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Dr. Renesh Bedre
Texas A&M AgriLife Research & Extension Center, Texas A&M University 2415 E. Hwy. 83, Weslaco, TX 78596, USA

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0 Biostatistics
0 Computational Biology
0 Genomics
0 Machine Learning

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Preprint content
Published: 24 July 2020
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Use of high-throughput sequencing (HTS) has become indispensable in life science research. Raw HTS data contains several sequencing artifacts, and as a first step it is imperative to remove the artifacts for reliable downstream bioinformatics analysis. Although there are multiple stand-alone tools available that can perform the various quality control steps separately, availability of an integrated tool that can allow one-step, automated quality control analysis of HTS datasets will significantly enhance handling large number of samples parallelly. Here, we developed HTSeqQC, a stand-alone, flexible, and easy-to-use software for one-step quality control analysis of raw HTS data. HTSeqQC can evaluate HTS data quality and perform filtering and trimming analysis in a single run. We evaluated the performance of HTSeqQC for conducting batch analysis of HTS datasets with 322 sample datasets with an average ∼1M (paired end) sequence reads per sample. HTSeqQC accomplished the QC analysis in ∼3 hours in distributed mode and ∼31 hours in shared mode, thus underscoring its utility and robust performance. In addition to command-line execution, we integrated HTSeqQC into the free, open-source, CyVerse cyberinfrastructure resource as a GUI interface, for wider access to experimental biologists who have limited computational resources and/or programming abilities.

ACS Style

Renesh H Bedre; Carlos A Avila; Kranthi Mandadi. HTSeqQC: A Flexible and One-Step Quality Control Software for High-throughput Sequence Data Analysis. 2020, 1 .

AMA Style

Renesh H Bedre, Carlos A Avila, Kranthi Mandadi. HTSeqQC: A Flexible and One-Step Quality Control Software for High-throughput Sequence Data Analysis. . 2020; ():1.

Chicago/Turabian Style

Renesh H Bedre; Carlos A Avila; Kranthi Mandadi. 2020. "HTSeqQC: A Flexible and One-Step Quality Control Software for High-throughput Sequence Data Analysis." , no. : 1.

Original research
Published: 04 December 2019 in Plant Direct
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Genome‐scale studies using high‐throughput sequencing (HTS) technologies generate substantial lists of differentially expressed genes under different experimental conditions. These gene lists need to be further mined to narrow down biologically relevant genes and associated functions in order to guide downstream functional genetic analyses. A popular approach is to determine statistically overrepresented genes in a user‐defined list through enrichment analysis tools, which rely on functional annotations of genes based on Gene Ontology (GO) terms. Here, we propose a new computational approach, GenFam, which allows annotation, classification, and enrichment of genes based on their gene family, thus simplifying identification of candidate gene families and associated genes that may be relevant to the query. GenFam and its integrated database comprises of three hundred and eighty‐four unique gene families and supports gene family analyses for sixty plant genomes. Four comparative case studies with plant species belonging to different clades and families were performed using GenFam which demonstrated its robustness and comprehensiveness over preexisting functional enrichment tools. To make it readily accessible for plant biologists, GenFam is available as a web‐based application where users can input gene IDs and export enrichment results in both tabular and graphical formats. Users can also customize analysis parameters by choosing from the various statistical enrichment tests and multiple testing correction methods. Additionally, the web‐based application, source code, and database are freely available to use and download. Website: http://mandadilab.webfactional.com/home/. Source code and database: http://mandadilab.webfactional.com/home/dload/.

ACS Style

Renesh Bedre; Kranthi Mandadi. GenFam: A web application and database for gene family‐based classification and functional enrichment analysis. Plant Direct 2019, 3, e00191 .

AMA Style

Renesh Bedre, Kranthi Mandadi. GenFam: A web application and database for gene family‐based classification and functional enrichment analysis. Plant Direct. 2019; 3 (12):e00191.

Chicago/Turabian Style

Renesh Bedre; Kranthi Mandadi. 2019. "GenFam: A web application and database for gene family‐based classification and functional enrichment analysis." Plant Direct 3, no. 12: e00191.

Journal article
Published: 01 December 2019 in Horticulture Research
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Minor alleles (MA) have been associated with disease incidence in human studies, enabling the identification of diagnostic risk factors for various diseases. However, allelic mapping has rarely been performed in plant systems. The goal of this study was to determine whether a difference in MA prevalence is a strong enough risk factor to indicate a likely significant difference in disease resistance against white rust (WR; Albugo occidentalis) in spinach (Spinacia oleracea). We used WR disease severity ratings (WR-DSRs) in a diversity panel of 267 spinach accessions to define resistant- and susceptibility-associated groups within the distribution scores and then tested the single-nucleotide polymorphism (SNP) variants to interrogate the MA prevalence in the most susceptible (MS) vs. most resistant (MR) individuals using permutation-based allelic association tests. A total of 448 minor alleles associated with WR severity were identified in the comparison between the 25% MS and the 25% MR accessions, while the MA were generally similar between the two halves of the interquartile range. The minor alleles in the MS group were distributed across all six chromosomes and made up ~71% of the markers that were also strongly associated with WR in parallel performed genome-wide association study. These results indicate that susceptibility may be highly determined by the disproportionate overrepresentation of minor alleles, which could be used to select for resistant plants. Furthermore, by focusing on the distribution tails, allelic mapping could be used to identify plant markers associated with quantitative traits on the most informative segments of the phenotypic distribution.

