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De Novo Assembly and Annotation of the Asian Tiger Mosquito (Aedes albopictus) Repeatome with dnaPipeTE from Raw Genomic Reads and Comparative Analysis with the Yellow Fever Mosquito (Aedes aegypti)

https://doi.org/10.1093/gbe/evv050
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1007/bf00224239openalex-snapshot
Intraspecific variation in nuclear DNA content among world populations of a mosquito, Aedes albopictus (Skuse)
inferredcites →https://doi.org/10.1016/j.cell.2008.09.022openalex-snapshot
Retrotransposons Revisited: The Restraint and Rehabilitation of Parasites
inferredcites →https://doi.org/10.1016/j.gene.2010.01.003openalex-snapshot
Jumping genes and epigenetics: Towards new species
inferredcites →https://doi.org/10.1016/j.gene.2010.11.009openalex-snapshot
Comparative analysis of transposable elements in the melanogaster subgroup sequenced genomes
inferredcites →https://doi.org/10.1016/j.gene.2012.07.042openalex-snapshot
The impact of transposable elements on eukaryotic genomes: From genome size increase to genetic adaptation to stressful environments
inferredcites →https://doi.org/10.1016/j.pt.2013.07.003openalex-snapshot
The invasive mosquito species Aedes albopictus: current knowledge and future perspectives
inferredcites →https://doi.org/10.1016/j.tig.2009.05.003openalex-snapshot
Dynamics of transposable elements: towards a community ecology of the genome
inferredcites →https://doi.org/10.1016/s0022-2836(05)80360-2openalex-snapshot
Basic Local Alignment Search Tool
inferredcites →https://doi.org/10.1017/s0016672300024289openalex-snapshot
Genome evolution in mosquitoes: intraspecific and interspecific variation in repetitive DNA amounts and organization
inferredcites →https://doi.org/10.1017/s0016672305007627openalex-snapshot
Phylogeography of Aedes ( Stegomyia ) aegypti (L.) and Aedes ( Stegomyia ) albopictus (Skuse) (Diptera: Culicidae) based on mitochondrial DNA variations
inferredcites →https://doi.org/10.1038/hdy.1987.120openalex-snapshot
Inter and intraspecific variation in nuclear DNA content in Aedes mosquitoes
inferredcites →https://doi.org/10.1038/hdy.1987.65openalex-snapshot
Intraspecific and interspecific variation in the sequence and abundance of highly repeated DNA among mosquitoes of the Aedes albopictus subgroup
inferredcites →https://doi.org/10.1038/hdy.1988.29openalex-snapshot
Breeding structure of a colonising species: Aedes albopictus (Skuse) in the United States
inferredcites →https://doi.org/10.1038/nbt.1883openalex-snapshot
Full-length transcriptome assembly from RNA-Seq data without a reference genome
inferredcites →https://doi.org/10.1038/nmeth.1923openalex-snapshot
Fast gapped-read alignment with Bowtie 2
inferredcites →https://doi.org/10.1038/nrg2165openalex-snapshot
A unified classification system for eukaryotic transposable elements
inferredcites →https://doi.org/10.1051/jbio/2004198040413openalex-snapshot
L’influence des éléments transposables sur la taille des génomes
inferredcites →https://doi.org/10.1073/pnas.0732024100openalex-snapshot
Molecular paleontology of transposable elements in the Drosophila melanogaster genome
inferredcites →https://doi.org/10.1093/aesa/76.3.388openalex-snapshot
Comparison of Allozyme and Morphological Relationships in Some Aedes (Stegomyia) Mosquitoes (Diptera: Culicidae)
inferredcites →https://doi.org/10.1093/bioinformatics/btl158openalex-snapshot
Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences
inferredcites →https://doi.org/10.1093/bioinformatics/btu365openalex-snapshot
Tedna: a transposable element de novo assembler
inferredcites →https://doi.org/10.1093/molbev/msg189openalex-snapshot
Non-LTR Retrotransposons in the African Malaria Mosquito, Anopheles gambiae: Unprecedented Diversity and Evidence of Recent Activity
inferredcites →https://doi.org/10.1093/nar/gkp1137openalex-snapshot
The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants
inferredcites →https://doi.org/10.1093/nar/gkt484openalex-snapshot
The Genome of Anopheles darlingi , the main neotropical malaria vector
inferredcites →https://doi.org/10.1093/nar/gku210openalex-snapshot
RepARK—de novo creation of repeat libraries from whole-genome NGS reads
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a025989openalex-snapshot
Structural, genomic, and phylogenetic analysis of Lian, a novel family of non-LTR retrotransposons in the yellow fever mosquito, Aedes aegypti
inferredcites →https://doi.org/10.1101/gr.074492.107openalex-snapshot
Velvet: Algorithms for de novo short read assembly using de Bruijn graphs
inferredcites →https://doi.org/10.1101/gr.9.9.868openalex-snapshot
CAP3: A DNA Sequence Assembly Program
