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Deep sequencing identifies novel and conserved microRNAs in peanuts (Arachis hypogaea L.). BMC Plant Biol

High-Tech Research Center, Shandong Academy of Agricultural Sciences, Key Laboratory of Crop Genetic Improvement and Biotechnology, Huanghuaihai, Ministry of Agriculture, Jinan 250100, PR China.
BMC Plant Biology (Impact Factor: 3.94). 01/2010; 10(1):3. DOI: 10.1186/1471-2229-10-3
Source: PubMed

ABSTRACT MicroRNAs (miRNAs) are a new class of small, endogenous RNAs that play a regulatory role in the cell by negatively affecting gene expression at the post-transcriptional level. miRNAs have been shown to control numerous genes involved in various biological and metabolic processes. There have been extensive studies on discovering miRNAs and analyzing their functions in model species, such as Arabidopsis and rice. Increasing investigations have been performed on important agricultural crops including soybean, conifers, and Phaselous vulgaris but no studies have been reported on discovering peanut miRNAs using a cloning strategy.
In this study, we employed the next generation high through-put Solexa sequencing technology to clone and identify both conserved and species-specific miRNAs in peanuts. Next generation high through-put Solexa sequencing showed that peanuts have a complex small RNA population and the length of small RNAs varied, 24-nt being the predominant length for a majority of the small RNAs. Combining the deep sequencing and bioinformatics, we discovered 14 novel miRNA families as well as 75 conserved miRNAs in peanuts. All 14 novel peanut miRNAs are considered to be species-specific because no homologs have been found in other plant species except ahy-miRn1, which has a homolog in soybean. qRT-PCR analysis demonstrated that both conserved and peanut-specific miRNAs are expressed in peanuts.
This study led to the discovery of 14 novel and 22 conserved miRNA families from peanut. These results show that regulatory miRNAs exist in agronomically important peanuts and may play an important role in peanut growth, development, and response to environmental stress.

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    • "In recent times, high-throughput sequencing platforms are showing significant promise for small RNA discovery and genomewide transcriptome analysis at single-base pair resolution [23] [31]. Sequencing techniques such as the Solexa Platform, SOLiD, and 454 Technology as well as other massively parallel sequencing strategies have been successfully applied in order to identify miRNAs in many plant species, such as rice [32], alfalfa [33], grape [34], tomato [35], orange [36], soybean [37], peanut [38], poplar [39], and black gram [40]. In comparison with microarray, deep sequencing has several advantages, the major one being its application in comprehensive identification and profiling of small previously unknown RNA populations [23]. "
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    ABSTRACT: MicroRNAs play a pivotal role in regulating a broad range of biological processes, acting by cleaving mRNAs or by translational repression. A group of plant microRNAs are evolutionarily conserved; however, others are expressed in a species specific manner. Jute is an agro-economically important fibre crop; nonetheless, no practical information is available for microRNAs in jute till date. In this study, Illumina sequencing revealed a total of 227 known microRNAs and 17 potential novel microRNA candidates in jute; of which 164 belong to 23 conserved families and the remaining 63 belong to 58 non-conserved families. Among a total of 81 identified microRNA families, 116 potential target genes were predicted for 39 families and 11 targets were predicted for 4 among the 17 identified novel microRNAs. For understanding better the functions of microRNAs, target genes were analyzed by Gene Ontology and their pathways illustrated by KEGG pathway analyses. The presence of microRNAs identified in jute were validated by stem loop RT-PCR followed by end point PCR and qPCR for randomly selected 20 known and novel microRNAs. This study exhaustively identifies microRNAs and their target genes in jute which will ultimately pave the way for understanding their role in this and other crops. Keywords: Illumina sequencing, microRNA, novel microRNA, stem loop RT PCR, end point PCR, q-RT PCR, jute.
    Comparative and Functional Genomics 02/2015;
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    • "Because targets complementary to the miRNA 5′ end appear to be critical, mismatches other than G:U18 wobbles at positions 2–7 at the 5′ end were further penalized by 0.5 point in the final score. Sequences were considered to be miRNA targets if the total score was less than 3.0 points (Zhao et al. 2010). For the identification of miRNA targets involved in thermotolerance pathways, we retrieved the mRNA transcript sequences from the public biological databases based on the literature search. "
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    ABSTRACT: MicroRNAs (miRNAs) are small endogenous RNAs of ~22 nucleotides that have been shown to play regulatory role by negatively affecting the expression of genes at the post-transcriptional level. Information of miRNAs on some important crops like soybean, Arabidopsis, and rice, etc. are available, but no study on heat-responsive novel miRNAs has yet been reported in wheat (Triticum aestivum L.). In the present investigation, a popular wheat cultivar HD2985 was used in small RNA library construction and Illumina HiSeq 2000 was used to perform high-throughput sequencing of the library after cluster generation; 110,896,604 and 87,743,861 reads were generated in the control (22 °C) and heat-treated (42 °C for 2 h) samples, respectively. Forty-four precursor and mature miRNAs were found in T. aestivum from miRBase v 19. The frequencies of the miRNA families varied from 2 (tae-miR1117) to 60,672 (tae-miR159b). We identify 1052 and 902 mature miRNA sequences in HD2985 control and HS-treated samples by mapping on reference draft genome of T. aestivum. Maximum identified miRNAs were located on IWGSC_CSS_3B_scaff (chromosome 3B). We could identify 53 and 46 mature miRNA in the control and HS samples and more than 516 target genes by mapping on the reference genome of Oryza sativa, Zea mays, and Sorghum bicolor. Using different pipelines and plant-specific criteria, 37 novel miRNAs were identified in the control and treated samples. Six novel miRNA were validated using qRT-PCR to be heat-responsive. A negative correlation was, however, observed between the expression of novel miRNAs and their targets. Target prediction and pathway analysis revealed their involvement in the heat stress tolerance. These novel miRNAs are new additions to miRNA database of wheat, and the regulatory network will be made use of in deciphering the mechanism of thermotolerance in wheat.
    Functional and Integrative Genomics 12/2014; 15(3). DOI:10.1007/s10142-014-0421-0
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    • "High-throughput sequencing has proved to be a powerful strategy for the identification of miRNAs. Hundreds of novel miRNAs have been identified from wheat, rice, barley , Arabidopsis, peanuts, and other plants (Lertpanyasampatha et al., 2012; Pelaez et al., 2012; Sunkar et al., 2008; Zhao et al., 2010). In rice, Liu et al. discovered 32 new miRNAs from rice seedlings under control and H 2 O 2 stress conditions, and one of these miRNAs was a putative exonic miRNA located in the exon of AK106348 (Li et al., 2011). "
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    ABSTRACT: Plant microRNAs (miRNAs) play important roles as modulators of gene expression at the post-transcriptional level. Previous studies have shown that high-throughput sequencing is a powerful tool for the identification of miRNAs, and it is believed that many more miRNAs remain to be discovered. Here, we found 23 novel conserved miRNAs from three rice cultivars by high-throughput sequencing and further identified these through subsequent cloning and quantitative real-time polymerase chain reaction (qPCR). Eight of these novel miRNAs were detected with significant signals in the three rice cultivars by northern blotting assays. The quantitative analysis of their expression profiles showed that most of these miRNAs were perfectly or imperfectly negatively correlated with their target genes, which suggests that these miRNAs may play important roles during rice development. This is the first genome-wide investigation of miRNAs from different rice cultivars, and the data obtained expand the known rice miRNA inventory and provide further information about the regulatory roles played by miRNAs in rice development.
    Gene 07/2014; 548(2). DOI:10.1016/j.gene.2014.07.048
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