Browsing by Author "Naganeeswaran, S."

Now showing 1 - 16 of 16
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    Amplification and sequencing of partial–length disease resistant gene homologues coding NBS LRR-type proteins in coconut
    (2012-11) Rachana, K.E.; Naganeeswaran, S.; Rajesh, M.K.
    Pseudomonas spp. and compared with other gene predicting tools. This tool can be used for the functional annotation of the microbial genome data providing insights into genome evolution and identifying different strains containing LTTR genes.
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    Analysis of expressed sequence tags (ESTs) from cocoa (Theobroma cacao L) upon infection with Phytophthora megakarya
    (2012) Naganeeswaran, S.; Elain Apshara, S.; Manimekalai, R.
    Phytophthora megakarya, the causative agent of cacao black pod disease in West African countries causes an extensive loss of yield. In this study we have analyzed 4 libraries of ESTs derived from Phytophthora megakarya infected cocoa leaf and pod tissues. Totally 6379 redundant sequences were retrieved from ESTtik database and EST processing was performed using seqclean tool. Clustering and assembling using CAP3 generated 3333 non-redundant (907 contigs and 2426 singletons) sequences. The primary sequence analysis of 3333 non-redundant sequences showed that the GC percentage was 42.7 and the sequence length ranged from 101 – 2576 nucleotides. Further, functional analysis (Blast, Interproscan, Gene ontology and KEGG search) were executed and 1230 orthologous genes were annotated. Totally 272 enzymes corresponding to 114 metabolic pathways were identified. Functional annotation revealed that most of the sequences are related to molecular function, stress response and biological processes. The annotated enzymes are aldehyde dehydrogenase (E.C: 1.2.1.3), catalase (E.C: 1.11.1.6), acetyl-CoA C-acetyltransferase (E.C: 2.3.1.9), threonine ammonia-lyase (E.C: 4.3.1.19), acetolactate synthase (E.C: 2.2.1.6), O-methyltransferase (E.C: 2.1.1.68) which play an important role in amino acid biosynthesis and phenyl propanoid biosynthesis. All this information was stored in MySQL database management system to be used in future for reconstruction of biotic stress response pathway in cocoa.
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    Analysis of genetic diversity among Indian Ocean coconut accessions through microsatellite markers
    (2016-03) Devakumar, K.; Neema Babu; Uma Maheswari, T.S.; Naganeeswaran, S.; Niral, V.; Augustine Jerard, B.
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    Cocoa EST database: Comprehensive database of Cocoa Expressed Sequence Tags (ESTs)
    (2015) Naganeeswaran, S.; Elain Apshara, S.; Manimekalai, R.; Amal Vasu; Malhotra, S.K.
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    Computational prediction and characterization of miRNA from coconut leaf transcriptome
    (2015) Naganeeswaran, S.; Fayas, T.P.; Rachana, K.E.; Rajesh, M.K.
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    Development of EST‑SSR markers for genetic diversity analysis in coconut (Cocos nucifera L.)
    (2020) Preeti P; Shafeeq Rahman; Naganeeswaran, S.; Sabana, A.A.; Gangaraj, K.P.; Jerard, B.A; Niral, V.; Rajesh, M.K.
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    A Machine Learning Approach for Prediction of Gibberellic Acid Metabolic Enzymes in Monocotyledonous Plants
    (2014-08) Sreepriya, P.; Naganeeswaran, S.; Hemalatha, N.; Sreejisha, P.; Rajesh, M.K.
    Gibberellins (GA) are one of the most important phytohormones that control different aspects of plant growth and influence various developments such as seed germination, stem elongation and floral induction. More than 130 GAs have been identified; however, only a small number of them are biologically active. In this study, five enzymes in GA metabolic pathway in monocots have been thoroughly researched namely, ent-copalyl-diphosphate synthase (CPS), ent-kaurene synthase (KS), ent-kaurene oxidase (KO), GA 20-oxidase (GA20ox), and GA 2-oxidase (GA2ox). We have designed and implemented a high performance prediction tool for these enzymes using machine learning algorithms. ‘GAPred’ is a web-based system to provide a comprehensive collection of enzymes in GA metabolic pathway and a systematic framework for the analysis of these enzymes for monocots. WEKA-based classifiers (Naïve-Bayes) and Support Vector Machine (SVM) based-modules were developed using dipeptide composition and high accuracies were obtained. In addition, BLAST and Hidden Markov Model (HMMER-based model) were also developed for searching sequence databases for homolog’s of enzymes of GA metabolic pathway, and for making protein sequence alignments.
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    MAPS: A web-based tool for detection of microsatellites in whole genome sequences
    (2015) Jamshinath, T.P.; Naganeeswaran, S.; Jomon K. Jose; Rajesh, M.K
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    Morphological and molecular characterization of a large fruited unique coconut accession from Vaibhavwadi, Maharashtra, India
    (2013) Niral, V.; Devakumar, K.; Umamaheswari, T.S.; Naganeeswaran, S.; Nair, R.V.; Jerard, B.A.