inferredcites →https://doi.org/10.1111/brv.12017openalex-snapshot
Distinguishing ecological from evolutionary approaches to transposable elements
inferredcites →https://doi.org/10.1111/evo.12281openalex-snapshot
HUMAN IMPACTS HAVE SHAPED HISTORICAL AND RECENT EVOLUTION IN AEDES AEGYPTI , THE DENGUE AND YELLOW FEVER MOSQUITO
inferredcites →https://doi.org/10.1111/j.1365-313x.2012.05072.xopenalex-snapshot
The sunflower (Helianthus annuus L.) genome reflects a recent history of biased accumulation of transposable elements
inferredcites →https://doi.org/10.1111/mec.12170openalex-snapshot
The impact of transposable elements in environmental adaptation
inferredcites →https://doi.org/10.1111/mec.12925openalex-snapshot
Human‐aided and natural dispersal drive gene flow across the range of an invasive mosquito
inferredcites →https://doi.org/10.1126/science.1076181openalex-snapshot
The Genome Sequence of the Malaria Mosquito Anopheles gambiae
inferredcites →https://doi.org/10.1126/science.1138878openalex-snapshot
Genome Sequence of Aedes aegypti , a Major Arbovirus Vector
inferredcites →https://doi.org/10.1146/annurev-genom-082509-141802openalex-snapshot
LINE-1 Elements in Structural Variation and Disease
inferredcites →https://doi.org/10.1159/000084979openalex-snapshot
Repbase Update, a database of eukaryotic repetitive elements
inferredcites →https://doi.org/10.1159/000084983openalex-snapshot
Transposable elements in mosquitoes
inferredcites →https://doi.org/10.1186/1471-2105-11-378openalex-snapshot
Graph-based clustering and characterization of repetitive sequences in next-generation sequencing data
inferredcites →https://doi.org/10.1186/1471-2164-12-606openalex-snapshot
The mosquito Aedes aegypti has a large genome size and high transposable element load but contains a low proportion of transposon-specific piRNAs
inferredcites →https://doi.org/10.1186/1471-2164-15-42openalex-snapshot
Genome sequence of Anopheles sinensis provides insight into genetics basis of mosquito competence for malaria parasites
inferredcites →https://doi.org/10.1186/1745-6150-6-44openalex-snapshot
Families of transposable elements, population structure and the origin of species
inferredcites →https://doi.org/10.1371/journal.pone.0088992openalex-snapshot
A Genome-Wide Survey of Genetic Instability by Transposition in Drosophila Hybrids
inferredcites →https://doi.org/10.1603/me09154openalex-snapshot
Dispersal and Survival of Aedes albopictus (Diptera: Culicidae) Males in Italian Urban Areas and Significance for Sterile Insect Technique Application

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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Repetitive Element Expansions Contribute to Genome Size Gigantism in Pamphagidae (Orthoptera: Acridoidea)
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Analyzing Horizontal Transfer of Transposable Elements on a Large Scale: Challenges and Prospects
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Finding and Characterizing Repeats in Plant Genomes
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Assembly-Free Detection and Quantification of Transposable Elements with dnaPipeTE
inferred← citeshttps://doi.org/10.1007/978-1-0716-4583-3_5openalex-snapshot
A Concise Guide for the Characterization and Curation of Transposable Elements in Insect Genomes
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Transposable Elements: Classification, Identification, and Their Use As a Tool For Comparative Genomics
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A step forward in the genome characterization of the sugarcane borer, Diatraea saccharalis: karyotype analysis, sex chromosome system and repetitive DNAs through a cytogenomic approach
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Diverse mobilome of Dichotomius (Luederwaldtinia) schiffleri (Coleoptera: Scarabaeidae) reveals long-range horizontal transfer events of DNA transposons
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Evaluation of non-invasive dsRNA delivery methods for the development of RNA interference in the Asian tiger mosquito Aedes albopictus
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Genomic population structure and diversity of the endangered Aphanius iberus: strategies for killifish conservation
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Nuclear genome annotation of wheel animals and thorny-headed worms: inferences about the last common ancestor of Syndermata (Rotifera s.l.)
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inferred← citeshttps://doi.org/10.1016/b978-0-12-809633-8.20227-6openalex-snapshot
Repeat in Genomes: How and Why You Should Consider Them in Genome Analyses?
