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Thangavelu R, Edwin Raj E, P P, Muthukathan G, Murugan L, Uma S. Draft Genome Resource of a Novel Virulent Fusarium oxysporum f. sp. cubense Race 1 Strain (VCG 0124) Infecting Cavendish (AAA) Group of Banana in India. Plant Dis 2021; 105:2708-2710. [PMID: 33728958 DOI: 10.1094/pdis-12-20-2737-a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Fusarium oxysporum f. sp. cubense is one of the most destructive soilborne fungi causing Fusarium wilt disease in banana. Generally, F. oxysporum f. sp. cubense race 1 (R1) severely affects most of the banana varieties, except Cavendish banana (AAA). Here, we present the draft genome of an isolate of VCG 0124, a novel virulent R1 strain that severely affects the Cavendish group of banana isolated from the Theni district of Tamil Nadu, India. The genome assembly of R1 comprises 61,471,473 bp with 88 contigs and 18,377 protein-coding regions. The genome contains homologs of F. oxysporum f. sp. cubense race-specific secreted-in-xylem (SIX) genes SIX1, SIX5, SIX9, and SIX13. The absence of SIX4 and SIX6 and deletion of a peptide in SIX1 virulence factor genes in the R1 (VCG 0124) strain might be the contributing factor for strains infecting Cavendish banana in India.
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Affiliation(s)
- Raman Thangavelu
- Indian Council of Agricultural Research National Research Centre for Banana, Tiruchirappalli 620102, Tamil Nadu, India
| | - Esack Edwin Raj
- Indian Council of Agricultural Research National Research Centre for Banana, Tiruchirappalli 620102, Tamil Nadu, India
| | - Pushpakanth P
- Indian Council of Agricultural Research National Research Centre for Banana, Tiruchirappalli 620102, Tamil Nadu, India
| | - Gopi Muthukathan
- Indian Council of Agricultural Research National Research Centre for Banana, Tiruchirappalli 620102, Tamil Nadu, India
| | - Loganathan Murugan
- Indian Council of Agricultural Research National Research Centre for Banana, Tiruchirappalli 620102, Tamil Nadu, India
| | - Subbaraya Uma
- Indian Council of Agricultural Research National Research Centre for Banana, Tiruchirappalli 620102, Tamil Nadu, India
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Senthilkumar M, Pushpakanth P, Arul Jose P, Krishnamoorthy R, Anandham R. Diversity and functional characterization of endophytic Methylobacterium isolated from banana cultivars of South India and its impact on early growth of tissue culture banana plantlets. J Appl Microbiol 2021; 131:2448-2465. [PMID: 33891792 DOI: 10.1111/jam.15112] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 03/28/2021] [Accepted: 04/11/2021] [Indexed: 11/27/2022]
Abstract
AIMS This study aimed at determining the distribution, colonization and growth promoting nature of Methylobacterium spp. in tissue culture banana plantlets. METHODS AND RESULTS Leaf samples from different field grown banana cultivars were used for Methylobacterium spp., isolation. Metabolic profile and functional characterization for plant growth-promoting traits of the isolates were assessed. The isolates were confirmed using 16S rRNA gene sequencing analysis, which resulted in six distinct species of Methylobacterium namely M. radiotolerans, M. salsuginis, M. thiocyanatum, M. rhodesianum, M. rhodinum and M. populi. Methylobacterium spp. inoculation experiment was conducted under hydroponic system in tissue culture banana plantlets (germ free) with eight selected isolates. A significant increase in growth parameters of Methylobacterium treated plantlets compared to uninoculated control was observed. Methylobacterium salsuginis TNMB03-gfp29 was developed and colonization micrograph was obtained using confocal laser scanning microscopy (CLSM) and scanning electron microscopy in different parts of banana plantlets (root, stem and leaves). CONCLUSION Field grown banana plants found to harbour diverse endophytic Methylobacterium population. Our finding suggests that endophytic Methylobacterium species may provide significant plant growth promoting compounds/nutrients to the banana plants. The experimental results demonstrated the efficacy of Methylobacterium spp. as a potential bioinoculant and can be exploited as a phyllosphere and rhizosphere based bioinoculant for the initial establishment and growth of tissue culture banana plantlets. SIGNIFICANCE AND IMPACT OF THE STUDY This study extended our knowledge on the distribution of Methylobacterium spp. in banana plants and endophytic colonization nature of this particular genus in plants. In addition, efficient isolate (M. salsuginis TNMB03) identified in this study may be promoted as bio-inoculants for banana plants after field evaluation.
