated an extensive amount of data, yielding a range of 10 to 31 million paired-end raw reads per sample, resulting in a cumulative raw data size of 11-50 GB. These raw reads were aligned against the reference genome of Musa acuminata ssp. malaccensis version 2 (DH Pahang), as well as the pathogen genomes of Foc race 1 and Foc TR4, using the HISAT2 alignment tool. The focal point of this study was the investigation of differential gene expression patterns of Musa spp. upon Foc infection. In Foc race1 resistant and susceptible root samples across the designated day intervals, a significant number of genes displayed up-regulation (ranging from 1 to 228) and down-regulation (ranging from 1 to 274). In corm samples, the up-regulated genes ranged from 1 to 149, while down-regulated genes spanned from 3 to 845. For Foc TR4 resistant and susceptible root samples, the expression profiles exhibited a notable up-regulation of genes (ranging from 31 to 964), along with a down-regulation range of 316-1315. In corm samples, up-regulated genes ranged from 57 to 929, while down-regulated genes were observed in the range of 40-936. In addition to the primary analysis, a comprehensive secondary analysis was conducted, including Gene Ontology (GO), euKaryotic Orthologous Groups (KOG) classification, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, and investigations into Simple Sequence Repeats (SSRs), Single Nucleotide Polymorphisms (SNPs), and microRNA (miRNA). The complete dataset was carefully curated and housed at ICAR-NRCB, Trichy, ensuring its accuracy and accessibility for the duration of the study. Further, the raw transcriptome read datasets have been successfully submitted to the National Center for Biotechnology Information - Sequence Read Archive (NCBI-SRA) database, ensuring the accessibility and reproducibility of this valuable dataset for further research endeavors.

Identification of sources resistant to a virulent Fusarium wilt strain (VCG 0124) infecting Cavendish bananas.

Bananas are vital for food security in many countries, and half of banana production relies solely on 'Cavendish' (AAA), which is presently threatened by the fungal pathogen Fusarium oxysporum f. sp. cubense (Foc) tropical race 4. This particular virulent Foc strain was also found to attack other banana varieties of commercial importance. As there is no single effective management practice available so far, this study was undertaken to determine resistant sources from the genotype collection available at the ICAR-National Research Centre for Banana, Tiruchirappalli, Tamil Nadu, India for direct use by farmers and/or in breeding programmes to develop resistant hybrids. A total of 258 genotypes of different ploidies and genomic constitutions were tested against Foc race 1 (VCG 0124). In total, 19 genotypes (AA Unique-6, BB type-2, AAA Unique-1, AAA Cavendish-1, AAB Mysore-3, AAB Pome-1, AAB Plantain-4 and AAAB-1) were found to be immune; eight genotypes (AA Unique-1, BB type-3, AAA Cavendish-1, AAB Mysore-1, AAB Unique-1, AAB Plantain-1) were highly resistant; and nine genotypes (AA Unique-1, AAA Cavendish-3, AAB Silk-1, AAB Pome-4) were resistant. The genotypes that are resistant to the virulent Foc race 1 (VCG 0124) strain can be exploited directly for commercialization and/or in breeding programs to develop resistant hybrids.

Draft Genome of Fusarium oxysporum f. sp. cubense Strain Tropical Race-4 Infecting Cavendish (AAA) Group of Banana in India.

Fusarium wilt, caused by the fungus Fusarium oxysporum f. sp. cubense, is the most serious pandemic disease of banana. In this study, we report the draft genome of F. oxysporum f. sp. cubense vegetative compatibility group (VCG) 01213/16 of strain tropical race 4 (TR4) that infects the Cavendish (AAA) group of banana collected from the subtropical region in India. The genome assembly of SFoc TR4 comprises 47,384,463 bp with 4,034 contigs and 15,508 protein-coding regions. Based on VCG analysis, the fungal isolate belongs to F. oxysporum f. sp. cubense TR4 but the genome sequence of SFoc TR4 shows differences in secreted-in-xylem (SIX) protein gene clusters (specifically, SIX8) in comparison with the reference genome of F. oxysporum f. sp. lycopersici and F. oxysporum f. sp. cubense TR4.

Rapid and sensitive detection of Pseudocercospora eumusae pathogen causing eumusae leaf spot disease of banana by loop-mediated isothermal amplification (LAMP) method.

