PT  - JOURNAL ARTICLE
AU  - Fatemeh Sharifi
AU  - Yuzhen Ye
TI  - Identification and Classification of Reverse Transcriptases in Bacterial Genomes and Metagenomes
AID  - 10.1101/2021.01.26.428298
DP  - 2021 Jan 01
TA  - bioRxiv
PG  - 2021.01.26.428298
4099  - http://biorxiv.org/content/early/2021/01/26/2021.01.26.428298.short
4100  - http://biorxiv.org/content/early/2021/01/26/2021.01.26.428298.full
AB  - Reverse Transcriptases (RTs) are found in different systems including group II introns, Diversity Generating Retroelements (DGRs), retrons, CRISPR-Cas systems, and Abortive Infection (Abi) systems in prokaryotes. Different classes of RTs can play different roles, such as template switching and mobility in group II introns, spacer acquisition in CRISPR-Cas systems, mutagenic retrohoming in DGRs, programmed cell suicide in Abi systems, and recently discovered phage defense in retrons. While some classes of RTs have been studied extensively, others remain to be characterized. There is a lack of computational tools for identifying and characterizing various classes of RTs. In this study, we built a tool (called myRT) for identification and classification of prokaryotic RTs. In addition, our tool provides information about the genomic neighborhood of each RT, providing potential functional clues. We applied our tool to predict and classify RTs in all complete and draft bacterial genomes, and created a collection that can be used for exploration of putative RTs. Application of myRT to gut metagenomes showed that gut metagenomes encode proportionally more RTs related to DGRs, outnumbering retron-related RTs, as compared to the collection of reference genomes. MyRT is both available as a standalone software and also through a website.Competing Interest StatementThe authors have declared no competing interest.