1
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Langschied F, Leisegang MS, Brandes RP, Ebersberger I. ncOrtho: efficient and reliable identification of miRNA orthologs. Nucleic Acids Res 2023; 51:e71. [PMID: 37260093 PMCID: PMC10359484 DOI: 10.1093/nar/gkad467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 05/04/2023] [Accepted: 05/30/2023] [Indexed: 06/02/2023] Open
Abstract
MicroRNAs (miRNAs) are post-transcriptional regulators that finetune gene expression via translational repression or degradation of their target mRNAs. Despite their functional relevance, frameworks for the scalable and accurate detection of miRNA orthologs are missing. Consequently, there is still no comprehensive picture of how miRNAs and their associated regulatory networks have evolved. Here we present ncOrtho, a synteny informed pipeline for the targeted search of miRNA orthologs in unannotated genome sequences. ncOrtho matches miRNA annotations from multi-tissue transcriptomes in precision, while scaling to the analysis of hundreds of custom-selected species. The presence-absence pattern of orthologs to 266 human miRNA families across 402 vertebrate species reveals four bursts of miRNA acquisition, of which the most recent event occurred in the last common ancestor of higher primates. miRNA families are rarely modified or lost, but notable exceptions for both events exist. miRNA co-ortholog numbers faithfully indicate lineage-specific whole genome duplications, and miRNAs are powerful markers for phylogenomic analyses. Their exceptionally low genetic diversity makes them suitable to resolve clades where the phylogenetic signal is blurred by incomplete lineage sorting of ancestral alleles. In summary, ncOrtho allows to routinely consider miRNAs in evolutionary analyses that were thus far reserved to protein-coding genes.
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Affiliation(s)
- Felix Langschied
- Applied Bioinformatics Group, Institute of Cell Biology and Neuroscience, Goethe University, Frankfurt, Germany
| | - Matthias S Leisegang
- Institute for Cardiovascular Physiology, Goethe University, Frankfurt, Germany
- German Center of Cardiovascular Research (DZHK), Partner site RheinMain, Frankfurt, Germany
| | - Ralf P Brandes
- Institute for Cardiovascular Physiology, Goethe University, Frankfurt, Germany
- German Center of Cardiovascular Research (DZHK), Partner site RheinMain, Frankfurt, Germany
| | - Ingo Ebersberger
- Applied Bioinformatics Group, Institute of Cell Biology and Neuroscience, Goethe University, Frankfurt, Germany
- Senckenberg Biodiversity and Climate Research Centre (S-BIK-F), Frankfurt am Main, Germany
- LOEWE Centre for Translational Biodiversity Genomics (TBG), Frankfurt am Main, Germany
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2
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Liu Y, Xu Y, Yu M. MicroRNA‑4722‑5p and microRNA‑615‑3p serve as potential biomarkers for Alzheimer's disease. Exp Ther Med 2022; 23:241. [PMID: 35222718 PMCID: PMC8815048 DOI: 10.3892/etm.2022.11166] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 11/09/2021] [Indexed: 12/05/2022] Open
Abstract
The aim of the present study was to investigate the expression levels of microRNA(miR)-4722-5p and miR-615-3p in Alzheimer's disease (AD) and their diagnostic value. Blood samples were collected from 33 patients with AD and 33 healthy controls, and an β-amyloid (Aβ)25-35-induced PC12 cell model was also established. The relative mRNA expression levels of miR-4722-5p and miR-615-3p were detected using reverse transcription-quantitative PCR. The correlations between the mRNA expression levels of the two miRNAs and the mini-mental state examination (MMSE) scores were analyzed, and the receiver operating characteristic curve was used to assess the diagnostic value of miR-4722-5p and miR-615-3p in AD. Functional enrichment analysis of the miRNA target genes was performed using The Database for Annotation, Visualization and Integrated Discovery database and the R language analysis package. The mRNA expression levels of miR-4722-5p and miR-615-3p were increased in patients with AD and the Aβ25-35-induced PC12 cell model. The mRNA expression levels of miR-4722-5p and miR-615-3p were negatively correlated with MMSE scores, and the combination of the two miRNAs for AD had an improved diagnostic value than that of each miRNA alone. The results of Gene Ontology (GO) enrichment analysis showed that the target genes of miR-4722-5p were found in the cytoplasm and cytosol, and were mainly involved in protein folding and cell division. The molecular functions included protein binding and GTPase activator activity. The results of Kyoto Encyclopedia of Genes and Genomes analysis showed that miR-4722-5p was associated with the regulation of dopaminergic synapses and mTOR signaling pathways. GO enrichment analysis also revealed that the target genes of miR-615-3p were located in the nucleus and cytoplasm, were involved in the regulation of transcription and protein phosphorylation, and were associated with protein binding, metal ion binding and transcription factor activity. The target genes of miR-615-3p played important roles in the regulation of the Ras and FoxO signaling pathways. In conclusion, miR-4722-5p and miR-615-3p may be potential biomarkers in the early diagnosis of AD.
