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Tree Genetics & Genomes

, 11:107 | Cite as

A survey of Gypsy and Copia LTR-retrotransposon superfamilies and lineages and their distinct dynamics in the Populus trichocarpa (L.) genome

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

Abstract

In this work, we report a comprehensive study of long terminal repeat retrotransposons of Populus trichocarpa. Our research group studied the retrotransposon component of the poplar genome in 2012, isolating 1479 putative full-length elements. However, in that study, it was not possible to identify the superfamily to which the majority of isolated full-length elements belonged. Moreover, during recent years, the genome sequence of P. trichocarpa has been updated, deciphering thek sequences of a number of previously unresolved loci. In this work, we performed a complete scan of the updated version of the genome sequence to isolate full-length retrotransposons based on sequence and structural features. The new dataset showed a reduced number of elements (958), and 21 full-length elements were discovered for the first time. The majority of retroelements belonged to the Gypsy superfamily (57 %), while Copia elements amounted to 41.1 % of the dataset. Full-length elements were dispersed throughout the chromosomes. However, Gypsy and, to a lesser extent, Copia elements accumulated preferentially at putative centromeres. Gypsy elements were more active in retrotransposition than Copia elements, with the exception of during the past million years, in which Copia elements were the most active. Improved annotation procedures also allowed us to determine the specific lineages to which isolated elements belonged. The three Gypsy lineages, Athila, OGRE, and Chromovirus (in the decreasing order), were by far the most abundant. On the other hand, each identified Copia lineage represented less than 1 % of the genome. Significant differences in the insertion age were found among lineages, suggesting specific activation mechanisms. Moreover, different chromosomal regions were affected by retrotransposition in different ages. In all chromosomes, putative pericentromeric regions were filled with elements older than the mean insertion age. Overall, results demonstrate structural and functional differences among plant retrotransposon lineages and further support the view of retrotransposons as a community of different organisms in the genome.

Keywords

Copia Gypsy LTR-retrotransposon lineages Poplar genome Populus trichocarpa 

Abbreviations

RE

Retrotransposon

LTR-RE

LTR-retrotransposon

LTR

Long terminal repeat

MY

Million of years

Notes

Acknowledgments

Research work was funded by the Department of Agriculture, Food, and Environment, University of Pisa, project PLANTOMICS.

Data archiving statement

All sequences described in this work were isolated from the 2014 version of the sequenced genome of P. trichocarpa (Tuskan et al. 2006; Slavov et al. 2012), deposited at NCBI (project number AARH02, http://www.ncbi.nlm.nih.gov/assembly/GCF_000002775.3). Coordinates and annotation of each sequence are reported in the Supplementary Material 1. Sequences are also available at the Department of Agriculture, Food, and Environment of Pisa University repository website (http://www.agr.unipi.it/Sequence-Repository.358.0.html).

Supplementary material

11295_2015_937_MOESM1_ESM.xlsx (160 kb)
ESM 1 (XLSX 159 kb)
11295_2015_937_MOESM2_ESM.pdf (303 kb)
ESM 2 (PDF 302 kb)
11295_2015_937_MOESM3_ESM.pdf (91 kb)
ESM 3 (PDF 91 kb)
11295_2015_937_MOESM4_ESM.pdf (277 kb)
ESM 4 (PDF 277 kb)

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Copyright information

© Springer-Verlag Berlin Heidelberg 2015

Authors and Affiliations

  • Lucia Natali
    • 1
  • Rosa Maria Cossu
    • 1
    • 2
  • Flavia Mascagni
    • 1
  • Tommaso Giordani
    • 1
  • Andrea Cavallini
    • 1
    Email author
  1. 1.Department of Agricultural, Food, and EnvironmentUniversity of PisaPisaItaly
  2. 2.Institute of Life SciencesScuola Superiore Sant’AnnaPisaItaly

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