Catoni, M. | Search bioRxiv

bioRxiv2018

Mobilization of Pack-CACTA transposons in Arabidopsis reveals the mechanism of gene shuffling

Pack-TYPE transposons are a unique class of potentially mobile non-autonomous elements that can capture, merge and relocate fragments of chromosomal DNA. It has been postulated that their activity accelerates the evolution of host genes. However, this important presumption is based only on the sequences of currently inactive Pack-TYPE transposons and the acquisition of chromosomal DNA has not been recorded in real time. We have now for the first time witnessed the mobilization of novel Pack-TYPE elements related to the CACTA transposon family over several plant generations. Remarkably, these elements tend to insert into genes as closely spaced direct repeats and they frequently undergo incomplete excisions, resulting in the deletion of one of the end sequences. These properties constitute a mechanism of efficient acquisition of genic DNA residing between neighbouring Pack-TYPE transposons and its subsequent mobilization. Our work documents crucial steps in the formation in vivo of novel Pack-TYPE transposons and thus the mechanism of gene shuffling mediated by this type of mobile element.

genetics↗

bioRxiv2018

Sensitive detection of pre-integration intermediates of LTR retrotransposons in crop plants

Retrotransposons have played an important role in the evolution of host genomes1,2. Their impact on host chromosomes is mainly deduced from the composition of DNA sequences, which have been fixed over evolutionary time. These studies provide important \"snapshots\" reflecting historical activities of transposons but do not predict current transposition potential. We previously reported Sequence-Independent Retrotransposon Trapping (SIRT) as a methodology that, by identification of extrachromosomal linear DNA (eclDNA), revealed the presence of active LTR retrotransposons in Arabidopsis9. Unfortunately, SIRT cannot be applied to large and transposon-rich genomes of crop plants. We have since developed an alternative approach named ALE-seq (amplification of LTR of eclDNAs followed by sequencing). ALE-seq reveals sequences of 5 LTRs of eclDNAs after two-step amplification: in vitro transcription and subsequent reverse transcription. Using ALE-seq in rice, we detected eclDNAs for a novel Copia family LTR retrotransposon, Go-on, which is activated by heat stress. Sequencing of rice accessions revealed that Go-on has preferentially accumulated in indica rice grown at higher temperatures. Furthermore, ALE-seq applied to tomato fruits identified a developmentally regulated Gypsy family of retrotransposons. Importantly, a bioinformatic pipeline adapted for ALE-seq data analyses allows the direct and reference-free annotation of new active retroelements. This pipeline allows assessment of LTR retrotransposon activities in organisms for which genomic sequences and/or reference genomes are unavailable or are of low quality.

plant biology↗