Identification of single nucleotide polymorphism in ginger using expressed sequence tags

Chandrasekar, A.; Riju, Aikkal; Sithara, Kandiyl; Anoop, Sahadevan; Eapen, Santhosh J.

doi:10.6026/97320630004119

Cited by 19 publications

(10 citation statements)

References 24 publications

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“…The reported abundance of A/T ratio as well as its reverse complement remains unexplained. Out of total SNPs substitutions detected in this attempt, transversions of all tissues is/are comparatively higher than the transitions which corroborates previous report on the ginger SNPs detection and assigns the reason of ginger is being vegetative propagated crop through rhizome [ 43 ].…”

Section: Discussionsupporting

confidence: 91%

“…Our study for the first time provides information about high quality SNPs (8810) and 1008 indels polymorphisms in addition to information about potential SNPs (11523) because of the use of triple filtration based on stringent analysis of ESTs database using QualitySNP when compared with the pearl script AutoSNP version 1.0 based analysis of ginger ESTs with higher number of potential 64026 SNPs sites and 7034 indels polymorphisms [ 43 ]. The present analysis provides additional information about tissues wise presence of haplotypes (222) distribution of high quality exonic (2355) and intronic (6455) SNPs and information about singletons (17421) in addition to contigs ( Figure 1(a), 1(b), 1(c) and Table 1- 4 ).…”

Section: Discussionmentioning

confidence: 99%

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High quality SNPs/Indels mining and characterization in ginger from ESTs data base

2015

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Ginger (Zingiber officinale Rosc.) is an important herb of the family Zingiberaceae. It is accepted as a universal cure for a multitude of diseases in Indian systems of medicine and its rhizomes are equally popular as a spice ingredient throughout Asia. SNPs, the definitive genetic markers, representing the finest resolution of a DNA sequence, are abundantly found in populations having a lower rate of mutation and are used for genomic analysis. The public ESTs sequences mostly lack quality files, making high quality SNPs detection more difficult since it is exclusively based on sequence comparisons. In the present study, current dbESTs of NCBI was mined and 38115 ginger ESTs sequences were obtained and assembled into contigs using CAP3 program. In this analysis, recent software tool QualitySNP was used to detect 11523 potential SNPs sites, 8810 high quality SNPs and 1008 indels polymorphisms with a frequency of 1.61 SNPs / 10 kbp. Of ESTs libraries generated from three ginger tissues together, rhizomes had a frequency of 0.32 SNPs and 0.03 indels per 10 kbp whereas the leaves had a frequency of 2.51 SNPs and 0.23 indels per 10 kbp and root is showing relative frequency of 0.76/10 kbp SNPs and 0.02/10 kbp indels. The present analysis provides additional information about the tissue wise presence of haplotypes (222), distribution of high quality exonic (2355) and intronic (6455) SNPs and information about singletons (7538) in addition to contigs transitions and transversions ratio (0.57). Among all tissue detected SNPs, transversions number is higher in comparison to the number of transitions. Quality SNPs detected in this work can be used as markers for further ginger genetic experiments.

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Section: Discussionsupporting

confidence: 91%

Section: Discussionmentioning

confidence: 99%

High quality SNPs/Indels mining and characterization in ginger from ESTs data base

2015

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“…Identified SNPs were found to be under the influence of transition biases i.e occurrence of higher transition as compared to transversion27. However, a contrasting result was observed in ginger EST leaves sequences28. The occurrence of higher transition as compared to transversion might be associated to the high frequency of the C to T variation after methylation29.…”

Section: Discussionmentioning

confidence: 94%

In Silico identification of SNP diversity in cultivated and wild tomato species: insight from molecular simulations

Bhardwaj

Dhar

Asif

et al. 2016

Sci Rep

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Single Nucleotide Polymorphisms (SNPs), an important source of genetic variations, are often used in crop improvement programme. The present study represented comprehensive In silico analysis of nucleotide polymorphisms in wild (Solanum habrochaites) and cultivated (Solanum lycopersicum) species of tomato to explore the consequence of substitutions both at sequence and structure level. A total of 8978 SNPs having Ts/Tv (Transition/Transversion) ratio 1.75 were identified from the Expressed Sequence Tag (EST) and Next Generation Sequence (NGS) data of both the species available in public databases. Out of these, 1838 SNPs were non-synonymous and distributed in 988 protein coding genes. Among these, 23 genes containing 96 SNPs were involved in traits markedly different between the two species. Furthermore, there were 28 deleterious SNPs distributed in 27 genes and a few of these genes were involved in plant pathogen interaction and plant hormone pathways. Molecular docking and simulations of several selected proteins showed the effect of SNPs in terms of compactness, conformation and interaction ability. Observed SNPs exhibited various types of motif binding effects due to nucleotide changes. SNPs that provide the evidence of differential motif binding and interaction behaviour could be effectively used for the crop improvement program.

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“…Ginger ( Zingiber officinale Rosc), a well-known plant for its medicinal applications, was successfully applied for the development of high-throughput methods for the detection of SNPs and small indels (insertion/deletion). In that study, 64026 SNP sites and 7034 indel polymorphisms with frequency of 0.84 SNPs/100 bp were found and among the three tissues from which the EST libraries were generated, rhizomes had high frequency of 1.08 SNPs/indels per 100 bp whereas the leaves had lowest frequency of 0.63 per 100 bp and root showed relative frequency of 0.82/100 bp (Chandrasekar et al 2009 ). Work has been done for authentication of medicinal plants by SNP-based Multiplex PCR, where highly variable intergenic spacer and intron regions from nuclear and cytoplasmic DNA have been used for species identification (Lee et al 2012 ).…”

Section: Use Of Single Nucleotide Polymorphism (Snps)mentioning

confidence: 94%

Genomic profile of the plants with pharmaceutical value

2014

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There is an ample genetic diversity of plants with medicinal importance around the globe and this pool of genetic variation serves as the base for selection as well as for plant improvement. Thus, identification, characterization and documentation of the gene pool of medicinal plants are essential for this purpose. Genomic information of many a medicinal plant species has increased rapidly since the past decade and genetic resources available for domestication and improvement programs include genome sequencing, expressed sequence tags sequencing, transcript profiling, gene transmit, molecular markers in favor of mapping and breeding. In recent years, multiple endeavors have been undertaken for genomic characterization of medicinal plant species with the aid of molecular markers for sustainable utilization of gene pool, its conservation and future studies. Recent advancement in genomics is so fast that only some researches have been published till date and to a large extent documentation is restricted to electronic resources. Whole genome profiling of the identified medicinal plant species, carried out by several researchers, based on the DNA fingerprinting, is well documented in the present review. This review will facilitate preparing a database of the widely used, economically important medicinal plant species, based on their genomic organization.

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Identification of single nucleotide polymorphism in ginger using expressed sequence tags

Cited by 19 publications

References 24 publications

High quality SNPs/Indels mining and characterization in ginger from ESTs data base

High quality SNPs/Indels mining and characterization in ginger from ESTs data base

In Silico identification of SNP diversity in cultivated and wild tomato species: insight from molecular simulations

Genomic profile of the plants with pharmaceutical value

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