Perspective: transposable elements, parasitic DNA, and genome evolution, Evolution, vol.55, pp.1-24, 2001. ,
Eukaryote DIRS1-like retrotransposons: an overview, BMC Genomics, vol.12, issue.1, 2011. ,
LINEs between species: evolutionary dynamics of LINE-1 retrotransposons across the eukaryotic tree of life, Genome Biol Evol, vol.8, pp.3301-3323, 2016. ,
A unified classification system for eukaryotic transposable elements, Nat Rev Genet, vol.8, pp.973-82, 2007. ,
URL : https://hal.archives-ouvertes.fr/hal-00169819
Origin and evolution of retroelements based upon their reverse transcriptase sequences, EMBO J, vol.9, pp.3353-62, 1990. ,
Evolution of retroposons by acquisition or deletion of retrovirus-like genes, Mol Biol Evol, vol.8, pp.835-56, 1991. ,
Translational recoding signals between gag and pol in diverse LTR retrotransposons, RNA, vol.9, pp.1422-1452, 2003. ,
Filamentous ascomycete genomes provide insights into Copia retrotransposon diversity in fungi, BMC Genomics, vol.18, 2017. ,
URL : https://hal.archives-ouvertes.fr/hal-01529914
Network dynamics of eukaryotic LTR retroelements beyond phylogenetic trees, Biol Direct, vol.4, p.41, 2009. ,
A group of deuterostome Ty3/gypsy-like retrotransposons with Ty1/copia-like pol-domain orders, Mol Gen Genomics, vol.267, pp.481-91, 2002. ,
The Gypsy Database (GyDB) of mobile genetic elements: release 2.0, Nucleic Acids Res, vol.39, issue.suppl_1, pp.70-74, 2011. ,
BEL/Pao retrotransposons in metazoan genomes, BMC Evol Biol, vol.11, issue.1, 2011. ,
LTRRetrotransposons in R exoculata and Other Crustaceans: The Outstanding Success of GalEa-Like Copia Elements, Plos One, vol.8, p.57675, 2013. ,
LTR retrotransposons in Fungi, PLoS One, vol.6, p.29425, 2011. ,
GalEa retrotransposons from galatheid squat lobsters (Decapoda, Anomura) define a new clade of Ty1/copia-like elements restricted to aquatic species, Mol Gen Genomics, vol.279, pp.63-73, 2008. ,
The Red Queen Am Nat, vol.111, pp.809-819, 1977. ,
The Sinbad retrotransposon from the genome of the human blood fluke, Schistosoma mansoni, and the distribution of related Pao-like elements, BMC Evol Biol, vol.5, p.20, 2005. ,
Invertebrate evolution: bringing order to the molluscan chaos, Curr Biol, vol.21, pp.964-970, 2011. ,
Pearl, a novel Family of Putative Transposable Elements in Bivalve Mollusks, J Mol Evol, vol.56, pp.308-324, 2003. ,
The Tc1/mariner DNA transposons in the genome of mollusk Littorina saxatilis, Russ J Genet, vol.53, pp.1358-65, 2017. ,
RUDI, a short interspersed element of the V-SINE superfamily widespread in molluscan genomes, Mol Gen Genomics, vol.291, pp.1419-1448, 2016. ,
Mobile element evolution playing jigsaw-SINEs in gastropod and bivalve mollusks ,
, Genome Biol Evol, vol.8, pp.253-70, 2016.
Activation of transcription and retrotransposition of a novel retroelement, Steamer, in neoplastic hemocytes of the mollusk Mya arenaria, Proc Natl Acad Sci, vol.111, pp.14175-80, 2014. ,
Horizontal transfer of retrotransposons between bivalves and other aquatic species of multiple phyla, Proc Natl Acad Sci, 2018. ,
Repbase update, a database of repetitive elements in eukaryotic genomes, Mob DNA, vol.6, 2015. ,
Insights into bilaterian evolution from three spiralian genomes, Nature, vol.493, pp.526-557, 2013. ,
The octopus genome and the evolution of cephalopod neural and morphological novelties, Nature, vol.524, pp.220-224, 2015. ,
Genome structure analysis of molluscs revealed whole genome duplication and lineage specific repeat variation, Gene, vol.483, pp.63-71, 2011. ,
Draft genome of the pearl oyster Pinctada fucata: a platform for understanding bivalve biology, DNA Res Int J Rapid Publ Rep Genes Genomes, vol.19, pp.117-147, 2012. ,
The oyster genome reveals stress adaptation and complexity of shell formation, Nature, vol.490, pp.49-54, 2012. ,
Screening of repetitive motifs inside the genome of the flat oyster (Ostrea edulis): transposable elements and short tandem repeats, Mar Genomics, vol.24, pp.335-376, 2015. ,
A first insight into the genome of the filter-feeder mussel Mytilus galloprovincialis, PLoS One, vol.11, 2016. ,
The snail (Biomphalaria glabrata) genome project, Trends Parasitol, vol.22, pp.148-51, 2006. ,
DOI : 10.1016/j.pt.2006.02.008
Structural features of conopeptide genes inferred from partial sequences of the Conus tribblei genome, Mol Gen Genomics, vol.291, pp.411-433, 2016. ,
LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons, BMC Bioinformatics, vol.9, p.18, 2008. ,
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 ,
URL : https://hal.archives-ouvertes.fr/hal-01227710
, Genome Biol Evol, vol.7, pp.1192-205, 2015.
