RepeatModeler2 for automated genomic discovery of transposable element families

2020/04/16 by Jullien M. Flynn, Robert Hubley, Clément Goubert +4 · 186 citations
Agricultural and Biological Sciences · Biochemistry, Genetics and Molecular Biology · #Chromosomal and Genetic Variations #Genomics and Phylogenetic Studies #RNA and protein synthesis mechanisms

paper · doi:10.1073/pnas.1921046117

openalex publication_date 2020/04/16 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/30

Abstract

The accelerating pace of genome sequencing throughout the tree of life is driving the need for improved unsupervised annotation of genome components such as transposable elements (TEs). Because the types and sequences of TEs are highly variable across species, automated TE discovery and annotation are challenging and time-consuming tasks. A critical first step is the de novo identification and accurate compilation of sequence models representing all of the unique TE families dispersed in the genome. Here we introduce RepeatModeler2, a pipeline that greatly facilitates this process. This program brings substantial improvements over the original version of RepeatModeler, one of the most widely used tools for TE discovery. In particular, this version incorporates a module for structural discovery of complete long terminal repeat (LTR) retroelements, which are widespread in eukaryotic genomes but recalcitrant to automated identification because of their size and sequence complexity. We benchmarked RepeatModeler2 on three model species with diverse TE landscapes and high-quality, manually curated TE libraries: Drosophila melanogaster (fruit fly), Danio rerio (zebrafish), and Oryza sativa (rice). In these three species, RepeatModeler2 identified approximately 3 times more consensus sequences matching with >95% sequence identity and sequence coverage to the manually curated sequences than the original RepeatModeler. As expected, the greatest improvement is for LTR retroelements. Thus, RepeatModeler2 represents a valuable addition to the genome annotation toolkit that will enhance the identification and study of TEs in eukaryotic genome sequences. RepeatModeler2 is available as source code or a containerized package under an open license ( https://github.com/Dfam-consortium/RepeatModeler , http://www.repeatmasker.org/RepeatModeler/ ).

Citations

• The zebrafish reference genome sequence and its relationship to the human genome

