miREvo: an integrative microRNA evolutionary analysis platform for next-generation sequencing experiments

BackgroundMicroRNAs (miRNAs) are small (~19-24nt) non-coding RNAs that play important roles in various biological processes. To date, the next-generation sequencing (NGS) technology has been widely used to discover miRNAs in plants and animals. Although evolutionary analysis is important to reveal the functional dynamics of miRNAs, few computational tools have been developed to analyze the evolution of miRNA sequence and expression across species, especially the newly emerged ones,ResultsWe developed miREvo, an integrated software platform with a graphical user interface (GUI), to process deep-sequencing data of small RNAs and to analyze miRNA sequence and expression evolution based on the multiple-species whole genome alignments (WGAs). Three major features are provided by miREvo: (i) to identify novel miRNAs in both plants and animals, based on a modified miRDeep algorithm, (ii) to detect miRNA homologs and measure their pairwise evolutionary distances among multiple species based on a WGA, and (iii) to profile miRNA expression abundances and analyze expression divergence across multiple species (small RNA libraries). Moreover, we demonstrated the utility of miREvo with Illumina data sets from Drosophila melanogaster and Arabidopsis, respectively.ConclusionThis work presents an integrated pipline, miREvo, for exploring the expressional and evolutionary dynamics of miRNAs across multiple species. MiREvo is standalone, modular, and freely available at http://evolution.sysu.edu.cn/software/mirevo.htm under the GNU/GPL license.

• Publication year

  2012

• Venue

  BMC Bioinformatics

• Publication date

  2012-06-21

• Fields of study

  Biology, Medicine, Computer Science

• Identifiers
  DOI 10.1186/1471-2105-13-140PMID 22720726PMCID 3410788
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades

  2011cited by this paper
• Characterization of statistical features for plant microRNA prediction

  2011cited by this paper
• Deep annotation of Drosophila melanogaster microRNAs yields insights into their processing, modification, and emergence.

  2011cited by this paper
• Deep small RNA sequencing from the nematode Ascaris reveals conservation, functional diversification, and novel developmental profiles.

  2011cited by this paper
• Testing hypotheses on the rate of molecular evolution in relation to gene expression using microRNAs

  2011cited by this paper
• A high-resolution map of human evolutionary constraint using 29 mammals

  2011cited by this paper
• miRDeep-P: a computational tool for analyzing the microRNA transcriptome in plants

  2011cited by this paper
• Adverse interactions between micro-RNAs and target genes from different species

  2010influential reference
• Aligning Short Sequencing Reads with Bowtie

  2010influential reference
• MicroRNA Gene Evolution in Arabidopsis lyrata and Arabidopsis thaliana[W][OA]

  2010influential reference
• Deep sequencing discovery of novel and conserved microRNAs in trifoliate orange (Citrus trifoliata)

  2010cited by this paper
• Desperately seeking microRNA targets

  2010cited by this paper
• Origin, biogenesis, and activity of plant microRNAs.

  2009cited by this paper
• miRanalyzer: a microRNA detection and analysis tool for next-generation sequencing experiments

  2009cited by this paper
• miRExpress: Analyzing high-throughput sequencing data for profiling microRNA expression

  2009cited by this paper
• Characterization and comparative profiling of the small RNA transcriptomes in two phases of locust

  2009cited by this paper
• High-resolution profiling and discovery of planarian small RNAs

  2009cited by this paper
• Parallel DNA pyrosequencing unveils new zebrafish microRNAs

  2009cited by this paper
• miROrtho: computational survey of microRNA genes

  2008influential reference
• miRNAminer: A tool for homologous microRNA gene search

  2008cited by this paper
• Criteria for Annotation of Plant MicroRNAs

  2008cited by this paper
• Identification of phylogenetically conserved microRNA cis-regulatory elements across 12 Drosophila species

  2008cited by this paper
• Adaptive evolution of newly emerged micro-RNA genes in Drosophila.

  2008influential reference
• A toolkit for analysing large-scale plant small RNA datasets

  2008cited by this paper
• Discovering microRNAs from deep sequencing data using miRDeep

  2008cited by this paper
• The birth and death of microRNA genes in Drosophila

  2008influential reference
• Effects of dependence in high-dimensional multiple testing problems

  2008cited by this paper
• Conservation and evolution of miRNA regulatory programs in plant development.