A rapid and sensitive loop-mediated isothermal amplification (LAMP) method was developed for the specific detection of Pseudocercospora eumusae. The LAMP primers designed based on the specific SCAR (Sequence Characterized Amplified Region) marker sequence of P. eumusae proved highly specific to P. eumusae and there was no cross reactivity with closely related Pseudocercospora spp. (P. fijiensis and P. musicola) and 17 other leaf spot causing fungal pathogens of banana. The developed LAMP method exhibited greater sensitivity as the minimum detectable concentration of P. eumusae genomic DNA was 10 Æ¿g/µl which was 100 times lower than that of conventional PCR (1 ng/µl).This method also detected the target pathogen from crude DNA of the mycelium and single leaf spot tissues which eliminates laborious purification steps in DNA isolation and requires less operational time. To the best of our knowledge, this is the first report on the development of this LAMP method to specifically detect and diagnose P. eumusae pathogen from pure cultures and leaf spot tissues.

Improvement of banana cv. Rasthali (Silk, AAB) against Fusarium oxysporum f.sp. cubense (VCG 0124/5) through induced mutagenesis: Determination of LD50 specific to mutagen, explants, toxins and in vitro and in vivo screening for Fusarium wilt resistance.

Shoot tips and in vitro grown proliferating buds of banana cv. Rasthali (Silk, AAB) were treated with various concentrations and durations of chemical mutagens viz., EMS, NaN3 and DES. LD50 for shoot tips based on 50% reduction in fresh weight was determined as 2% for 3 h, 0.02% for 5 h and 0.15% for 5 h, while for proliferating buds, they were 0.6% for 30 min, 0.01% for 2 h and 0.06% for 2 h for the mutagens EMS, NaN3 and DES, respectively. Subsequently, the mutated explants were screened in vitro against fusarium wilt using selection agents like fusaric acid and culture filtrate. LD50 for in vitro selection agents calculated based on 50% survival of explants was 0.050 mM and 7% for fusaric acid and culture filtrate, respectively and beyond which a rapid decline in growth was observed. This was followed by pot screening which led to the identification of three putative resistant mutants with an internal disease score of 1 (corm completely clean, no vascular discolouration). The putative mutants identified in the present study have also been mass multiplied in vitro.

Genome-wide analysis and differential expression of chitinases in banana against root lesion nematode (Pratylenchus coffeae) and eumusa leaf spot (Mycosphaerella eumusae) pathogens.

Knowledge on structure and conserved domain of Musa chitinase isoforms and their responses to various biotic stresses will give a lead to select the suitable chitinase isoform for developing biotic stress-resistant genotypes. Hence, in this study, chitinase sequences available in the Musa genome hub were analyzed for their gene structure, conserved domain, as well as intron and exon regions. To identify the Musa chitinase isoforms involved in Pratylenchus coffeae (root lesion nematode) and Mycosphaerella eumusae (eumusa leaf spot) resistant mechanisms, differential gene expression analysis was carried out in P. coffeae- and M. eumusae-challenged resistant and susceptible banana genotypes. This study revealed that more number of chitinase isoforms (CIs) were responses upon eumusa leaf spot stress than nematode stress. The nematode challenge studies revealed that class II chitinase (GSMUA_Achr9G16770_001) was significantly overexpressed with 6.75-fold (with high fragments per kilobase of exon per million fragments mapped (FPKM)) in resistant genotype (Karthobiumtham-ABB) than susceptible (Nendran-AAB) genotype, whereas when M. eumusae was challenge inoculated, two class III CIs (GSMUA_Achr9G25580_001 and GSMUA_Achr8G27880_001) were overexpressed in resistant genotype (Manoranjitham-AAA) than the susceptible genotype (Grand Naine-AAA). However, none of the CIs were found to be commonly overexpressed under both stress conditions. This study reiterated that the chitinase genes are responding differently to different biotic stresses in their respective resistant genotypes.

Genetic diversity of Fusarium oxysporum f.sp. cubense isolates (Foc) of India by inter simple sequence repeats (ISSR) analysis.