Cited by

• Chromosome‐scale genome assembly of the endangered aquatic plant <i>Ottelia songmingensis</i> elucidates genomic features and conservation implications
• Genome Assembly of the Dyeing Poison Frog Provides Insights into the Dynamics of Transposable Element and Genome-Size Evolution
• Haplotype‐resolved chromosome‐level genome assembly of the endangered tree <i>Phoebe zhennan</i>
• Genome analysis of Channel millet reveals a wild dodecaploid shaped by environmental variability
• Ancient origin and dynamic evolution of bivalent spider toxins
• Haplotype-Resolved Genome of the Critically Endangered, Paleo-endemic Tree, <i>Eidothea hardeniana</i>
• From Adam's rib: the Siberian moth's female W chromosome is derived from its Z counterpart
• Chromosome‐Scale Haplotype Genome Assemblies for the Australian Mango ‘Kensington Pride’ and a Wild Relative, <i>Mangifera laurina</i> , Provide Insights Into Anthracnose‐Resistance and Volatile Compound Biosynthesis Genes
• Annotation of 200 Insect Genomes with BRAKER for Consistent Comparisons across Species
• Phylogeny of waterfowl (Anseriformes) constructed using genome sequences provides insights into topological incongruences
• Comparative Genomics of the Testacea Group of <i>Drosophila</i> Reveals Introgression and Variation in Chromosome Size and Structure
• Resolving the Stasis-Dynamism Paradox: Genome Evolution in Tree Ferns
• A Reference Genome for the Critically Endangered Philippine Eagle ( <i>Pithecophaga jefferyi</i> ), the National Bird of the Philippines
• The Nuclear and Mitochondrial Genomes of the Lined Rockskipper, <i>Istiblennius lineatus</i> (Teleostei: Blenniidae)
• Patterns and Processes of Genomic Evolution Inferred From the Ten Smallest Vertebrate Genomes
• A haplotype-resolved reference genome for <i>Eucalyptus grandis</i>
• Adaptive radiation and social evolution of the ants
• Genome assembly of <i>Bougainvillia</i> cf. <i>muscus</i> (Cnidaria: Hydrozoa)
• De Novo Whole Genome Assemblies of Unusual Case‐Making Caddisflies (Trichoptera) Highlight Genomic Convergence in the Composition of the Major Silk Gene ( <i>h‐fibroin</i> )
• Draft Genome Assembly of Root Knot Nematode, <i>Meloidogyne fallax</i>
• The genome of the Australian water dragon (<i>Intellagama lesueurii</i>), an agamid model for urban adaptation
• Differential Conservation and Loss of CR1 Retrotransposons in Squamates Reveals Lineage-Specific Genome Dynamics across Reptiles
• Genome evolution and introgression in the New Zealand mud snails <i>Potamopyrgus estuarinus</i> and <i>Potamopyrgus kaitunuparaoa</i>
• Two independent origins of XY sex chromosomes in <i>Asparagus</i>
• Arms races between selfish genetic elements and their host defence in termites
• Evaluating inbreeding and assessing the risk of outbreeding depression in genetic rescue using whole-genome sequence data
• The Golden Lancehead Genome Reveals Distinct Selective Processes Acting on Venom Genes of an Island Endemic Snake
• Anuran genome size evolution is driven by relatively recent retrotransposon activity and by life history
• Contrasting Genomic Trajectories of <i>Bartonellaceae</i> Symbionts of Planthoppers
• Genomic Features Underlying the Origin of Sociality and the Diversification of Caste Systems in Termites
• Nuclear and Mitochondrial Genome Assemblies of <i>Indrella ampulla</i> , a Terrestrial Gastropod Endemic to the Western Ghats
• Sugar beet long-read reference assembly of genotype KWS2320
• Genome of the parasitoid wasp <i>Dinocampus coccinellae</i> reveals extensive duplications, accelerated evolution, and independent origins of thelytokous parthenogeny and solitary behavior
• The Oryza australiensis genome reveals potential as a source of genes for rice improvement
• Comparative analysis of the mobilome yields new insights into its diversity, dynamics and evolution in parasites of the Trypanosomatidae family
• Comparative Genomics Reveals Intra and Inter Species Variation in the Pathogenic Fungus <i>Batrachochytrium dendrobatidis</i>
• The Genome of <scp><i>Lolium multiflorum</i></scp> Reveals the Genetic Architecture of Paraquat Resistance
• Subtelomeric repeat expansion in Hydractinia symbiolongicarpus chromosomes
• Selection on the vascular-remodeling <i>BMPER</i> gene is associated with altitudinal adaptation in an insular lizard
• The <i>Silene latifolia</i> genome and its giant Y chromosome
