1
|
Nithya K, Parameswari B, Kumar S, Annadurai A, Nithyanantham R, Mahadevaswamy HK, Viswanathan R. Prospecting true ScYLV resistance in Saccharum hybrid parental population in India by symptom phenotyping and viral titre quantification. 3 Biotech 2023; 13:125. [PMID: 37041801 PMCID: PMC10082694 DOI: 10.1007/s13205-023-03541-y] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Accepted: 03/28/2023] [Indexed: 04/13/2023] Open
Abstract
In sugarcane (Saccharum spp. hybrids) cultivation, viral diseases pose a great challenge across the globe. Yellow leaf (YL) disease is one of the important viral diseases caused by Sugarcane yellow leaf virus (ScYLV), a positive-sense ssRNA virus, genus Polerovirus, family Solemoviridae. The disease symptoms appear in later stages of crop growth during grand growth to maturity phase with intense midrib yellowing in the abaxial leaf surface. At present, this disease is managed through tissue (meristem) culture and healthy seed nurseries in India. However, the virus-free plants are infected quickly by secondary inoculum from aphid vectors in the field, which necessitates the importance of developing YL-resistant varieties. We screened about 600-625 sugarcane parental clones to identify true YL resistance based on 0-5 disease rating scale since 2015 and categorised them as resistant, moderately resistant, moderately susceptible, susceptible and highly susceptible. Leaf samples were collected from all these categories of plants during 2018-20 for the viral titre estimation through absolute quantification method (qRT-PCR assay). The viral load was invariably high in all categories of susceptible samples that ranged from 4.40 × 102 to 8.429 × 106, whereas in YL-free asymptomatic clones, the viral load ranged from 82.35 ± 5.90 to 5.121 × 104. The results clearly indicated that highest viral titre of 105-107 copies was present in all the susceptible clones irrespective of their disease severity grades. Our results clearly established that about 22.85% of apparently resistant sugarcane clones remained free from YL symptoms with significantly low ScYLV titre although we could not find a significant correlation between virus titre and symptom expression. The identified resistant parents will serve as sources of YL resistance to develop virus resistant sugarcane varieties. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03541-y.
Collapse
Affiliation(s)
- K. Nithya
- ICAR-Sugarcane Breeding Institute, Coimbatore, 641007 India
| | - B. Parameswari
- ICAR-National Bureau of Plant Genetic Resources, Regional Station, Hyderabad, 500030 India
- ICAR-Sugarcane Breeding Institute, Research Centre, Karnal, Haryana 132001 India
| | - Subham Kumar
- ICAR-Sugarcane Breeding Institute, Research Centre, Karnal, Haryana 132001 India
| | - A. Annadurai
- ICAR-Sugarcane Breeding Institute, Coimbatore, 641007 India
| | | | | | - R. Viswanathan
- ICAR-Sugarcane Breeding Institute, Coimbatore, 641007 India
| |
Collapse
|
2
|
Nithya K, Vardhan JV, Balasaravanan S, Kaverinathan K, Viswanathan R. Natural infection of Ca. Phytoplasma sacchari causing sugarcane grassy shoot disease in Sorghum bicolor. Vegetos 2023. [DOI: 10.1007/s42535-022-00560-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
|
3
|
Janiga PK, Nithya K, Viswanathan R. Dynamics of Genetic Diversity Among Indian Sugarcane Bacilliform Virus Species and Implications of Associated Recombination Events in the Virus. Sugar Tech 2022. [DOI: 10.1007/s12355-022-01224-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
|
4
|
Geetha N, Viswanathan R, Ramasubramanian T, Salin KP, Yogambal C, Devi PN, Karthigeyan S, Chitra N. Phenacoccus saccharifolii (Green) (Pseudococcidae: Hemiptera) on sugarcane in Tamil Nadu, India. CURR SCI INDIA 2022. [DOI: 10.18520/cs/v123/i9/1142-1151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
|
5
|
Walder M, Edelstein E, Carroll M, Lazarev S, Fajardo JE, Fiser A, Viswanathan R. Integrated structure-based protein interface prediction. BMC Bioinformatics 2022; 23:301. [PMID: 35879651 PMCID: PMC9316365 DOI: 10.1186/s12859-022-04852-2] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 07/18/2022] [Indexed: 11/29/2022] Open
Abstract
Background Identifying protein interfaces can inform how proteins interact with their binding partners, uncover the regulatory mechanisms that control biological functions and guide the development of novel therapeutic agents. A variety of computational approaches have been developed for predicting a protein’s interfacial residues from its known sequence and structure. Methods using the known three-dimensional structures of proteins can be template-based or template-free. Template-based methods have limited success in predicting interfaces when homologues with known complex structures are not available to use as templates. The prediction performance of template-free methods that only rely only upon proteins’ intrinsic properties is limited by the amount of biologically relevant features that can be included in an interface prediction model. Results We describe the development of an integrated method for protein interface prediction (ISPIP) to explore the hypothesis that the efficacy of a computational prediction method of protein binding sites can be enhanced by using a combination of methods that rely on orthogonal structure-based properties of a query protein, combining and balancing both template-free and template-based features. ISPIP is a method that integrates these approaches through simple linear or logistic regression models and more complex decision tree models. On a diverse test set of 156 query proteins, ISPIP outperforms each of its individual classifiers in identifying protein binding interfaces. Conclusions The integrated method captures the best performance of individual classifiers and delivers an improved interface prediction. The method is robust and performs well even when one of the individual classifiers performs poorly on a particular query protein. This work demonstrates that integrating orthogonal methods that depend on different structural properties of proteins performs better at interface prediction than any individual classifier alone. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-022-04852-2.
