Comparative genomics analysis of repetitive elements in ten gymnosperm species: “dark repeatome” and its abundance in conifer and gnetum species

Avi Titievsky, Yuliya A. Putintseva, Elizaveta A. Taranenko, Sofya Baskin, Natalia V. Oreshkova, Elia Brodsky, Alexandra V. Sharova, Vadim V. Sharov, Julia Panov, Dmitry A. Kuzmin, Leonid Brodsky, Konstantin V. Krutovsky

Research output: Contribution to journalArticlepeer-review

Abstract

Repetitive elements (RE) and transposons (TE) can comprise up to 80% of some plant genomes and may be essential for regulating their evolution and adaptation. The “repeatome” information is often unavailable in assembled genomes because genomic areas of repeats are challenging to assemble and are often missing from final assembly. However, raw genomic sequencing data contain rich information about RE/TEs. Here, raw genomic NGS reads of 10 gymnosperm species were studied for the content and abundance patterns of their “repeatome”. We utilized a combi-nation of alignment on databases of repetitive elements and de novo assembly of highly repetitive sequences from genomic sequencing reads to characterize and calculate the abundance of known and putative repetitive elements in the genomes of 10 conifer plants: Pinus taeda, Pinus sylvestris, Pinus sibirica, Picea glauca, Picea abies, Abies sibirica, Larix sibirica, Juniperus communis, Taxus baccata, and Gnetum gnemon. We found that genome abundances of known and newly discovered putative repeats are specific to phylogenetically close groups of species and match biological taxa. The grouping of species based on abundances of known repeats closely matches the grouping based on abundances of newly discovered putative repeats (kChains) and matches the known taxonomic relations.

Original languageEnglish
Article number1234
JournalLife
Volume11
Issue number11
DOIs
StatePublished - Nov 2021

Bibliographical note

Funding Information:
Acknowledgments: We acknowledge support by the Open Access Publication Funds of the University of Göttingen.

Funding Information:
This study was supported by a grant to Tauber Bioinformatics Research Center from the Laszlo N. Tauber Family Foundation and by Research Grant No. 14.Y26.31.0004 from the Government of the Russian Federation to the Genome Research and Education Center, Siberian Federal University. Acknowledgments: We acknowledge support by the Open Access Publication Funds of the University of G?ttingen.

Funding Information:
Funding: This study was supported by a grant to Tauber Bioinformatics Research Center from the Laszlo N. Tauber Family Foundation and by Research Grant No. 14.Y26.31.0004 from the Government of the Russian Federation to the Genome Research and Education Center, Siberian Federal University.

Publisher Copyright:
© 2021 by the authors. Licensee MDPI, Basel, Switzerland.

Keywords

  • Gymnosperms
  • Principal component analysis
  • Repetitive elements

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Biochemistry, Genetics and Molecular Biology (all)
  • Space and Planetary Science
  • Paleontology

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