Systematic survey of plant LTR-retrotransposons elucidates phylogenetic relationships of their polyprotein domains and provides a reference for element classification View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2019-12

AUTHORS

Pavel Neumann, Petr Novák, Nina Hoštáková, Jiří Macas

ABSTRACT

Background: Plant LTR-retrotransposons are classified into two superfamilies, Ty1/copia and Ty3/gypsy. They are further divided into an enormous number of families which are, due to the high diversity of their nucleotide sequences, usually specific to a single or a group of closely related species. Previous attempts to group these families into broader categories reflecting their phylogenetic relationships were limited either to analyzing a narrow range of plant species or to analyzing a small numbers of elements. Furthermore, there is no reference database that allows for similarity based classification of LTR-retrotransposons. Results: We have assembled a database of retrotransposon encoded polyprotein domains sequences extracted from 5410 Ty1/copia elements and 8453 Ty3/gypsy elements sampled from 80 species representing major groups of green plants (Viridiplantae). Phylogenetic analysis of the three most conserved polyprotein domains (RT, RH and INT) led to dividing Ty1/copia and Ty3/gypsy retrotransposons into 16 and 14 lineages respectively. We also characterized various features of LTR-retrotransposon sequences including additional polyprotein domains, extra open reading frames and primer binding sites, and found that the occurrence and/or type of these features correlates with phylogenies inferred from the three protein domains. Conclusions: We have established an improved classification system applicable to LTR-retrotransposons from a wide range of plant species. This system reflects phylogenetic relationships as well as distinct sequence and structural features of the elements. A comprehensive database of retrotransposon protein domains (REXdb) that reflects this classification provides a reference for efficient and unified annotation of LTR-retrotransposons in plant genomes. Access to REXdb related tools is implemented in the RepeatExplorer web server (https://repeatexplorer-elixir.cerit-sc.cz/) or using a standalone version of REXdb that can be downloaded seaparately from RepeatExplorer web page (http://repeatexplorer.org/). More... »

PAGES

1

References to SciGraph publications

  • 1999-12. Phylogenetic evidence for Ty1-copia-like endogenous retroviruses in plant genomes in GENETICA
  • 2012-12. MASiVEdb: the Sirevirus Plant Retrotransposon Database in BMC GENOMICS
  • 2013-12. Sirevirus LTR retrotransposons: phylogenetic misconceptions in the plant world in MOBILE DNA
  • 2018-12. Impact of transposable elements on genome structure and evolution in bread wheat in GENOME BIOLOGY
  • 2008-11. Experimental evidence for splicing of intron-containing transcripts of plant LTR retrotransposon Ogre in MOLECULAR GENETICS AND GENOMICS
  • 2018-12. Nomenclature for endogenous retrovirus (ERV) loci in RETROVIROLOGY
  • 2010-05-30. Recent Insights into Mechanisms of Genome Size Change in Plants in JOURNAL OF BOTANY
  • 2002-09. Long terminal repeat retrotransposons of Oryza sativa in GENOME BIOLOGY
  • 2014-12. From algae to angiosperms–inferring the phylogeny of green plants (Viridiplantae) from 360 plastid genomes in BMC EVOLUTIONARY BIOLOGY
  • 2007-12. Repetitive DNA in the pea (Pisum sativum L.) genome: comprehensive characterization using 454 sequencing and comparison to soybean and Medicago truncatula in BMC GENOMICS
  • 2003-10. Highly abundant pea LTR retrotransposon Ogre is constitutively transcribed and partially spliced in PLANT MOLECULAR BIOLOGY
  • 1997-03. What makes Grande1 retrotransposon different? in GENETICA
  • 2007-02. Characterization of AFLAV, a Tf1/Sushi retrotransposon from Aspergillus flavus in MYCOPATHOLOGIA
  • 2001-05. A new gypsy-type retrotransposon, RIRE7: preferential insertion into the tandem repeat sequence TrsD in pericentromeric heterochromatin regions of rice chromosomes in MOLECULAR GENETICS AND GENOMICS
  • 2006-09. Retand: a novel family of gypsy-like retrotransposons harboring an amplified tandem repeat in MOLECULAR GENETICS AND GENOMICS
  • 2008-10. Structure and dynamics of retrotransposons at wheat centromeres and pericentromeres in CHROMOSOMA
  • 2011-12. Plant centromeric retrotransposons: a structural and cytogenetic perspective in MOBILE DNA
  • 2009-12. Network dynamics of eukaryotic LTR retroelements beyond phylogenetic trees in BIOLOGY DIRECT
  • 2007-12. A unified classification system for eukaryotic transposable elements in NATURE REVIEWS GENETICS
  • 2001-03. Vertebrate LTR Retrotransposons of the Tf1/Sushi Group in JOURNAL OF MOLECULAR EVOLUTION
  • 2010-12. Evolutionary genomics revealed interkingdom distribution of Tcn1-like chromodomain-containing Gypsy LTR retrotransposons among fungi and plants in BMC GENOMICS
  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1186/s13100-018-0144-1

    DOI

    http://dx.doi.org/10.1186/s13100-018-0144-1

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1111105173

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/30622655


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