Collapse
Affiliation(s)
- M Walder
- Department of Chemistry, Yeshiva College, Yeshiva University, New York, NY, 10033, USA
| | - E Edelstein
- Department of Chemistry, Yeshiva College, Yeshiva University, New York, NY, 10033, USA
| | - M Carroll
- Department of Chemistry, Yeshiva College, Yeshiva University, New York, NY, 10033, USA
| | - S Lazarev
- Department of Chemistry, Yeshiva College, Yeshiva University, New York, NY, 10033, USA
| | - J E Fajardo
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - A Fiser
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - R Viswanathan
- Department of Chemistry, Yeshiva College, Yeshiva University, New York, NY, 10033, USA.
| |
Collapse
|
6
|
Sathyabhama M, Viswanathan R, Prasanth CN, Malathi P, Sundar AR. Differential host responses of sugarcane to Colletotrichum falcatum reveal activation of probable effector triggered immunity (ETI) in defence responses. Plant Cell Rep 2022; 41:1461-1476. [PMID: 35415786 DOI: 10.1007/s00299-022-02870-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 03/22/2022] [Indexed: 02/05/2023]
Abstract
KEY MESSAGE The differential compatibility responses of sugarcane to Colletotrichum falcatum pathotypes depend on the nature of both host primary defence signalling cascades and pathogen virulence. The complex polyploidy of sugarcane genome and genetic variations in different cultivars of sugarcane remain a challenge to identify and characterise specific genes controlling the compatible and incompatible interactions between sugarcane and the red rot pathogen, Colletotrichum falcatum. To avoid host background variation in the interaction study, suppression subtractive hybridization (SSH)-based next-generation sequencing (NGS) technology was used in a sugarcane cultivar Co 7805 which is compatible with one C. falcatum pathotype but incompatible with another one. In the incompatible interaction (ICI-less virulent) 10,038 contigs were assembled from ~ 54,699,263 raw reads, while 4022 contigs were assembled from ~ 52,509,239 in the compatible interaction (CI-virulent). The transcripts homologous to CEBiP receptor and those involved in the signalling pathways of ROS, Ca2+, BR, and ABA were expressed in both interaction responses. In contrast, MAPK, ET, PI signalling pathways and JA amino conjugation related transcripts were found only in ICI. In temporal gene expression assays, 16 transcripts showed their highest induction in ICI than CI. Further, more than 17 transcripts specific to the pathogen were found only in CI, indicating that the pathogen colonizes the host tissue whereas it failed to do so in ICI. Overall, this study has identified for the first time that a probable PAMP triggered immunity (PTI) in both responses, while a more efficient effector triggered immunity (ETI) was found only in ICI. Moreover, pathogen proliferation could be predicted in CI based on transcript expression, which were homologous to Glomerella graminicola, the nearest clade to the perfect stage of C. falcatum (G. tucumanensis).
Collapse
Affiliation(s)
- M Sathyabhama
- Plant Pathology Section, Division of Crop Protection, ICAR-Sugarcane Breeding Institute, Coimbatore, 641007, India
- Department of Biotechnology, PSG College of Arts and Science, Coimbatore, 641014, India
| | - R Viswanathan
- Plant Pathology Section, Division of Crop Protection, ICAR-Sugarcane Breeding Institute, Coimbatore, 641007, India.
| | - C N Prasanth
- Plant Pathology Section, Division of Crop Protection, ICAR-Sugarcane Breeding Institute, Coimbatore, 641007, India
| | - P Malathi
- Plant Pathology Section, Division of Crop Protection, ICAR-Sugarcane Breeding Institute, Coimbatore, 641007, India
| | - A Ramesh Sundar
- Plant Pathology Section, Division of Crop Protection, ICAR-Sugarcane Breeding Institute, Coimbatore, 641007, India
| |
Collapse
|
7
|
Prasanth CN, Viswanathan R, Malathi P, Sundar AR. Carbohydrate active enzymes (CAZy) regulate cellulolytic and pectinolytic enzymes in Colletotrichum falcatum causing red rot in sugarcane. 3 Biotech 2022; 12:48. [PMID: 35127303 PMCID: PMC8787009 DOI: 10.1007/s13205-022-03113-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [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: 07/01/2021] [Accepted: 01/08/2022] [Indexed: 02/05/2023] Open
Abstract
Colletotrichum falcatum, an ascomycete pathogen causes red rot of sugarcane which is specialized to infect cane stalks. Cellulolytic and pectinolytic enzymes are necessary for degradation of plant cell wall which stands as barrier for successful fungal pathogenesis. In the study, we have confined to the CAZy genes that regulate cellulolytic and pectinolytic enzymes in two distinctive pathotypes of C. falcatum. Comparative transcriptome analysis revealed that a number of CAZy genes producing cellulolytic and pectinolytic enzyme were present in the virulent (Cf671) and least virulent (RoC) pathotypes. Two consecutive transcriptome analyses (in vitro) were performed using Illumina Hi Seq 2500, further analysis was done with various bioinformatic tools. In vitro expression analysis of cutinase, glycoside hydrolyase and pectin-related genes revealed number of genes that attributes virulence. Numerous pectin-related genes involved in degradation of plant cell wall, pectinase and pectin lyase are considered to be key precursor in degradation of pectin in sugarcane. These results suggest that cellulolytic enzymes, cutinase and pectin-related genes are essential for degradation of sugarcane cell wall and considered to be an important pathogenic factor in C. falcatum. This is the first detailed report on sugarcane cell wall-degrading enzymes during its interaction with C. falcatum and also this comparative transcriptome analysis provided more insights into pathogen mechanism on C. falcatum. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13205-022-03113-6.