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Affiliation(s)
- Yan Liu
- Department of Neurology, The Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu 212001, P.R. China
| | - Yuhao Xu
- Department of Neurology, The Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu 212001, P.R. China
| | - Ming Yu
- Department of Neurology, The Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu 212001, P.R. China
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3
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Barela Hudgell MA, Smith LC. Sequence Diversity, Locus Structure, and Evolutionary History of the SpTransformer Genes in the Sea Urchin Genome. Front Immunol 2021; 12:744783. [PMID: 34867968 PMCID: PMC8634487 DOI: 10.3389/fimmu.2021.744783] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 10/12/2021] [Indexed: 11/13/2022] Open
Abstract
The generation of large immune gene families is often driven by evolutionary pressure exerted on host genomes by their pathogens, which has been described as the immunological arms race. The SpTransformer (SpTrf) gene family from the California purple sea urchin, Strongylocentrotus purpuratus, is upregulated upon immune challenge and encodes the SpTrf proteins that interact with pathogens during an immune response. Native SpTrf proteins bind both bacteria and yeast, and augment phagocytosis of a marine Vibrio, while a recombinant SpTrf protein (rSpTrf-E1) binds a subset of pathogens and a range of pathogen associated molecular patterns. In the sequenced sea urchin genome, there are four SpTrf gene clusters for a total of 17 genes. Here, we report an in-depth analysis of these genes to understand the sequence complexities of this family, its genomic structure, and to derive a putative evolutionary history for the formation of the gene clusters. We report a detailed characterization of gene structure including the intron type and UTRs with conserved transcriptional start sites, the start codon and multiple stop codons, and locations of polyadenylation signals. Phylogenetic and percent mismatch analyses of the genes and the intergenic regions allowed us to predict the last common ancestral SpTrf gene and a theoretical evolutionary history of the gene family. The appearance of the gene clusters from the theoretical ancestral gene may have been driven by multiple duplication and deletion events of regions containing SpTrf genes. Duplications and ectopic insertion events, indels, and point mutations in the exons likely resulted in the extant genes and family structure. This theoretical evolutionary history is consistent with the involvement of these genes in the arms race in responses to pathogens and suggests that the diversification of these genes and their encoded proteins have been selected for based on the survival benefits of pathogen binding and host protection.
