Long Tandem Arrays of Cassandra Retroelements and Their Role in Genome Dynamics in Plants

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.

DNA profiling and assessment of genetic diversity of relict speciesAllium altaicumPall. on the territory of Altai

“…Reproducibility of PCR and high polymorphism can be used as an express technology in assessing the ecogeographic diversity of any plant species ( Kumar et al, 2018 ; Phong et al, 2016 ). Retrotransposons are activated in response to the influence of various forms of abiotic and biotic stresses, and this can lead to genome destabilization ( Belyayev et al, 2010 ; Kalendar et al, 2020 ; Vicient et al, 2001 ; Wessler, 1996 ). Retrotransposons can be one of the sources of genetic variability induced by the appearance of adaptation traits due to accidental insertions/deletions of retrotransposons.…”

“…Therefore, under stress conditions, bursts in activity of retrotransposons and transposons can be fixed genetically in plants with vegetative reproduction. The induced genetic rearrangements and insertions of mobile genetic elements in regions of active euchromatin contribute to genome alteration, which leads to “genomic stress” ( Belyayev et al, 2010 ; Capy et al, 2000 ; Kalendar et al, 2020 ). Transcriptionally active retrotransposons can potentially participate indirectly in gene regulation and adaptation to environmental stress, since their activity is induced by stressful environmental conditions ( Belyayev et al, 2010 ; Capy et al, 2000 ; Vicient et al, 2001 ; Wessler, 1996 ).…”

Comparative Study of Pine Reference Genomes Reveals Transposable Element Interconnected Gene Networks

“…Consequently, comparison of genomes assembled with different approaches and of varying quality should be performed with caution to avoid errors when interpreting the results. Additionally, widespread gene capture by TEs has often been described for large plant genomes [ 42 , 101 , 102 , 103 ] and this phenomenon could introduce additional errors in short-read genome assemblies [ 103 ]. Considering the high copy number and the structural and functional differences from protein-coding genes, it is advisable to annotate TE-associated sequences in separate data sets even though many TE families bear open reading frames.…”

“…The internal region of autonomous RLXs contain gag- and polyprotein-coding domains that produce the proteins necessary for retrotransposition, namely, protease, reverse transcriptase, and integrase. Non-autonomous elements contain empty, partial, or disrupted polyprotein sequences and use proteins produced by autonomous elements, sometimes integrating more effectively than their autonomous partner [ 35 , 40 , 41 , 42 ]. Reverse transcription processes introduce mutations and can produce chimeric elements by template switching [ 43 ].…”

Figure 1: Places of collection of samples of rare and endemic species of onions in the territory of Kazakhstani Altai.

“…Therefore, under stress conditions, bursts in activity of retrotransposons and transposons can be fixed genetically in plants with vegetative reproduction. The induced genetic rearrangements and insertions of mobile genetic elements in regions of active euchromatin contribute to genome alteration, which leads to "genomic stress" (Belyayev et al, 2010;Capy et al, 2000;Kalendar et al, 2020). Transcriptionally active retrotransposons can potentially participate indirectly in gene regulation and adaptation to environmental stress, since their activity is induced by stressful environmental conditions (Belyayev et al, 2010;Capy et al, 2000;Vicient et al, 2001;Wessler, 1996).…”