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The genomic and cellular basis of biosynthetic innovation in rove beetles
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Comprehensive Chromosome End Remodeling during Programmed DNA Elimination
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Chromosome fusion and programmed DNA elimination shape karyotypes of nematodes
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The dynamics of transposable element content in the genome of the human pathogen Histoplasma
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Low coverage sequencing provides insights into the key features of the nuclear and mitochondrial genomes of the Alligator Snapping Turtle Macrochelys temminckii
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Mobilome characterization of the beetle Euchroma gigantea (Buprestidae) uncovers multiple long range Tc1-Mariner horizontal transfer events
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Gigantic Genomes Provide Empirical Tests of Transposable Element Dynamics Models
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Contribution of the satellitome to the exceptionally large genome of dinoflagellates: The case of the harmful alga Alexandrium minutum
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Genetic diversity and distribution differ between long-established and recently introduced populations in the invasive mosquito Aedes albopictus
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The untapped potential of short-read sequencing in biodiversity research
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Variations in genome size between wild and domesticated lineages of fowls belonging to the Gallus gallus species
inferred← citeshttps://doi.org/10.1016/j.ygeno.2024.110896openalex-snapshot
Repetitive element expansions contribute to genome size gigantism in Pamphagidae: A comparative study (Orthoptera, Acridoidea)
inferred← citeshttps://doi.org/10.1038/hdy.2016.35openalex-snapshot
Population genetics of the Asian tiger mosquito Aedes albopictus, an invasive vector of human diseases
inferred← citeshttps://doi.org/10.1038/s41437-020-0327-7openalex-snapshot
High dynamism for neo-sex chromosomes: satellite DNAs reveal complex evolution in a grasshopper
inferred← citeshttps://doi.org/10.1038/s41437-021-00470-5openalex-snapshot
Out of patterns, the euchromatic B chromosome of the grasshopper Abracris flavolineata is not enriched in high-copy repeats
inferred← citeshttps://doi.org/10.1038/s41467-022-28482-7openalex-snapshot
Small RNA pathways in the nematode Ascaris in the absence of piRNAs
inferred← citeshttps://doi.org/10.1038/s41467-024-50239-7openalex-snapshot
Ecological genomics in the Northern krill uncovers loci for local adaptation across ocean basins
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Interspecies association mapping links reduced CG to TG substitution rates to the loss of gene-body methylation
inferred← citeshttps://doi.org/10.1038/s41576-018-0050-xopenalex-snapshot
Computational tools to unmask transposable elements
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Global analysis of repetitive DNA from unassembled sequence reads using RepeatExplorer2
inferred← citeshttps://doi.org/10.1038/s41597-019-0017-6openalex-snapshot
The survey and reference assisted assembly of the Octopus vulgaris genome
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Evolutionary dynamics of repetitive elements and genome size in Tetrigidae (Orthoptera: Caelifera)
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DNA gains and losses in gigantic genomes do not track differences in transposable element-host silencing interactions
inferred← citeshttps://doi.org/10.1073/pnas.1910106116openalex-snapshot
Expansion of a single transposable element family is associated with genome-size increase and radiation in the genus Hydra
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A bird-like genome from a frog: Mechanisms of genome size reduction in the ornate burrowing frog, Platyplectrum ornatum
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Genomic divergence of the Italian drywood termites Kalotermes italicus and K. flavicollis (Blattodea Kalotermitidae): insights from genome skimming
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Genome-wide codon usage profiling of ocular infectiveChlamydia trachomatisserovars and drug target identification
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Endogenous non-retroviral elements in genomes of Aedes mosquitoes and vector competence
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Life without a Sporophyte: The Origin and Genomic Consequences of Asexual Reproduction in a Gametophyte-Only Fern
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Consistent accumulation of transposable elements in species of the Hawaiian Tetragnatha spiny-leg adaptive radiation across the archipelago chronosequence
inferred← citeshttps://doi.org/10.1093/g3journal/jkab050openalex-snapshot
Rapid divergence of the male reproductive proteins in the Drosophila dunni group and implications for postmating incompatibilities between species
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Genome size evolution in the beetle genus Diabrotica