• Genomic signature of repeated transitions to diurnality in spiders
• Kingdom-wide evolutionary characterization of RNA editing factors in Archaeplastida
• Genome Scanning Reveals the Genetic Basis of a Color Pattern Morphotype in an Island Population of the European Adder ( <i>Vipera berus</i> )
• Retrotransposed gene copies persist under relaxed selection in wild <i>Spodoptera frugiperda</i>
• Chromosome‐level genome of the green odorous frog ( <i>Odorrana margaretae</i> ) provides insights into the evolution of transposable elements and olfaction‐related gene families in frogs
• Absence of the luciferase gene in the genome of the kleptoprotein bioluminescent fish Parapriacanthus ransonneti
• Chromosome-Scale Reference Genome Assemblies for Two <i>Anoplophora</i> Longhorned Beetle Species (Coleoptera: Cerambycidae)
• Ensembl 2022
• Targeted genetic manipulation and yeast-like evolutionary genomics in the green alga <i>Auxenochlorella</i>
• The genome of <i>Eleocharis vivipara</i> elucidates the genetics of C₃–C₄ photosynthetic plasticity and karyotype evolution in the Cyperaceae
• Chromosome-level genome assemblies and genetic maps reveal heterochiasmy and macrosynteny in endangered Atlantic Acropora
• An episodic burst of massive genomic rearrangements and the origin of non-marine annelids
• Earl Grey: A Fully Automated User-Friendly Transposable Element Annotation and Analysis Pipeline
• Repeated loss of function at HD mating-type genes and of recombination in anther-smut fungi
• The genome of a low‐seeded mandarin, Premier, displays major structural changes due to gamma irradiation
• EDTA-GUI: a plant-optimized graphical implementation of the EDTA pipeline enabling lineage-level classification and analysis
• Genome Variation in Three <i>Anthophora</i> Bee Species Reflects Divergent Demographic Histories
• A Field Guide to Eukaryotic Transposable Elements
• Coexisting Y haplotypes reveal cyclic sex chromosome differentiation around a shared sex-determining region
• Neo-sex Chromosomes Track the Mitochondrial Phylogeny and Exhibit an Extensive Added Stratum of Recombination Suppression in Honeyeaters (Aves: Meliphagidae)
• The nuclear and mitochondrial genomes of the bellicose bumblebee (<i>Bombus bellicosus</i>, Hymenoptera: Apidae), a threatened pollinator in a changing South American landscape
• Intraspecies sequence-graph analysis of the <i>Phytophthora theobromicola</i> genome reveals a dynamic structure and variable effector repertoires
• The cytonuclear interactions during grapevine domestication
• A high-quality reference genome for the Ural Owl (<i>Strix uralensis</i>) enables investigations of cell cultures as a genomic resource for endangered species
• Pooled, Long-read Sequencing for Structural Variant Characterization in Schistosome Populations
• Repeatome diversity in sea anemone genomics (Cnidaria: Actiniaria) based on the Actiniaria-REPlib library
• Systematic identification of cargo-mobilizing genetic elements reveals new dimensions of eukaryotic diversity
• Characterization of the transposable element landscape shaping the Ectocarpus genome
• Drought stress responses revealed by genomic and transcriptomic analyses of two macrofungi (Inonotus hispidus and Inocutis levis) from Populus euphratica
• Chromosome-Level Genome Assembly of the Asian Tramp Snail <i>Bradybaena similaris</i> (Stylommatophora: Camaenidae)
• A Segregating Structural Variant Defines Novel Venom Phenotypes in the Eastern Diamondback Rattlesnake
• Optimization and Evaluation of the <scp>bestRAD</scp> Sequencing Approach: Towards Ascertainment of the Invasion Routes of the Oriental Fruit Fly, <i>Bactrocera dorsalis</i>
• Recent neo-X and Y sex chromosomes in an ant cricket
• A Near Complete Genome Assembly of the Oshima Cherry Cerasus speciosa
• Demographic history of the Malayan tapirs ( <scp> <i>Tapirus indicus</i> </scp> ) in Southeast Asia
• Genome assembly variation and its implications for gene discovery in nematodes
• A <i>k-</i>mer-Based Approach for Phylogenetic Classification of Taxa in Environmental Genomic Data
• Long-Read–Based Genome Assembly Reveals Numerous Endogenous Viral Elements in the Green Algal Bacterivore <i>Cymbomonas tetramitiformis</i>
• Comprehensive profiling of insertion sequences and eukaryotic-like transposons across archaeal genomes
