Evolving Together: Cassandra Retrotransposons Gradually Mirror Promoter Mutations of the 5S rRNA Genes

Abstract

The 5S rRNA genes are among the most conserved nucleotide sequences across all species. Similar to the 5S preservation we observe the occurrence of 5S-related nonautonomous retrotransposons, so-called Cassandras. Cassandras harbor highly conserved 5S rDNA-related sequences within their long terminal repeats, advantageously providing them with the 5S internal promoter. However, the dynamics of Cassandra retrotransposon evolution in the context of 5S rRNA gene sequence information and structural arrangement are still unclear, especially: (1) do we observe repeated or gradual domestication of the highly conserved 5S promoter by Cassandras and (2) do changes in 5S organization such as in the linked 35S-5S rDNA arrangements impact Cassandra evolution? Here, we show evidence for gradual co-evolution of Cassandra sequences with their corresponding 5S rDNAs. To follow the impact of 5S rDNA variability on Cassandra TEs, we investigate the Asteraceae family where highly variable 5S rDNAs, including 5S promoter shifts and both linked and separated 35S-5S rDNA arrangements have been reported. Cassandras within the Asteraceae mirror 5S rDNA promoter mutations of their host genome, likely as an adaptation to the host's specific 5S transcription factors and hence compensating for evolutionary changes in the 5S rDNA sequence. Changes in the 5S rDNA sequence and in Cassandras seem uncorrelated with linked/separated rDNA arrangements. We place all these observations into the context of angiosperm 5S rDNA-Cassandra evolution, discuss Cassandra's origin hypotheses (single or multiple) and Cassandra's possible impact on rDNA and plant genome organization, giving new insights into the interplay of ribosomal genes and transposable elements.

The Genome Organization of 5S rRNA Genes in the Model Organism Tribolium castaneum and Its Sibling Species Tribolium freemani

“…For example, so-called Cassandras, the 5S-related nonautonomous retrotransposons in plants, harbor highly conserved 5S rDNA sequences within their long terminal repeats [ 30 ]. Moreover, recent work has shown evidence for a gradual coevolution of Cassandra transposons with their corresponding 5S rDNAs [ 11 ]. However, the organization of 5S rDNA clusters in T. freemani is, as far as we know, the first example of 5S rRNA genes being associated with two types of the most abundant repetitive sequences, satDNA and TE.…”

“…The DNA sequence of Mutsu retrotransposons is approximately 5500 bp long and consists of two open reading frames (ORFs) flanked by untranslated regions (UTRs). Recent evidence has shown the occurrence of 5S-related nonautonomous retrotransposons, so-called Cassandras, in plants [ 11 ]. Cassandras harbor highly conserved 5S rDNA-related sequences within their long terminal repeats.…”

The Dynamic Interplay Between Ribosomal DNA and Transposable Elements: A Perspective From Genomics and Cytogenetics

“…To our knowledge, there are no 5S-derived SINEs in plants. Instead, plants harbor non-autonomous LTR retrotransposons with 5S rDNA promoter sequences in their LTRs, named Cassandra ( Kalendar et al 2008 , 2020 ; Maiwald et al 2021 , 2024 ; a recent study also found analogous retrotranspons in ribbon worms, named Ajax ( Kojima 2024 )). Cassandras were first described in 50 plant species including ferns, monocots, and eudicots and later (re)confirmed in several angiosperm lineages ( Yin et al 2014 ; Gao et al 2016 ; Kalendar et al 2020 ), including Arabidopsis ( Sampath and Yang 2014 ), Agave ( Tamayo-Ordóñez et al 2018 ), and beets ( Maiwald et al 2021 ).…”

“…At present, there are no reports of Cassandras in gymnosperms. Looking closely at the Asteraceae, the plant family with most variability in the 5S rDNA, including rDNA arrangements ( Garcia et al 2010 ) and promoter shifts ( Garcia et al 2012 ), Maiwald et al (2024) found that Cassandra retrotransposons closely mimic the promoter motif changes, thus providing a recent example of rDNA–TE co-evolution.…”