Collapse
Affiliation(s)
- C. Naveen Prasanth
- Division of Crop Protection, Sugarcane Breeding Institute, Indian Council of Agricultural Research (ICAR), Tamil Nadu, Coimbatore, 641007 India
| | - R. Viswanathan
- Division of Crop Protection, Sugarcane Breeding Institute, Indian Council of Agricultural Research (ICAR), Tamil Nadu, Coimbatore, 641007 India
| | - P. Malathi
- Division of Crop Protection, Sugarcane Breeding Institute, Indian Council of Agricultural Research (ICAR), Tamil Nadu, Coimbatore, 641007 India
| | - A. Ramesh Sundar
- Division of Crop Protection, Sugarcane Breeding Institute, Indian Council of Agricultural Research (ICAR), Tamil Nadu, Coimbatore, 641007 India
| |
Collapse
|
8
|
Viswanathan R, Singh SP, Selvakumar R, Singh D, Bharti YP, Chhabra ML, Parameswari B, Sharma A, Minnatullah M. Varietal Break Down to Red Rot in the Sugarcane Variety Co 0238 Mimics Vertifolia Effect: Characterizing New Colletotrichum falcatum Pathotype CF13. Sugar Tech 2022. [DOI: 10.1007/s12355-021-01070-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
|
9
|
Viswanathan R, Ramasubramanian T, Chinnaraja C, Selvakumar R, Pathy TL, Manivannan K, Nithyanantham R. Population dynamics of Melanaphis sacchari (Zehntner), the aphid vector of sugarcane yellow leaf virus under tropical conditions in India. Trop plant pathol 2022. [DOI: 10.1007/s40858-021-00483-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
|
10
|
Balan S, Nithya K, Cherian KA, Viswanathan R. True Seed Transmission of Sugarcane bacilliform virus (SCBV) in Sugarcane. Sugar Tech 2021. [DOI: 10.1007/s12355-021-01031-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
|
11
|
Viswanathan R, Selvakumar R, Geetha N, Balaji CG, Annadurai A, Pazhani AS, Malathi P, Sundar AR, Nithiyanantham R, Manivannan K. Epidemiology of sugarcane wilt: predisposition by root borer Polyocha depresella a myth or reality. Indian Phytopathology 2021. [DOI: 10.1007/s42360-021-00398-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
|
12
|
Viswanathan R, Rao GP, Solomon S. Measures to Minimize the Growing Menace of Red Rot of Sugarcane in Subtropical India. Sugar Tech 2021. [DOI: 10.1007/s12355-021-01013-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
|
13
|
Viswanathan R. Impact of yellow leaf disease in sugarcane and its successful disease management to sustain crop production. Indian Phytopathology 2021. [DOI: 10.1007/s42360-021-00391-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
|
14
|
Parameswari B, Nithya K, Kumar S, Holkar SK, Chabbra ML, Kumar P, Viswanathan R. Genome wide association studies in sugarcane host pathogen system for disease resistance: an update on the current status of research. Indian Phytopathology 2021. [DOI: 10.1007/s42360-021-00323-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
|
15
|
Nandakumar M, Malathi P, Sundar AR, Viswanathan R. Expression Analyses of Resistance-Associated Candidate Genes During Sugarcane-Colletotrichum falcatum Went Interaction. Sugar Tech 2021. [DOI: 10.1007/s12355-021-00976-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
|
16
|
Nandakumar M, Malathi P, Sundar AR, Rajadurai CP, Philip M, Viswanathan R. Role of miRNAs in the host-pathogen interaction between sugarcane and Colletotrichum falcatum, the red rot pathogen. Plant Cell Rep 2021; 40:851-870. [PMID: 33818644 DOI: 10.1007/s00299-021-02682-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 03/15/2021] [Indexed: 02/08/2023]
Abstract
KEY MESSAGE Sugarcane microRNAs specifically involved during compatible and incompatible interactions with red rot pathogen Colletotrichum falcatum were identified. We have identified how the miRNAs regulate their gene targets and elaborated evidently on the underlying molecular mechanism of sugarcane defense response to C. falcatum for the first time. Resistance against the fungal pathogen Colletotrichum falcatum causing red rot is one of the most desirable traits for sustainable crop cultivation in sugarcane. To gain new insight into the host defense mechanism against C. falcatum, we studied the role of sugarcane microRNAs during compatible and incompatible interactions by adopting the NGS platform. We have sequenced a total of 80 miRNA families that comprised 980 miRNAs, and the putative targets of the miRNAs include transcription factors, membrane-bound proteins, glutamate receptor proteins, lignin biosynthesis proteins, signaling cascade proteins, transporter proteins, mitochondrial proteins, ER proteins, defense-related, stress response proteins, translational regulation proteins, cell proliferation, and ubiquitination proteins. Further, qRT-PCR analyses of 8 differentially regulated miRNAs and 26 gene transcript targets expression indicated that these miRNAs have a regulatory effect on the expression of respective target genes in most of the cases. Also, the results suggest that certain miRNA regulates many target genes that are involved in inciting early responses to the pathogen infection, signaling pathways, endoplasmic reticulum stress, and resistance gene activation through feedback response from various cellular processes during the compatible and incompatible interaction with the red rot pathogen C. falcatum. The present study revealed the role of sugarcane miRNAs and their target genes during sugarcane-C. falcatum interaction and provided new insight into the miRNA-mediated defense mechanism in sugarcane for the first time.
