Characterization of Mariner transposons in seven species of Rhus gall aphids

1. Charlesworth, B., Sniegowski, P. & Stephan, W. The evolutionary dynamics of repetitive DNA in…

  • 1.

    Charlesworth, B., Sniegowski, P. & Stephan, W. The evolutionary dynamics of repetitive DNA in eukaryotes. Nature 371, 215–220 (1994).

    ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • 2.

    Brunet, F., Giraud, T., Godin, F. & Capy, P. Do deletions of Mos1-like elements occur randomly in the Drosophilidae family? J. Mol. Evol. 54, 227–234 (2002).

    ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • 3.

    Dechaud, C., Volff, J. N., Schartl, M. & Naville, M. Sex and the TEs: Transposable elements in sexual development and function in animals. Mob. DNA 10, 1–15 (2019).

    Article 

    Google Scholar
     

  • 4.

    Mittapalli, O. R. L. et al. Cloning and characterization of mariner-like elements in the soybean aphid, Aphis glycines Matsumura. Bull. Entomol. Res. 101, 697–704 (2011).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • 5.

    Petersen, M. et al. Diversity and evolution of the transposable element repertoire in arthropods with particular reference to insects. BMC Evol. Biol. 19, 11 (2019).

    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • 6.

    Moschetti, R., Palazzo, A., Lorusso, P., Viggiano, L. & Massimiliano Marsano, R. “What you need, baby, I got it”: Transposable elements as suppliers of cis-operating sequences in drosophila. Biology. 9, 25 (2020).

    CAS 
    PubMed Central 
    Article 
    PubMed 

    Google Scholar
     

  • 7.

    Gao, B. et al. Evolution of pogo, a separate superfamily of IS630-Tc1-mariner transposons, revealing recurrent domestication events in vertebrates. Mob. DNA 11, 1–5 (2020).

    Article 
    CAS 

    Google Scholar
     

  • 8.

    Makałowski, W., Gotea, V., Pande, A. & Makałowska, I. Transposable elements: Classification, identification, and their use as a tool for comparative genomics. In Evolutionary Genomics (ed. Anisimova, M.) 177–207 (Humana, 2019).

    Chapter 

    Google Scholar
     

  • 9.

    Feschotte, C. et al. Miniature inverted-repeat transposable elements and their relationship to established DNA transposons. In Mobile DNA II (eds Craig, N. L. et al.) 1147–1158 (American Society of Microbiology, 2002).

    Chapter 

    Google Scholar
     

  • 10.

    Marini, M. M. et al. Identification and characterization of Tc1/mariner-like DNA transposons in genomes of the pathogenic fungi of the Paracoccidioides species complex. BMC Genomics 11(1), 130 (2010).

    MathSciNet 
    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar
     

  • 11.

    Wicker, T. et al. A unified classification system for eukaryotic transposable elements. Nat. Rev. Genet. 8, 973–982 (2007).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • 12.

    Kapitonov, V. V. & Jurka, J. A universal classification of eukaryotic transposable elements implemented in Repbase. Nat. Rev. Genet. 9, 411–412 (2008).

    PubMed 
    Article 

    Google Scholar
     

  • 13.

    Wicker, T. et al. A unified classification system for eukaryotic transposable elements should reflect their phylogeny. Nat. Rev. Genet. 10, 276–276 (2009).

    CAS 
    Article 

    Google Scholar
     

  • 14.

    Rouault, J. D. et al. Automatic classification within families of transposable elements: Application to the mariner Family. Gene 448, 227–232 (2009).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • 15.

    Plasterk, R. H., Izsvák, Z. & Ivics, Z. Resident aliens: The Tc1/mariner superfamily of transposable elements. Trends Genet. 15, 326–332 (1999).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • 16.

    Shao, H. & Tu, Z. Expanding the diversity of the IS630-Tc1-mariner superfamily: Discovery of a unique DD37E transposon and reclassification of the DD37D and DD39D transposons. Genetics 159, 1103–1115 (2001).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • 17.

    Chalopin, D., Naville, M., Plard, F., Galiana, D. & Volff, J. N. Comparative analysis of transposable elements highlights mobilome diversity and evolution in vertebrates. Genome Biol. Evol. 7, 567–580 (2015).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • 18.