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Affiliation(s)
- M Senthilkumar
- Department of Agricultural Microbiology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| | - P Pushpakanth
- Department of Agricultural Microbiology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| | - P Arul Jose
- Department of Agricultural Microbiology, Agricultural College and Research Institute, Madurai, Tamil Nadu, India
| | - R Krishnamoorthy
- Department of Crop Management, Vanavarayar Institute of Agriculture, Pollachi, Tamil Nadu, India
| | - R Anandham
- Department of Agricultural Microbiology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
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Loganathan M, Thangavelu R, P P, Kalimuthu M, Ramesh R, Selvarajan R, Uma S. First report of rhizome rot of banana caused by Klebsiella variicola in India. Plant Dis 2021; 105:2011. [PMID: 33673773 DOI: 10.1094/pdis-10-20-2316-pdn] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Rhizome rot or soft rot disease is one of the major problems in banana (Musa spp.) cultivation, as it causes germination failure and death of early stage plants. A roving survey conducted during 2017 to 2019 in the major banana growing states of India indicated a 5-30% incidence of rhizome rot in commercial cultivars. The symptoms observed were yellowing of leaves, necrotic drying with or without heart rot, and yellow or brown water soaked spots with dark brown margins in the rhizomes. Decay of tissues, cavity formation and brown ooze with foul smell, and toppling were also observed. To isolate bacteria, dissected diseased tissues were surface sterilized and plated on Crystal Violet Pectate (CVP) medium. Of 60 samples plated on CVP medium, three samples collected from cvs. NeyPoovan-AB (Karur, Tamil Nadu, 10°56'36.8"N;78°24'12.5"E), Grand Naine-AAA (Tiruchirappalli, Tamil Nadu, 10°47'26.1"N;78°34'14.8"E) and Thellachakkarakeli-AAA (East-Godavari, Andhra Pradesh, 16°51'32.1"N;81°46'08.4"E), did not yield any bacteria; however, when plated on nutrient agar, they produced whitish to dull white, mucoid, raised, round and translucent colonies, and three isolates were named as NPK-3-48, GTC-5 and 1-1B-3, respectively. Because these colonies were distinct from colonies obtained on CVP medium (which were analyzed and confirmed separately as Pectobaterium sp.) (Gokul et al. 2019), they were further characterized. Amplification of 16S rDNA genes of NPK-3-48, GTC-5 and 1-1B-3 isolates using universal primers (27F 5' - AGAGTTTGATCCTGGCTCAG - 3'; 1492 R 5' - GGTTACCTTGTTACGACTT - 3') and rpoB gene (Rosenblueth et al. 2004) was carried; the amplicons were sequenced and deposited in NCBI (Accessions MW036529-MW036531; MW497572-MW497574). Phylogenetic analysis of rpoB clearly showed that the isolates NPK-3-48, GTC-5, 1-1B-3 are Klebsiella variicola (Rosenblueth et al. 2004) Besides, biochemical tests also indicated that all three isolates were Gram negative, catalase positive, oxidase negative and able to utilize glucose, maltose and citrate (Ajayasree and Borkar 2018). Therefore, the above said morphological, molecular and biochemical analyses carried out indicated that NPK-3-48, GTC-5, 1-1B-3 are of K. variicola. Earlier, K. variicola causing soft rot has been reported on banana in China (Fan et al. 2016), plantain soft rot in Haiti (Fulton et al. 2020) and carrot soft rot in India (Chandrashekar et al. 2018). For pathogenicity tests, these three isolates were grown in nutrient broth for 48 h at 37±1°C and the cells were harvested by centrifugation. Five milliliters of the culture suspension (2×108 CFUmL-1) taken in a syringe was injected into rhizomes of three month old tissue cultured Grand Naine plants. Each bacterial isolate was injected into eight banana plants at soil level. Appropriate controls were maintained. Inoculated plants were maintained in a glasshouse at 32±2°C and after 30-35 days, rhizome rot symptoms appeared in all the three bacterial isolates inoculated plants but in none of the control plants. The Koch's postulates were proved by re-isolation and identification.To the best of our knowledge, this is the first report of K. variicola causing rhizome rot disease of banana in India.
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Affiliation(s)
- Murugan Loganathan
- ICAR-National Research Centre for Banana, Plant Pathology, ICAR National Research Centre for Banana , Thogamalai Road, Thayanur (Post), Tiruchirapalli-620 102, Tiruchirapalli, Tamil Nadu, India, 620102
- ICAR;
| | - Raman Thangavelu
- ICAR-National Research Centre for Banana, Plant Pathology, ICAR-National, Tiruchirapalli, India, 620102
- 4/115, 16th cross, shanmuganagar UKTIndia;
| | - Pushpakanth P
- ICAR-National Research Centre for Banana, Plant Pathology, Tiruchirapalli, Tamil Nadu, India;
| | - Muthubharathi Kalimuthu
- ICAR-National Research Centre for Banana, Plant Pathology, Tiruchirapalli, Tamil Nadu, India;
| | - R Ramesh
- ICAR Central Coastal Agricultural Research Institute, 105112, Ela, Goa, India;
| | - Ramasamy Selvarajan
- NRC Banana, Plant Pathology - Molecular Virology lab, Thogamali road, Thayanur post, Trichy, Tamil Nadu, India, 620 102;
| | - Subbaraya Uma
- ICAR-National Research Centre for Banana, Crop Improvement, Tiruchirapalli, India;
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Thangavelu R, Edwin Raj E, Pushpakanth P, Loganathan M, Uma S. Draft Genome of Fusarium oxysporum f. sp. cubense Strain Tropical Race-4 Infecting Cavendish (AAA) Group of Banana in India. Plant Dis 2021; 105:481-483. [PMID: 32748718 DOI: 10.1094/pdis-06-20-1170-a] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
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.
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Affiliation(s)
- R Thangavelu
- ICAR-National Research Centre for Banana, Tiruchirappalli 620 102, India
| | - E Edwin Raj
- ICAR-National Research Centre for Banana, Tiruchirappalli 620 102, India
| | - P Pushpakanth
- ICAR-National Research Centre for Banana, Tiruchirappalli 620 102, India
| | - M Loganathan
- ICAR-National Research Centre for Banana, Tiruchirappalli 620 102, India
| | - S Uma
- ICAR-National Research Centre for Banana, Tiruchirappalli 620 102, India
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