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Comparative Analysis of Genomic Repeat Content in Gomphocerine Grasshoppers Reveals Expansion of Satellite DNA and Helitrons in Species with Unusually Large Genomes
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The Transposable Elements of the Drosophila serrata Reference Panel
inferred← citeshttps://doi.org/10.1093/gbe/evab255openalex-snapshot
Comparative Population Genomics of Cryptic Speciation and Adaptive Divergence in Bicknell’s and Gray-Cheeked Thrushes (Aves: Catharus bicknelli and Catharus minimus )
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Genome Evolution and Introgression in the New Zealand mud Snails Potamopyrgus estuarinus and Potamopyrgus kaitunuparaoa
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Genetic Variation in Jamaican Populations of the Coffee Berry Borer, Hypothenemus hampei
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inferred← citeshttps://doi.org/10.1093/gbe/evx032openalex-snapshot
An Annotated Draft Genome for Radix auricularia (Gastropoda, Mollusca)
inferred← citeshttps://doi.org/10.1093/gbe/evx091openalex-snapshot
Transposable Element Misregulation Is Linked to the Divergence between Parental piRNA Pathways in Drosophila Hybrids
inferred← citeshttps://doi.org/10.1093/gbe/evx163openalex-snapshot
Rapid Increase in Genome Size as a Consequence of Transposable Element Hyperactivity in Wood-White (Leptidea) Butterflies
inferred← citeshttps://doi.org/10.1093/gbe/evy184openalex-snapshot
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Heterochromatin-based silencing of a foreign tandem repeat in Drosophila melanogaster shows unusual biochemistry and temperature sensitivity
inferred← citeshttps://doi.org/10.1093/gigascience/giac011openalex-snapshot
Genome size evolution in the diverse insect order Trichoptera
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Analysis of the Aedes albopictus C6/36 genome provides insight into cell line utility for viral propagation
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Leveraging Short-Read Sequencing to Explore the Genomics of Sepiolid Squid
inferred← citeshttps://doi.org/10.1093/jhered/esaa031openalex-snapshot
Genomic Features of Parthenogenetic Animals
inferred← citeshttps://doi.org/10.1093/jhered/esab032openalex-snapshot
A Chromosome-Level Genome Assembly of the Parasitoid Wasp,Cotesia glomerata(Hymenoptera: Braconidae)
inferred← citeshttps://doi.org/10.1093/molbev/msaa030openalex-snapshot
A Behavior-Manipulating Virus Relative as a Source of Adaptive Genes forDrosophilaParasitoids
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The Drosophila Y Chromosome Affects Heterochromatin Integrity Genome-Wide
inferred← citeshttps://doi.org/10.1093/molbev/msaf111openalex-snapshot
Relaxed Purifying Selection is Associated with an Accumulation of Transposable Elements in Flies
inferred← citeshttps://doi.org/10.1093/molbev/msag051openalex-snapshot
Intraspecific genome size variation is attributed to adaptive silencing of transposable elements in Hordeum species
inferred← citeshttps://doi.org/10.1093/molbev/msy236openalex-snapshot
Degenerative Expansion of a Young Supergene
inferred← citeshttps://doi.org/10.1093/molbev/msz059openalex-snapshot
The Genome of Drosophila innubila Reveals Lineage-Specific Patterns of Selection in Immune Genes
inferred← citeshttps://doi.org/10.1093/nar/gkw953openalex-snapshot
TEtools facilitates big data expression analysis of transposable elements and reveals an antagonism between their activity and that of piRNA genes
inferred← citeshttps://doi.org/10.1098/rsbl.2016.0407openalex-snapshot
Strong phylogenetic inertia on genome size and transposable element content among 26 species of flies
inferred← citeshttps://doi.org/10.1098/rspb.2020.1441openalex-snapshot
Genome size evolution: towards new model systems for old questions
inferred← citeshttps://doi.org/10.1101/049197openalex-snapshot
High-Throughput Sequencing of Transposable Element Insertions Suggests Adaptive Evolution of the Invasive Asian Tiger Mosquito Towards Temperate Environments
inferred← citeshttps://doi.org/10.1101/2020.11.22.393231openalex-snapshot
Uncovering transposable element variants and their potential adaptive impact in urban populations of the malaria vector Anopheles coluzzii
inferred← citeshttps://doi.org/10.1101/2020.11.22.393231v1openalex-snapshot
Impact of transposable elements on the genome of the urban malaria vector Anopheles coluzzii
inferred← citeshttps://doi.org/10.1101/2021.03.14.435331openalex-snapshot
Ecological correlates of gene family size in a pine-feeding sawfly genome and across Hymenoptera
inferred← citeshttps://doi.org/10.1101/2021.06.02.446622openalex-snapshot
Transposable element accumulation drives size differences among polymorphic Y chromosomes in Drosophila
inferred← citeshttps://doi.org/10.1101/2022.06.02.494618openalex-snapshot
600+ insect genomes reveal repetitive element dynamics and highlight biodiversity-scale repeat annotation challenges
inferred← citeshttps://doi.org/10.1101/2022.07.21.500944openalex-snapshot
TrEMOLO: Accurate transposable element allele frequency estimation using long-read sequencing data combining assembly and mapping-based approaches