Collapse
Affiliation(s)
- M Nandakumar
- ICAR-Sugarcane Breeding Institute, Coimbatore, Tamil Nadu, 641007, India
| | - P Malathi
- ICAR-Sugarcane Breeding Institute, Coimbatore, Tamil Nadu, 641007, India
| | - A R Sundar
- ICAR-Sugarcane Breeding Institute, Coimbatore, Tamil Nadu, 641007, India
| | - C P Rajadurai
- AgriGenome Labs, Infopark-Smart City Short Rd, Kochi, Kerala, 682030, India
| | - Manuel Philip
- AgriGenome Labs, Infopark-Smart City Short Rd, Kochi, Kerala, 682030, India
| | - R Viswanathan
- ICAR-Sugarcane Breeding Institute, Coimbatore, Tamil Nadu, 641007, India.
| |
Collapse
|
17
|
Nandakumar M, Viswanathan R, Malathi P, Ramesh Sundar A. Selection of reference genes for normalization of microRNA expression in sugarcane stalks during its interaction with Colletotrichum falcatum. 3 Biotech 2021; 11:72. [PMID: 33489689 DOI: 10.1007/s13205-020-02632-4] [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: 07/16/2020] [Accepted: 12/28/2020] [Indexed: 02/05/2023] Open
Abstract
The microRNAs role in various cellular and metabolic functions is gaining more limelight in line with second-generation NGS technology. For the validation of candidate miRNA genes, the quantitative real-time PCR is the widely trusted and efficient method to follow. Sugarcane miRNAs are less explored in sugarcane defense response during their interaction with Colletotrichum falcatum inciting red rot. Further, for RT-qPCR experiments involving sugarcane miRNA expression studies, a stable internal reference gene is required. Hence, we have taken a study involving 20 candidate genes to identify stable expressing reference genes using NormFinder, geNorm, BestKeeper, and deltaCt statistical algorithms. The candidate reference genes included miRNAs and protein-coding genes. The results indicated that there is a variation in ranking among the algorithms. We found miR1862c as the stably expressed miRNA reference gene among the candidates and miR444b.2 along miR1862c formed the best reference gene pair combination, which can be used in the experiments aiming to explore sugarcane miRNAs in the defense mechanism against C. falcatum. The stable miRNA reference gene was further validated with other lesser stable reference gene candidates to assess the effect of stable reference genes during normalization. The present study evaluating the sugarcane miRNAs as reference genes for normalizing RT-qPCR expression data involving miRNAs during sugarcane × C. falcatum interaction is the first of its kind. Further, this systematic approach can be followed to assess the reference gene in various experimental conditions involving sugarcane miRNAs.
Collapse
Affiliation(s)
- M Nandakumar
- ICAR-Sugarcane Breeding Institute, Coimbatore, Tamil Nadu 641007 India
| | - R Viswanathan
- ICAR-Sugarcane Breeding Institute, Coimbatore, Tamil Nadu 641007 India
| | - P Malathi
- ICAR-Sugarcane Breeding Institute, Coimbatore, Tamil Nadu 641007 India
| | - A Ramesh Sundar
- ICAR-Sugarcane Breeding Institute, Coimbatore, Tamil Nadu 641007 India
| |
Collapse
|
18
|
Patel V, Viswanathan R, Ruffner R, Peris-Celda M, Pinheiro-Neto CD. Comparing nasal physiology after superior ethmoidal and traditional endoscopic anterior cranial base approaches. Rhinology 2021; 58:629-631. [PMID: 32926008 DOI: 10.4193/rhin20.325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- V Patel
- Division of Otolaryngology / Head and Neck Surgery, Department of Surgery, Albany Medical Center, Albany, NY, USA
| | | | - R Ruffner
- Division of Otolaryngology / Head and Neck Surgery, Department of Surgery, Albany Medical Center, Albany, NY, USA
| | - M Peris-Celda
- Department of Neurosurgery, Albany Medical Center, Albany, NY, USA;Adjunct Assistant Professor, Department of Neurosurgery, Mayo Clinic, Rochester, MN, USA
| | - C D Pinheiro-Neto
- Division of Otolaryngology / Head and Neck Surgery, Department of Surgery, Albany Medical Center, Albany, NY, USA; Department of Neurosurgery, Albany Medical Center, Albany, NY, USA
| |
Collapse
|
19
|
Gopi R, Mahendran B, Chandran K, Nisha M, Viswanathan R. Plant and Weather Factors on Resistance of Saccharum officinarum Germplasm Against Ring Spot Disease. Sugar Tech 2021. [DOI: 10.1007/s12355-020-00943-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
|
20
|
Prasanth CN, Viswanathan R, Malathi P, Sundar AR. Development and characterization of genomic SSR marker for virulent strain-specific Colletotrichum falcatum infecting sugarcane. 3 Biotech 2021; 11:20. [PMID: 33442518 DOI: 10.1007/s13205-020-02572-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 07/19/2020] [Accepted: 11/28/2020] [Indexed: 02/05/2023] Open
Abstract
Colle totrichum falcatum, an intriguing pathogen causing red rot in sugarcane, exhibits enormous variation for pathogenicity under field conditions. A species-specific marker is very much needed to classify the virulence among the varying population and to identify the potential of a pathotype by mining the microsatellites, which are considered to be the largest genetic source to develop molecular markers for an organism. In this study, we have mined the C. falcatum genome using MISA database which yielded 12,121 SSRs from 48.1 Mb and 2745 SSRs containing sequences. The most frequent SSR types from the genome of C. falcatum was di-nucleotide which constitutes 50.89% followed by tri-nucleotide 39.60%, hepta-nucleotide 6.7%, hexa-nucleotide 1.38% and penta-nucleotide 1.3%. Over 90 SSR containing sequences from the genome were predicted using BlastX which are found to be non-homologs. Most of the annotated SSR containing sequences fell in CAZy superfamilies, proteases, peptidases, plant cell wall degrading enzymes (PCDWE) and membrane transporters which are considered to be pathogenicity gene clusters. Among them, glycosyl hydrolases (GH) were found to be abundant in SSR containing sequences which again proved our previous transcriptome results. Our in-silico results suggested that the mined microsatellites from C. falcatum genome show absence of homolog sequences which suggests that these markers could be used as an ideal species-specific molecular marker. Two virulence specific markers were characterized using conventional PCR assays from C. falcatum along with virulent species-specific (VSS) marker developed for C. gloeosporioides. The study lays the foundation for the development of C. falcatum specific molecular marker to phenotype the pathotypes based on virulence.
