University of Cambridge, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences
Jungnam Cho1,2,3*, Matthias Benoit1, Marco Catoni1,4, Hajk-Georg Drost1, Anna Brestovitsky1, Matthijs Oosterbeek1,5 and Jerzy Paszkowski1,6*
1 The Sainsbury Laboratory, University of Cambridge, Cambridge, UK. 2 National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai, China. 3 CAS-JIC Centre of Excellence for Plant and Microbial Science, Chinese Academy of Sciences, Shanghai, China. 4 School of Biosciences, University of Birmingham, Birmingham, UK. 5 Present address: Laboratory of Nematology, Wageningen University, Wageningen, the Netherlands. 6Present address: Radachowka 37, Kolbiel, Poland.
*Correspondence to Jungnam Cho or Jerzy Paszkowski
Retrotransposons have played an important role in the evolution of host genomes 1,2. Their impact is mainly deduced from the composition of DNA sequences that have been fixed over evolutionary time 2. Such studies provide important ‘snapshots’ reflecting the historical activities of transposons but do not predict current transposition potential. We previously reported sequence-independent retrotransposon trapping (SIRT) as a method that, by identification of extrachromosomal linear DNA (eclDNA), revealed the presence of active long terminal repeat (LTR) retrotransposons in Arabidopsis 3. However, SIRT cannot be applied to large and transposon-rich genomes, as found in crop plants. We have developed an alternative approach named ALE-seq (amplification of LTR of eclDNAs followed by sequencing) for such situations. 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 Oryza sativa ssp. indica rice grown at higher temperatures. Furthermore, ALE-seq applied to tomato fruits identified a developmentally regulated Gypsy family of retrotransposons. A bioinformatic pipeline adapted for ALE-seq data analyses is used for 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 either unavailable or of low quality.