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Affiliation(s)
| | - L. Courtney Smith
- Department of Biological Sciences, George Washington University, Washington, DC, United States
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4
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Roy S, Sharma B, Mazid MI, Akhand RN, Das M, Marufatuzzahan M, Chowdhury TA, Azim KF, Hasan M. Identification and host response interaction study of SARS-CoV-2 encoded miRNA-like sequences: an in silico approach. Comput Biol Med 2021; 134:104451. [PMID: 34020131 PMCID: PMC8078050 DOI: 10.1016/j.compbiomed.2021.104451] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Revised: 04/20/2021] [Accepted: 04/22/2021] [Indexed: 01/08/2023]
Abstract
COVID-19, a global pandemic caused by an RNA virus named SARS-CoV-2 has brought the world to a standstill in terms of infectivity, casualty, and commercial plummet. RNA viruses can encode microRNAs (miRNAs) capable of modulating host gene expression, and with that notion, we aimed to predict viral miRNA like sequences of MERS-CoV, SARS-CoV and SARS-CoV-2, analyze sequence reciprocity and investigate SARS-CoV-2 encoded potential miRNA-human genes interaction using bioinformatics tools. In this study, we retrieved 206 SARS-CoV-2 genomes, executed phylogenetic analysis, and the selected reference genome (MT434792.1) exhibited about 99% similarities among the retrieved genomes. We predicted 402, 137, and 85 putative miRNAs of MERS-CoV (NC_019843.3), SARS-CoV (NC_004718.3), and SARS-CoV-2 (MT434792.1) genome, respectively. Sequence similarity was analyzed among 624 miRNAs which revealed that the predicted miRNAs of SARS-CoV-2 share a cluster with the clad of miRNAs from MERS-CoV and SARS-CoV. Only SARS-CoV-2 derived 85 miRNAs were encountered for target prediction and 29 viral miRNAs seemed to target 119 human genes. Moreover, Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) analysis suggested the involvement of respective genes in various pathways and biological processes. Finally, we focused on eight putative miRNAs influencing 14 genes that are involved in the adaptive hypoxic response, neuroinvasion and hormonal regulation, and tumorigenic progression in patients with COVID-19. SARS-CoV-2 encoded miRNAs may cause misexpression of some critical regulators and facilitate viral neuroinvasion, altered hormonal axis, and tumorigenic events in the human host. However, these propositions need validation from future studies.
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Affiliation(s)
- Sawrab Roy
- Department of Microbiology and Immunology, Sylhet Agricultural University, Sylhet, 3100, Bangladesh
| | - Binayok Sharma
- Department of Medicine, Sylhet Agricultural University, Sylhet, 3100, Bangladesh
| | | | - Rubaiat Nazneen Akhand
- Department of Biochemistry and Chemistry, Sylhet Agricultural University, Sylhet, 3100, Bangladesh
| | - Moumita Das
- Department of Epidemiology and Public Health, Sylhet Agricultural University, Sylhet, 3100, Bangladesh
| | | | - Tanjia Afrin Chowdhury
- Department of Microbial Biotechnology, Sylhet Agricultural University, Sylhet, 3100, Bangladesh
| | - Kazi Faizul Azim
- Department of Microbial Biotechnology, Sylhet Agricultural University, Sylhet, 3100, Bangladesh
| | - Mahmudul Hasan
- Department of Pharmaceuticals and Industrial Biotechnology, Sylhet Agricultural University, Sylhet, 3100, Bangladesh,Corresponding author. Department of Pharmaceuticals and Industrial Biotechnology, Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet, 3100, Bangladesh
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5
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Ma X, He K, Shi Z, Li M, Li F, Chen XX. Large-Scale Annotation and Evolution Analysis of MiRNA in Insects. Genome Biol Evol 2021; 13:6255746. [PMID: 33905491 PMCID: PMC8126727 DOI: 10.1093/gbe/evab083] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/19/2021] [Indexed: 12/22/2022] Open
Abstract
Insects are among the most diverse and successful groups of animals and exhibit great morphological diversity and complexity. The innovation of wings and metamorphosis are some examples of the fascinating biological evolution of insects. Most microRNAs (miRNAs) contribute to canalization by conferring robustness to gene networks and thus increase the heritability of important phenotypes. Though previous studies have demonstrated how miRNAs regulate important phenotypes, little is still known about miRNA evolution in insects. Here, we used both small RNA-seq data and homology searching methods to annotate the miRNA repertoires of 152 arthropod species, including 135 insects and 17 noninsect arthropods. We identified 16,212 miRNA genes, and classified them into highly conserved (62), insect-conserved (90), and lineage-specific (354) miRNA families. The phylogenetic relationship of miRNA binary presence/absence dynamics implies that homoplastic loss of conserved miRNA families tends to occur in far-related morphologically simplified taxa, including scale insects (Coccoidea) and twisted-wing insects (Strepsiptera), leading to inconsistent phylogenetic tree reconstruction. The common ancestor of Insecta shares 62 conserved miRNA families, of which five were rapidly gained in the early winged-insects (Pterygota). We also detected extensive miRNA losses in Paraneoptera that are correlated with morphological reduction, and miRNA gains in early Endopterygota around the time holometabolous metamorphosis appeared. This was followed by abundant miRNA gains in Hymenoptera and Lepidoptera. In summary, we provide a comprehensive data set and a detailed evolutionary analysis of miRNAs in insects. These data will be important for future studies on miRNA functions associated with insect morphological innovation and trait biodiversity.
