A transcriptionally active copia-like retroelement in Citrus limon

Abstract

Abstract:The plant nuclear genome is largely composed of mobile DNA, which can rearrange genomes and other individual gene structure and also affect gene regulation through various promoted activities: transposition, insertion, excision, chromosome breakage, and ectopic recombination. Ty1-copia-like retrotransposon is a widespread class of transposable elements in the plant kingdom, representing a large part of the total DNA content. Here, a novel retrotransposon-like sequence was isolated and identified as the Ty1-copia-like reverse transcriptase domain (named here CLCoy1), based on the homology of known elements. Fluorescence in situ hybridization, revealed that CLCoy1 was mainly located in telomeric and sub-telomeric regions along the Citrus chromosomes. CLCoy1 composes 3.6% of the genome and, interestingly, while transposons are mostly specific to a species, this element was identified in other Citrus species such as Citrus aurantium, Fortunella margarita and Citrus paradisi, but undetected in Poncirus trifoliata. We also determined that wounding, salt and cell culture stress produced transcriptional activation of this novel retroelement in Citrus limon. The novel Ty1-copia-like element CLCoy1 may have played a major role in shaping genome structure and size during Citrus species evolution.

Retrotransposons Control Fruit-Specific, Cold-Dependent Accumulation of Anthocyanins in Blood Oranges

“…Different accessions of blood orange demonstrate the high levels of recombination and transposition associated with the retroelements and suggest that they may be responsible for generating much of the diversity available to Citrus breeders (Tao et al, 2005;Rico-Cabanas, and Martínez-Izquierdo, 2007;De Felice et al, 2009). However, recombination between Tcs1 LTRs at the Ruby locus does not result in phenotypic changes in the levels of anthocyanins produced, confirming that the solo LTR carries all the information for the control of Ruby expression in Sicilian blood oranges.…”

The Ty1-copia families SALIRE and Cotzilla populating the Beta vulgaris genome show remarkable differences in abundance, chromosomal distribution, and age

“…While the localization of Ty1-copia retrotransposons on chromosomes has been previously reported Heslop-Harrison et al 1997;Francki 2001;de Felice et al 2008;Jia et al 2009), only one study describes the chromosomal distribution of Sireviruses (Mroczek and Dawe 2003). Members of the Cotzilla family and the maize elements Opie and PREM-2 analyzed by Mroczek and Dawe (2003) show a similar localization with a dispersed distribution along chromosomes.…”

“…Generally, most Ty1-copia retroelements are present on both arms of chromosomes with exclusion of centromeres, telomeres, and the 18S-5.8S-25S rRNA gene arrays . Exceptions are a family of A. thaliana Ty1-copia retrotransposons which are located at 4′,6′-diamidino-2-phenylindole (DAPI)-positive, ATrich regions at centromeres interspersed with a satellite family Heslop-Harrison et al 1997) or CLCoy elements of Citrus limon that are localized at subtelomeric positions of two chromosomes (de Felice et al 2008). In contrast, Ty3-gypsy-like retrotransposons tend to accumulate in centromeric regions (Nagaki et al 2004, Wu et al 2004, Weber and Schmidt 2009).…”

Different scales of Ty1/copia-like retrotransposon proliferation in the genomes of three diploid hybrid sunflower species

“…Environmental stress has been implicated as a causal agent of LTR retrotransposon derepression and proliferation in plants. It thus seems conceivable that the different habitats and associated environmental stresses experienced by the hybrid species could be associated with these different scales of proliferation, especially given that exposure of plants to high salt concentrations has been shown to induce Ty1/copia-like transcriptional activity in other species (Tapia et al, 2005;De Felice et al, 2009). A survey of Ty1/copia-like diversity (based on the RT region) within the genomes of these sunflower taxa using degenerate PCR followed by sequencing of multiple clones revealed considerable element heterogeneity, with sequence diversity estimates (p) ranging from 0.194 to 0.314 (Table 1).…”