ACS Style

Henry O. Awika; Thiago G. Marconi; Renesh Bedre; Kranthi K. Mandadi; Carlos A. Avila. Minor alleles are associated with white rust (Albugo occidentalis) susceptibility in spinach (Spinacia oleracea). Horticulture Research 2019, 6, 1 -15.

AMA Style

Henry O. Awika, Thiago G. Marconi, Renesh Bedre, Kranthi K. Mandadi, Carlos A. Avila. Minor alleles are associated with white rust (Albugo occidentalis) susceptibility in spinach (Spinacia oleracea). Horticulture Research. 2019; 6 (1):1-15.

Chicago/Turabian Style

Henry O. Awika; Thiago G. Marconi; Renesh Bedre; Kranthi K. Mandadi; Carlos A. Avila. 2019. "Minor alleles are associated with white rust (Albugo occidentalis) susceptibility in spinach (Spinacia oleracea)." Horticulture Research 6, no. 1: 1-15.

Original article
Published: 10 November 2019 in Plant Breeding
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Anthracnose (Colletotrichum dematium) is an important disease in spinach (Spinacia oleracea). Sources of resistance must be identified, and molecular tools must be developed to expedite cultivar development. In this study, a diverse collection of 276 spinach accessions was scored for anthracnose disease severity. We then evaluated marker identification approaches by testing how well haplotype‐based trait modelling compares to single markers in identifying strong association signals. Alleles in linkage disequilibrium were tagged in haplotype blocks, and anthracnose‐associated molecular markers were identified using single‐SNP (sSNP), pairwise haplotype (htP) and multi‐marker haplotype (htM) SNP tagging approaches. We identified 49 significantly associated markers distributed on several spinach chromosomes using all methods. The sSNP approach identified 13 markers, while htP identified 24 (~63% more) and htM 34 (~162% more). Of these markers, four were uniquely identified by the sSNP approach, nine by htP and nineteen by htM. The results indicate that resistance to anthracnose is polygenic and that haplotype‐based analysis may have more power than sSNP. Using a combination of these methods can improve the identification of molecular markers for spinach breeding.

ACS Style

Henry O. Awika; Kimberly Cochran; Vijay Joshi; Renesh Bedre; Kranthi K. Mandadi; Carlos A. Avila. Single‐marker and haplotype‐based association analysis of anthracnose ( Colletotrichum dematium) resistance in spinach ( Spinacia oleracea ). Plant Breeding 2019, 139, 402 -418.

AMA Style

Henry O. Awika, Kimberly Cochran, Vijay Joshi, Renesh Bedre, Kranthi K. Mandadi, Carlos A. Avila. Single‐marker and haplotype‐based association analysis of anthracnose ( Colletotrichum dematium) resistance in spinach ( Spinacia oleracea ). Plant Breeding. 2019; 139 (2):402-418.

Chicago/Turabian Style

Henry O. Awika; Kimberly Cochran; Vijay Joshi; Renesh Bedre; Kranthi K. Mandadi; Carlos A. Avila. 2019. "Single‐marker and haplotype‐based association analysis of anthracnose ( Colletotrichum dematium) resistance in spinach ( Spinacia oleracea )." Plant Breeding 139, no. 2: 402-418.

Journal article
Published: 01 November 2019 in The Plant Genome
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Despite advances in sequencing for genotyping, the lack of rapid, accurate, and reproducible phenotyping platforms has hampered efforts to use genetic analysis to predict traits of interest. Therefore, the use of high-throughput systems to phenotype traits related to crop growth, yield, quality, and resistance to biotic and abiotic stresses has become a major asset for breeding. Here, we assessed the efficacy of unmanned aircraft system (UAS)-based high-throughput phenotyping to obtain data for molecular marker development for spinach (Spinacia oleracea L.) improvement. We used a UAS equipped with a red–green–blue sensor to capture raw images of 284 spinach accessions throughout the crop cycle. Processed images generated orthomosaic and digital surface models for estimating canopy cover, canopy volume, and excess greenness index models. In addition, we manually recorded the number of days to bolting. Genome-wide association studies against a single-nucleotide polymorphism (SNP) panel obtained by ddRADseq identified 99 SNPs significantly associated with growth parameters. Some of these SNPs are in transcription factor and stress-response genes with possible roles in plant growth and development. The results underscore the utility of combining aerial imaging and genomic data analysis to optimize marker development. This study lays the foundation for the use of UAS-based high-throughput phenotyping for the molecular breeding of spinach. Copyright © 2019. . © 2019 The Author(s).

ACS Style

Henry O. Awika; Renesh Bedre; Junho Yeom; Thiago G. Marconi; Juan Enciso; Kranthi K. Mandadi; Jinha Jung; Carlos A. Avila. Developing Growth‐Associated Molecular Markers Via High‐Throughput Phenotyping in Spinach. The Plant Genome 2019, 12, 190027 -19.

AMA Style

Henry O. Awika, Renesh Bedre, Junho Yeom, Thiago G. Marconi, Juan Enciso, Kranthi K. Mandadi, Jinha Jung, Carlos A. Avila. Developing Growth‐Associated Molecular Markers Via High‐Throughput Phenotyping in Spinach. The Plant Genome. 2019; 12 (3):190027-19.

Chicago/Turabian Style

Henry O. Awika; Renesh Bedre; Junho Yeom; Thiago G. Marconi; Juan Enciso; Kranthi K. Mandadi; Jinha Jung; Carlos A. Avila. 2019. "Developing Growth‐Associated Molecular Markers Via High‐Throughput Phenotyping in Spinach." The Plant Genome 12, no. 3: 190027-19.