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Affiliation(s)
- Xingzhou Ma
- State Key Laboratory of Rice Biology & Ministry of Agriculture and Rural Affairs Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China.,College of Plant Protection, Nanjing Agricultural University, China
| | - Kang He
- State Key Laboratory of Rice Biology & Ministry of Agriculture and Rural Affairs Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Zhenmin Shi
- State Key Laboratory of Rice Biology & Ministry of Agriculture and Rural Affairs Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Meizhen Li
- State Key Laboratory of Rice Biology & Ministry of Agriculture and Rural Affairs Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Fei Li
- State Key Laboratory of Rice Biology & Ministry of Agriculture and Rural Affairs Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Xue-Xin Chen
- State Key Laboratory of Rice Biology & Ministry of Agriculture and Rural Affairs Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
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6
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Fromm B, Tarbier M, Smith O, Marmol-Sanchez E, Dalen L, Gilbert TP, Friedlander MR. Ancient microRNA profiles of a 14,300-year-old canid samples confirm taxonomic origin and give glimpses into tissue-specific gene regulation from the Pleistocene. RNA (NEW YORK, N.Y.) 2020; 27:rna.078410.120. [PMID: 33323528 PMCID: PMC7901840 DOI: 10.1261/rna.078410.120] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 12/09/2020] [Indexed: 05/04/2023]
Abstract
DNA sequencing is the current key technology for historic or ancient biological samples and has led to many exciting discoveries in the field of paleogenomics. However, functional insights into tissue identity, cellular composition or gene regulation cannot be gained from DNA. Recent analyses have shown that, under favorable conditions, RNA can also be sequenced from ancient samples, enabling studies at the transcriptomic and regulatory level. Analyzing ancient RNA data from a Pleistocene canid, we find hundreds of intact microRNAs that are taxonomically informative, show tissue-specificity and have functionally predictive characteristics. With an extraordinary age of 14,300 years, these microRNA sequences are by far the oldest ever reported. The authenticity of the sequences is further supported by a) the presence of canid / Caniformia-specific sequences that never evolved outside of this clade, b) tissue-specific expression patterns (cartilage, liver and muscle) that resemble those of modern dogs and c) RNA damage patterns that are clearly distinct from those of fresh samples. By performing computational microRNA-target enrichment analyses on the ancient sequences, we predict microRNA functions consistent with their tissue pattern of expression. For instance, we find a liver-specific microRNA that regulates carbohydrate metabolism and starvation responses in canids. In summary, we show that straightforward paleotranscriptomic microRNA analyses can give functional glimpses into tissue identity, cellular composition and gene regulatory activity of ancient samples and biological processes that took place in the Pleistocene, thus holding great promise for deeper insights into gene regulation in extinct animals based on ancient RNA sequencing. .
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Affiliation(s)
- Bastian Fromm
- Stockholm University, The Wenner-Gren Institute, Department of Molecular Biosciences, SciLifelab;
| | - Marcel Tarbier
- Stockholm University, The Wenner-Gren Institute, Department of Molecular Biosciences, SciLifelab
| | - Oliver Smith
- University of Copenhagen, Section for Evolutionary Genomics, The Globe Institute, Faculty of Health and Medical Sciences
| | - Emilio Marmol-Sanchez
- Stockholm University, The Wenner-Gren Institute, Department of Molecular Biosciences, SciLifelab
| | - Love Dalen
- Stockholm University, Centre for Palaeogenetics
| | - Tom P Gilbert
- University of Copenhagen, Section for Evolutionary Genomics, The Globe Institute, Faculty of Health and Medical Sciences
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7