• nQuack: An R package for predicting ploidal level from sequence data using site‐based heterozygosity
• The Telomere-to-Telomere Genome and Lifestyle Transcriptome Profiling of <i>Discula destructiva</i> , the Causal Agent of Dogwood Anthracnose
• Big Spider, Big Genome: Chromosome-Level Genome of a North American Tarantula ( <i>Aphonopelma marxi</i> ) and Comparative Genomics Across 300 Million Years of Spider Evolution
• Genome Assembly of <i>Spinifex sericeus</i> Provides Insights into Repetitive Content and Haplotype Variation in a Dioecious Coastal Grass
• Genome Evolution and the Enigmatic Axial Skeleton of the Hero Shew (Soricidae: <i>Scutisorex Somereni</i> )
• <scp>RepeatOBserver</scp> : Tandem Repeat Visualisation and Putative Centromere Detection
• Chromosome-level reference genome of the beach false foxglove, <i>Agalinis fasciculata</i> (Orobanchaceae)
• Lifestyles shape genome size and gene content in fungal pathogens
• Three Novel Genomes Broaden the Wild Side of the <i>Capsicum</i> Pangenome
• Genetic basis for broad interspecific compatibility in <i>Solanum verrucosum</i>
• <scp> <i>detectEVE</i> </scp> : Fast, Sensitive and Precise Detection of Endogenous Viral Elements in Genomic Data
• Genomic insights into deleterious mutations and their impact on agronomic traits during pear domestication
• The complete genomes of two hybridizing field crickets, <i>Gryllus pennsylvanicus</i> and <i>Gryllus firmus</i>
• No silver bullet: Patterns of macrosynteny recapitulate systemic conflicts in the higher-level relationships of the arachnids
• FaNUDT19 contributes to 5′ cap quality control by modulating NAD+ capped RNA dynamics during strawberry fruit ripening
• Genome assembly and annotation of the olive grass mouse Abrothrix olivacea reveal transcriptomic and cellular adaptations across contrasting biomes
• Haplotype-resolved genomes of Phlebopus portentosus reveal nuclear differentiation, TE-mediated variation, and saprotrophic potential
• Genomic Patterns of Loss of Distyly and Polyploidization in Primroses
• Comparative Genomics of <i>Chloropicon primus</i> and <i>Chloropicon roscoffensis</i> Provide Insights into the Evolutionary Dynamics and Ecological Success of These Tiny Green Algae in Marine Environments
• The Genome of <i>Apera spica-venti</i>: A Major Grass Weed
• Genome assembly of the endangered Santa Marta Harlequin Toad, <i>Atelopus laetissimus</i> , endemic to the Sierra Nevada de Santa Marta of Colombia
• A phased chromosome-level genome of the annelid tubeworm <i>Galeolaria caespitosa</i>
• <scp> <i>FHY3/FAR1</i> </scp> transposable elements generate adaptive genetic variation in the <scp> <i>Bassia scoparia</i> </scp> genome
• Insights into longhorn beetle (Cerambycidae) evolution from comparative analyses of the red-headed ash borer (<i>Neoclytus acuminatus acuminatus</i>) genome
• Three new Pseudogymnoascus species (Pseudeurotiaceae, Thelebolales) described from Antarctic soils
• Single specimen genome assembly of Culicoides stellifer shows evidence of a non-retroviral endogenous viral element
• Genomics, Population Divergence, and Historical Demography of the World's Largest and Endangered Butterfly, The Queen Alexandra's Birdwing
• Genomic basis of adaptation to serpentine soil in two <i>Alyssum</i> species shows convergence with <i>Arabidopsis</i> across 20 million years of divergence
• Atypical epigenetic and small RNA control of degenerated transposons and their fragments in clonally reproducing <i>Spirodela polyrhiza</i>
• The genome of the sapphire damselfish Chrysiptera cyanea: a new resource to support further investigation of the evolution of Pomacentrids
• The chromosome-level genome assembly of the red swamp crayfish Procambarus clarkii
• Tiberius: End-to-End Deep Learning with an HMM for Gene Prediction
• Effective Purging and Conservation of Heterozygous Regions During Independent Evolution to High‐Level Inbreeding in Wild Paradise Fishes
• Transposable element accumulation drives genome size increase in <i>Hylesia metabus</i> (Lepidoptera: Saturniidae), an urticating moth species from South America
• Distinct genomic routes underlie transitions to specialised symbiotic lifestyles in deep-sea annelid worms
• Comparative Genomics Provide Insight Into the Evolution of European <i>Aphanomyces euteiches</i> Strains
• Conspecific Scaffold‐Level Genome Assembly Outperforms Heterospecific Chromosome‐Level Assemblies for Assessing Genetic Indicators in a Threatened Marine Fish
