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

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http://hdl.handle.net/10138/316717

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Kalendar , R , Raskina , O , Belyayev , A & Schulman , A 2020 , ' Long tandem arrays of Cassandra retroelements and their role in genome dynamics in plants ' , International Journal of Molecular Sciences , vol. 21 , no. 8 , 2931 . https://doi.org/10.3390/ijms21082931

Title: Long tandem arrays of Cassandra retroelements and their role in genome dynamics in plants
Author: Kalendar, Ruslan; Raskina, Olga; Belyayev, Alexander; Schulman, Alan
Other contributor: University of Helsinki, Department of Agricultural Sciences
University of Helsinki, Institute of Biotechnology

Date: 2020-04-22
Language: eng
Number of pages: 20
Belongs to series: International Journal of Molecular Sciences
ISSN: 1422-0067
DOI: https://doi.org/10.3390/ijms21082931
URI: http://hdl.handle.net/10138/316717
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. 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.
Subject: 5S RNA gene
AEGILOPS
BARLEY
CHROMOSOME
COPY NUMBER VARIATION
Cassandra TRIM
EVOLUTION
FAST PRIMER
RECOMBINATION
RETROTRANSPOSONS
TRANSPOSABLE ELEMENTS
VARIABILITY
ectopic recombination
genome evolution
long tandem array
retrotransposon
1182 Biochemistry, cell and molecular biology
1184 Genetics, developmental biology, physiology
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