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Fromm B, Tosar JP, Aguilera F, Friedländer MR, Bachmann L, Hejnol A. Evolutionary Implications of the microRNA- and piRNA Complement of Lepidodermella squamata (Gastrotricha). Noncoding RNA 2019; 5:E19. [PMID: 30813358 PMCID: PMC6468455 DOI: 10.3390/ncrna5010019] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 02/15/2019] [Accepted: 02/19/2019] [Indexed: 02/06/2023] Open
Abstract
Gastrotrichs-'hairy bellies'-are microscopic free-living animals inhabiting marine and freshwater habitats. Based on morphological and early molecular analyses, gastrotrichs were placed close to nematodes, but recent phylogenomic analyses have suggested their close relationship to flatworms (Platyhelminthes) within Spiralia. Small non-coding RNA data on e.g., microRNAs (miRNAs) and PIWI-interacting RNAs (piRNA) may help to resolve this long-standing question. MiRNAs are short post-transcriptional gene regulators that together with piRNAs play key roles in development. In a 'multi-omics' approach we here used small-RNA sequencing, available transcriptome and genomic data to unravel the miRNA- and piRNA complements along with the RNAi (RNA interference) protein machinery of Lepidodermella squamata (Gastrotricha, Chaetonotida). We identified 52 miRNA genes representing 35 highly conserved miRNA families specific to Eumetazoa, Bilateria, Protostomia, and Spiralia, respectively, with overall high similarities to platyhelminth miRNA complements. In addition, we found four large piRNA clusters that also resemble flatworm piRNAs but not those earlier described for nematodes. Congruently, transcriptomic annotation revealed that the Lepidodermella protein machinery is highly similar to flatworms, too. Taken together, miRNA, piRNA, and protein data support a close relationship of gastrotrichs and flatworms.
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Affiliation(s)
- Bastian Fromm
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, S-10691 Stockholm, Sweden.
| | - Juan Pablo Tosar
- Functional Genomics Unit, Institut Pasteur de Montevideo, Montevideo 11400, Uruguay.
- Nuclear Research Center, Faculty of Science, Universidad de la República, Montevideo 11400, Uruguay.
| | - Felipe Aguilera
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universidad de Concepción, Casilla 160_C, Concepción 3349001, Chile.
- Sars International Centre for Marine Molecular Biology, University of Bergen, 5006 Bergen, Norway.
| | - Marc R Friedländer
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, S-10691 Stockholm, Sweden.
| | - Lutz Bachmann
- Research group Frontiers in Evolutionary Zoology, Natural History Museum, University of Oslo, 0318 Oslo, Norway.
| | - Andreas Hejnol
- Sars International Centre for Marine Molecular Biology, University of Bergen, 5006 Bergen, Norway.
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8
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Kang W, Eldfjell Y, Fromm B, Estivill X, Biryukova I, Friedländer MR. miRTrace reveals the organismal origins of microRNA sequencing data. Genome Biol 2018; 19:213. [PMID: 30514392 PMCID: PMC6280396 DOI: 10.1186/s13059-018-1588-9] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 11/15/2018] [Indexed: 12/27/2022] Open
Abstract
We present here miRTrace, the first algorithm to trace microRNA sequencing data back to their taxonomic origins. This is a challenge with profound implications for forensics, parasitology, food control, and research settings where cross-contamination can compromise results. miRTrace accurately (> 99%) assigns real and simulated data to 14 important animal and plant groups, sensitively detects parasitic infection in mammals, and discovers the primate origin of single cells. Applying our algorithm to over 700 public datasets, we find evidence that over 7% are cross-contaminated and present a novel solution to clean these computationally, even after sequencing has occurred. miRTrace is freely available at https://github.com/friedlanderlab/mirtrace .
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Affiliation(s)
- Wenjing Kang
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Yrin Eldfjell
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Bastian Fromm
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Xavier Estivill
- Genetics and Genomics Department, Sidra Medicine, Doha, Qatar
| | - Inna Biryukova
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Marc R Friedländer
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden.
