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ExplorATE test data: a pipeline to explore active transposable elements from RNAseq data without a reference genome

ABSTRACT: Transposable elements (TEs) are ubiquitous in genomes. Many of these TEs remain active and are an important fraction of the transcriptomes with potential effects on the host genomes. The functional impact of TEs is well known for model organisms, however, in transcriptomes analysis of non-model organisms, this information is ignored due to the difficulty in identifying and quantifying TEs. Here we develop ExplorATE, a pipeline that allows the identification and quantification of active TEs in non-model organisms that can be easily implemented within the R environment. Based on simulated data, we show that our pipeline accurately identifies and quantifies TEs, over-performing the commonly used tools in model organisms. We show the implementation of ExplorATE using real data for RNA-seq samples from different tissues (liver, ovary, and brain) of Liolaemus parthenos, the only parthenogenetic lizard known to date in the entire clade Iguanidae (pleurodonta). Our results show that a significant fraction of the transcriptome contains repeats, however many of these are co-expressed with genes. The implementation of our pipeline in real data allowed the identification of the most abundant transposon families in each tissue. The ERV2, CR1, and SINE3 families were particularly abundant in the liver. A test data set is provided in the ExplorATE package.

ORGANISM(S): Liolaemus parthenos

PROVIDER: GSE173261 | GEO | 2021/07/30

REPOSITORIES: GEO

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Project description:Background: Transcriptional activation of structurally autonomous transposable elements (TEs) is a precursor to both autonomous and non-autonomous transposition in host genomes. However, the identification of those transcribed TE loci that are competent autonomous elements, their genomic locations and the specific conditions under which these loci can contribute to mobilisation of both autonomous and non-autonomous elements remains largely unknown. Results: A three-channel analysis pipeline was established to identified expressed TE loci. This pipeline is mainly comprised of three different existing tools (htseq-count, bedtools, and TEFingerprint) for mapped read quantification. Using Vitis vinifera embryogenic callus as a model, we exposed the callus to live cultures of an endemic grapevine yeast Hanseniaspora uvarum to determine the landscape and properties of expressed TE loci. In this system, only 1.7%-2.5% of total annotated TE loci were transcribed, of which 5%-10% of these were full-length (>90% length integrity). Collectively, these TE loci (including fragmented and structurally ‘autonomous’ loci) exhibited a significant tendency to be found within introns of expressed genes. This strong location bias towards expressed genes was also observed in Arabidopsis thaliana wild-type and ibm2, but not in ddm1. Moreover, in the grapevine model, differentially expressed TE loci tend to present similar expression pattern with co-localized differentially expressed genes. Nonetheless, utilizing Oxford Nanopore Technology (ONT) cDNA sequencing, we found a strong correlation between the inclusion of intronic TEs in gene transcripts and the presence of premature termination codons in these transcripts. Finally, we identified full-length transcripts derived from structurally autonomous TE loci in our grapevine system, although the level of these transcripts was low. Conclusions: Our observations in the two disparate plant model systems reveal the closely connected transcriptional relationship between TEs and co-localized genes when the epigenetic silencing system is not compromised. Furthermore, we found that the stress treatment alone was not sufficient to induce large scale full length transcription from structurally intact TE loci, a precursor for mobilisation of non-autonomous and autonomous elements.

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ExplorATE test data: a pipeline to explore active transposable elements from RNAseq data without a reference genome

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