Characterisation of pararetrovirus-like sequences in the genome of potato <i>(Solanum tuberosum)</i>

Abstract

Three families of pararetrovirus-like sequences were isolated from the genome of potato using PCR of a characteristic fragment extending from the end of the transactivator domain. The potato pararetrovirus-like sequences are abundant in the nuclear genome of potato as demonstrated by their hybridisation to high-molecular weight DNA in Southern transfers and by fluorescence in situ hybridisation. Sequencing of cloned PCR products demonstrated that the potato pararetrovirus-like sequences were similar to other pararetroviral sequences and also to some expressed sequences from tobacco and tomato, notably from callus and Agrobacterium-infected tissue. It is possible that the potato pararetroviral sequences defend against viral genes via silencing mechanisms, although, as in Petunia or banana, their transcription and recombination may cause infection under stress conditions.

Endogenous pararetroviral sequences in tomato (Solanum lycopersicum) and related species

“…The absence of copies with a full-length coding sequence or a functional promoter region in the genomic library does not exclude the existence of a full copy elsewhere in the genome since the cDNAs were not identical to the genomic copies sequenced. EPRV-like EST matches from normal and stressed tissue respectively were also reported for the EPRV family SoTu in the potato genome [4]. …”

“…which revealed up to 86 to 92% sequence identity on the nucleotide level. The conserved 272 to 282 bp box has an overall identity of up to 70% with its counterpart in S.tuberosum , SoTu [4] and 80% to the IGR of Nicotiana EPRVs with several highly conserved motives. Some IGR sequences contained short (27 to 104 bp) AT-rich structures of low complexity (Lh2, Lh5, Le4, Le5) while others revealed short (12 to 24 bp) direct repeats which were not conserved between the different IGRs (Lh2, Lh5, Lh7, Le5).…”

“…Our results demonstrate that Lyc EPRVs and related sequences are common in many species of Solanum subsection lycopersicon. Given that tomato and potato are in the same genus, Lyc EPRVs are more similar to known EPRVs from Nicotiana than to the SoTu EPRV family [4] from potato.…”

“…If retroelements constitute some 50% of the genome [24,45,46], then the association is little different from random, particularly if there is a preference for EPRVs and metaviridae elements to cluster in the genomic regions such as the centromere (see Fig 3. and [4,8] for petunia and potato). Nevertheless, it is tempting to suggest functional associations: pararetroviruses do not encode an integrase, so intact retrotransposons may supply this function in trans and related structural sites [14].…”

“…Unlike other retroelements, such as retroviruses and retrotransposons, integration into the host genome is not essential during their replication cycle. Nevertheless, in recent years there have been accumulating reports of endogenous pararetroviral sequences (EPRVs) in the nuclear genomes of several plants including tobacco ( Nicotiana tabacum ) and other Nicotiana species [1-3], potato [4], banana [5-7], petunia [8] and rice [9]. EPRVs are assumed to integrate by illegitimate recombination into the host genome, where they may accumulate to high copy numbers [1,10].…”