Broken, silent, and in hiding: tamed endogenous pararetroviruses escape elimination from the genome of sugar beet (Beta vulgaris)

Abstract

Background and Aims Endogenous pararetroviruses (EPRVs) are widespread components of plant genomes that originated from episomal DNA viruses of the Caulimoviridae family. Due to fragmentation and rearrangements, most EPRVs have lost their ability to replicate through reverse transcription and to initiate viral infection. Similar to the closely related retrotransposons, extant EPRVs were retained and often amplified in plant genomes for several million years. Here, we characterize the complete genomic EPRV fraction of the crop sugar beet (Beta vulgaris, Amaranthaceae) to understand how they shaped the beet genome and to suggest explanations for their absent virulence. Methods Using next- and third-generation sequencing data and the genome assembly, we reconstructed full-length in silico representatives for the three host-specific EPRVs (beetEPRVs) in the B. vulgaris genome. Focusing on the endogenous caulimovirid beetEPRV3, we investigated its chromosomal localization, abundance, and distribution by fluorescent in situ and Southern hybridization. Key Results BeetEPRVs range between 7.5 and 10.7 kb (0.3 % of the B. vulgaris genome) and are heterogeneous in structure and sequence. Although all three beetEPRVs were assigned to the florendoviruses, they showed variably arranged protein-coding domains, different fragmentation, and preferences for diverse sequence contexts. We observed small RNAs that specifically target the individual beetEPRVs, indicating stringent epigenetic suppression. BeetEPRV3 sequences occur along all sugar beet chromosomes, preferentially in vicinity to each other and are associated with heterochromatic, centromeric, and intercalary satellite DNAs. BeetEPRV3 members also exist in genomes of related wild species, indicating an initial beetEPRV3 integration 13.4 to 7.2 million years ago. Conclusions Our study in beet illustrates the variability of EPRV structure and sequence in a single host genome. Evidence of sequence fragmentation and epigenetic silencing imply possible plant strategies to cope with long-term persistence of EPRVs, including amplification, fixation in the heterochromatin, and containment of EPRV virulence.

Comparative Repeat Profiling of Two Closely Related Conifers (Larix decidua and Larix kaempferi) Reveals High Genome Similarity With Only Few Fast-Evolving Satellite DNAs

“…The similarities include both, repeat family and abundance. In line with evidence from other conifers (Prunier et al, 2016), these results also suggest the limited TE elimination, usually carried out by recombination, reshuffling, fragmentation, or removal as aftermath to genomic rearrangements (Ma et al, 2004;Ren et al, 2018;Kögler et al, 2020;Maiwald et al, 2021;Schmidt et al, 2021). Along the same lines, we did not observe any transpositional bursts of amplification during the speciation of the larches.…”

Participation of Multifunctional RNA in Replication, Recombination and Regulation of Endogenous Plant Pararetroviruses (EPRVs)

“…ERPVs have been found accumulated in heterochromatin, in particular in AT-rich regions and next to TA dinucleotide-rich ( Oryza sp. : Kunii et al, 2004 ; and Liu et al, 2012 ; various species: Geering et al, 2014 , Beta vulgaris : Schmidt et al, 2021 ), but also next to retroelements and transposons (tomato: Staginnus et al, 2007 ; Petunia: Richert-Pöggeler et al, 2003 ; Schwarzacher et al, 2016 ). The latter would support an alternative mode of integration for pararetroviruses together with retrotransposons during reverse transcription when template switches can occur between viral RNA strands ( Hohn, 1994 ).…”

“…Often EPRVs form clusters and can occupy large parts of the genome (e.g., tobacco: Lockhart et al, 2000 ; Petunia, Richert-Pöggeler et al, 2003 ; rice: Liu et al, 2012 ; Citrinae spp. : Yu et al, 2019 ; Beta vulgaris : Schmidt et al, 2021 ) and could result from the simultaneous integration of several EPRV copies in tandem or nested, or from recombination of episomal viruses with already integrated sequences ( Hohn et al, 2008 ). Amplifications of EPRVs within the host genome can further lead to the substantial amount of EPRVs found in many plant genomes.…”

“…In order to control EPRVs, copies are frequently inactivated by sequence degeneration or fragmentation to render transcription of entire virus components ineffective ( Figure 1B ). Alternatively, epigenetic silencing through methylation and small RNAs (sRNAs) has been observed ( Noreen et al, 2007 ; Staginnus et al, 2007 ; Schmidt et al, 2021 , and see below). Heterochromatin that is generally transcriptionally inactive and shows low recombination rates ( Heslop-Harrison and Schwarzacher, 2011 ) therefore can be viewed as safe havens for EPRVs ( Schmidt et al, 2021 ) and similar to retroelements can influence the genome organization and recombination landscape ( Kent et al, 2017 ).…”

“…Endogenous TVCV-like sequences in Solanum species show CHH methylation ( Staginnus et al, 2007 ), further supporting RdDM based transcriptional silencing of EPRVs, and Fri EPRV showed abundant 24 nt siRNAs, a hallmark of TGS by RdRM ( Becher et al, 2014 ). In Beta vulgaris , sRNAs between 18 and 30 nt were found, indicating that florendovirus beet EPRVs, although not present as active forms in nature, are nevertheless silenced by TGS and PTGS ( Schmidt et al, 2021 ). In citrus, Cit EPRV was assembled from 24 nt sRNAs, while other non-endogenous viral genomes in this study were assembled from 21–22 nt sRNAs ( Barrero et al, 2017 ).…”