Journal article
Published: 20 June 2019 in Scientific Reports
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Alternative splicing (AS) promotes transcriptome and proteome diversity during growth, development, and stress responses in eukaryotes. Genome-wide studies of AS in sugarcane (Saccharum spp.) are lacking, mainly due to the absence of a high-quality sequenced reference genome, sugarcane's large, complex genome, and the variable chromosome numbers and polyploidy of sugarcane cultivars. Here, we analyzed changes in the sugarcane isoform-level transcriptome and AS landscape during infection with the smut fungus (Sporisorium scitamineum) using a hybrid approach involving Sorghum bicolor reference-based and Trinity de novo mapping tools. In total, this analysis detected 16,039 and 15,379 transcripts (≥2 FPKM) at 5 and 200 days after infection, respectively. A conservative estimate of isoform-level expression suggested that approximately 5,000 (14%) sugarcane genes undergo AS. Differential expression analysis of the alternatively spliced genes in healthy and smut-infected sugarcane revealed 896 AS events modulated at different stages of infection. Gene family and gene ontology functional enrichment analysis of the differentially spliced genes revealed overrepresentation of functional categories related to the cell wall, defense, and redox homeostasis pathways. Our study provides novel insight into the AS landscape of sugarcane during smut disease interactions.

ACS Style

Renesh Bedre; Sonia Irigoyen; Patricia D. C. Schaker; Claudia Barros Monteiro-Vitorello; Jorge A. Da Silva; Kranthi K. Mandadi. Genome-wide alternative splicing landscapes modulated by biotrophic sugarcane smut pathogen. Scientific Reports 2019, 9, 8876 .

AMA Style

Renesh Bedre, Sonia Irigoyen, Patricia D. C. Schaker, Claudia Barros Monteiro-Vitorello, Jorge A. Da Silva, Kranthi K. Mandadi. Genome-wide alternative splicing landscapes modulated by biotrophic sugarcane smut pathogen. Scientific Reports. 2019; 9 (1):8876.

Chicago/Turabian Style

Renesh Bedre; Sonia Irigoyen; Patricia D. C. Schaker; Claudia Barros Monteiro-Vitorello; Jorge A. Da Silva; Kranthi K. Mandadi. 2019. "Genome-wide alternative splicing landscapes modulated by biotrophic sugarcane smut pathogen." Scientific Reports 9, no. 1: 8876.

Opinion article
Published: 04 June 2019 in Frontiers in Plant Science
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New Era in Plant Alternative Splicing Analysis Enabled by Advances in High-Throughput Sequencing (HTS) Technologies

ACS Style

Renesh Bedre; Sonia Irigoyen; Ezequiel Petrillo; Kranthi K. Mandadi. New Era in Plant Alternative Splicing Analysis Enabled by Advances in High-Throughput Sequencing (HTS) Technologies. Frontiers in Plant Science 2019, 10, 740 .

AMA Style

Renesh Bedre, Sonia Irigoyen, Ezequiel Petrillo, Kranthi K. Mandadi. New Era in Plant Alternative Splicing Analysis Enabled by Advances in High-Throughput Sequencing (HTS) Technologies. Frontiers in Plant Science. 2019; 10 ():740.

Chicago/Turabian Style

Renesh Bedre; Sonia Irigoyen; Ezequiel Petrillo; Kranthi K. Mandadi. 2019. "New Era in Plant Alternative Splicing Analysis Enabled by Advances in High-Throughput Sequencing (HTS) Technologies." Frontiers in Plant Science 10, no. : 740.

Journal article
Published: 01 January 2019 in American Journal of Plant Sciences
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Genetic variation developed in plant breeding programs is fundamental to creating new combinations that result in cultivars with enhanced characteristics. Over the years, tomato (Solanum lycopersicum) breeding programs associated with the Texas A&M University system have developed morphologically diverse lines of tomatoes selected for heat tolerance, fruit quality, and disease resistance to adapt them to Texas growing conditions. Here we explored the intraspecific genetic variations of 322 cultivated tomato genotypes, including 300 breeding lines developed by three Texas A&M breeding programs, as an initial step toward implementing molecular breeding approaches. Genotyping by sequencing using low coverage whole-genome sequencing (SkimGBS) identified 10,236 high-quality single-nucleotide polymorphisms (SNPs) that were used to assess genetic diversity, population structure, and phylogenetic relationship between genotypes and breeding programs. Model-based population structure analysis, phylogenetic tree construction, and principal component analysis indicated that the genotypes were grouped into two main clusters. Genetic distance analysis revealed greater genetic diversity among the products of the three breeding programs. The germplasm developed at Texas A&M programs at Weslaco, College Station, and by Dr. Paul Leeper exhibited genetic diversity ranges of 0.175 - 0.434, 0.099 - 0.392, and 0.183 - 0.347, respectively, suggesting that there is enough variation within and between the lines from the three programs to perform selection for cultivar development. The SNPs identified here could be used to develop molecular tools for selecting various traits of interest and to select parents for future tomato breeding.

ACS Style

Devi R. Kandel; Renesh Bedre; Kranthi K. Mandadi; Kevin Crosby; Carlos A. Avila. Genetic Diversity and Population Structure of Tomato (Solanum lycopersicum) Germplasm Developed by Texas A&M Breeding Programs. American Journal of Plant Sciences 2019, 10, 1154 -1180.

AMA Style

Devi R. Kandel, Renesh Bedre, Kranthi K. Mandadi, Kevin Crosby, Carlos A. Avila. Genetic Diversity and Population Structure of Tomato (Solanum lycopersicum) Germplasm Developed by Texas A&M Breeding Programs. American Journal of Plant Sciences. 2019; 10 (07):1154-1180.