Collapse
Affiliation(s)
- C Naveen Prasanth
- Division of Crop Protection, Sugarcane Breeding Institute, Indian Council of Agricultural Research, Tamil Nadu, Coimbatore, 641007 India
| | - R Viswanathan
- Division of Crop Protection, Sugarcane Breeding Institute, Indian Council of Agricultural Research, Tamil Nadu, Coimbatore, 641007 India
| | - P Malathi
- Division of Crop Protection, Sugarcane Breeding Institute, Indian Council of Agricultural Research, Tamil Nadu, Coimbatore, 641007 India
| | - A Ramesh Sundar
- Division of Crop Protection, Sugarcane Breeding Institute, Indian Council of Agricultural Research, Tamil Nadu, Coimbatore, 641007 India
| |
Collapse
|
21
|
|
22
|
Jayakumar V, Ramesh Sundar A, Viswanathan R. Biocontrol of Colletotrichum falcatum with volatile metabolites produced by endophytic bacteria and profiling VOCs by headspace SPME coupled with GC–MS. Sugar Tech 2020. [DOI: 10.1007/s12355-020-00891-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
|
23
|
|
24
|
Ovalle W, Viswanathan R. Sustaining Sugarcane Production in Guatemala and Nicaragua Through Efficient Disease Management Approaches. Sugar Tech 2020. [DOI: 10.1007/s12355-020-00801-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
|
25
|
Nandakumar M, Malathi P, Sundar AR, Viswanathan R. Use of Green Fluorescent Protein Expressing Colletotrichum falcatum, the Red Rot Pathogen for Precise Host–Pathogen Interaction Studies in Sugarcane. Sugar Tech 2019. [DOI: 10.1007/s12355-019-00751-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
|
26
|
Viswanathan R, Bingham A, Raghav S, Arjunan SP, Jelfs B, Kempster P, Kumar DK. Normalized Mutual Information of phonetic sound to distinguish the speech of Parkinson's disease. Annu Int Conf IEEE Eng Med Biol Soc 2019; 2019:3523-3526. [PMID: 31946638 DOI: 10.1109/embc.2019.8857112] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
This study has investigated the use of inter-personnel mutual information computed from the phonetic sound recordings to differentiate between Parkinson's disease (PD) and control subjects. The normalized mutual information (NMI) denotes the amount of information shared between the voice recordings of people within the same group: PD and Control. The hypothesis of this study was that within group NMI will be significantly different when compared with inter- group NMI. For each phonetic sound, the NMI was computed for every pairing of recordings for both the PD and control groups. Pearson correlation coefficient analysis was used to determine the association of NMI with clinical parameters including Unified Parkinson's Disease Rating Scale (UPDRS), Montreal cognitive assessment (MoCA) and disease duration. ANOVA test for the three phonetic sounds of control and PD subjects showed that there is significant difference between the intra-group mean NMI for the two groups (p <; 0.003) and also showed significant association with the UPDRS motor examination score, MoCA and disease duration.