    The morphological and molecular characterization of a large fruited coconut population was undertaken using twentythree morphological traits, six tender nut traits and eight fruit component traits. Fruit component analysis of the nuts of this accession indicated that they have low husk to nut weight ratio typical of the Niu vai type cultivated in South East Asia. The microsatellite analysis indicated that Vaibhavwadi coconut population (MAHT) is generally close to the South East Asian coconut accessions and has proximity with dwarf accessions in the conserved germplasm of India. Though, genetic assignment test did not identify this accession specifically with any particular cultivar in the microsatellite database, the probable origin of this type could be identified as Borneo Tall (60% similarity) a cultivar which is known to produce large coconuts. It is suggested to conserve the MAHT in the National Coconut Gene Bank of India for its utilization in the breeding programme.
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    De novo assembly and characterization of global transcriptome of coconut palm (Cocos nucifera L.) embryogenic calli using Illumina paired-end sequencing
    (2016) Rajesh, M.K.; Fayas, T.P.; Naganeeswaran, S.; Rachana, K.E.; Bhavyashree, U.; Sajini, K.K.; Anitha Karun
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    De novo assembly and characterization of global transcriptome of coconut palm (Cocos nucifera L.) embryogenic calli using Illumina paired-end sequencing
    (2016) Rajesh, M.K.; Fayas, T.P.; Naganeeswaran, S.; Rachana, K.E.; Bhavyashree, U.; Sajini, K.K.; Anitha Karun
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    De novo assembly and characterization of global transcriptome of coconut palm (Cocos nucifera L.) embryogenic calli using Illumina paired-end sequencing
    (2016) Rajesh, M.K.; Fayas, T.P.; Naganeeswaran, S.; Rachana, K.E.; Bhavyashree, U.; Sajini, K.K.; Anitha Karun
    Production and supply of quality planting material is significant to coconut cultivation but is one of the major constraints in coconut productivity. Rapid multiplication of coconut through in vitro techniques, therefore, is of paramount importance. Although somatic embryogenesis in coconut is a promising technique that will allow for the mass production of high quality palms, coconut is highly recalcitrant to in vitro culture. In order to overcome the bottlenecks in coconut somatic embryogenesis and to develop a repeatable protocol, it is imperative to understand, identify, and characterize molecular events involved in coconut somatic embryogenesis pathway. Transcriptome analysis (RNA-Seq) of coconut embryogenic calli, derived from plumular explants of West Coast Tall cultivar, was undertaken on an Illumina HiSeq 2000 platform. After de novo transcriptome assembly and functional annotation, we have obtained 40,367 transcripts which showed significant BLASTx matches with similarity greater than 40 % and E value of ≤10−5. Fourteen genes known to be involved in somatic embryogenesis were identified. Quantitative real-time PCR (qRT-PCR) analyses of these 14 genes were carried in six developmental stages. The result showed that CLV was upregulated in the initial stage of callogenesis. Transcripts GLP, GST, PKL, WUS, and WRKY were expressed more in somatic embryo stage. The expression of SERK, MAPK, AP2, SAUR, ECP, AGP, LEA, and ANTwere higher in the embryogenic callus stage compared to initial culture and somatic embryo stages. This study provides the first insights into the gene expression patterns during somatic embryogenesis in coconut.
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    De novo assembly and characterization of global transcriptome of coconut palm (Cocos nucifera L.) embryogenic calli using Illumina paired-end sequencing
    (2016) Rajesh, M.K.; Fayas, T.P.; Naganeeswaran, S.; Rachana, K.E.; Bhavyashree, U.; Sajini, K.K.; Anitha Karun
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    PhzPred – A Tool for Prediction of Phenazine Synthesizing Genes in Plant Growth Promoting Pseudomonas spp
    (2014-10) Shilpa, S.; Anil Paul; Naganeeswaran, S.; Hemalatha, N.; Rajesh, M.K.
    Phenazines are natural products produced by the bacterial strain of Pseudomonas spp. which possess anti-microbial activities and include more than 50 pigmented heterocyclic nitrogen containing secondary metabolites. Seven core phenazine biosynthetic genes have been identified in nearly all identified bacterial strains that produce phenazine compounds. In this study, a model has been developed to predict the phenazine biosynthetic genes from a set of protein sequences usingmachine learning algorithms from whole genomes of Pseudomonas spp. Initially, protein sequences from the Pseudomonas spp. were retrieved from public databases and used to train the WEKA models. To train the different classifiers in WEKA, three amino acid compositions were used: monomer amino acids, dipeptide amino acids, and a hybridmethod. The trained models were then used for the prediction of phenazine synthesizing gene in anuser submitted sequence. The best WEKA modules were selected based on the performance of different classifiers in training and testing. The performances of the classifier’s were then evaluated based on 10-fold cross validation and independent data set validation techniques. In the proposed methodology, better performance was observed for the hybrid feature extraction method. The development of a genome wide prediction tool for phenazinesynthesizing genes will substantially have an impact on bacterial genome annotation and devising crop protection strategies using plant growth promoting rhizobacteria.
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    Virtual screening and in vitro evaluation of potential growth regulators against somatic embryogenesis receptor- like kinase(SERK) in Cocos nucifera L.
    (2015) Rajesh, M.K.; Gangaraj, K.P.; Jamshinath, T.P.; Fayas, T.P.; Naganeeswaran, S.; Sajini, K.K.; Anitha Karun