Chicago/Turabian Style

Devi R. Kandel; Renesh Bedre; Kranthi K. Mandadi; Kevin Crosby; Carlos A. Avila. 2019. "Genetic Diversity and Population Structure of Tomato (Solanum lycopersicum) Germplasm Developed by Texas A&M Breeding Programs." American Journal of Plant Sciences 10, no. 07: 1154-1180.

Research article
Published: 31 May 2018 in Plant Biotechnology Journal
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Actin‐depolymerizing factors (ADFs) maintain the cellular actin network dynamics by regulating severing and disassembly of actin filaments in response to environmental cues. An ADF isolated from a monocot halophyte, Spartina alterniflora (SaADF2), imparted significantly higher level of drought and salinity tolerance when expressed in rice than its rice homologue OsADF2. SaADF2 differs from OsADF2 by a few amino acid residues, including a substitution in the regulatory phosphorylation site serine‐6, which accounted for its weak interaction with OsCDPK6 (calcium‐dependent protein kinase), thus resulting in an increased efficacy of SaADF2 and enhanced cellular actin dynamics. SaADF2 overexpression preserved the actin filament organization better in rice protoplasts under desiccation stress. The predicted tertiary structure of SaADF2 showed a longer F‐loop than OsADF2 that could have contributed to higher actin‐binding affinity and rapid F‐actin depolymerization in vitro by SaADF2. Rice transgenics constitutively overexpressing SaADF2 (SaADF2‐OE) showed better growth, relative water content, and photosynthetic and agronomic yield under drought conditions than wild‐type (WT) and OsADF2 overexpressers (OsADF2‐OE). SaADF2‐OE preserved intact grana structure after prolonged drought stress, whereas WT and OsADF2‐OE presented highly damaged and disorganized grana stacking. The possible role of ADF2 in transactivation was hypothesized from the comparative transcriptome analyses, which showed significant differential expression of stress‐related genes including interacting partners of ADF2 in overexpressers. Identification of a complex, differential interactome decorating or regulating stress‐modulated cytoskeleton driven by ADF isoforms will lead us to key pathways that could be potential target for genome engineering to improve abiotic stress tolerance in agricultural crops.

ACS Style

Sonali Sengupta; Venkata Mangu; Luis Sanchez; Renesh Bedre; Rohit Joshi; Kanniah Rajasekaran; Niranjan Baisakh. An actin‐depolymerizing factor from the halophyte smooth cordgrass, Spartina alterniflora ( Sa ADF 2 ), is superior to its rice homolog ( Os ADF 2 ) in conferring drought and salt tolerance when constitutively overexpressed in rice. Plant Biotechnology Journal 2018, 17, 188 -205.

AMA Style

Sonali Sengupta, Venkata Mangu, Luis Sanchez, Renesh Bedre, Rohit Joshi, Kanniah Rajasekaran, Niranjan Baisakh. An actin‐depolymerizing factor from the halophyte smooth cordgrass, Spartina alterniflora ( Sa ADF 2 ), is superior to its rice homolog ( Os ADF 2 ) in conferring drought and salt tolerance when constitutively overexpressed in rice. Plant Biotechnology Journal. 2018; 17 (1):188-205.

Chicago/Turabian Style

Sonali Sengupta; Venkata Mangu; Luis Sanchez; Renesh Bedre; Rohit Joshi; Kanniah Rajasekaran; Niranjan Baisakh. 2018. "An actin‐depolymerizing factor from the halophyte smooth cordgrass, Spartina alterniflora ( Sa ADF 2 ), is superior to its rice homolog ( Os ADF 2 ) in conferring drought and salt tolerance when constitutively overexpressed in rice." Plant Biotechnology Journal 17, no. 1: 188-205.

Short communication
Published: 22 March 2018 in Physiology and Molecular Biology of Plants
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A comparative transcriptome analysis was performed using the genes significantly differentially expressed in cotton, corn and peanut in response to aflatoxin producing fungus Aspergillus flavus with an objective of identifying candidate resistance genes in cotton. Two-way analyses identified 732 unique genes to be differentially regulated by the fungus with only 26 genes common across all three crops that were considered candidate A. flavus resistance genes with an assumption that these genes have specific roles in conferring the resistance trait. Genes of membrane cellular component involved in DNA binding with involvement in defense responses were highly represented among the differentially expressed unique genes. Most (six) of these genes coded for 2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase superfamily proteins. Genes encoding helix loop helix protein, alcohol dehydrogenase and UDP glycosylation transferase which were upregulated in response to both atoxigenic and toxigenic strains of A. flavus, could be potential resistance candidate genes for downstream functional manipulation to confer resistance.

ACS Style

Muthamilarasan Mehanathan; Renesh Bedre; Venkata Mangu; Kanniah Rajasekaran; Deepak Bhatnagar; Niranjan Baisakh. Identification of candidate resistance genes of cotton against Aspergillus flavus infection using a comparative transcriptomics approach. Physiology and Molecular Biology of Plants 2018, 24, 513 -519.

AMA Style

Muthamilarasan Mehanathan, Renesh Bedre, Venkata Mangu, Kanniah Rajasekaran, Deepak Bhatnagar, Niranjan Baisakh. Identification of candidate resistance genes of cotton against Aspergillus flavus infection using a comparative transcriptomics approach. Physiology and Molecular Biology of Plants. 2018; 24 (3):513-519.

Chicago/Turabian Style

Muthamilarasan Mehanathan; Renesh Bedre; Venkata Mangu; Kanniah Rajasekaran; Deepak Bhatnagar; Niranjan Baisakh. 2018. "Identification of candidate resistance genes of cotton against Aspergillus flavus infection using a comparative transcriptomics approach." Physiology and Molecular Biology of Plants 24, no. 3: 513-519.

