Table 1.

Summary of approaches used to identify actively transposing elements.

Strategy used to identify actively transposing TEs	Main drawbacks	Recommendations for efficient targeting actively transposing TEs
Targeting TE-derived transcripts	- existence of TE-derived transcripts not competent for transposition (chimeric transcripts; transcripts involved in epigenetic silencing of TEs; post-transcriptional suppression mechanisms by TE-derived sequences)	- combine with another technique targeting products from the final phases of the transposition process (e.g. eclDNA, eccDNA)
Targeting TE-derived proteins	- non-transposing TEs can still express proteins - requires equipment that is not so common in molecular genetics laboratories	- combine with another technique targeting products from the final phases of the transposition process (e.g. eclDNA, eccDNA) - PIT (Proteomics Informed by Transcriptomics)
Targeting eclDNA	- eclDNA can occur as a result of other cellular processes (e.g. cell lysis, existence of micro-eclDNA)	- include a selective step to enrich TE-derived eclDNAs (e.g. PBS complementary to MET-iCAT tRNA) - combine with high throughput sequencing (ALE-Seq)
Targeting eccDNA	- eccDNA does not directly participate in the process of transposition - eccDNA can occur as a result of other cellular processes	- combine with high throughput sequencing to identify novel insertion sites
Identification of novel insertion sites by using TE-based genotyping platforms	- laborious and time consuming and error-prone	- use PST-PCR v.2 as a less laborious method
High throughput sequencing	- availability of a high quality reference genome or a large set of resequenced genomes of related accessions - inaccuracies related to short reads provided by the Illumina technology (problems with longer TEs, such as LTR-RTs; insertions in repetitive regions)	- use technologies producing long reads, e.g. Oxford Nanopore