De novo Transcriptome Sequencing Reveals a Considerable Bias in the Incidence of Simple Sequence Repeats towards the Downstream of ‘Pre-miRNAs’ of Black Pepper

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.

Unravelling the complexity of microRNA-mediated gene regulation in black pepper (Piper nigrum L.) using high-throughput small RNA profiling

“…Two conserved miRNAs (miR166 and miR171) were identified using experimental in silico approach from black pepper ). In addition, a (CT) dinucleotide SSR in the hairpin precursors of miRNA (Joy and Soniya 2012) and potential microsatellite derived miRNAs (Joy et al 2013) were identified from black pepper. In this paper, we report the first small RNA profiling using Illumina high-throughput sequencing for the comprehensive investigation of miRNAs of black pepper.…”

“…In this paper, we report the first small RNA profiling using Illumina high-throughput sequencing for the comprehensive investigation of miRNAs of black pepper. The secondary stem-loop precursors of conserved and novel miRNAs were identified from recently sequenced black pepper mRNA transcriptome data (Joy et al 2013). Expression pattern of eight conserved miRNAs were verified and potential targets of majority of the miRNAs were predicted.…”

SSR Development and Utilization with Rehmannia glutinosa Transcriptome

“…This reflects that SSRs loci in R. glutinosa obviously prefer to particular category of genes. Additionally, 35 SSRs were found to locate in non-coding transcripts, in who's derived SSRs a bias of base composition was obviously observed, that was also found in other animals and plants Joy et al, 2013;Asadi and Monfared, 2014). It was reported that EST-SSR markers were identified on transcribed regions of DNA that were often considered as putative functional sequences (Jiang et al, 2012).…”

High-Throughput Transcriptome Analysis of Plant Stress Responses

“…KEGG database enables to understand biological functions of genes with the Pathway annotation. The KEGG pathway database records networks of molecular interactions in the cells, and variants of them specifi c to particular organisms (Kanehisa et al 2010 ;Joy et al 2013 ).…”