To find out the genetic diversity of Indian Foc isolates of banana, a total of 107 isolates of Fusarium which includes 98 Foc isolates obtained from different banana growing regions of India and seven Foc isolates belong to all known VCGs obtained from Australia and two non-pathogenic Fusarium oxysporum (npFo) isolates were subjected to ISSR analysis. In the initial screening of ISSR primers, out of 34, 10 primers which generated more polymorphic bands were selected for further analysis. The Phylogenetic analysis carried out based on the fingerprints obtained through ISSR analysis indicated the presence of wide genetic diversity among the Foc isolates of India and also its polyphyletic nature. Totally, seven different clusters were obtained and these clusters differentiated the Foc isolates of India based on the races/VCGs. Besides, the cluster analysis clearly distinguished the freshly emerged Foc strain obtained from cv. Grand Naine (Cavendish-AAA) and Poovan (Mysore-AAB) from the other Foc isolates. The non-pathogenic F. oxysporum isolates which have been included for comparison purpose also clustered separately. All these above said findings indicates for the first time the discriminatory power of ISSR to clearly distinguish and separate the Foc isolates according to its race/VCGs and also its virulence. This study would be useful not only to design and develop effective management strategies but also useful for quarantine purposes.

First Report on the Occurrence of a Virulent Strain of Fusarium Wilt Pathogen (Race-1) Infecting Cavendish (AAA) Group of Bananas in India.

Banana wilt disease caused by Fusarium oxysporum f. sp. cubense is one of the most significant threats to banana production worldwide. Strains of F. oxysporum f. sp. cubense have been grouped into race-1, -2, or -4 on the basis of differential virulence among different genotypes of banana. In India, though the disease is reported among susceptible varieties of races 1 and 2, the disease is not reported from Cavendish cultivars, which are the differential host to race-4. Recent surveys of the Cumbum areas (Theni District, Tamil Nadu) revealed symptoms (e.g., yellowing and drooping of leaves around the pseudostem and longitudinal splitting of pseudostem) on cv. Grand Naine (Cavendish group - AAA). F. oxysporum f. sp. cubense was recovered and single-spore isolates had characteristic white-to-purple aerial mycelia producing single-celled, oval microconidia in false heads on branched monophialides and sickle-shaped macroconidia with an attenuated apical cell and a foot-shaped basal cell. Pathogenicity was demonstrated on cv. Grand Naine by inoculation with sand maize meal inoculum (20 g per pot containing 106 spores per g). Vegetative compatibility, using 33 nit-M testers of all known vegetative compatibility groups (2), showed that nit-1 mutants generated from a wild strain of F. oxysporum f. sp. cubense isolated from cv. Grand Naine formed robust heterokaryons with nit-M tester 0124 of the Department of Employment, Economic Development and Innovation, Brisbane, Australia and also with nit-M tester obtained from an isolate of F. oxysporum f. sp. cubense from Karpuravalli (Pisang Awak-ABB). Further characterization of this new Cavendish strain was studied on the basis of volatile odor production (3) using VCGs 0125 for race-1 ('inodoratum group') and 0120 for race 4 ('odoratum group') as positive controls and sterile medium as a negative control. This new F. oxysporum f. sp. cubense strain of Cavendish belonged to 'inodoratum' group of F. oxysporum f. sp. cubense. Pathogenicity was demonstrated on potted plants (10 per cultivar) of cvs. Rasthali (Silk-AAB), Karpuravalli (Pisang Awak-ABB), Ney Poovan (AB), Poovan (Mysore-AAB), Red Banana (AAA), Nendran (French plantain-AAB), Monthan (ABB), and Grand Naine (Cavendish-AAA) by inoculation with sand maize meal inoculum (20 g per pot containing 106 spores per g) in three replicate experiments. Plants were uprooted 2 months postinoculation and disease severity was estimated by rating internal vascular discoloration in the corm (1). The result showed that all cultivars, except Red Banana and Nendran, had the highest rating for disease severity, 6. To our knowledge, this is the first report of a virulent strain of F. oxysporum f. sp. cubense VCG 0124 of race-1on Cavendish banana. References: (1) J. Carlier et al. Technical Guidelines Number 6. INIBAP, Montpellier, France, 2002. (2) J. C. Correll et al. Phytopathology 77:1640, 1987. (3) N. Y. Moore. Aust. J. Bot 39:161, 1991.