Collapse
|
27
|
Malathi P, Viswanathan R, Jothi R. Specific adaptation of colletotrichum falcatum pathotypes to sugarcane cultivars. Sugar Tech 2018. [DOI: 10.1007/bf02943742] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
|
28
|
Anandakumar L, Bagyalakshmi K, Nithya K, Parameswari B, Viswanathan R. Reverse Transcription Loop-Mediated Isothermal Amplification (RT-LAMP) Assay for Rapid Diagnosis of Sugarcane yellow leaf virus in Sugarcane. Sugar Tech 2018. [DOI: 10.1007/s12355-018-0606-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
|
29
|
Arun Prakash VR, Viswanathan R. Microwave-shielding behavior of silanized Cu and Cu–Fe3O4 compound particle-reinforced epoxy resin composite in E-, F-, I-, and J-band frequencies. Polym Bull (Berl) 2018. [DOI: 10.1007/s00289-017-2262-1] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|
30
|
Ashwin NMR, Barnabas L, Ramesh Sundar A, Malathi P, Viswanathan R, Masi A, Agrawal GK, Rakwal R. Advances in proteomic technologies and their scope of application in understanding plant–pathogen interactions. J Plant Biochem Biotechnol 2017. [DOI: 10.1007/s13562-017-0402-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
|
31
|
Kaverinathan K, Scindiya M, Malathi P, Viswanathan R, Ramesh Sundar A. Role of Melanin in Colletotrichum falcatum Pathogenesis Causing Sugarcane Red Rot. Sugar Tech 2017. [DOI: 10.1007/s12355-017-0519-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
|
32
|
Barnabas L, Ashwin NMR, Kaverinathan K, Trentin AR, Pivato M, Sundar AR, Malathi P, Viswanathan R, Rosana OB, Neethukrishna K, Carletti P, Arrigoni G, Masi A, Agrawal GK, Rakwal R. Proteomic analysis of a compatible interaction between sugarcane and Sporisorium scitamineum. Proteomics 2016; 16:1111-22. [PMID: 26857420 DOI: 10.1002/pmic.201500245] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [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: 06/23/2015] [Revised: 01/05/2016] [Accepted: 02/02/2016] [Indexed: 02/05/2023]
Abstract
Smut caused by Sporisorium scitamineum is one of the important diseases of sugarcane with global significance. Despite the intriguing nature of sugarcane, S. scitamineum interaction, several pertinent aspects remain unexplored. This study investigates the proteome level alterations occurring in the meristem of a S. scitamineum infected susceptible sugarcane cultivar at whip emergence stage. Differentially abundant proteins were identified by 2DE coupled with MALDI-TOF/TOF-MS. Comprehensively, 53 sugarcane proteins identified were related to defence, stress, metabolism, protein folding, energy, and cell division; in addition, a putative effector of S. scitamineum, chorismate mutase, was identified. Transcript expression vis-à-vis the activity of phenylalanine ammonia lyase was relatively higher in the infected meristem. Abundance of seven candidate proteins in 2D gel profiles was in correlation with its corresponding transcript expression levels as validated by qRT-PCR. Furthermore, this study has opened up new perspectives on the interaction between sugarcane and S. scitamineum.
Collapse
Affiliation(s)
- Leonard Barnabas
- Division of Crop Protection, ICAR-Sugarcane Breeding Institute, Indian Council of Agricultural Research, Coimbatore, India
| | - N M R Ashwin
- Division of Crop Protection, ICAR-Sugarcane Breeding Institute, Indian Council of Agricultural Research, Coimbatore, India
| | - K Kaverinathan
- Division of Crop Protection, ICAR-Sugarcane Breeding Institute, Indian Council of Agricultural Research, Coimbatore, India
| | - Anna Rita Trentin
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, Padova, Italy
| | - Micaela Pivato
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, Padova, Italy
| | - A Ramesh Sundar
- Division of Crop Protection, ICAR-Sugarcane Breeding Institute, Indian Council of Agricultural Research, Coimbatore, India
| | - P Malathi
- Division of Crop Protection, ICAR-Sugarcane Breeding Institute, Indian Council of Agricultural Research, Coimbatore, India
| | - R Viswanathan
- Division of Crop Protection, ICAR-Sugarcane Breeding Institute, Indian Council of Agricultural Research, Coimbatore, India
| | - O B Rosana
- Bioinformatics Center, ICAR-Indian Institute of Spices Research, Kozhikode, India
| | - K Neethukrishna
- Bioinformatics Center, ICAR-Indian Institute of Spices Research, Kozhikode, India
| | - Paolo Carletti
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, Padova, Italy
| | - Giorgio Arrigoni
- Proteomics Center of Padova University, Padova, Italy.,Department of Biomedical Sciences, University of Padova, Padova, Italy
| | - Antonio Masi
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, Padova, Italy
| | - Ganesh Kumar Agrawal
- Research Laboratory for Biotechnology and Biochemistry (RLABB), Kathmandu, Nepal.,GRADE (Global Research Arch for Developing Education) Academy Private Limited, Birgunj, Nepal
| | - Randeep Rakwal
- Research Laboratory for Biotechnology and Biochemistry (RLABB), Kathmandu, Nepal.,GRADE (Global Research Arch for Developing Education) Academy Private Limited, Birgunj, Nepal.,Tsukuba International Academy for Sport Studies (TIAS) and Faculty of Health and Sport Sciences, University of Tsukuba, Ibaraki, Japan
| |
Collapse
|
33
|
Viswanathan R. Pathogen Virulence in Sugarcane Red Rot Pathogen Versus Varieties in Cultivation: Classical Case of Loss in Virulence in the Pathotype CF06 (Cf671). Sugar Tech 2016. [DOI: 10.1007/s12355-016-0458-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
|
34
|
Chhabra ML, Parameswari B, Viswanathan R. Pathogenic behaviour pattern of Colletotrichum falcatum isolates of sugarcane in sub-tropical India. ACTA ACUST UNITED AC 2016. [DOI: 10.5958/2229-4473.2016.00103.8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
|
35
|
Chinnaraja C, Viswanathan R. Quantification of sugarcane yellow leaf virus in sugarcane following transmission through aphid vector, Melanaphis sacchari. Virusdisease 2015; 26:237-42. [PMID: 26645033 PMCID: PMC4663716 DOI: 10.1007/s13337-015-0267-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [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: 05/13/2015] [Accepted: 07/07/2015] [Indexed: 02/05/2023] Open
Abstract
Yellow leaf caused by Sugarcane yellow leaf virus (SCYLV) is a serious constraint to sugarcane production in India and currently the disease epidemics occur on many of the susceptible varieties under field conditions. Studies were conducted on the virus transmission by sugarcane aphid Melanaphis sacchari in sugarcane by inoculating virus-free meristem derived from micro- propagated plants of sugarcane cv Co 86032 with viruliferous aphids. Virus transmission was confirmed through RT-PCR assays and subsequently SCYLV population was established through RT-qPCR. A maximum of 22.3 × 10(3), 3.16 × 10(6) and 4.78 × 10(6) copies of SCYLV-RNA targets were recorded in the plants after 7, 180 and 300 days, respectively. This study showed that the aphid species M. sacchari acts as an effective vector of SCYLV. The relative standard curve method in RT-qPCR efficiently detected the increment in SCYLV copy numbers in sugarcane following transmission through M. sacchari.