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9
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Tarver JE, Taylor RS, Puttick MN, Lloyd GT, Pett W, Fromm B, Schirrmeister BE, Pisani D, Peterson KJ, Donoghue PCJ. Well-Annotated microRNAomes Do Not Evidence Pervasive miRNA Loss. Genome Biol Evol 2018; 10:1457-1470. [PMID: 29788279 PMCID: PMC6007596 DOI: 10.1093/gbe/evy096] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/11/2018] [Indexed: 12/18/2022] Open
Abstract
microRNAs are conserved noncoding regulatory factors implicated in diverse physiological and developmental processes in multicellular organisms, as causal macroevolutionary agents and for phylogeny inference. However, the conservation and phylogenetic utility of microRNAs has been questioned on evidence of pervasive loss. Here, we show that apparent widespread losses are, largely, an artefact of poorly sampled and annotated microRNAomes. Using a curated data set of animal microRNAomes, we reject the view that miRNA families are never lost, but they are rarely lost (92% are never lost). A small number of families account for a majority of losses (1.7% of families account for >45% losses), and losses are associated with lineages exhibiting phenotypic simplification. Phylogenetic analyses based on the presence/absence of microRNA families among animal lineages, and based on microRNA sequences among Osteichthyes, demonstrate the power of these small data sets in phylogenetic inference. Perceptions of widespread evolutionary loss of microRNA families are due to the uncritical use of public archives corrupted by spurious microRNA annotations, and failure to discriminate false absences that occur because of incomplete microRNAome annotation.
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Affiliation(s)
- James E Tarver
- School of Earth Sciences and School of Biological Sciences, University of Bristol, United Kingdom
| | - Richard S Taylor
- School of Earth Sciences and School of Biological Sciences, University of Bristol, United Kingdom
| | - Mark N Puttick
- School of Earth Sciences and School of Biological Sciences, University of Bristol, United Kingdom
- Department of Biology and Biochemistry, University of Bath, United Kingdom
| | - Graeme T Lloyd
- School of Earth and Environment, University of Leeds, United Kingdom
| | - Walker Pett
- Department of Ecology, Evolution and Organismal Biology, Iowa State University
| | - Bastian Fromm
- Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, Norway
| | - Bettina E Schirrmeister
- School of Earth Sciences and School of Biological Sciences, University of Bristol, United Kingdom
| | - Davide Pisani
- School of Earth Sciences and School of Biological Sciences, University of Bristol, United Kingdom
| | - Kevin J Peterson
- Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire
| | - Philip C J Donoghue
- School of Earth Sciences and School of Biological Sciences, University of Bristol, United Kingdom
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10
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Whelan NV, Halanych KM. Who Let the CAT Out of the Bag? Accurately Dealing with Substitutional Heterogeneity in Phylogenomic Analyses. Syst Biol 2018; 66:232-255. [PMID: 27633354 DOI: 10.1093/sysbio/syw084] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2015] [Accepted: 09/04/2016] [Indexed: 11/14/2022] Open
Abstract
As phylogenetic datasets have increased in size, site-heterogeneous substitution models such as CAT-F81 and CAT-GTR have been advocated in favor of other models because they purportedly suppress long-branch attraction (LBA). These models are two of the most commonly used models in phylogenomics, and they have been applied to a variety of taxa, ranging from Drosophila to land plants. However, many arguments in favor of CAT models have been based on tenuous assumptions about the true phylogeny, rather than rigorous testing with known trees via simulation. Moreover, CAT models have not been compared to other approaches for handling substitutional heterogeneity such as data partitioning with site-homogeneous substitution models. We simulated amino acid sequence datasets with substitutional heterogeneity on a variety of tree shapes including those susceptible to LBA. Data were analyzed with both CAT models and partitioning to explore model performance; in total over 670,000 CPU hours were used, of which over 97% was spent running analyses with CAT models. In many cases, all models recovered branching patterns that were identical to the known tree. However, CAT-F81 consistently performed worse than other models in inferring the correct branching patterns, and both CAT models often overestimated substitutional heterogeneity. Additionally, reanalysis of two empirical metazoan datasets supports the notion that CAT-F81 tends to recover less accurate trees than data partitioning and CAT-GTR. Given these results, we conclude that partitioning and CAT-GTR perform similarly in recovering accurate branching patterns. However, computation time can be orders of magnitude less for data partitioning, with commonly used implementations of CAT-GTR often failing to reach completion in a reasonable time frame (i.e., for Bayesian analyses to converge). Practices such as removing constant sites and parsimony uninformative characters, or using CAT-F81 when CAT-GTR is deemed too computationally expensive, cannot be logically justified. Given clear problems with CAT-F81, phylogenies previously inferred with this model should be reassessed. [Data partitioning; phylogenomics, simulation, site-heterogeneity, substitution models.].
