Tree Genetics & Genomes

, 13:96 | Cite as

Comparative genome-wide analysis of repetitive DNA in the genus Populus L.

  • Gabriele Usai
  • Flavia Mascagni
  • Lucia Natali
  • Tommaso Giordani
  • Andrea CavalliniEmail author
Original Article
Part of the following topical collections:
  1. Genome Biology


Genome skimming was performed, using Illumina sequence reads, in order to obtain a detailed comparative picture of the repetitive component of the genome of Populus species. Read sets of seven Populus and two Salix species (as outgroups) were subjected to clustering using RepeatExplorer (Novák et al. BMC Bioinformatics 11:378 2010). The repetitive portion of the genome ranged from 33.8 in Populus nigra to 46.5% in Populus tremuloides. The large majority of repetitive sequences were long terminal repeat-retrotransposons. Gypsy elements were over-represented compared to Copia ones, with a mean ratio Gypsy to Copia of 6.7:1. Satellite DNAs showed a mean genome proportion of 2.2%. DNA transposons and ribosomal DNA showed genome proportions of 1.8 and 1.9%, respectively. The other repeat types accounted for less of 1% each. Long terminal repeat-retrotransposons were further characterized, identifying the lineage to which they belong and studying the proliferation times of each lineage in the different species. The most abundant lineage was Athila, which showed large differences among species. Concerning Copia lineages, similar transpositional profiles were observed among all the analysed species; by contrast, differences in transpositional peaks of Gypsy lineages were found. The genome proportions of repeats were compared in the seven species, and a phylogenetic tree was built, showing species separation according to the botanical section to which the species belongs, although significant differences could be found within sections, possibly related to the different geographical origin of the species. Overall, the data indicate that the repetitive component of the genome in the poplar genus is still rapidly evolving.


Populus LTR-retrotransposons Repetitive DNA Comparative retrotransposon dynamics 



This research work was supported by the Department of Agriculture, Food and Environment, University of Pisa, Italy, project Plantomics.

Supplementary material

11295_2017_1181_MOESM1_ESM.docx (181 kb)
ESM 1 (DOCX 181 kb)


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Copyright information

© Springer-Verlag GmbH Germany 2017

Authors and Affiliations

  • Gabriele Usai
    • 1
  • Flavia Mascagni
    • 1
  • Lucia Natali
    • 1
  • Tommaso Giordani
    • 1
  • Andrea Cavallini
    • 1
    Email author
  1. 1.Department of Agriculture, Food and EnvironmentUniversity of PisaPisaItaly

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