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

Tanner A Robison,Paul G Wolf

doi:10.1002/aps3.1216

Abstract

Premise of the StudyIn 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 ResultsWe 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.ConclusionsCompared 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.

Highlights

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
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
As of September 2018, more than 2700 plastome sequences from green plants have been published in public databases, which has in turn aided in the resolution of deep phylogenetic relationships across plant diversity (Ruhfel et al, 2014; Tonti-Filippini et al, 2017; Gitzendanner et al, 2018)

Summary

Introduction

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.

Results

Conclusion