Potential impact of stress activated retrotransposons on genome evolution in a marine diatom, BMC Genomics, vol.10, p.624, 2009. ,
Retroviral-like element in a marine invertebrate, Proc Natl Acad Sci, vol.88, pp.8401-8405, 1991. ,
CsRn1, a novel active retrotransposon in a parasitic trematode, Clonorchis sinensis, discloses a new phylogenetic clade of Ty3/gypsy-like LTR retrotransposons, Mol Biol Evol, vol.18, pp.1474-83, 2001. ,
Sequence analysis of transposable elements in the sea squirt, Oikopleura dioica, Mol Biol Evol, vol.17, pp.1685-94, 2000. ,
Retroelement dynamics and a novel type of chordate retroviruslike element in the miniature genome of the tunicate Oikopleura dioica, Mol Biol Evol, vol.21, pp.2022-2055, 2004. ,
Adaptation to deep-sea chemosynthetic environments as revealed by mussel genomes, Nat Ecol Evol, vol.1, p.121, 2017. ,
DOI : 10.1038/s41559-017-0121
URL : https://www.nature.com/articles/s41559-017-0121.pdf
Developing tools for the study of molluscan immunity: the sequencing of the genome of the eastern oyster, Crassostrea virginica, Fish Shellfish Immunol, vol.46, pp.2-4, 2015. ,
The venomous cocktail of the vampire snail Colubraria reticulata (Mollusca, Gastropoda), BMC Genomics, vol.16, 2015. ,
Assembly of a reference transcriptome for the gymnosome pteropod Clione limacina and profiling responses to short-term CO2 exposure, Mar Genomics, vol.34, pp.39-45, 2017. ,
Comparative transcriptomics of alternative developmental phenotypes in a marine gastropod, J Exp Zoolog B Mol Dev Evol, vol.326, pp.151-67, 2016. ,
De novo assembly and annotation of the European abalone Haliotis tuberculata transcriptome, Mar Genomics, vol.28, pp.11-17, 2016. ,
URL : https://hal.archives-ouvertes.fr/hal-01483234
Evolutionary history of LTR-retrotransposons among 20 Drosophila species, Mob DNA, vol.8, 2017. ,
URL : https://hal.archives-ouvertes.fr/hal-02049656
Diversity and evolution of Ty1-copia retroelements within Chalcidoidea by reverse transcriptase domain analysis, Insect Mol Biol, vol.24, pp.503-519, 2015. ,
Transcriptional Differences between Diapausing and Non-Diapausing D montana Females Reared under the Same Photoperiod and Temperature, PLOS One, vol.11, p.161852, 2016. ,
DOI : 10.1371/journal.pone.0161852
URL : https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0161852&type=printable
Structure and evolution of mtanga, a retrotransposon actively expressed on the Y chromosome of the African malaria vector Anopheles gambiae, Mol Biol Evol, vol.19, pp.149-62, 2002. ,
Two different clades of copia-like retrotransposons in the red alga, Porphyra yezoensis, Gene, vol.424, pp.153-161, 2008. ,
Genomic analysis of Caenorhabditis elegans reveals ancient families of retroviral-like elements, Genome Res, vol.9, pp.924-959, 1999. ,
The complete sequence of mag, a new retrotransposon in Bombyx mori, Nucleic Acids Res, vol.18, p.674, 1990. ,
Structural and evolutionary analyses of the Ty3/gypsy Group of LTR retrotransposons in the genome of Anopheles gambiae, Mol Biol Evol, vol.22, pp.29-39, 2005. ,
Jule from the fish Xiphophorus is the first complete vertebrate Ty3/gypsy retrotransposon from the mag family, Mol Biol Evol, vol.18, pp.101-112, 2001. ,
Evolution of sea urchin retroviral-like (SURL) elements: evidence from 40 echinoid species, Mol Biol Evol, vol.16, pp.938-52, 1999. ,
Database resources of the national center for biotechnology information, Nucleic Acids Res, vol.44, p.7, 2016. ,
Basic local alignment search tool, J Mol Biol, vol.215, pp.403-413, 1990. ,
MAFFT multiple sequence alignment software version 7: improvements in performance and usability, Mol Biol Evol, vol.30, pp.772-80, 2013. ,
, , 2013.
Fast and accurate long-read alignment with burrowswheeler transform, Bioinformatics, vol.26, pp.589-95, 2010. ,
The neighbor-joining method: a new method for reconstructing phylogenetic trees, Mol Biol Evol, vol.4, pp.406-431, 1987. ,
MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods, Mol Biol Evol, vol.28, pp.2731-2740, 2011. ,
TOPALi: software for automatic identification of recombinant sequences within DNA multiple alignments, Bioinformatics, vol.20, pp.1806-1813, 2004. ,
The rapid generation of mutation data matrices from protein sequences, Bioinformatics, vol.8, pp.275-82, 1992. ,
Confidence limits on phylogenies: an approach using the bootstrap, Evolution, vol.39, p.783, 1985. ,