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Affiliation(s)
- Nathan V Whelan
- Department of Biological Sciences, Molette Biology Laboratory for Environmental and Climate Change Studies, Auburn University, 101 Life Sciences Building, Auburn, AL 36849, USA
| | - Kenneth M Halanych
- Department of Biological Sciences, Molette Biology Laboratory for Environmental and Climate Change Studies, Auburn University, 101 Life Sciences Building, Auburn, AL 36849, USA
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11
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Tarver JE, Dos Reis M, Mirarab S, Moran RJ, Parker S, O'Reilly JE, King BL, O'Connell MJ, Asher RJ, Warnow T, Peterson KJ, Donoghue PCJ, Pisani D. The Interrelationships of Placental Mammals and the Limits of Phylogenetic Inference. Genome Biol Evol 2016; 8:330-44. [PMID: 26733575 PMCID: PMC4779606 DOI: 10.1093/gbe/evv261] [Citation(s) in RCA: 123] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Placental mammals comprise three principal clades: Afrotheria (e.g., elephants and tenrecs), Xenarthra (e.g., armadillos and sloths), and Boreoeutheria (all other placental mammals), the relationships among which are the subject of controversy and a touchstone for debate on the limits of phylogenetic inference. Previous analyses have found support for all three hypotheses, leading some to conclude that this phylogenetic problem might be impossible to resolve due to the compounded effects of incomplete lineage sorting (ILS) and a rapid radiation. Here we show, using a genome scale nucleotide data set, microRNAs, and the reanalysis of the three largest previously published amino acid data sets, that the root of Placentalia lies between Atlantogenata and Boreoeutheria. Although we found evidence for ILS in early placental evolution, we are able to reject previous conclusions that the placental root is a hard polytomy that cannot be resolved. Reanalyses of previous data sets recover Atlantogenata + Boreoeutheria and show that contradictory results are a consequence of poorly fitting evolutionary models; instead, when the evolutionary process is better-modeled, all data sets converge on Atlantogenata. Our Bayesian molecular clock analysis estimates that marsupials diverged from placentals 157-170 Ma, crown Placentalia diverged 86-100 Ma, and crown Atlantogenata diverged 84-97 Ma. Our results are compatible with placental diversification being driven by dispersal rather than vicariance mechanisms, postdating early phases in the protracted opening of the Atlantic Ocean.
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Affiliation(s)
- James E Tarver
- Department of Biology, The National University of Ireland, Maynooth, Ireland School of Earth Sciences, University of Bristol, United Kingdom
| | - Mario Dos Reis
- Department of Genetics, Evolution and Environment, University College London, United Kingdom School of Biological and Chemical Sciences, Queen Mary University of London, United Kingdom
| | - Siavash Mirarab
- Department of Computer Science, University of Texas at Austin Department of Electrical and Computer Engineering, University of California, San Diego
| | - Raymond J Moran
- Computational and Molecular Evolutionary Biology Group, School of Biology, Faculty of Life Sciences, University of Leeds
| | - Sean Parker
- School of Earth Sciences, University of Bristol, United Kingdom
| | | | - Benjamin L King
- Mount Desert Island Biological Laboratory, Salisbury Cove, Maine
| | - Mary J O'Connell
- Computational and Molecular Evolutionary Biology Group, School of Biology, Faculty of Life Sciences, University of Leeds
| | - Robert J Asher
- Museum of Zoology, University of Cambridge, United Kingdom
| | - Tandy Warnow
- Department of Computer Science, University of Texas at Austin Department of Electrical and Computer Engineering, University of California, San Diego Departments of Bioengineering and Computer Science, University of Illinois at Urbana-Champaign
| | - Kevin J Peterson
- Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire
| | | | - Davide Pisani
- School of Earth Sciences, University of Bristol, United Kingdom School of Biological Sciences, University of Bristol, United Kingdom
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12
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Fromm B, Billipp T, Peck LE, Johansen M, Tarver JE, King BL, Newcomb JM, Sempere LF, Flatmark K, Hovig E, Peterson KJ. A Uniform System for the Annotation of Vertebrate microRNA Genes and the Evolution of the Human microRNAome. Annu Rev Genet 2015; 49:213-42. [PMID: 26473382 DOI: 10.1146/annurev-genet-120213-092023] [Citation(s) in RCA: 361] [Impact Index Per Article: 40.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Although microRNAs (miRNAs) are among the most intensively studied molecules of the past 20 years, determining what is and what is not a miRNA has not been straightforward. Here, we present a uniform system for the annotation and nomenclature of miRNA genes. We show that less than a third of the 1,881 human miRBase entries, and only approximately 16% of the 7,095 metazoan miRBase entries, are robustly supported as miRNA genes. Furthermore, we show that the human repertoire of miRNAs has been shaped by periods of intense miRNA innovation and that mature gene products show a very different tempo and mode of sequence evolution than star products. We establish a new open access database--MirGeneDB ( http://mirgenedb.org )--to catalog this set of miRNAs, which complements the efforts of miRBase but differs from it by annotating the mature versus star products and by imposing an evolutionary hierarchy upon this curated and consistently named repertoire.
