ReFernment: An R Package for Annotating RNA Editing in Plastid Genomes

Authors

Tanner A. Robison, Utah State UniversityFollow
Paul G. Wolf, Utah State UniversityFollow

Document Type

Article

Journal/Book Title/Conference

Applications in Plant Sciences

Volume

7

Issue

2

Publisher

Wiley Periodicals, Inc.

Publication Date

1-30-2019

Creative Commons License

This work is licensed under a Creative Commons Attribution 4.0 License.

First Page

1

Last Page

2

Abstract

PREMISE OF THE STUDY: In the absence of cDNA, the annotation of RNA editing in plastomes must be done manually, representing a significant time cost to those studying the organellar genomes of ferns and hornworts.

METHODS AND RESULTS: We developed an R package to automatically annotate apparent nonsense mutations in plastid genomes. The software successfully annotates such sites and results in no false positives for data with no sequencing or assembly errors.

CONCLUSIONS: Compared to manual annotation, ReFernment offers greater speed and accuracy for annotating RNA editing sites. This software should be especially useful for researchers generating large numbers of plastome sequences for taxa with high levels of RNA editing.

Recommended Citation

Robison, T. A., and P. G. Wolf. 2019. ReFernment: An R package for annotating RNA editing in plastid genomes. Applications in Plant Sciences 7(2): e1216.