Biology Commons^™

Refernment: An R Package For Annotating Rna Editing In Plastid Genomes, Tanner A. Robison, Paul G. Wolf

Biology Faculty Publications

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 …

Genetic Relationships Between Two Rare Plant Species, Aliciella Caespitosa And A. Tenuis, And Their Putative Progenitor, A. Subnuda, Carrie L. Mccracken

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Isolated populations have potential to become new species that should have less genetic variation than their ancestors. Small populations are more likely to lose genetic variation, which is, thus, expected to be greater in ancestors. Aliciella caespitosa and A. tenuis, two endemic species, may be derived from small populations of A. subnuda, a widespread species. Chloroplast DNA sequences were used to test this hypothesis. Allozyme data were used to compare genetic variation and numbers of alleles. Chloroplast data do not support the proposed relationships between A. subnuda and the other two species. Allozyme data were not more variable …