Performance comparison and evaluation of software tools for microRNA deep-sequencing data analysis

Li, Yue; Zhang, Zhuo; Liu, Feng; Vongsangnak, Wanwipa; Jing, Qing; Shen, Bairong

doi:10.1093/nar/gks043

Cited by 126 publications

(119 citation statements)

References 18 publications

Supporting

Mentioning

119

Contrasting

Order By: Relevance

“…The unique sequences were mapped in the M. truncatula genome version 4.0 (http://www.medicagohapmap.org/?genome) using BWA [38] to get premiRNA sequences for new miRNAs prediction. Novel miRNAs were predicted by using Mireap [39]. Novel miRNA candidates were identified according to the criteria reported by [40].…”

Section: Identification Of Known and Novel Mirnasmentioning

confidence: 99%

Identification of Drought-Responsive microRNAs from Roots and Leaves of Alfalfa by High-Throughput Sequencing

Li¹,

Wan²,

Bi³

et al. 2017

Preprint

Self Cite

View full text Add to dashboard Cite

Alfalfa, an important legume forage, is an ideal crop for sustainable agriculture and a potential bioenergy plant. Drought, one of the most common environmental stresses, substantially affects plants' growth, development and productivity. MicroRNAs (miRNAs) are newly discovered gene expression regulators that have been linked to several plant stress responses. To elucidate the role of miRNAs in drought stress regulation of alfalfa, a high-throughput sequencing approach was used to analyze 12 small RNA libraries comprising of 4 samples, each with 3 biological replicates. We identified 348 known miRNAs, belonging to 80 miRNA families, from the 12 libraries and 281 novel miRNAs using Mireap software. 18 known miRNAs in roots and 12 known miRNAs in leaves were screened out as drought-responsive miRNAs. Except for miR319d and miR157a which were upregulated under drought stress, the expression pattern of drought-responsive miRNAs were different between roots and leaves in alfalfa. This is the first study discovering miR157a, miR1507, miR3512, miR3630, miR5213, miR5294, miR5368 and miR6173 are drought-responsive miRNAs. Target transcripts of drought-responsive miRNAs were computationally predicted. All 447 target genes for the known miRNAs were predicted using an online tool. This study provides a significant insight on understanding drought-responsive mechanisms of alfalfa.

show abstract

Section: Identification Of Known and Novel Mirnasmentioning

confidence: 99%

Identification of Drought-Responsive microRNAs from Roots and Leaves of Alfalfa by High-Throughput Sequencing

Li¹,

Wan²,

Bi³

et al. 2017

Preprint

Self Cite

View full text Add to dashboard Cite

show abstract

“…Much attention has been given to the specific problem of annotating MIRNA genes from small RNA-seq data, and several tools for this purpose have been described to date (for review, see Li et al 2012). Less attention has been devoted to the broader problem of all-inclusive annotations based on reference-aligned small RNA-seq data.…”

Section: Introductionmentioning

confidence: 99%

ShortStack: Comprehensive annotation and quantification of small RNA genes

Axtell

2013

RNA

394

398

View full text Add to dashboard Cite

Small RNA sequencing allows genome-wide discovery, categorization, and quantification of genes producing regulatory small RNAs. Many tools have been described for annotation and quantification of microRNA loci (MIRNAs) from small RNA-seq data. However, in many organisms and tissue types, MIRNA genes comprise only a small fraction of all small RNA-producing genes. ShortStack is a stand-alone application that analyzes reference-aligned small RNA-seq data and performs comprehensive de novo annotation and quantification of the inferred small RNA genes. ShortStack's output reports multiple parameters of direct relevance to small RNA gene annotation, including RNA size distributions, repetitiveness, strandedness, hairpin-association, MIRNA annotation, and phasing. In this study, ShortStack is demonstrated to perform accurate annotations and useful descriptions of diverse small RNA genes from four plants (Arabidopsis, tomato, rice, and maize) and three animals (Drosophila, mice, and humans). ShortStack efficiently processes very large small RNA-seq data sets using modest computational resources, and its performance compares favorably to previously described tools.

show abstract

“…Above these programs are based on specific miRNA hairpin stem-loop structures and minimal free energies (MFE) . In the study, the novel candidate miRNAs were predicted using the MIREAP software by studying the stem-loop structure, minimum free energy, and Dicer cleavage site (Li et al, 2012).Then, the predicted candidate novel miRNAs and known miRNAs were further validated by real-time fluorescent PCR (Figure 3). …”

Section: Northern Blot Analysismentioning

confidence: 99%

Discovery of two novel miRNAs from the Ovis aries by a combinatorial approach of experiments and bioinformatics

Chang

Wang

Zhang

et al. 2017

IJAR

View full text Add to dashboard Cite

In the study, we successful constructed a library from the ovine testis using next-generation sequencing technology, and identified 219 novel miRNAs by bioinformatics. Two of the novel miRNAs (ovis_aries_testis-m0052_5p a nd ovis_aries_testis-m0165_5p), which were expressed in the sheep testis and ovary, and were confirmed by real-time PCR and northern blotting. Ovis_aries_testis-m0052_5p was 23 nucleotides in length, was located on chromosome 15, and had 100% similarity to mmu-miR-34c-5p, hsa-miR-34c-5p, gga-miR-34c-5p, and cfa-miR-34c. Ovis_aries_testis-m0165_5p was 21 nucleotides in length, located on chromosome 5, and had 100% similarity to mmu-miR-145a-5p, hsa-miR-145-5p, ssc-miR-145-5p, and bta-miR-145. The pre-miRNAs for Ovis_aries_testis-m0052_5p and Ovis_aries_testis-m0165_5p were 75 and 81 nucleotides in length, and both had a standard hairpin stem-loop structure. From the consistency of the sequence and structure, we speculated that ovis_aries_testis-m0052_5p had a function similar to hsa-miR-34c-5p, mmumiR-34c-5p, and ovis_aries_testis-m0165_5p had a function similar to hsa-miR-145-5p, which were involved in the fine regulation of cell survival, spermatozoon generate, breeding activities. Therefore, we defined the identified miRNAs as oar-miR-34c-5p and oar-miR-145-5p. The results will enrich the miRNA database, and provide the basis for research into the regulatory mechanisms of miRNA in relation to breeding activities.

show abstract

Performance comparison and evaluation of software tools for microRNA deep-sequencing data analysis

Cited by 126 publications

References 18 publications

Identification of Drought-Responsive microRNAs from Roots and Leaves of Alfalfa by High-Throughput Sequencing

Identification of Drought-Responsive microRNAs from Roots and Leaves of Alfalfa by High-Throughput Sequencing

ShortStack: Comprehensive annotation and quantification of small RNA genes

Discovery of two novel miRNAs from the Ovis aries by a combinatorial approach of experiments and bioinformatics

Contact Info

Product

Resources

About