• The telomere-to-telomere (T2T) genome of <i>Peucedanum praeruptorum</i> Dunn provides insights into the genome evolution and coumarin biosynthesis
• Draft genome of <i>Neofabraea vagabunda</i> , the agent of bull's eye rot
• Chromosome-level genome assembly and methylome profile yield insights for the conservation of endangered loggerhead sea turtles
• Spread of a Single Superclone Drives Insecticide Resistance in <i>Acyrthosiphon kondoi</i> Across an Invasive Range
• Episodic and Ongoing Mechanisms Drive Plastid-Derived Nuclear DNA Evolution in Angiosperms
• Origin and de novo domestication of sweet orange
• Global changes in alternative splicing are associated with insecticide response and resistance
• Chromosome-level genome assembly and annotation of the transverse lady beetle <i>Coccinella transversoguttata</i>
• Two chromosome-scale genomes of wild <i>Aedes aegypti aegypti</i> mosquitoes from North America and South-East Asia
• Long-read de novo assembly of the spekboom (Portulacaria afra) genome
• Chromosome-scale genomes of two wild flowering cherrys ( <i>Cerasus itosakura</i> and <i>C. jamasakura</i> ) provide insights into structural evolution in <i>Prunus</i>
• Chromosome level assembly and annotation of <i>Cuscuta campestris</i> Yunck. (“field dodder”), a model parasitic plant
• Genome assembly of the Antipodean and Gibson’s albatrosses ( <i>Diomedea antipodensis antipodensis</i> and <i>D. a. gibsoni</i> )
• The telomere-to-telomere gapless genome of grass carp provides insights for genetic improvement
• Functional and evolutionary insights into chemosensation and specialized herbivory from the genome of the red milkweed beetle, <i>Tetraopes tetrophthalmus</i> (Cerambycidae: Lamiinae)
• Chromosome-level reference genome for the medically important Arabian horned viper ( <i>Cerastes gasperettii</i> )
• Three novel genomes broaden the wild side of the <i>Capsicum</i> pangenome
• Telomere-to-telomere genome of common bean (<i>Phaseolus vulgaris</i> L., YP4)
• Genomic and <i>Cis</i> ‐Regulatory Basis of a Plastic C ₃ ‐C ₄ Photosynthesis in <i>Eleocharis Baldwinii</i>
• Chromosomal fusions reshape gene expression and environmental responses in <i>Corbicula</i> Clams
• A Chromosome-scale Genome Assembly of <i>Meloidogyne hapla</i> Reveals Localized Recombination Hotspots Enriched with Effector Proteins
• Gag proteins encoded by endogenous retroviruses are required for zebrafish development
• A chromosome-level genome assembly of the Chinese herring ( <i>Ilisha elongata</i> ) uncovered its population dynamics and genes related to lipid metabolism
• Multiomics Reveal Associations Between CpG Methylation, Histone Modifications and Transcription in a Species That has Lost DNMT3, the Colorado Potato Beetle
• Distinct genomic contexts predict gene presence–absence variation in different pathotypes of <i>Magnaporthe oryzae</i>
• The molecular basis of octocoral calcification revealed by genome and skeletal proteome analyses
• De novo genome assembly of a Geomyid rodent, Botta’s pocket gopher (<i>Thomomys bottae bottae</i>)
• Genomic and transcriptomic analyses of <i>Heteropoda venatoria</i> reveal the expansion of P450 family for starvation resistance in spiders
• Genome assembly and annotation of Acropora pulchra from Mo’orea French Polynesia
• Phylogenomics and adaptive evolution of the Colletotrichum gloeosporioides species complex
• Insights into the evolution and mechanisms of response to heat stress by whole genome sequencing and comparative proteomics analysis of the domesticated edible mushroom <i>Lepista sordida</i>
• First reference genomes for two mesophotic, reef-building coral species: <i>Leptoseris</i> cf. <i>scabra</i> and <i>Montipora</i> cf. <i>grisea</i>
• Evaluating the Benefits and Limits of Multiple Displacement Amplification With Whole‐Genome Oxford Nanopore Sequencing
• Sequencing a botanical monument: a chromosome-level assembly of the 400-year-old Goethe’s Palm ( <i>Chamaerops humilis</i> L.) at the Botanical Garden of the University of Padua (Italy)
• IMA GENOME - F20 A draft genome assembly of Agroathelia rolfsii, Ceratobasidium papillatum, Pyrenopeziza brassicae, Neopestalotiopsis macadamiae, Sphaerellopsis filum and genomic resources for Colletotrichum spaethianum and Colletotrichum fructicola