Other
Published: 26 February 2018
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Genome-scale studies using high-throughput sequencing (HTS) technologies generate substantial lists of differentially expressed genes under different experimental conditions. These gene lists need to be further mined to narrow down biologically relevant genes and associated functions in order to guide downstream functional genetic analyses. A popular approach is to determine statistically overrepresented genes in a user-defined list through enrichment analysis tools, which rely on functional annotations of genes based on Gene Ontology (GO) terms. Here, we propose a new approach, GenFam, which allows classification and enrichment of genes based on their gene family, thus simplifying identification of candidate gene families and associated genes that may be relevant to the query. GenFam and its integrated database comprises of three-hundred and eighty-four unique gene families and supports gene family classification and enrichment analyses for sixty plant genomes. Four comparative case studies with plant species belonging to different clades and families were performed using GenFam which demonstrated its robustness and comprehensiveness over preexisting functional enrichment tools. To make it readily accessible for plant biologists, GenFam is available as a web-based application where users can input gene IDs and export enrichment results in both tabular and graphical formats. Users can also customize analysis parameters by choosing from the various statistical enrichment tests and multiple testing correction methods. Additionally, the web-based application, source code and database are freely available to use and download. Website: http://mandadilab.webfactional.com/home/. Source code and database: http://mandadilab.webfactional.com/home/dload/.

ACS Style

Renesh Bedre; Kranthi Mandadi. GenFam: A web application and database for gene family-based classification and functional enrichment analysis. 2018, 272187 .

AMA Style

Renesh Bedre, Kranthi Mandadi. GenFam: A web application and database for gene family-based classification and functional enrichment analysis. . 2018; ():272187.

Chicago/Turabian Style

Renesh Bedre; Kranthi Mandadi. 2018. "GenFam: A web application and database for gene family-based classification and functional enrichment analysis." , no. : 272187.

Original research article
Published: 08 January 2018 in Frontiers in Chemistry
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Drought stress is a constant threat to rice production worldwide. Most modern rice cultivars are sensitive to drought, and the effect is severe at the reproductive stage. Conventional breeding for drought resistant (DR) rice varieties is slow and limited due to the quantitative nature of the DR traits. Identification of genes (QTLs)/markers associated with DR traits is a prerequisite for marker-assisted breeding. Grain yield is the most important trait and to this end drought yield QTLs have been identified under field conditions. The present study reports identification of drought yield QTLs under controlled conditions without confounding effects of other factors prevalent under natural conditions. A linkage map covering 1,781.5 cM with an average resolution of 9.76 cM was constructed using an F2 population from a cross between two Japonica cultivars, Cocodrie (drought sensitive) and Vandana (drought tolerant) with 213 markers distributed over 12 rice chromosomes. A subset of 59 markers (22 genic SSRs and 37 SNPs) derived from the transcriptome of the parents were also placed in the map. Single marker analysis using 187 F2 : 3 progeny identified 6 markers distributed on chromosomes 1, 5, and 8 to be associated with grain yield under drought (GYD). Composite interval mapping identified six genomic regions/quantitative trait loci (QTL) on chromosome 1, 5, 8, and 9 to be associated with GYD. QTLs located on chromosome 1 (qGYD1.2, qGYD1.3), chromosome 5 (qGYD5.1) and chromosome 8 (qGYD8.1) were contributed by Vandana alleles, whereas the QTLs, qGYD1.1 and qQYD9.1 were contributed by Cocodrie alelles. The additive positive phenotypic variance explained by the QTLs ranged from 30.0 to 34.0%. Candidate genes annotation within QTLs suggested the role of transcription factors and genes involved in osmotic potential regulation through catalytic/metabolic pathways in drought tolerance mechanism contributing to yield.

ACS Style

Julio Solis; Andres Gutierrez; Venkata Mangu; Eduardo Sanchez; Renesh Bedre; Steve Linscombe; Niranjan Baisakh. Genetic Mapping of Quantitative Trait Loci for Grain Yield under Drought in Rice under Controlled Greenhouse Conditions. Frontiers in Chemistry 2018, 5, 129 .

AMA Style

Julio Solis, Andres Gutierrez, Venkata Mangu, Eduardo Sanchez, Renesh Bedre, Steve Linscombe, Niranjan Baisakh. Genetic Mapping of Quantitative Trait Loci for Grain Yield under Drought in Rice under Controlled Greenhouse Conditions. Frontiers in Chemistry. 2018; 5 ():129.

Chicago/Turabian Style

Julio Solis; Andres Gutierrez; Venkata Mangu; Eduardo Sanchez; Renesh Bedre; Steve Linscombe; Niranjan Baisakh. 2018. "Genetic Mapping of Quantitative Trait Loci for Grain Yield under Drought in Rice under Controlled Greenhouse Conditions." Frontiers in Chemistry 5, no. : 129.

Correction
Published: 28 December 2017 in ACS Chemical Biology
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ACS Style

Ashish Gupta; Renesh Bedre; Sudarshan Singh Thapa; Afsana Sabrin; Guannan Wang; Maheshi Dassanayake; Anne Grove. Correction to Global Awakening of Cryptic Biosynthetic Gene Clusters in Burkholderia thailandensis. ACS Chemical Biology 2017, 13, 282 -282.

AMA Style

Ashish Gupta, Renesh Bedre, Sudarshan Singh Thapa, Afsana Sabrin, Guannan Wang, Maheshi Dassanayake, Anne Grove. Correction to Global Awakening of Cryptic Biosynthetic Gene Clusters in Burkholderia thailandensis. ACS Chemical Biology. 2017; 13 (1):282-282.