Collapse
Affiliation(s)
- C. Chinnaraja
- Plant Pathology Section, Sugarcane Breeding Institute, Indian Council of Agricultural Research, Coimbatore, 641007 India
| | - R. Viswanathan
- Plant Pathology Section, Sugarcane Breeding Institute, Indian Council of Agricultural Research, Coimbatore, 641007 India
| |
Collapse
|
36
|
Sathyabhama M, Viswanathan R, Nandakumar M, Malathi P, Ramesh Sundar A. Understanding sugarcane defence responses during the initial phase of Colletotrichum falcatum pathogenesis by suppression subtractive hybridization (SSH). Physiological and Molecular Plant Pathology 2015. [DOI: 10.1016/j.pmpp.2015.07.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
|
37
|
Viswanathan R, Rana R, Lee Y, Alagkiozidis I, Reinhardt M, Arain A, Tolentino J, Pradhan T. Relationship of locus of control and depression to treatment adherence in gynecologic oncology patients. Gynecol Oncol 2015. [DOI: 10.1016/j.ygyno.2015.01.203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
|
38
|
|
39
|
Sathyabhama M, Viswanathan R, Malathi P, Ramesh Sundar A. Identification of Differentially Expressed Genes in Sugarcane During Pathogenesis of Colletotrichum falcatum by Suppression Subtractive Hybridization (SSH). Sugar Tech 2015. [DOI: 10.1007/s12355-014-0364-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
|
40
|
Rahul PR, Ganesh Kumar V, Viswanathan R, Ramesh Sundar A, Malathi P, Naveen Prasanth C, Pratima PT. Defense Transcriptome Analysis of Sugarcane and Colletotrichum falcatum Interaction Using Host Suspension Cells and Pathogen Elicitor. Sugar Tech 2014. [DOI: 10.1007/s12355-014-0356-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
|
41
|
Parameswari B, Bagyalakshmi K, Chinnaraja C, Viswanathan R. Molecular characterization of Indian Sugarcane streak mosaic virus isolates reveals recombination and negative selection in the P1 gene. Gene 2014; 552:199-203. [PMID: 25225126 DOI: 10.1016/j.gene.2014.09.021] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2013] [Revised: 09/05/2014] [Accepted: 09/12/2014] [Indexed: 02/08/2023]
|
42
|
Anna Durai A, Premachandran MN, Govindaraj P, Malathi P, Viswanathan R. Variability in Breeding Pool of Sugarcane (Saccharum spp.) for Yield, Quality and Resistance to Different Biotic and Abiotic Stress Factors. Sugar Tech 2014. [DOI: 10.1007/s12355-014-0301-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
|
43
|
Viswanathan R. Infectious hepatitis in Delhi (1955-56): a critical study-epidemiology. 1957. Natl Med J India 2013; 26:362-377. [PMID: 25074004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Affiliation(s)
- R Viswanathan
- (First published Indian J Med Res 1957;45 [Suppl 12] : 1-29)
| |
Collapse
|
44
|
Prathima PT, Raveendran M, Kumar KK, Rahul PR, Kumar VG, Viswanathan R, Sundar AR, Malathi P, Sudhakar D, Balasubramaniam P. Differential regulation of defense-related gene expression in response to red rot pathogen Colletotrichum falcatum infection in sugarcane. Appl Biochem Biotechnol 2013; 171:488-503. [PMID: 23861092 DOI: 10.1007/s12010-013-0346-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Accepted: 06/17/2013] [Indexed: 02/08/2023]
Abstract
Red rot is a serious disease of sugarcane caused by the fungus Colletotrichum falcatum imposing a considerable economic loss annually in all sugarcane-producing countries. In this study, we analyzed the early resistance response of sugarcane to red rot fungus by comparing the differences between control and inoculated stalk tissues. Differential display reverse transcription polymerase chain reaction (DD-RT-PCR) was employed to identify altered expression of genes in disease-resistant cv Co 93009, in response to pathogen infection. DD-RT-PCR identified 300 differentially expressed transcripts of which 112 were selected for further analysis. Cloning and sequence analysis of the isolated cDNA fragments resulted in functional categorization of these clones into five categories, of which the defense/stress/signaling group was the largest, with clones homologous to genes known to be actively involved in various pathogenesis-related functions in plant species. This group showed overexpression of several transcripts related to ethylene-mediated and jasmonic acid pathway of plant defense mechanisms. Of the 112 expressed sequence tags, validation of expression was carried out for five important genes whose role in plant defense mechanisms is well established. This is the first report of Colletotrichum-mediated gene regulation in sugarcane which has provided a set of candidate genes for detailed molecular dissection of signaling and defense responses in tropical sugarcane during the onset of red rot resistance.