  2007cited by this paper
• Rapid evolution of an X-linked microRNA cluster in primates.

  2007cited by this paper
• High-Throughput Sequencing of Arabidopsis microRNAs: Evidence for Frequent Birth and Death of MIRNA Genes

  2007cited by this paper
• Statistical analysis and significance testing of serial analysis of gene expression data using a Poisson mixture model

  2007cited by this paper
• Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures

  2007cited by this paper
• Identification of plant microRNA homologs

  2006cited by this paper
• Plant and animal microRNAs: similarities and differences

  2005influential reference
• Phylogenetic shadowing and computational identification of human microRNA genes.

  2005cited by this paper
• Computational prediction of miRNAs in Arabidopsis thaliana.

  2005cited by this paper
• Intensified Cloning Efforts Have Revealed Numer

  2004cited by this paper
• Aligning multiple genomic sequences with the threaded blockset aligner.

  2004cited by this paper
• Evolution's cauldron: Duplication, deletion, and rearrangement in the mouse and human genomes

  2003cited by this paper
• Comparative analyses of multi-species sequences from targeted genomic regions

  2003cited by this paper
• Human-mouse alignments with BLASTZ.

  2003influential reference
• Tandem repeats finder: a program to analyze DNA sequences.

  1999cited by this paper
• Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.

  1997influential reference
• BIOINFORMATICS APPLICATIONS

  year unknowninfluential reference

• Integrated mRNA-miRNA Analysis Reveals the Regulatory Network Under Salt–Alkali Stress in Alfalfa (Medicago sativa L.)

  2026cites this paper
• Genome‐Wide Analysis of the lncRNAs and miRNAs Involved in Flower Development in Radish

  2026cites this paper
• Transcriptome Sequencing Unveils a Novel Mechanism Underlying Breed Distinctions Between Thin- and Fat-Tailed Sheep.

  2026cites this paper
• The microRNA Targeting Cu/Zn-SOD Increases the Susceptibility To WSSV Under Ammonia Stress in Pacific White Shrimp Litopenaeus vannamei

  2026cites this paper
• Comparative analysis of microRNA expression in serum-derived extracellular vesicles from sudden infant death syndrome cases.

  2026cites this paper
• Regulatory role of miR319a and functional validation of its target gene ArMYB33 in leaf color change of Acer rubrum.

  2026cites this paper
• Integrating transcriptome, rhizosphere microbiome, and exosome microRNA analyses unravels the response of tobacco (Nicotiana tabacum L.) to atrazine stress

  2025cites this paper
• Elucidating the molecular basis of salt tolerance in potatoes through miRNA expression and phenotypic analysis

  2025influential citation
• Non-coding RNAs and regulatory networks involved in the Ameson portunus (Microsporidia)-Portunus trituberculatus interaction.

  2025cites this paper
• The Small RNA Landscape in Azoospermia: Implications for Male Infertility and Sperm Retrieval—A Preliminary Study

  2025cites this paper
• The Novel miR_146-Tfdp2 Axis Antagonizes METH-Induced Neuron Apoptosis and Cell Cycle Abnormalities in Tree Shrew.

  2025cites this paper
• Identification of Novel 58-5p and SREBF1 Interaction and Effects on Apoptosis of Ovine Ovarian Granulosa Cell

  2025cites this paper
• Identification of sex-biased and gonadal developmental miRNAs during critical windows of early gonadal differentiation in the Chinese giant salamander (Andrias davidianus)

  2025cites this paper
• miR3398‐VqMYB15 Regulates the Synthesis of Stilbene in Vitis quinquangularis

  2025cites this paper
• Integrating exosome wide associations study and Mendelian randomization identified causal miRNAs for type 2 diabetes mellitus and its complications

  2025cites this paper
• AAT-MSC-EVs: Novel implications for suppressing ferroptosis, fibrosis and pain associated with chronic pancreatitis.