inferred← citeshttps://doi.org/10.1101/2023.12.21.572835openalex-snapshot
Chromosome fusion and programmed DNA elimination shape karyotypes of parasitic nematodes
inferred← citeshttps://doi.org/10.1101/2024.01.03.574070openalex-snapshot
Consistent accumulation of transposable elements in species of the Hawaiian Tetragnatha spiny-leg adaptive radiation across the archipelago chronosequence
inferred← citeshttps://doi.org/10.1101/2024.07.22.604708openalex-snapshot
Size evolution of gigantic genomes suggests stochastic outcomes of transposable element/host silencing interactions
inferred← citeshttps://doi.org/10.1101/2024.09.30.614436openalex-snapshot
Genomic stability in the Galápagos Scalesia adaptive radiation: Consistent transposable element accumulation despite hybridization and ecological niche shifts
inferred← citeshttps://doi.org/10.1101/2025.01.10.632341openalex-snapshot
Manual versus automatic annotation of transposable elements: case studies in Drosophila melanogaster and Aedes albopictus , balancing accuracy and biological relevance
inferred← citeshttps://doi.org/10.1101/2025.09.26.678839openalex-snapshot
Genome size variation is attributed to adaptive purging of transposable elements
inferred← citeshttps://doi.org/10.1101/497495openalex-snapshot
Genomic features of parthenogenetic animals
inferred← citeshttps://doi.org/10.1101/gr.275761.121openalex-snapshot
Transposable element variants and their potential adaptive impact in urban populations of the malaria vector Anopheles coluzzii
inferred← citeshttps://doi.org/10.1101/gr.275996.121openalex-snapshot
Transposable element accumulation drives size differences among polymorphic Y Chromosomes in Drosophila
inferred← citeshttps://doi.org/10.1101/gr.277387.122openalex-snapshot
Analyses of 600+ insect genomes reveal repetitive element dynamics and highlight biodiversity-scale repeat annotation challenges
inferred← citeshttps://doi.org/10.1101/gr.277966.123openalex-snapshot
Transposable elements drive the evolution of metazoan zinc finger genes
inferred← citeshttps://doi.org/10.1111/1365-2435.13317openalex-snapshot
Biological invasion: The influence of the hidden side of the (epi)genome
inferred← citeshttps://doi.org/10.1111/1744-7917.70276openalex-snapshot
Coevolutionary interactions between transposable elements and host silencing factors in genome gigantism of Caeliferans (Orthoptera)
inferred← citeshttps://doi.org/10.1111/1755-0998.13030openalex-snapshot
DeviaTE: Assembly‐free analysis and visualization of mobile genetic element composition
inferred← citeshttps://doi.org/10.1111/1755-0998.13080openalex-snapshot
TERAD: Extraction of transposable element composition from RADseq data
inferred← citeshttps://doi.org/10.1111/1755-0998.13305openalex-snapshot
RepeatProfiler: A pipeline for visualization and comparative analysis of repetitive DNA profiles
inferred← citeshttps://doi.org/10.1111/evo.14287openalex-snapshot
Cytogenomic analysis unveils mixed molecular evolution and recurrent chromosomal rearrangements shaping the multigene families onSchistocercagrasshopper genomes
inferred← citeshttps://doi.org/10.1111/imb.12599openalex-snapshot
Insect genomes: progress and challenges
inferred← citeshttps://doi.org/10.1111/imb.13013openalex-snapshot
A new piece in the repeatome puzzle of Triatominae bugs: The analysis of Triatoma rubrofasciata reveals the role of satellite DNAs in the karyotypic evolution of distinct lineages
inferred← citeshttps://doi.org/10.1111/mec.14184openalex-snapshot
High‐throughput sequencing of transposable element insertions suggests adaptive evolution of the invasive Asian tiger mosquito towards temperate environments
inferred← citeshttps://doi.org/10.1111/mec.14963openalex-snapshot
Population‐specific dynamics and selection patterns of transposable element insertions in European natural populations
inferred← citeshttps://doi.org/10.1111/mec.16099openalex-snapshot
Transposable elements and introgression introduce genetic variation in the invasive ant Cardiocondyla obscurior
inferred← citeshttps://doi.org/10.1111/mec.17567openalex-snapshot
Orthopteran Neo‐Sex Chromosomes Reveal Dynamics of Recombination Suppression and Evolution of Supergenes
inferred← citeshttps://doi.org/10.1111/mve.70040openalex-snapshot
Transposable elements in the transcriptome of Aedes (Stegomyia) aegypti (Linnaeus, 1762)
inferred← citeshttps://doi.org/10.1111/nph.15715openalex-snapshot
Adding color to a century‐old enigma: multi‐color chromosome identification unravels the autotriploid nature of saffron ( Crocus sativus ) as a hybrid of wild Crocus cartwrightianus cytotypes
inferred← citeshttps://doi.org/10.1111/pbi.14570openalex-snapshot
Deciphering recent transposition patterns in plants through comparison of 811 genome assemblies
inferred← citeshttps://doi.org/10.1111/syen.12629openalex-snapshot
Evolutionary dynamics of genome size and transposable elements in crickets ( Ensifera: Gryllidea )
inferred← citeshttps://doi.org/10.1111/tpj.14705openalex-snapshot
Satellite DNA landscapes after allotetraploidization of quinoa ( Chenopodium quinoa ) reveal unique A and B subgenomes
inferred← citeshttps://doi.org/10.1126/sciadv.abg3842openalex-snapshot
Convergent consequences of parthenogenesis on stick insect genomes
inferred← citeshttps://doi.org/10.1126/sciadv.adj6823openalex-snapshot