Chicago/Turabian Style

Ashish Gupta; Renesh Bedre; Sudarshan Singh Thapa; Afsana Sabrin; Guannan Wang; Maheshi Dassanayake; Anne Grove. 2017. "Correction to Global Awakening of Cryptic Biosynthetic Gene Clusters in Burkholderia thailandensis." ACS Chemical Biology 13, no. 1: 282-282.

Research article
Published: 08 November 2017 in ACS Chemical Biology
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Many bacteria encode biosynthetic proteins that produce a vast array of natural products. These compounds are often synthesized during host invasion as they function as virulence factors. In addition, such secondary metabolites have yielded numerous molecular scaffolds with pharmaceutical and clinical importance. The gene clusters that encode proteins responsible for synthesis of these compounds are typically silenced or “cryptic” under laboratory growth conditions, hampering discovery of novel lead compounds. We report here that MftR is a global repressor of secondary metabolite synthesis in Burkholderia thailandensis and that urate functions as a physiologically relevant inducer of gene expression. Biosynthetic gene clusters under MftR control include those associated with production of the antimicrobial bactobolins, the iron siderophore malleobactin, and the virulence factor malleilactone. MftR also controls additional genes associated with survival in a host environment, such as genes encoding components of the type III secretion system (T3SS) and proteins linked to anaerobic respiration. This observation not only has implications for understanding activation of gene regulatory networks during host invasion, but it also paves the way for isolation of novel therapeutic leads.

ACS Style

Ashish Gupta; Renesh Bedre; Sudarshan Singh Thapa; Afsana Sabrin; Guannan Wang; Maheshi Dassanayake; Anne Grove. Global Awakening of Cryptic Biosynthetic Gene Clusters in Burkholderia thailandensis. ACS Chemical Biology 2017, 12, 3012 -3021.

AMA Style

Ashish Gupta, Renesh Bedre, Sudarshan Singh Thapa, Afsana Sabrin, Guannan Wang, Maheshi Dassanayake, Anne Grove. Global Awakening of Cryptic Biosynthetic Gene Clusters in Burkholderia thailandensis. ACS Chemical Biology. 2017; 12 (12):3012-3021.

Chicago/Turabian Style

Ashish Gupta; Renesh Bedre; Sudarshan Singh Thapa; Afsana Sabrin; Guannan Wang; Maheshi Dassanayake; Anne Grove. 2017. "Global Awakening of Cryptic Biosynthetic Gene Clusters in Burkholderia thailandensis." ACS Chemical Biology 12, no. 12: 3012-3021.

Protocol
Published: 17 October 2017 in Advanced Structural Safety Studies
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Alternative splicing (AS) promotes transcriptome and proteome diversity in plants, which influences growth and development, and host responses to stress. Advancements in next-generation sequencing, bioinformatics, and computational biology tools have allowed biologists to investigate AS landscapes on a genome-wide scale in several plant species. Furthermore, the development of Brachypodium distachyon (Brachypodium) as a model system for grasses has facilitated comparative studies of AS within the Poaceae. These analyses revealed a plethora of genes in several biological processes that are alternatively spliced and identified conserved AS patterns among monocot and dicot plants. In this chapter, using a Brachypodium-virus pathosystem as a research template, we provide an overview of genomic and bioinformatic tools that can be used to investigate constitutive and alternative splicing in plants.

ACS Style

Sonia Irigoyen; Renesh H. Bedre; Karen-Beth G. Scholthof; Kranthi K. Mandadi. Genomic Approaches to Analyze Alternative Splicing, A Key Regulator of Transcriptome and Proteome Diversity in Brachypodium distachyon. Advanced Structural Safety Studies 2017, 1667, 73 -85.

AMA Style

Sonia Irigoyen, Renesh H. Bedre, Karen-Beth G. Scholthof, Kranthi K. Mandadi. Genomic Approaches to Analyze Alternative Splicing, A Key Regulator of Transcriptome and Proteome Diversity in Brachypodium distachyon. Advanced Structural Safety Studies. 2017; 1667 ():73-85.

Chicago/Turabian Style

Sonia Irigoyen; Renesh H. Bedre; Karen-Beth G. Scholthof; Kranthi K. Mandadi. 2017. "Genomic Approaches to Analyze Alternative Splicing, A Key Regulator of Transcriptome and Proteome Diversity in Brachypodium distachyon." Advanced Structural Safety Studies 1667, no. : 73-85.

Review
Published: 01 September 2016 in Biology, Engineering, Medicine and Science Reports
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ACS Style

Renesh Bedre; Utkarsh Raj; Pritish Varadwaj. Efficacy of Sucralfate in Reflux Disease in comparison to H2 – Receptor Antagonist: A Meta-Analysis of Randomized Trials. Biology, Engineering, Medicine and Science Reports 2016, 2, 18 -22.

AMA Style

Renesh Bedre, Utkarsh Raj, Pritish Varadwaj. Efficacy of Sucralfate in Reflux Disease in comparison to H2 – Receptor Antagonist: A Meta-Analysis of Randomized Trials. Biology, Engineering, Medicine and Science Reports. 2016; 2 (1):18-22.

Chicago/Turabian Style

Renesh Bedre; Utkarsh Raj; Pritish Varadwaj. 2016. "Efficacy of Sucralfate in Reflux Disease in comparison to H2 – Receptor Antagonist: A Meta-Analysis of Randomized Trials." Biology, Engineering, Medicine and Science Reports 2, no. 1: 18-22.