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Affiliation(s)
- Bastian Fromm
- Department of Tumor Biology, Institute for Cancer Research
| | - Tyler Billipp
- Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire 03755;
| | - Liam E Peck
- Department of Biology and Health Sciences, New England College, Henniker, New Hampshire 03242
| | | | - James E Tarver
- Department of Biology, The National University of Ireland, Maynooth, Kildare, Ireland.,School of Earth Sciences, University of Bristol, BS8 1TQ Bristol, United Kingdom
| | - Benjamin L King
- Kathryn W. Davis Center for Regenerative Biology and Medicine, Mount Desert Island Biological Laboratory, Salisbury Cove, Maine 04672
| | - James M Newcomb
- Department of Biology and Health Sciences, New England College, Henniker, New Hampshire 03242
| | - Lorenzo F Sempere
- Center for Cancer and Cell Biology, Van Andel Research Institute, Grand Rapids, Michigan 49503
| | - Kjersti Flatmark
- Department of Tumor Biology, Institute for Cancer Research.,Department of Gastroenterological Surgery.,Institute of Clinical Medicine
| | - Eivind Hovig
- Department of Tumor Biology, Institute for Cancer Research.,Institute of Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Nydalen, N-0424 Oslo, Norway.,Department of Informatics, University of Oslo, Blindern, N-0318 Oslo, Norway
| | - Kevin J Peterson
- Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire 03755;
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13
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Kenny NJ, Namigai EKO, Marlétaz F, Hui JHL, Shimeld SM. Draft genome assemblies and predicted microRNA complements of the intertidal lophotrochozoans Patella vulgata (Mollusca, Patellogastropoda) and Spirobranchus (Pomatoceros) lamarcki (Annelida, Serpulida). Mar Genomics 2015; 24 Pt 2:139-46. [PMID: 26319627 DOI: 10.1016/j.margen.2015.07.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Revised: 06/19/2015] [Accepted: 07/14/2015] [Indexed: 12/01/2022]
Abstract
MicroRNAs (miRNA) are small non-coding RNAs that act post-transcriptionally to regulate gene expression levels. Some studies have indicated that microRNAs may have low homoplasy, and as a consequence the phylogenetic distribution of microRNA families has been used to study animal evolutionary relationships. Limited levels of lineage sampling, however, may distort such analyses. Lophotrochozoa is an under-sampled taxon that includes molluscs, annelids and nemerteans, among other phyla. Here, we present two novel draft genomes, those of the limpet Patella vulgata and polychaete Spirobranchus (Pomatoceros) lamarcki. Surveying these genomes for known microRNAs identifies numerous potential orthologues, including a number that have been considered to be confined to other lineages. RT-PCR demonstrates that some of these (miR-1285, miR-1287, miR-1957, miR-1983 and miR-3533), previously thought to be found only in vertebrates, are expressed. This study provides genomic resources for two lophotrochozoans and reveals patterns of microRNA evolution that could be hidden by more restricted sampling.
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Affiliation(s)
- Nathan J Kenny
- Simon F.S. Li Marine Science Laboratory of School of Life Sciences and Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong; Department of Zoology, University of Oxford, Oxford OX1 3PS, UK
| | | | | | - Jerome H L Hui
- Simon F.S. Li Marine Science Laboratory of School of Life Sciences and Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong.
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