A nuclear genome assembly of an extinct flightless bird, the little bush moa
inferred← citeshttps://doi.org/10.1126/science.aau0099openalex-snapshot
Males as somatic investment in a parthenogenetic nematode
inferred← citeshttps://doi.org/10.1134/s1022795421110156openalex-snapshot
Phenotypically Unstable Mutations as Markers of Chromosomal Rearrangements Involving DNA Transposons
inferred← citeshttps://doi.org/10.1179/2047773215y.0000000031openalex-snapshot
A draft genome sequence of an invasive mosquito: an ItalianAedes albopictus
inferred← citeshttps://doi.org/10.1186/s12711-023-00821-2openalex-snapshot
Taming transposable elements in livestock and poultry: a review of their roles and applications
inferred← citeshttps://doi.org/10.1186/s12864-018-4763-1openalex-snapshot
A transposable element annotation pipeline and expression analysis reveal potentially active elements in the microalga Tisochrysis lutea
inferred← citeshttps://doi.org/10.1186/s12864-018-5200-1openalex-snapshot
Mollusc genomes reveal variability in patterns of LTR-retrotransposons dynamics
inferred← citeshttps://doi.org/10.1186/s12864-019-5859-yopenalex-snapshot
Small, but surprisingly repetitive genomes: transposon expansion and not polyploidy has driven a doubling in genome size in a metazoan species complex
inferred← citeshttps://doi.org/10.1186/s12864-020-6764-0openalex-snapshot
Functional insights from the GC-poor genomes of two aphid parasitoids, Aphidius ervi and Lysiphlebus fabarum
inferred← citeshttps://doi.org/10.1186/s12864-021-07700-4openalex-snapshot
Historical genomics reveals the evolutionary mechanisms behind multiple outbreaks of the host-specific coffee wilt pathogen Fusarium xylarioides
inferred← citeshttps://doi.org/10.1186/s12864-021-07857-yopenalex-snapshot
Genomics and transcriptomics of epizoic Seisonidea (Rotifera, syn. Syndermata) reveal strain formation and gradual gene loss with growing ties to the host
inferred← citeshttps://doi.org/10.1186/s12864-023-09953-7openalex-snapshot
Insights into the genome of the ‘Loco’ Concholepas concholepas (Gastropoda: Muricidae) from low-coverage short-read sequencing: genome size, ploidy, transposable elements, nuclear RNA gene operon, mitochondrial genome, and phylogenetic placement in the family Muricidae
inferred← citeshttps://doi.org/10.1186/s12864-024-11025-3openalex-snapshot
Chromosome-level genome assemblies and genetic maps reveal heterochiasmy and macrosynteny in endangered Atlantic Acropora
inferred← citeshttps://doi.org/10.1186/s12864-025-11591-0openalex-snapshot
Repeatome diversity in sea anemone genomics (Cnidaria: Actiniaria) based on the Actiniaria-REPlib library
inferred← citeshttps://doi.org/10.1186/s12864-025-11794-5openalex-snapshot
A first nuclear and mitochondrial genomic portrait of Robinson Crusoe’s (Juan Fernández Island) spiny lobster Jasus frontalis (Crustacea: Decapoda: Achelata)
inferred← citeshttps://doi.org/10.1186/s12864-026-12600-6openalex-snapshot
Repeat-associated heterochromatin expansion in Acyclania tenebrosa, a noctuid with one of the largest lepidopteran genomes
inferred← citeshttps://doi.org/10.1186/s12915-021-01158-2openalex-snapshot
The transposable element-rich genome of the cereal pest Sitophilus oryzae
inferred← citeshttps://doi.org/10.1186/s12915-022-01441-wopenalex-snapshot
Transposable element expansion and low-level piRNA silencing in grasshoppers may cause genome gigantism
inferred← citeshttps://doi.org/10.1186/s12915-023-01539-9openalex-snapshot
Genomic profiling of dioecious Amaranthus species provides novel insights into species relatedness and sex genes
inferred← citeshttps://doi.org/10.1186/s12915-025-02370-0openalex-snapshot
The impact of insertion bias into piRNA clusters on the invasion of transposable elements
inferred← citeshttps://doi.org/10.1186/s13059-023-02911-2openalex-snapshot
TrEMOLO: accurate transposable element allele frequency estimation using long-read sequencing data combining assembly and mapping-based approaches
inferred← citeshttps://doi.org/10.1186/s13071-016-1815-8openalex-snapshot
Developmental piRNA profiles of the invasive vector mosquito Aedes albopictus
inferred← citeshttps://doi.org/10.1186/s13100-017-0088-xopenalex-snapshot
LoRTE: Detecting transposon-induced genomic variants using low coverage PacBio long read sequences
inferred← citeshttps://doi.org/10.1186/s13100-017-0103-2openalex-snapshot
Using bioinformatic and phylogenetic approaches to classify transposable elements and understand their complex evolutionary histories
inferred← citeshttps://doi.org/10.1186/s13100-018-0123-6openalex-snapshot
Extensive exchange of transposable elements in the Drosophila pseudoobscura group
inferred← citeshttps://doi.org/10.1186/s13100-018-0127-2openalex-snapshot
Drosophila parasitoid wasps bears a distinct DNA transposon profile
inferred← citeshttps://doi.org/10.1186/s13100-020-00213-zopenalex-snapshot
Transposable elements in Drosophila
inferred← citeshttps://doi.org/10.1186/s13100-021-00252-0openalex-snapshot
Comparative genomic and transcriptomic analyses of transposable elements in polychaetous annelids highlight LTR retrotransposon diversity and evolution
inferred← citeshttps://doi.org/10.1186/s13100-022-00270-6openalex-snapshot