Journal article
Published: 19 August 2016 in BMC Genomics
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Soil salinity affects growth and yield of crop plants. Plants respond to salinity by physiological and biochemical adjustments through a coordinated regulation and expression of a cascade of genes. Recently, halophytes have attracted attention of the biologists to understand their salt adaptation mechanisms. Spartina alterniflora (smooth cordgrass) is a Louisiana native monocot halophyte that can withstand salinity up to double the strength of sea water. To dissect the molecular mechanisms underlying its salinity adaptation, leaf and root transcriptome of S. alterniflora was sequenced using 454/GS-FLX. Altogether, 770,690 high quality reads with an average length 324-bp were assembled de novo into 73,131 contigs (average 577-bp long) with 5.9X sequence coverage. Most unigenes (95 %) annotated to proteins with known functions, and had more than 90 % similarity to rice genes. About 28 % unigenes were considered specific to S. alterniflora. Digital expression profiles revealed significant enrichment (P < 0.01) of transporters, vacuolar proton pump members and transcription factors under salt stress, which suggested the role of ion homeostasis and transcriptional regulation in the salinity adaptation of this grass. Also, 10,805 SSRs markers from 9457 unigenes were generated and validated through genetic diversity analysis among 13 accessions of S. alterniflora. The present study explores the transcriptome of S. alterniflora to understand the gene regulation under salt stress in halophytes. The sequenced transcriptome (control and salt-regulated) of S. alterniflora provides a platform for further gene finding studies in grasses. This study and our previously published studies suggested that S. alterniflora is a rich reservoir of salt tolerance genes that can be used to develop salt tolerant cereal crops, especially rice, a major food crop of global importance.

ACS Style

Renesh Bedre; Venkata Ramanarao Mangu; Subodh Srivastava; Luis Eduardo Sanchez; Niranjan Baisakh. Transcriptome analysis of smooth cordgrass (Spartina alterniflora Loisel), a monocot halophyte, reveals candidate genes involved in its adaptation to salinity. BMC Genomics 2016, 17, 1 -18.

AMA Style

Renesh Bedre, Venkata Ramanarao Mangu, Subodh Srivastava, Luis Eduardo Sanchez, Niranjan Baisakh. Transcriptome analysis of smooth cordgrass (Spartina alterniflora Loisel), a monocot halophyte, reveals candidate genes involved in its adaptation to salinity. BMC Genomics. 2016; 17 (1):1-18.

Chicago/Turabian Style

Renesh Bedre; Venkata Ramanarao Mangu; Subodh Srivastava; Luis Eduardo Sanchez; Niranjan Baisakh. 2016. "Transcriptome analysis of smooth cordgrass (Spartina alterniflora Loisel), a monocot halophyte, reveals candidate genes involved in its adaptation to salinity." BMC Genomics 17, no. 1: 1-18.

Review
Published: 01 March 2016 in Indian Journal of Gastroenterology
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Nucleotide/nucleoside analogues (antiviral therapy) are used in the therapy of HBeAg positive and HBeAg negative chronic hepatitis B. We analyzed ten selected randomized controlled with 2557 patients to estimate the effect of antiviral drugs in chronic hepatitis B with compared to placebo. Virological response, biochemical response, histological response, seroconversion of HBeAg, and loss of HBeAg were estimated as primary efficacy measures. The included studies were subjected for heterogeneity and publication bias. The heterogeneity was assessed with χ2 and I2 statistics. Publication bias was assessed by funnel plot. Greater rates of improvement obtained in antiviral group for virological response [43.96 % vs. 3.15 %, RR = 0.57, 95 % CI = 0.54–0.61, p-value <0.00001], biochemical response [58.37 % vs. 21.87 %, RR = 0.52, 95 % CI = 0.48–0.56, p-value <0.00001], histological response [58.99 % vs. 27.13 %, RR = 0.56, 95 % CI = 0.50–0.63, p-value <0.0001], seroconversion of HBeAg [10.66 % vs. 5.56 %, RR = 0.94, 95 % CI = 0.91–0.97, p-value = 0.0005], and HBeAg loss [14.59 % vs. 9.64 %, RR = 0.92, 95 % CI = 0.88–0.96, p-value = 0.0002]. The safety analysis were carried out for adverse events such as headache [17.22 % vs. 17.34 %, OR = 1.09, 95 % CI = 0.81–1.46, p-value = 0.58], abdominal pain [16.46 % vs. 14.34 %, OR = 1.24, 95 % CI = 0.90–1.72, p-value = 0.19], and pharyngitis [22.22 % vs. 18.23 %, OR = 1.12, 95 % CI = 0.86–1.45, p-value = 0.40]. Excluding adverse events, all primary efficacy measures shown statistical significant result for chronic hepatitis treatment (p-value <0.05). Antiviral therapy provided significant benefit for the treatment of chronic hepatitis B with no measurable adverse effects.

ACS Style

Renesh H. Bedre; Utkarsh Raj; Sri Prakash Misra; Pritish Kumar Varadwaj. Antiviral therapy with nucleotide/nucleoside analogues in chronic hepatitis B: A meta-analysis of prospective randomized trials. Indian Journal of Gastroenterology 2016, 35, 75 -82.

AMA Style

Renesh H. Bedre, Utkarsh Raj, Sri Prakash Misra, Pritish Kumar Varadwaj. Antiviral therapy with nucleotide/nucleoside analogues in chronic hepatitis B: A meta-analysis of prospective randomized trials. Indian Journal of Gastroenterology. 2016; 35 (2):75-82.

