Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 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.

PubMed Disclaimer

References

    1. Gitzendanner, M. A. , Soltis P. S., Wong G. K.‐S., Ruhfel B. R., and Soltis D. E.. 2018. Plastid phylogenomic analysis of green plants: A billion years of evolutionary history. American Journal of Botany 105: 291–301. - PubMed
    1. Hein, A. , Polsakiewicz M., and Knoop V.. 2016. Frequent chloroplast RNA editing in early‐branching flowering plants: Pilot studies on angiosperm‐wide coexistence of editing sites and their nuclear specificity factors. BMC Evolutionary Biology 16: 23. - PMC - PubMed
    1. Jung, J. , Kim J. I., Jeong Y.‐S., and Yi G.. 2018. AGORA: Organellar genome annotation from the amino acid and nucleotide references. Bioinformatics 34: 2661–2663. - PubMed
    1. Krause, K. 2008. From chloroplasts to “cryptic” plastids: Evolution of plastid genomes in parasitic plants. Current Genetics 54: 111–121. - PubMed
    1. Kugita, M. , Yamamoto Y., Fujikawa T., Matsumoto T., and Yoshinaga K.. 2003. RNA editing in hornwort chloroplasts makes more than half the genes functional. Nucleic Acids Research 31: 2417–2423. - PMC - PubMed