Identification and characterization of microRNAs (miRNAs) and their transposable element origins in the saltwater crocodile, Crocodylus porosus

Arnab Ghosh; Roy N Platt 2nd; Michael W Vandewege; Rabia Tabassum; Chuan-Yu Hsu; Sally R Isberg; Daniel G Peterson; John W Finger Jr; Troy J Kieran; Travis C Glenn; Jaime Gongora; David A Ray

doi:10.1016/j.ab.2020.113781

Identification and characterization of microRNAs (miRNAs) and their transposable element origins in the saltwater crocodile, Crocodylus porosus

Anal Biochem. 2020 Aug 1:602:113781. doi: 10.1016/j.ab.2020.113781. Epub 2020 May 30.

Authors

Affiliations

¹ Department of Biological Sciences, Texas Tech University, Lubbock, TX, USA.
² Department of Biological Sciences, Texas Tech University, Lubbock, TX, USA; Department of Biology, Eastern New Mexico University, Portales, NM, USA.
³ Charles Darwin University, Australia.
⁴ Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, MS, USA.
⁵ Sydney School of Veterinary Science, Faculty of Science, University of Sydney, Sydney, NSW, Australia; The Centre for Crocodile Research, Darwin, NT, Australia.
⁶ Department of Environmental Health Science, University of Georgia, Athens, GA, USA; Department of Biological Sciences, Auburn University, Auburn, AL, USA.
⁷ Department of Environmental Health Science, University of Georgia, Athens, GA, USA.
⁸ Sydney School of Veterinary Science, Faculty of Science, University of Sydney, Sydney, NSW, Australia.
⁹ Department of Biological Sciences, Texas Tech University, Lubbock, TX, USA. Electronic address: david.4.ray@gmail.com.

PMID: 32485163
DOI: 10.1016/j.ab.2020.113781

Abstract

MicroRNAs (miRNAs) are 18-24 nucleotide regulatory RNAs. They are involved in the regulation of genetic and biological pathways through post transcriptional gene silencing and/or translational repression. Data suggests a slow evolutionary rate for the saltwater crocodile (Crocodylus porosus) over the past several million years when compared to birds, the closest extant relatives of crocodilians. Understanding gene regulation in the saltwater crocodile in the context of relatively slow genomic change thus holds potential for the investigation of genomics, evolution, and adaptation. Utilizing eleven tissue types and sixteen small RNA libraries, we report 644 miRNAs in the saltwater crocodile with >78% of miRNAs being novel to crocodilians. We also identified potential targets for the miRNAs and analyzed the relationship of the miRNA repertoire to transposable elements (TEs). Results suggest an increased association of DNA transposons with miRNAs when compared to retrotransposons. This work reports the first comprehensive analysis of miRNAs in Crocodylus porosus and addresses the potential impacts of miRNAs in regulating the genome in the saltwater crocodile. In addition, the data suggests a supporting role of TEs as a source for miRNAs, adding to the increasing evidence that TEs play a significant role in the evolution of gene regulation.

Keywords: Crocodilian; Crocodylus porosus; Phylogeny; Small RNA; miRDeep2; miRNA.

Publication types

Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Alligators and Crocodiles
Animals
DNA Transposable Elements / genetics*
Gene Library
MicroRNAs / genetics*
Salinity

Substances

DNA Transposable Elements
MicroRNAs