Collapse
Affiliation(s)
- P T Prathima
- Sugarcane Breeding Institute, Coimbatore-7, India.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
45
|
Viswanathan R, Ganesh Kumar V, Karuppaiah R, Scindiya M, Chinnaraja C. Development of Duplex-Immunocapture (Duplex-IC) RT-PCR for the Detection of Sugarcane streak mosaic virus and Sugarcane mosaic virus in Sugarcane. Sugar Tech 2013. [DOI: 10.1007/s12355-013-0216-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
|
46
|
Karuppaiah R, Viswanathan R, Kumar VG. Genetic diversity of Sugarcane bacilliform virus isolates infecting Saccharum spp. in India. Virus Genes 2013; 46:505-16. [PMID: 23430710 DOI: 10.1007/s11262-013-0890-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Accepted: 02/05/2013] [Indexed: 02/05/2023]
Abstract
Sugarcane bacilliform virus (SCBV), which causes leaf freckle in sugarcane, is a member of the genus Badnavirus. Studies were conducted to characterize SCBV in Saccharum officinarum germplasm and cultivated varieties in India by sequencing the complete genomes of five isolates. Genome lengths ranged from 7,553 to 7,884 nucleotides. Duplications in ORF3 and insertions in the RNase H-domain in some of the isolates were found to contribute to the large size of their genomes. The Indian SCBV isolates share identities of 69-85 % for the complete genomic sequence, indicating wide genetic diversity among them, and share 70-82 % identity with Sugarcane bacilliform Ireng Maleng virus (SCBIMV) and Sugarcane bacilliform Morocco virus (SCBMV), as well as 43-46 % identity with Banana streak virus (BSV) and BSV-related SCBV species from Guadeloupe, indicating that the Indian SCBV isolates are distinct from SCBV isolates reported to date. Irrespective of the region compared, SCBV isolates from India, Australia, and Morocco clustered together. BSV and BSV-related SCBV isolates from Guadeloupe formed another cluster. A phylogenetic analysis based on the partial RT/RNase H-sequence separated SCBV and BSV-related SCBV sequences into 11 SCBV groups viz. SCBV-A to -K. Among the 11 groups, the SCBV sequences separated under H, I, J, and K are newly identified in this study, representing three new species and are tentatively named as SCBBBV, SCBBOV, and SCBBRV. Thus, the PASC and phylogenetic analyses evidenced that the symptoms associated with badnaviruses in sugarcane in India are caused by at least three new species, SCBBBV, SCBBOV, and SCBBRV, besides SCBIMV and SCBMV represented by SCBV-BT and SCBV-Iscam, respectively.
Collapse
Affiliation(s)
- R Karuppaiah
- Plant Pathology Section, Sugarcane Breeding Institute, Indian Council of Agricultural Research, Coimbatore, 641007, India
| | | | | |
Collapse
|
47
|
Parameswari B, Bagyalakshmi K, Viswanathan R, Chinnaraja C. Molecular characterization of Indian sugarcane streak mosaic virus isolate. Virus Genes 2012; 46:186-9. [PMID: 23011777 DOI: 10.1007/s11262-012-0827-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2011] [Accepted: 09/14/2012] [Indexed: 02/05/2023]
Abstract
Sugarcane streak mosaic virus (SCSMV), a member of the genus Poacevirus, family Potyviridae, is an important viral pathogen affecting sugarcane cultivation in India. The complete nucleotide sequence of a SCSMV isolate from India (SCSMV-IND) was determined. The linear, assembled, single-stranded positive-sense RNA genome of SCSMV-IND was 9,786 nucleotides in length (excluding the poly (A) tail) and encoded a polyprotein of 3,131 amino acid residues. The genome of SCSMV-IND shared high degree of sequence identity with SCSMV-PAK (93 % at nucleotide and 97 % at amino acid), and shared only 81 % nucleotide and 94 % amino acid identities with all the four SCSMV isolates (SCSMV-JP1, -JP2, -ID, and -THA). Phylogenetic tree analysis of the complete genome sequences of SCSMV isolates revealed that they can be clustered into two groups. SCSMV-IND and -AP isolates showed 18 % (nucleotide) divergence within the highly conserved 3' partial genome, suggesting a high level of genetic diversity among the Indian SCSMV isolates.
Collapse
Affiliation(s)
- B Parameswari
- Sugarcane Breeding Institute Regional Centre, Karnal, Haryana, India
| | | | | | | |
Collapse
|
48
|
Chinnaraja C, Viswanathan R, Karuppaiah R, Bagyalakshmi K, Malathi P, Parameswari B. Complete genome characterization of Sugarcane yellow leaf virus from India: Evidence for RNA recombination. Eur J Plant Pathol 2012. [DOI: 10.1007/s10658-012-0090-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
|
49
|
Malathi P, Viswanathan R. Identification of Pathogenicity Determinants in Colletotrichum falcatum Using Wild and Mutant Cultures. Sugar Tech 2012. [DOI: 10.1007/s12355-012-0161-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
|
50
|
Malathi P, Viswanathan R. Variation in Colletotrichum falcatum-Red Rot Pathogen of Sugarcane in Relation to Host Resistance. Sugar Tech 2012. [DOI: 10.1007/s12355-012-0150-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
|