ArticlePloS one2013
De novo transcriptome sequencing reveals a considerable bias in the incidence of simple sequence repeats towards the downstream of 'Pre-miRNAs' of black pepper.
Article in PloS one, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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24 citing papers in PubMed, 61 citations in OpenAlex.
- Genome-wide identification of copy number variation in diverse black pepper accessions.Planta · 2025Article
- De novo transcriptome profiling revealing genes involved in piperine biosynthetic pathway in Piper longum L.Scientific reports · 2025Article
- Transcriptional regulation of hormone signalling genes in black pepper in response to Phytophthora capsici.BMC genomics · 2024Article
- Development of miRNA-SSR and target-SSR markers from yield-associate genes and their applicability in the assessment of genetic diversity and association mapping in rice (Molecular breeding : new strategies in plant improvement · 2024Article
- A comprehensive review on genomic resources in medicinally and industrially important major spices for future breeding programs: Status, utility and challenges.Current research in food science · 2023Review
- De novo transcriptome profiling unveils the regulation of phenylpropanoid biosynthesis in unripe Piper nigrum berries.BMC plant biology · 2022Article
- NCodR: A multi-class support vector machine classification to distinguish non-coding RNAs in Viridiplantae.Quantitative plant biology · 2022Article
- Genome-wide identification and functional prediction of salt- stress related long non-coding RNAs (lncRNAs) in chickpea (Physiology and molecular biology of plants : an international journal of functional plant biology · 2021Article
- Non-Targeted Metabolite Profiling Reveals Host Metabolomic Reprogramming during the Interaction of Black Pepper withInternational journal of molecular sciences · 2021Article
- Genome wide identification, characterization and validation of novel miRNA-based SSR markers in pomegranate (Physiology and molecular biology of plants : an international journal of functional plant biology · 2020Article
- Identification of stable reference gene for transcript normalization in black pepper-Physiology and molecular biology of plants : an international journal of functional plant biology · 2019Article
- A deeper view into the significance of simple sequence repeats in pre-miRNAs provides clues for its possible roles in determining the function of microRNAs.BMC genetics · 2018Article
- Differentially expressed genes in heads and tails of Angelica sinensis diels: Focusing on ferulic acid metabolism.Chinese journal of integrative medicine · 2017Article
- Transfer RNA Derived Small RNAs Targeting Defense Responsive Genes Are Induced during Phytophthora capsici Infection in Black Pepper (Piper nigrum L.).Frontiers in plant science · 2016Article
- Transcriptome- Assisted Label-Free Quantitative Proteomics Analysis Reveals Novel Insights into Piper nigrum-Phytophthora capsici Phytopathosystem.Frontiers in plant science · 2016Article
- A Genome-Wide Survey of the Microsatellite Content of the Globe Artichoke Genome and the Development of a Web-Based Database.PloS one · 2016Article
- Unravelling the complexity of microRNA-mediated gene regulation in black pepper (Piper nigrum L.) using high-throughput small RNA profiling.Plant cell reports · 2016Article
- Computational prediction of miRNAs and their targets in Phaseolus vulgaris using simple sequence repeat signatures.BMC plant biology · 2015Article
- De Novo Assembly and Characterization of Fruit Transcriptome in Black Pepper (Piper nigrum).PloS one · 2015Article
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4 authors at 1 institution in 1 country.
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Abstract
Next generation sequencing has an advantageon transformational development of species with limited available sequence data as it helps to decode the genome and transcriptome. We carried out the de novo sequencing using illuminaHiSeq™ 2000 to generate the first leaf transcriptome of black pepper (Piper nigrum L.), an important spice variety native to South India and also grown in other tropical regions. Despite the economic and biochemical importance of pepper, a scientifically rigorous study at the molecular level is far from complete due to lack of sufficient sequence information and cytological complexity of its genome. The 55 million raw reads obtained, when assembled using Trinity program generated 2,23,386 contigs and 1,28,157 unigenes. Reports suggest that the repeat-rich genomic regions give rise to small non-coding functional RNAs. MicroRNAs (miRNAs) are the most abundant type of non-coding regulatory RNAs. In spite of the widespread research on miRNAs, little is known about the hair-pin precursors of miRNAs bearing Simple Sequence Repeats (SSRs). We used the array of transcripts generated, for the in silico prediction and detection of '43 pre-miRNA candidates bearing different types of SSR motifs'. The analysis identified 3913 different types of SSR motifs with an average of one SSR per 3.04 MB of thetranscriptome. About 0.033% of the transcriptome constituted 'pre-miRNA candidates bearing SSRs'. The abundance, type and distribution of SSR motifs studied across the hair-pin miRNA precursors, showed a significant bias in the position of SSRs towards the downstream of predicted 'pre-miRNA candidates'. The catalogue of transcripts identified, together with the demonstration of reliable existence of SSRs in the miRNA precursors, permits future opportunities for understanding the genetic mechanism of black pepper and likely functions of 'tandem repeats' in miRNAs.
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