  2025cites this paper
• Transcriptome Sequencing Reveals ceRNA Networks and Molecular Signatures in Myopic Mouse Retina

  2025cites this paper
• Distinct microRNA signatures define sporadic PSP-RS and PD in patient-derived midbrain organoids

  2025cites this paper
• GSK-3α regulates miRNAs associated with transcriptional and metabolic processes in human cardiomyocytes under hypoxia

  2025cites this paper
• Integrated multi-omics analyses reveal the roles of apricot miR166a and miR396c in the growth and development of apricot-peach grafted chimera.

  2025cites this paper
• Comprehensive transcriptome of muscle development in Sichuan white rabbit

  2025cites this paper
• miR-34-5p mediates 20E-induced autophagy in the fat body of Bombyx mori by targeting Atg1

  2025cites this paper
• fru-miR-138 targeting SOCS3 modulates the immune response of Japanese pufferfish (Takifugu rubripes) upon Vibrio harveyi infection.

  2025cites this paper
• Whole‐Transcriptome Reveals Molecular Adaptation Mechanisms of Hypothalamus and Construction of Key ceRNA Networks During Reproductive State Transition in Precocious Goats

  2025cites this paper
• Dynamic responses during early development of the sea urchin Strongylocentrotus intermedius to CO2-driven ocean acidification: A microRNA-mRNA integrated analysis.

  2025cites this paper
• Polyploidization-driven transcriptomic dynamics in Medicago sativa neotetraploids: mRNA, smRNA and allele-specific gene expression

  2025cites this paper
• Increased miRNA-375 causes oxidative damage but promotes apoptosis resistance and cell migration in the clam Ruditapes philippinarum

  2025cites this paper
• Preliminary exploration of mRNA, lncRNA, and miRNA expressions in the bovine jejunum unveils novel aspects of Mycobacterium avium subspecies paratuberculosis infections

  2025cites this paper
• miRNA-seq analysis revealed a potential strategy underlying poplar root responses to low nitrogen stress

  2025cites this paper
• Exploration of Small Non-Coding RNAs as Molecular Markers of Ram Sperm Fertility

  2025cites this paper
• Role of Plasma-Derived Exosomal MicroRNAs in Mediating Type 2 Diabetes Remission

  2025cites this paper
• Characterisation of early fruit development-specific miRNAs and their targets in peach using small RNA and degradome sequencing

  2025cites this paper
• In-depth single-cell transcriptomic exploration of the regenerative dynamics in stony coral

  2025cites this paper
• High-throughput sequencing reveals the regulatory role of microRNAs in the Chinese mitten crab (Eriocheir sinensis) response to heat stress

  2025cites this paper
• Genome-wide landscape of miRNA-mRNA-lncRNA-circRNA ceRNA network in Nanos2 deficient mice

  2025cites this paper
• RNA sequencing-based profiling of differentially expressed microRNAs in endothelial cells from offspring of hypertensive pregnancies: a preliminary study

  2025cites this paper
• MicroRNA analysis of porcine muscle tissue involved in phosphoinositol metabolism

  2025cites this paper
• Integrative analysis of small RNA and degradome sequencing reveals the role of miRNAs in monoterpene biosynthesis in linalool-type Cinnamomum camphora

  2025cites this paper
• Analysis of Non‐Coding RNAs and N6‐Methyladenosine‐Modified Genes in Response to flg22 in Grape Immunity

  2025cites this paper
• Comprehensive Transcriptomics Reveals Putative Cytokinin-Triggered Non-coding RNA Networks Modulating Female Flower Formation in Cassava

  2025cites this paper
• Early changes in exosomal microRNAs after a one-week low-calorie diet predict sustained glycaemic and weight outcomes in patients with type 2 diabetes.

  2025cites this paper
• Screening and validation of key microRNAs regulating muscle development in Hanper sheep

  2025cites this paper
• Multi-omics integration identifies NK cell-mediated cytotoxicity as a therapeutic target in systemic lupus erythematosus

  2025cites this paper
• Pathological and miRNA-mRNA Analyses Provide New Insights into the Immune Response of Clams to Vibrio Infection

  2025cites this paper
• miR398‐Dirigent Module Negatively Regulates Cassava Resistance to Cassava Common Mosaic Virus by Affecting the Cell Wall Lignification and Thickness

  2025cites this paper
• Integrated Analysis of mRNA and miRNA Associated with Reproduction in Female and Male Gonads in Abalone (Haliotis discus hannai)

  2025influential citation
• Integrated analysis of lncRNA-miRNA-mRNA regulatory network revealing molecular mechanisms of immune response and ion transport in Eriocheir sinensis under alkalinity stress.