Characterization of transposable elements within the Bemisia tabaci species complex
inferred← citeshttps://doi.org/10.1186/s13100-023-00302-9openalex-snapshot
Teleost genomic repeat landscapes in light of diversification rates and ecology
inferred← citeshttps://doi.org/10.1186/s13100-024-00316-xopenalex-snapshot
Orthoptera-TElib: a library of Orthoptera transposable elements for TE annotation
inferred← citeshttps://doi.org/10.1186/s13100-025-00362-zopenalex-snapshot
No evidence of transposable element bursts in the Galápagos Scalesia adaptive radiation despite hybridization, diversification and ecological niche shifts
inferred← citeshttps://doi.org/10.1186/s13100-026-00396-xopenalex-snapshot
Massive proliferation of retrotransposons contributes to genome size expansion in species of the Pseudocercospora genus
inferred← citeshttps://doi.org/10.1186/s40693-024-00132-wopenalex-snapshot
Genomics resources for the Rapa Nui (Eastern Island) spiny lobster Panulirus pascuensis (Crustacea: Decapoda: Achelata)
inferred← citeshttps://doi.org/10.1371/journal.pbio.3001309openalex-snapshot
Massive colonization of protein-coding exons by selfish genetic elements in Paramecium germline genomes
inferred← citeshttps://doi.org/10.1371/journal.pbio.3002733openalex-snapshot
Diatom abundance in the polar oceans is predicted by genome size
inferred← citeshttps://doi.org/10.1371/journal.pgen.1008946openalex-snapshot
Mosquito genomes are frequently invaded by transposable elements through horizontal transfer
inferred← citeshttps://doi.org/10.1371/journal.pgen.1009438openalex-snapshot
Toxic Y chromosome: Increased repeat expression and age-associated heterochromatin loss in male Drosophila with a young Y chromosome
inferred← citeshttps://doi.org/10.1371/journal.pone.0232973openalex-snapshot
The genome, transcriptome, and proteome of the fish parasite Pomphorhynchus laevis (Acanthocephala)
inferred← citeshttps://doi.org/10.1534/g3.118.200865openalex-snapshot
Draft Genome Assembly and Population Genetics of an Agricultural Pollinator, the Solitary Alkali Bee (Halictidae: Nomia melanderi )
inferred← citeshttps://doi.org/10.21105/joss.00527openalex-snapshot
reper: Genome-wide identification, classification and quantification of repetitive elements without an assembled genome
inferred← citeshttps://doi.org/10.21203/rs.3.rs-41472/v1openalex-snapshot
Rapid Divergence Of The Copulation Proteins In The Drosophila Dunni Group Is Associated With Hybrid Post-Mating-Prezygotic Incompatibilities
inferred← citeshttps://doi.org/10.2139/ssrn.3318936openalex-snapshot
A Behavior-Manipulating Virus Relative As a Source of Adaptive Genes for Parasitoid Wasps
inferred← citeshttps://doi.org/10.22541/au.159242077.72607009openalex-snapshot
Selection and demography shape genomic variation in a ‘Sky Island’ species
inferred← citeshttps://doi.org/10.3389/fcell.2023.1124374openalex-snapshot
Transposable element and host silencing activity in gigantic genomes
inferred← citeshttps://doi.org/10.3389/fevo.2025.1664211openalex-snapshot
CYP genes are duplicated in Drosophila suzukii and carry transposable elements
inferred← citeshttps://doi.org/10.3389/fgene.2020.542437openalex-snapshot
In and Outs of Chuviridae Endogenous Viral Elements: Origin of a Potentially New Retrovirus and Signature of Ancient and Ongoing Arms Race in Mosquito Genomes
inferred← citeshttps://doi.org/10.3389/fpls.2026.1855960openalex-snapshot
REAPER: a project-centric workflow layer for comparative repeatome analysis
inferred← citeshttps://doi.org/10.3390/cells10071707openalex-snapshot
Impact of Repetitive DNA Elements on Snake Genome Biology and Evolution
inferred← citeshttps://doi.org/10.3390/cells9081776openalex-snapshot
A Transposon Story: From TE Content to TE Dynamic Invasion of Drosophila Genomes Using the Single-Molecule Sequencing Technology from Oxford Nanopore
inferred← citeshttps://doi.org/10.3390/genes10040258openalex-snapshot
On the Importance to Acknowledge Transposable Elements in Epigenomic Analyses
inferred← citeshttps://doi.org/10.3390/genes11020170openalex-snapshot
Homology-Free Detection of Transposable Elements Unveils Their Dynamics in Three Ecologically Distinct Rhodnius Species
inferred← citeshttps://doi.org/10.3390/genes11060614openalex-snapshot
Identification of Regulatory SNPs Associated with Vicine and Convicine Content of Vicia faba Based on Genotyping by Sequencing Data Using Deep Learning
inferred← citeshttps://doi.org/10.3390/genes13040709openalex-snapshot
Methodologies for the De novo Discovery of Transposable Element Families
inferred← citeshttps://doi.org/10.3390/ijms18112307openalex-snapshot
Mutational Biases and GC-Biased Gene Conversion Affect GC Content in the Plastomes of Dendrobium Genus
inferred← citeshttps://doi.org/10.3390/ijms22116052openalex-snapshot
Satellitome Analysis of Rhodnius prolixus, One of the Main Chagas Disease Vector Species
inferred← citeshttps://doi.org/10.3390/ijms23116220openalex-snapshot
Characterisation of LTR-Retrotransposons of Stevia rebaudiana and Their Use for the Analysis of Genetic Variability
inferred← citeshttps://doi.org/10.3390/ijms25084441openalex-snapshot
Study of Dispersed Repeats in the Cyanidioschyzon merolae Genome
inferred← citeshttps://doi.org/10.3390/ijms26136039openalex-snapshot
