Long tandem arrays of cassandra retroelements and their role in genome dynamics in plants

Ruslan Kalendar, Olga Raskina, Alexander Belyayev, Alan H. Schulman

Research output: Contribution to journalArticlepeer-review

Abstract

Retrotransposable elements are widely distributed and diverse in eukaryotes. Their copy number increases through reverse-transcription-mediated propagation, while they can be lost through recombinational processes, generating genomic rearrangements. We previously identified extensive structurally uniform retrotransposon groups in which no member contains the gag, pol, or env internal domains. Because of the lack of protein-coding capacity, these groups are non-autonomous in replication, even if transcriptionally active. The Cassandra element belongs to the non-autonomous group called terminal-repeat retrotransposons in miniature (TRIM). It carries 5S RNA sequences with conserved RNA polymerase (pol) III promoters and terminators in its long terminal repeats (LTRs). Here, we identified multiple extended tandem arrays of Cassandra retrotransposons within different plant species, including ferns. At least 12 copies of repeated LTRs (as the tandem unit) and internal domain (as a spacer), giving a pattern that resembles the cellular 5S rRNA genes, were identified. A cytogenetic analysis revealed the specific chromosomal pattern of the Cassandra retrotransposon with prominent clustering at and around 5S rDNA loci. The secondary structure of the Cassandra retroelement RNA is predicted to form super-loops, in which the two LTRs are complementary to each other and can initiate local recombination, leading to the tandem arrays of Cassandra elements. The array structures are conserved for Cassandra retroelements of different species. We speculate that recombination events similar to those of 5S rRNA genes may explain the wide variation in Cassandra copy number. Likewise, the organization of 5S rRNA gene sequences is very variable in flowering plants; part of what is taken for 5S gene copy variation may be variation in Cassandra number. The role of the Cassandra 5S sequences remains to be established.

Original languageEnglish
Article number2931
JournalInternational Journal of Molecular Sciences
Volume21
Issue number8
DOIs
StatePublished - 2 Apr 2020

Bibliographical note

Funding Information:
Funding: This work was supported under the Science Committee of the Ministry of Education and Science of the Republic of Kazakhstan in the framework of program funding for research (BR05236574) as well as Academy of Finland Decision 314961. The research was partly supported by the long-term research development project no. RVO 67985939 from the Academy of Sciences of the Czech Republic. Open access funding provided by University of Helsinki including Helsinki University Central Hospital.

Publisher Copyright:
© 2020 by the authors. Licensee MDPI, Basel, Switzerland.

Keywords

  • 5S RNA gene
  • Cassandra TRIM
  • Ectopic recombination
  • Genome evolution
  • Long tandem array
  • Retrotransposon

ASJC Scopus subject areas

  • Catalysis
  • Molecular Biology
  • Spectroscopy
  • Computer Science Applications
  • Physical and Theoretical Chemistry
  • Organic Chemistry
  • Inorganic Chemistry

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