    Mérel, V., Boulesteix, M., Fablet, M. & Vieira, C. Transposable elements in Drosophila. Mob. DNA 11, 1–20 (2020).

    Article 

    Google Scholar
     

  • 19.

    Bouallègue, M. et al. Diversity and evolution of mariner-like elements in aphid genomes. BMC Genomics 18, 494 (2017).

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar
     

  • 20.

    Kharrat, I. et al. Characterization of mariner-like transposons of the mauritiana subfamily in seven tree aphid species. Genetica 143, 63–72 (2015).

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar
     

  • 21.

    Jurka, J. Mariner families from Acyrthosiphon pisum. Repbase Rep. 8, 340 (2008).


    Google Scholar
     

  • 22.

    Ren, Z. et al. Another look at the phylogenetic relationships and intercontinental biogeography of eastern Asian-North American Rhus gall aphids (Hemiptera: Aphididae: Eriosomatinae): Evidence from mitogenome sequences via genome skimming. Mol. Phylogenet. Evol. 117, 102–110 (2017).

    PubMed 
    Article 
    PubMed Central 

    Google Scholar
     

  • 23.

    Ren, Z. et al. Congruent phylogenetic relationships of Melaphidina aphids (Aphididae: Eriosomatinae: Fordini) according to nuclear and mitochondrial DNA data with taxonomic implications on generic limits. PLoS ONE 14, e0213181 (2019).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • 24.

    Zhang, G. X., Qiao, G. X., Zhong, T. S. & Zhang, W. Y. Fauna Sinica Insecta 14. D274. InHomoptera: Mindaridae and Pemphigidae 256 (Science Press, 1999).


    Google Scholar
     

  • 25.

    Yang, Z. X., Chen, X. M., Havill, N. P., Feng, Y. & Chen, H. Phylogeny of Rhus gall aphids (Hemiptera: Pemphigidae) based on combined molecular analysis of nuclear EF-1a and mitochondrial COII genes. Entomol. Sci. 13, 351–357 (2010).

    Article 

    Google Scholar
     

  • 26.

    Skipper, K. A., Andersen, P. R., Sharma, N. & Mikkelsen, J. G. DNA transposon-based gene vehicles-scenes from an evolutionary drive. J. Biomed. Sci. 20, 1–23 (2013).

    Article 
    CAS 

    Google Scholar
     

  • 27.

    Yamada, K. et al. Widespread distribution and evolutionary patterns of mariner-like elements among various spiders and insects. J. Insect Biotechnol. Sericol. 84, 029–041 (2015).

    CAS 

    Google Scholar
     

  • 28.

    Quesneville, H. Impact of transposable elements on insect genomes and biology. Curr. Opin. Insect Sci. 7, 1–7 (2015).

    Article 

    Google Scholar
     

  • 29.

    Wallau, G. L., Capy, P., Loreto, E. & Hua-Van, A. Genomic landscape and evolutionary dynamics of mariner transposable elements within the Drosophila genus. BMC Genomics 15, 727 (2014).

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar
     

  • 30.

    Dunn, P. et al. Next generation sequencing methods for diagnosis of epilepsy syndromes. Front. Genet. 9, 20 (2018).

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar
     

  • 31.

    Doak, T. G., Doerder, F. P., Jahn, C. L. & Herrick, G. A proposed superfamily of transposase genes: Transposon-like elements in ciliated protozoa and a common “D35E” motif. Proc. Natl. Acad. Sci. 91, 942–946 (1994).

    ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • 32.

    Demattei, M. V. et al. Nuclear importation of mariner transposases among eukaryotes: Motif requirements and homo-protein interactions. PLoS ONE 6, e23693 (2011).

    ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • 33.

    Foottit, R. G., Maw, H. V., Von-Dohlen, C. D. & Hebert, P. D. Species identification of aphids (Insecta: Hemiptera: Aphididae) through DNA barcodes. Mol. Ecol. Resour. 6, 1189–1201 (2008).

    Article 
    CAS 

    Google Scholar
     

  • 34.

    Kim, H., Lee, S. & Jang, Y. Macroevolutionary patterns in the Aphidini aphids (Hemiptera: Aphididae): Diversification, host association, and biogeographic origins. PLoS ONE 6, e24749 (2011).

    ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • 35.

    Blackman, R. L. & Eastop, V. F. Taxonomic issues. Aphids Crop Pests 1, 1–29 (2007).