  2025cites this paper
• Characterization and analysis of MicroRNA during leg muscle development in embryonic stage of daozhou grey goose

  2025cites this paper
• MicroRNA-874-3p is a Potential Contributor to Primary Hyperparathyroidism-Induced Osteoporosis

  2025cites this paper
• Study on the Regulatory Mechanisms of Carapace Marking Formation in Marsupenaeus japonicus

  2025cites this paper
• Whole-transcriptome sequencing reveals the regulatory roles of non-coding RNAs during xylem development in Ginkgo biloba L.

  2025cites this paper
• Identifying microRNAs and their downstream transcriptional regulatory network during prickle development in Rubus spp

  2025cites this paper
• Identification of heavy metal transport-related genes and microRNAs in response to cadmium toxicity and micronutrient deficiency in barley roots.

  2025cites this paper
• A Comprehensive Transcriptome Atlas Reveals the Crucial Role of LncRNAs in Maintaining Nodulation Homeostasis in Soybean

  2024cites this paper
• microRNA as an Important Mediator in the Regulation of Male Gallus gallus domesticus Reproduction: Current State of the Problem

  2024cites this paper
• Constructing mRNA-meth-miRNA single-sample networks to reveal the molecular interaction patterns induced by lunar orbital stressors in rice (Oryzasativa).

  2024cites this paper
• Molecular Characterization of miRNAs in Myzus persicae Carrying Brassica Yellows Virus

  2024cites this paper
• Exosomal Micro RNA Isolation in White-Tailed Deer (Odocoileus virginianus) for Diagnostic Biomarker Discovery

  2024cites this paper
• Integrated Analysis of microRNAs and Transcription Factor Targets in Floral Transition of Pleioblastus pygmaeus

  2024cites this paper
• miRNA targeting Mpp53 is involved in UV‐B irradiation resistance in Myzus persicae

  2024cites this paper
• Genome-wide analysis of non-coding RNA reveals the role of a novel miR319c for tuber dormancy release process in potato

  2024cites this paper
• Integrated Analysis of the lncRNA-miRNA-mRNA Expression Profiles in Response to Meloidogyne incognita in Radish (Raphanus sativus L.)

  2024cites this paper
• MicroRNA Profile of Mouse Adipocyte-Derived Extracellular Vesicles

  2024cites this paper
• Pituitary-derived small extracellular vesicles promote liver repair by its cargo miR-143-3p

  2024cites this paper
• Exploring the Heat-Responsive miRNAs and their Target Gene Regulation in Ruditapes philippinarum Under Acute Heat Stress

  2024cites this paper
• Combined Analysis of Transcriptome and Small RNA Sequencing Reveals the Mechanism of UV-B-promoted Flavonoid Biosynthesis in Ginkgo biloba

  2024cites this paper
• MiRNAs profiles among three poplar varieties provide insights into different molecular responses in resistance to newly emerging bacterial pathogen.

  2024cites this paper
• Exploring the microRNA-mRNA regulatory network associated with solasonine in bladder cancer

  2024cites this paper
• Zhuang-Gu-Fang promotes osteoblast differentiation via myoblasts and myoblast-derived exosomal miRNAs:miR-5100, miR-126a-3p, miR-450b-5p, and miR-669a-5p.

  2024cites this paper
• Exploring the dynamic adaptive responses of Epimedium pubescens to phosphorus deficiency by Integrated transcriptome and miRNA analysis

  2024cites this paper
• MicroRNA expression profile of chicken liver at different times after Histomonas meleagridis infection.

  2024cites this paper
• MicroRNA bmo-miR-31-5p inhibits apoptosis and promotes BmNPV proliferation by targeting the CYP9e2 gene of Bombyx mori.

  2024cites this paper
• Transcriptome analysis of mRNA and miRNA in the development of LeiZhou goat muscles

  2024cites this paper
• Comprehensive analysis of differentially expressed mRNAs, circRNAs, and miRNAs and their ceRNA network in the testis of cattle-yak, yak, and cattle.

  2024cites this paper
• Transcriptome analysis reveals miRNA expression profiles in hypothalamus tissues during the sexual development of Jining grey goats

  2024cites this paper
• The expression patterns of exosomal miRNAs in the Pacific oyster after high-temperature stress or Vibrio stimulation.

  2024cites this paper
• Ferroptosis Altered microRNAs Expression in HT-1080 Fibrosarcoma Cells Based on Small RNA Sequencing and Bioinformatics Analysis

  2024cites this paper
• The grapevine miR827a regulates the synthesis of stilbenes by targeting VqMYB14 and gives rise to susceptibility in plant immunity

  2024cites this paper
• The Construction of lncRNA/circRNA–miRNA–mRNA Networks Reveals Functional Genes Related to Growth Traits in Schima superba

  2024cites this paper
• Exploring MicroRNAs Associated with Pomegranate Pistil Development: An Identification and Analysis Study

  2024cites this paper
• miRNA Expression Analysis of IPEC-J2 Cells Damaged by Soybean 7S Globulin Reveals ssc-miR-221-5p as the Factor Alleviating Cell Damage.

  2024cites this paper
• Maize miRNAs and their putative target genes involved in chilling stress response in 5-day old seedlings

  2024cites this paper
• Expression profiles of host miRNAs and circRNAs and ceRNA network during Toxoplasma gondii lytic cycle

  2024cites this paper
• Multi-omics analyses reveal microRNAs’ role in terpene biosynthesis regulation in slash pine

  2024cites this paper
• Deciphering the role of non-coding RNAs involved in sorafenib resistance

  2024cites this paper
• Integrated analysis of differently expressed microRNAs and mRNAs at different postnatal stages reveals intramuscular fat deposition regulation in goats (Capra hircus).

  2024cites this paper
• Non-coding RNA in the gut of the blood-feeding parasitic worm, Haemonchus contortus

  2024cites this paper
• The accumulation of modular serine protease mediated by a novel circRNA sponging miRNA increases Aedes aegypti immunity to fungus

  2024cites this paper
• Overexpression of Let-7a mitigates diploidization in mouse androgenetic haploid embryonic stem cells

  2024cites this paper
• Identification and construction of lncRNA-miRNA-mRNA ceRNA networks associated with temperature changes in Sebastiscus marmoratus

  2024cites this paper
• MicroRNA expression profile of chicken jejunum in different time points Eimeria maxima infection

  2024cites this paper
• Exosomes derived from mesenchymal stem cells ameliorate impaired glucose metabolism in myocardial Ischemia/reperfusion injury through miR-132-3p/PTEN/AKT pathway

  2024cites this paper
• miRNAs targeted transcription factors HaGATAa/b to mediate the post-mating switch in Helicoverpa armigera female reproductive behavior.

  2024cites this paper
• Analysis of microRNA Expression Profiles in Broiler Muscle Tissues by Feeding Different Levels of Guanidinoacetic Acid

  2024cites this paper
• MicroRNA Identification and Integrated Network Analyses for Age-Dependent Flavonoid Biosynthesis in Ginkgo biloba

  2023cites this paper
• Changes in the gut bacterial community affect miRNA profiles in Riptortus pedestris under different rearing conditions.

  2023cites this paper
• Seasonal patterns of miRNA and mRNA expression profiles in the testes of plateau zokors (Eospalax baileyi).

  2023cites this paper
• Multiomics studies with co-transformation reveal microRNAs via miRNA-TF-mRNA network participating in wood formation in Hevea brasiliensis

  2023cites this paper
• Transcriptome analysis reveals candidate miRNAs involved in skin color differentiation of juvenile Plectropomus leopardus in response to different background colors.

  2023cites this paper
• Comparative analysis of microRNA expression profiles in clam Ruditapes philippinarum after ammonia nitrogen exposure.

  2023cites this paper