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. 2019 Jan 30;7(2):e01216.
doi: 10.1002/aps3.1216. eCollection 2019 Feb.

ReFernment: An R package for annotating RNA editing in plastid genomes

Tanner A Robison  1 , Paul G Wolf  1
Affiliations

ReFernment: An R package for annotating RNA editing in plastid genomes

Tanner A Robison et al. Appl Plant Sci. .

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.

Keywords: GenBank; National Center for Biotechnology Information (NCBI); RNA editing; annotation; chloroplast; genome; plastome.

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