Repeatome Dynamics and Sex Chromosome Differentiation in the XY and XY1Y2 Systems of the Fish Hoplias malabaricus (Teleostei; Characiformes)
inferred← citeshttps://doi.org/10.3390/ijms27198720openalex-snapshot
Comparative Repeatomics Uncovers Genome Diversification in Gasteropelecidae Fishes
inferred← citeshttps://doi.org/10.3390/insects11120879openalex-snapshot
Screening of Helicoverpa armigera Mobilome Revealed Transposable Element Insertions in Insecticide Resistance Genes
inferred← citeshttps://doi.org/10.3390/life12040521openalex-snapshot
Satellitome Analysis and Transposable Elements Comparison in Geographically Distant Populations of Spodoptera frugiperda
inferred← citeshttps://doi.org/10.6084/m9.figshare.15139367openalex-snapshot
Additional file 1 of Genomics and transcriptomics of epizoic Seisonidea (Rotifera, syn. Syndermata) reveal strain formation and gradual gene loss with growing ties to the host
inferred← citeshttps://doi.org/10.6084/m9.figshare.16907267openalex-snapshot
Additional file 10 of Comparative genomic and transcriptomic analyses of transposable elements in polychaetous annelids highlight LTR retrotransposon diversity and evolution
inferred← citeshttps://doi.org/10.6084/m9.figshare.16907288openalex-snapshot
Additional file 1 of Comparative genomic and transcriptomic analyses of transposable elements in polychaetous annelids highlight LTR retrotransposon diversity and evolution
inferred← citeshttps://doi.org/10.6084/m9.figshare.16907291openalex-snapshot
Additional file 2 of Comparative genomic and transcriptomic analyses of transposable elements in polychaetous annelids highlight LTR retrotransposon diversity and evolution
inferred← citeshttps://doi.org/10.6084/m9.figshare.16907297openalex-snapshot
Additional file 4 of Comparative genomic and transcriptomic analyses of transposable elements in polychaetous annelids highlight LTR retrotransposon diversity and evolution
inferred← citeshttps://doi.org/10.6084/m9.figshare.16907306openalex-snapshot
Additional file 6 of Comparative genomic and transcriptomic analyses of transposable elements in polychaetous annelids highlight LTR retrotransposon diversity and evolution
inferred← citeshttps://doi.org/10.6084/m9.figshare.16907309openalex-snapshot
Additional file 7 of Comparative genomic and transcriptomic analyses of transposable elements in polychaetous annelids highlight LTR retrotransposon diversity and evolution
inferred← citeshttps://doi.org/10.6084/m9.figshare.16907315openalex-snapshot
Additional file 8 of Comparative genomic and transcriptomic analyses of transposable elements in polychaetous annelids highlight LTR retrotransposon diversity and evolution
inferred← citeshttps://doi.org/10.6084/m9.figshare.16907318openalex-snapshot
Additional file 9 of Comparative genomic and transcriptomic analyses of transposable elements in polychaetous annelids highlight LTR retrotransposon diversity and evolution
inferred← citeshttps://doi.org/10.6084/m9.figshare.22623680openalex-snapshot
Additional file 1 of TrEMOLO: accurate transposable element allele frequency estimation using long-read sequencing data combining assembly and mapping-based approaches
inferred← citeshttps://doi.org/10.6084/m9.figshare.22623683openalex-snapshot
Additional file 2 of TrEMOLO: accurate transposable element allele frequency estimation using long-read sequencing data combining assembly and mapping-based approaches
inferred← citeshttps://doi.org/10.6084/m9.figshare.25414889openalex-snapshot
Additional file 1 of Orthoptera-TElib: a library of Orthoptera transposable elements for TE annotation
inferred← citeshttps://doi.org/10.6084/m9.figshare.25415047openalex-snapshot
Additional file 2 of Orthoptera-TElib: a library of Orthoptera transposable elements for TE annotation
inferred← citeshttps://doi.org/10.6084/m9.figshare.26669517openalex-snapshot
Additional file 1 of Insights into the genome of the ‘Loco’ Concholepas concholepas (Gastropoda: Muricidae) from low-coverage short-read sequencing: genome size, ploidy, transposable elements, nuclear RNA gene operon, mitochondrial genome, and phylogenetic placement in the family Muricidae
inferred← citeshttps://doi.org/10.6084/m9.figshare.26944284openalex-snapshot
Additional file 1 of Genomics resources for the Rapa Nui (Eastern Island) spiny lobster Panulirus pascuensis (Crustacea: Decapoda: Achelata)
inferred← citeshttps://doi.org/10.64898/2026.01.28.702265openalex-snapshot
The transposable elements syndrome of wheat domestication
inferred← citeshttps://doi.org/10.70675/00dbd2ffz4271z4c8bz8b6azd41857860271openalex-snapshot
Dynamique des éléments transposables chez Drosophila suzukii
inferred← citeshttps://doi.org/10.70675/2cc987c0z9536z4449z9b00za8b607d01c0bopenalex-snapshot
Etude de l’activité des éléments mobiles chez Tisochrysis lutea dans un contexte d’amélioration des espèces de microalgues.
inferred← citeshttps://doi.org/10.70675/365deb88zeb80z45f6z88b9z386c76342273openalex-snapshot
Impact des éléments transposables sur l'évolution de la régulation des gènes : exemple du sexe chez les poissons téléostéens
inferred← citeshttps://doi.org/10.70675/725d5452z1adcz4104zb78dz430950e41644openalex-snapshot
Methods for genome-wide structural variation inference in skimming data using graph pangenome
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