Chicago/Turabian Style

Renesh H. Bedre; Utkarsh Raj; Sri Prakash Misra; Pritish Kumar Varadwaj. 2016. "Antiviral therapy with nucleotide/nucleoside analogues in chronic hepatitis B: A meta-analysis of prospective randomized trials." Indian Journal of Gastroenterology 35, no. 2: 75-82.

Research article
Published: 14 September 2015 in PLoS ONE
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Aflatoxins are toxic and potent carcinogenic metabolites produced from the fungi Aspergillus flavus and A. parasiticus. Aflatoxins can contaminate cottonseed under conducive preharvest and postharvest conditions. United States federal regulations restrict the use of aflatoxin contaminated cottonseed at >20 ppb for animal feed. Several strategies have been proposed for controlling aflatoxin contamination, and much success has been achieved by the application of an atoxigenic strain of A. flavus in cotton, peanut and maize fields. Development of cultivars resistant to aflatoxin through overexpression of resistance associated genes and/or knocking down aflatoxin biosynthesis of A. flavus will be an effective strategy for controlling aflatoxin contamination in cotton. In this study, genome-wide transcriptome profiling was performed to identify differentially expressed genes in response to infection with both toxigenic and atoxigenic strains of A. flavus on cotton (Gossypium hirsutum L.) pericarp and seed. The genes involved in antifungal response, oxidative burst, transcription factors, defense signaling pathways and stress response were highly differentially expressed in pericarp and seed tissues in response to A. flavus infection. The cell-wall modifying genes and genes involved in the production of antimicrobial substances were more active in pericarp as compared to seed. The genes involved in auxin and cytokinin signaling were also induced. Most of the genes involved in defense response in cotton were highly induced in pericarp than in seed. The global gene expression analysis in response to fungal invasion in cotton will serve as a source for identifying biomarkers for breeding, potential candidate genes for transgenic manipulation, and will help in understanding complex plant-fungal interaction for future downstream research.

ACS Style

Renesh Bedre; Kanniah Rajasekaran; Venkata Ramanarao Mangu; Luis Eduardo Sanchez Timm; Deepak Bhatnagar; Niranjan Baisakh. Genome-Wide Transcriptome Analysis of Cotton (Gossypium hirsutum L.) Identifies Candidate Gene Signatures in Response to Aflatoxin Producing Fungus Aspergillus flavus. PLoS ONE 2015, 10, e0138025 .

AMA Style

Renesh Bedre, Kanniah Rajasekaran, Venkata Ramanarao Mangu, Luis Eduardo Sanchez Timm, Deepak Bhatnagar, Niranjan Baisakh. Genome-Wide Transcriptome Analysis of Cotton (Gossypium hirsutum L.) Identifies Candidate Gene Signatures in Response to Aflatoxin Producing Fungus Aspergillus flavus. PLoS ONE. 2015; 10 (9):e0138025.

Chicago/Turabian Style

Renesh Bedre; Kanniah Rajasekaran; Venkata Ramanarao Mangu; Luis Eduardo Sanchez Timm; Deepak Bhatnagar; Niranjan Baisakh. 2015. "Genome-Wide Transcriptome Analysis of Cotton (Gossypium hirsutum L.) Identifies Candidate Gene Signatures in Response to Aflatoxin Producing Fungus Aspergillus flavus." PLoS ONE 10, no. 9: e0138025.

Journal article
Published: 15 May 2015 in Molecular Biology Reports
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MicroRNAs have been shown to be involved in regulating plant's response to environmental stresses, including salinity. There is no report yet on the miRNA-mediated posttranscriptional regulation of salt stress response of a grass halophyte by miRNAs. Here we report on the deep-sequencing followed by expression validation through (s)qRT-PCR of a selected set of salt-responsive miRNAs and their targets of the salt marsh monocot halophyte smooth cordgrass (Spartina alterniflora Loisel). Expression kinetics study of 12 miRNAs showed differential up/down-regulation in leaf and root tissues under salinity. Induction of expression of six putative novel microRNAs with high read counts in the sequence library suggested that the halophyte grass may possess different/novel gene posttranscriptional regulation of its salinity adaptation. Similarly, expression analysis of target genes of four selected miRNAs showed temporal and spatial variation in the up/down-regulation of their transcript accumulation under salt stress. The expression levels of miRNAs and their respective targets were coherent, non-coherent, or semi-coherent type. Understanding the gene regulation mechanism(s) at the miRNA level will broaden our fundamental understanding of the biology of the salt stress tolerance of the halophyte and provide novel positive regulators of salt stress tolerance for downstream research.

ACS Style

Hana Zandkarimi; Renesh Bedre; Julio Solis; Venkata Mangu; Niranjan Baisakh. Sequencing and expression analysis of salt-responsive miRNAs and target genes in the halophyte smooth cordgrass (Spartina alternifolia Loisel). Molecular Biology Reports 2015, 42, 1341 -1350.

AMA Style

Hana Zandkarimi, Renesh Bedre, Julio Solis, Venkata Mangu, Niranjan Baisakh. Sequencing and expression analysis of salt-responsive miRNAs and target genes in the halophyte smooth cordgrass (Spartina alternifolia Loisel). Molecular Biology Reports. 2015; 42 (8):1341-1350.

Chicago/Turabian Style

Hana Zandkarimi; Renesh Bedre; Julio Solis; Venkata Mangu; Niranjan Baisakh. 2015. "Sequencing and expression analysis of salt-responsive miRNAs and target genes in the halophyte smooth cordgrass (Spartina alternifolia Loisel)." Molecular Biology Reports 42, no. 8: 1341-1350.