Transcriptome-wide Identification and Expression Analysis of Brachypodium distachyon Transposons in Response to Viral Infection

Abstract

Transposable elements (TEs) are the most abundant group of genomic elements in plants that can be found in genic or intergenic regions of their host genomes. Several stimuli such as biotic or abiotic stress have roles in either activating their transcription or transposition. Here the effect of the Panicum mosaic virus (PMV) and its satellite virus (SPMV) infection on the transposon transcription of the Brachypodium distachyon model plant was investigated. To evaluate the transcription activity of TEs, transcriptomic data of mock and virus inoculated plants were compared. Our results indicate that major components of TEs are retroelements in all RNA-seq libraries. The number of transcribed TEs detected in mock inoculated plants is higher than virus inoculated plants. In comparison with mock inoculated plants 13% of the TEs showed at least two folds alteration upon PMV infection and 21% upon PMV+SPMV infection. Rather than inoculation with PMV alone inoculation with PMV+SPMV together also increased various TE encoding transcripts expressions. MuDR-N78C_OS encoding transcript was strongly up-regulated against both PMV and PMV+SPMV infection. The synergism generated by PMV and SPMV together enhanced TE transcripts expressions than PMV alone. It was observed that viral infection induced the transcriptional activity of several transposons. The results suggest that increased expressions of TEs might have a role in response to biotic stress in B. distachyon. Identification of TEs which are taking part in stress can serve useful information for functional genomics and designing novel breeding strategies in developing stress resistance crops.

A review of strategies used to identify transposition events in plant genomes

“…A global analysis of TE-derived transcripts can be produced with microarrays ( Picault et al., 2009 ; Rocheta et al., 2016 ). Comprehensive information about the whole spectrum of actively transcribed TEs can also be captured by RNA-seq based on massive parallel DNA sequencing technologies ( Gürkök, 2017 ; Oberlin et al., 2017 ; Qiu and Ungerer, 2018 ; Vangelisti et al., 2019 ; Jiménez-Ruiz et al., 2020 ; Kirov et al., 2020 ). RNA-seq data have been utilized and interpreted differently in reports aiming at the description of global activity of TEs.…”

“…RNA-seq data have been utilized and interpreted differently in reports aiming at the description of global activity of TEs. While some reports simply presented a spectrum of TEs captured in RNA-seq reads ( Gürkök, 2017 ; Jiménez-Ruiz et al., 2020 ), in other reports, especially those concerning plant species for which high quality reference genomes were available, TE-derived transcripts were mapped to the reference genome assembly ( Li et al., 2010 ; Hollister et al., 2011 ; Valdebenito-Maturana and Riadi, 2018 ). However, owing to the fact that some TE families comprise numerous copies and the evolutionary relationships among TE families can be complex, interpretation of the RNA-seq data remains challenging.…”