• Complexity of the lichen symbiosis revealed by metagenome and transcriptome analysis of Xanthoria parietina
• Chromosome‐level assemblies of <i>Amaranthus palmeri</i>, <i>Amaranthus retroflexus</i>, and <i>Amaranthus hybridus</i> allow for genomic comparisons and identification of a sex‐determining region
• Enhancing inbreeding estimation and global conservation insights through chromosome-level assemblies of the Chinese and Malayan pangolin
• Secrets of the Goo: The genome assembly of the Pacific banana slug, <i>Ariolimax columbianus</i>
• Grapevine pangenome facilitates trait genetics and genomic breeding
• Unexpectedly low recombination rates and presence of hotspots in termite genomes
• A high-quality chromosomal genome assembly of the sea cucumber <i>Chiridota heheva</i> and its hydrothermal adaptation
• A reference genome for ecological restoration of the sunflower sea star, <i>Pycnopodia helianthoides</i>
• Gapless Genome Assembly of Puccinia triticina Provides Insights into Chromosome Evolution in Pucciniales
• Haplotype-resolved assemblies provide insights into genomic makeup of the oldest grapevine cultivar (Munage) in China
• Rapid mid-Cretaceous diversification of squid and cuttlefish preceded radiation into coastal niches
• Comprehensive re-assembly and annotation dataset for the argan tree (Argania spinosa L., Sapotaceae) genome
• The Genome of <i>Pseudocercospora cladosporioides</i> : A Step Toward Understanding Olive Cercosporiosis
• RNA-sequencing Analysis of Hybrid Females Reveals a Dominance of Expression of Alleles From Outcrossing Species Over Those From Selfing Species
• Comparative Transcriptomics Reveals an Extracellular Worm Argonaute as an Ancestral Regulator of LTR Retrotransposons
• A transposon DNA/hAT-Ac insertion promotes the formation of yellow tepals in lotus (Nelumbo)
• Whole genome sequencing and assembly of the house sparrow, Passer domesticus
• Phylogenomics and the evolutionary history of the Oxyurida (pinworms)
• Draft Genome of <i>Entamoeba marina</i> Provides Insights Into the Attenuation of Pathogenicity and Adaptation to the Marine Environment
• Landscape of Somatic and Age‐Related Pathogenic Structural Variations in Hepatocellular Carcinoma Revealed by Long‐Read Sequencing
• Genome Assembly of Gangetic Dolphin ( <i>Platanista gangetica</i> ) Reveals Signature of Regressive Evolution
• A high-quality genome assembly and integrative data portal ( <i>Phabase</i> ) for the Mesoamerican black bean ( <i>Phaseolus vulgaris</i> cv. Negro Jamapa)
• Genome assembly of <i>Spinifex sericeus</i> provides insights into repetitive content and haplotype variation in a dioecious coastal grass
• A wild genome of the underutilized legume lablab ( <i>Lablab purpureus</i> ) reveals the genetic basis of domestication
• MycoMobilome: A community-focused non-redundant database of transposable element consensus sequences for the fungal kingdom
• Lifestyles shape genome size and gene content in fungal pathogens
• Arms races between selfish genetic elements and their host defence
• Structure and sequence evolution in the pennycress ( <i>Thlaspi arvense</i> ) pangenome
• Telomere to telomere flax (<i>Linum usitatissimum</i> L.) genome assembly unlocks insights beyond fatty acid metabolism pathways
• Domestication shaped the chromatin landscape of grain amaranth
• Chromosome-level genome assembly of the sacoglossan sea slug <i>Elysia atroviridis</i>
• The genome assembly of <i>Sphaerospora molnari</i> provides novel insights into the rapid evolution and diversification of unique lineage-specific gene groups in myxozoan parasites
• A pseudochromosomal reference genome of the golden jackal, <i>Canis aureus</i>
• A chromosome-level genome assembly for snowshoe hare ( <i>Lepus americanus</i> )
• Chromosome-Scale Genome Assemblies of Duckweeds Provide Insights Into Genomic Plasticity, Aquatic Adaptation, and Morphological Reduction

Related

• Earl Grey: A Fully Automated User-Friendly Transposable Element Annotation and Analysis Pipeline
• Terrier: A Deep Learning Repeat Classifier
• TE_Bench: a foundational benchmarking workflow for transposable element annotation pipelines
• The Dfam community resource of transposable element families, sequence models, and genome annotations
• A reference-free pipeline for detecting shared transposable elements from pan-genomes to retrace their dynamics in a species