Differentially expressed genes in incompatible interactions of Pratylenchus coffeae with Musa using suppression subtractive hybridization

Backiyarani, S.; Uma, S.; Arunkumar, Ganesan; Saraswathi, Marimuthu Somasundaram; Sundararaju, P.

doi:10.1016/j.pmpp.2014.02.002

Cited by 22 publications

(22 citation statements)

References 36 publications

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“…Similarly in the case of banana, more accumulation of endochitinases and putative chitinase transcripts, which are involved in fungal cell wall degradation, was reported in Mycosphaerella musicola-challenged leaves [10]. Overexpression of chitinase was also observed in P. coffeae-challenged resistant banana genotype compared to susceptible genotype [11]. These findings emphasized the important role of chitinase for conferring resistance to various biotic stresses in banana.…”

Section: Introductionmentioning

confidence: 53%

Genome-Wide Analysis and Differential Expression of Chitinases in Banana Against Root Lesion Nematode (Pratylenchus coffeae) and Eumusa Leaf Spot (Mycosphaerella eumusae) Pathogens

Backiyarani

Uma

Nithya

et al. 2015

Appl Biochem Biotechnol

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

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Section: Introductionmentioning

confidence: 53%

Genome-Wide Analysis and Differential Expression of Chitinases in Banana Against Root Lesion Nematode (Pratylenchus coffeae) and Eumusa Leaf Spot (Mycosphaerella eumusae) Pathogens

Backiyarani

Uma

Nithya

et al. 2015

Appl Biochem Biotechnol

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“…The SSH method has been used to identify genes differentially expressed at the mRNA level from different plant species under a wide range of biotic and abiotic stresses. Applications of SSH range from biological characteristics, such as the development and ripening of fruit [99], flowering [100], morphological differences with different physical function [12], the molecular processes underlying salt and water stress tolerance development [101][102][103], the molecular mechanism of plant defense against different pathogens [104][105][106][107][108], the identification of mineral upregulated responsive genes as food bio-fortification [109], and in improving the tolerance of plants under different chemical component stresses [110][111][112][113][114]. The results of a study considering the micropylar endosperm of germinated cress seeds using a tissue-specific subtracted cDNA library revealed the role of three peroxidase SALK activities in the germination phenotype.…”

Section: Application Of Different Techniques Involved In Gene Expressmentioning

confidence: 99%

Suppression Subtractive Hybridization Versus Next-Generation Sequencing in Plant Genetic Engineering: Challenges and Perspectives

et al. 2015

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Suppression subtractive hybridization (SSH) is an effective method to identify different genes with different expression levels involved in a variety of biological processes. This method has often been used to study molecular mechanisms of plants in complex relationships with different pathogens and a variety of biotic stresses. Compared to other techniques used in gene expression profiling, SSH needs relatively smaller amounts of the initial materials, with lower costs, and fewer false positives present within the results. Extraction of total RNA from plant species rich in phenolic compounds, carbohydrates, and polysaccharides that easily bind to nucleic acids through cellular mechanisms is difficult and needs to be considered. Remarkable advancement has been achieved in the next-generation sequencing (NGS) field. As a result of progress within fields related to molecular chemistry and biology as well as specialized engineering, parallelization in the sequencing reaction has exceptionally enhanced the overall read number of generated sequences per run. Currently available sequencing platforms support an earlier unparalleled view directly into complex mixes associated with RNA in addition to DNA samples. NGS technology has demonstrated the ability to sequence DNA with remarkable swiftness, therefore allowing previously unthinkable scientific accomplishments along with novel biological purposes. However, the massive amounts of data generated by NGS impose a substantial challenge with regard to data safe-keeping and analysis. This review examines some simple but vital points involved in preparing the initial material for SSH and introduces this method as well as its associated applications to detect different novel genes from different plant species. This review evaluates general concepts, basic applications, plus the probable results of NGS technology in genomics, with unique mention of feasible potential tools as well as bioinformatics.

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“…It revealed that cytochrome oxidase, lipoxygenase, metallothionein, flavin containing monoxygenase were upregulated only in the resistant cultivar within 48 h post inoculation (HPI) and these genes could be involved in M. eumusae leaf spot resistance mechanism. Backiyarani et al (2014) also identified 256 unique genes from the root lesion nematode ( Pratylenchus coffeae) challenged resistant cultivar (Karthobiumtham ABB) through SSH approach. Of these, 26.8 % were unigenes involved in defense and/or signal transduction including resistant gene homologues, disease resistance response proteins and protein kinase signaling.…”

Section: Suppression Subtractive Hybridisation (Ssh)mentioning

confidence: 99%

Sustainable Horticultural Systems

Nandwani¹

2014

Sustainable Development and Biodiversity

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This book series provides complete, comprehensive and broad subject based reviews about existing biodiversity of different habitats and conservation strategies in the framework of different technologies, ecosystem diversity, and genetic diversity. The ways by which these resources are used with sustainable management and replenishment are also dealt with. The topics of interest include but are not restricted only to sustainable development of various ecosystems and conservation of hotspots, traditional methods and role of local people, threatened and endangered species, global climate change and effect on biodiversity, invasive species, impact of various activities on biodiversity, biodiversity conservation in sustaining livelihoods and reducing poverty, and technologies available and required. The books in this series will be useful to botanists, environmentalists, marine biologists, policy makers, conservationists, and NGOs working for environment protection.More information about this series at

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Differentially expressed genes in incompatible interactions of Pratylenchus coffeae with Musa using suppression subtractive hybridization

Cited by 22 publications

References 36 publications

Genome-Wide Analysis and Differential Expression of Chitinases in Banana Against Root Lesion Nematode (Pratylenchus coffeae) and Eumusa Leaf Spot (Mycosphaerella eumusae) Pathogens

Genome-Wide Analysis and Differential Expression of Chitinases in Banana Against Root Lesion Nematode (Pratylenchus coffeae) and Eumusa Leaf Spot (Mycosphaerella eumusae) Pathogens

Suppression Subtractive Hybridization Versus Next-Generation Sequencing in Plant Genetic Engineering: Challenges and Perspectives

Sustainable Horticultural Systems

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