    Google Scholar
     

  • 36.

    Leclant, F. Aphids of Cultivated Crops: Identification Keys. Aphids of Cultivated Crops: Identification Keys. III Fruit Crops: Identification Keys. III Fruit Crops pp. 128 (2000).

  • 37.

    Park, D. S., Foottit, R., Maw, E. & Hebert, P. D. Barcoding bugs: DNA-based identification of the true bugs (Insecta: Hemiptera: Heteroptera). PLoS ONE 6, e18749 (2011).

    ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • 38.

    Lawrence, J. G. & Hartl, D. L. Inference of horizontal genetic transfer from molecular data: An approach using the bootstrap. Genetics 131, 753–760 (1992).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • 39.

    Clark, J. B., Maddison, W. P. & Kidwell, M. G. Phylogenetic analysis supports horizontal transfer of P transposable elements. Mol. Biol. Evol. 11, 40–50 (1994).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 40.

    Robertson, H. M. & Lampe, D. J. Recent horizontal transfer of a mariner transposable element among and between Diptera and Neuroptera. Mol. Biol. Evol. 12, 850–862 (1995).

    CAS 
    PubMed 

    Google Scholar
     

  • 41.

    Capy, P., Anxolabéhère, D. & Langin, T. The strange phylogenies of transposable elements: Are horizontal transfers the only explanation? Trends Genet. 10, 7–12 (1994).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • 42.

    Palazzo, A., Escuder, E., D’Addabbo, P., Lovero, D. & Marsano, R. M. A genomic survey of Tc1-mariner transposons in nematodes suggests extensive horizontal transposon transfer events. Mol. Phylogenet. Evol. 158, 107090 (2021).

    PubMed 
    Article 

    Google Scholar
     

  • 43.

    Zhou, M. B., Zhong, H. & Tang, D. Q. Isolation and characterization of seventy-nine full-length mariner-like transposase genes in the Bambusoideae subfamily. J. Plant. Res. 124, 607–617 (2011).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • 44.

    Dupeyron, M., Leclercq, S., Cerveau, N., Bouchon, D. & Gilbert, C. Horizontal transfer of transposons between and within crustaceans and insects. Mob. DNA 5, 4 (2014).

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar
     

  • 45.

    Han, G. et al. Characterization of a novel Helitron family in insect genomes: Insights into classification, evolution and horizontal transfer. Mob. DNA 10, 25 (2019).

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar
     

  • 46.

    Grace, C. A. & Carr, M. The evolutionary history of mariner elements in stalk-eyed flies reveals the horizontal transfer of transposons from insects into the genome of the cnidarian Hydra vulgaris. PLoS ONE 15, e0235984 (2020).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • 47.

    Wallau, G. L., Capy, P., Loreto, E., Le-Rouzic, A. & Hua-Van, A. VHICA, a new method to discriminate between vertical and horizontal transposon transfer: Application to the mariner family within Drosophila. Mol. Biol. Evol. 1, 1094–1109 (2016).

    Article 
    CAS 

    Google Scholar
     

  • 48.

    Bartolomé, C., Bello, X. & Maside, X. Widespread evidence for horizontal transfer of transposable elements across Drosophila genomes. Genome Biol. 10, 1–1 (2009).

    Article 
    CAS 

    Google Scholar
     

  • 49.

    Bolger, A. M., Lohse, M. & Usadel, B. Trimmomatic: A flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114–2120 (2014).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • 50.

    Bankevich, A. et al. SPAdes: A new genome assembly algorithm and its applications to single-cell sequencing. J. Comput. Biol. 19, 455–477 (2012).

    MathSciNet 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • 51.

    Marchler-Bauer, A. et al. CDD/SPARCLE: Functional classification of proteins via subfamily domain architectures. Nucleic Acids Res. 45, 200–203 (2017).

    Article 
    CAS 

    Google Scholar
     

  • 52.

    Kosugi, S., Hasebe, M., Tomita, M. & Yanagawa, H. Systematic identification of cell cycle-dependent yeast nucleocytoplasmic shuttling proteins by prediction of composite motifs. Proc. Natl. Acad. Sci. 106, 10171–10176 (2009).

    ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • 53.

    Stamatakis, A. RAxML version 8: A tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30, 1312–1313 (2014).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar