The Pentatricopeptide Repeat (PPR) gene family produces RNA-binding proteins that target organellar transcripts. The PPR family is expanded in land plants, with nearly 450 genes identified in Arabidopsis thaliana. In plants with a Cytoplasmic Male Sterility (CMS) phenotype, members of the PPR family can act as a RESTORER OF FERTILITY...
Despite knowledge that concerted evolution of high-copy loci is often imperfect,
studies that investigate the extent of intragenomic polymorphisms and comparisons
across a large number of species are rarely made. We present a bioinformatic pipeline
for characterizing polymorphisms within an individual among copies of a high-copy
locus. Results are presented...
The Leguminosae has emerged as a model for studying angiosperm plastome evolution because of its striking diversity of structural rearrangements and sequence variation. However, most of what is known about legume plastomes comes from few genera representing a subset of lineages in subfamily Papilionoideae. We investigate plastome evolution in subfamily...
Forest health issues are on the rise in the United States, resulting from introduction of alien pests and diseases, coupled with abiotic stresses related to climate change. Increasingly, forest scientists are finding genetic/genomic resources valuable in addressing forest health issues. For a set of ten ecologically and economically important native...
Eukaryotic small RNA (~20-30 nucleotides) are diverse regulatory molecules that repress gene expression at the transcriptional and post-transcriptional levels, defend hosts against invading viruses and defend genomes against selfish DNA elements. Small RNA populations are studied by high-throughput sequencing of the total small RNA fraction isolated from cells, however, the...
Whole-genome duplications are radical evolutionary events that have driven speciation and adaptation in many taxa. Higher-order
polyploids have complex histories often including interspecific hybridization and dynamic genomic changes. This chromosomal
reshuffling is poorly understood for most polyploid species, despite their evolutionary and agricultural importance, due to the
challenge of distinguishing...
Background: Recent mapping of eukaryotic transcriptomes and spliceomes using massively parallel RNA sequencing (RNA-seq) has revealed that the extent of alternative splicing has been considerably underestimated. Evidence also suggests that many pre-mRNAs undergo unproductive alternative splicing resulting in incorporation of in-frame premature termination codons (PTCs). The destinies and potential functions...
RNA interference pathways can involve amplification of secondary siRNAs by RNA-dependent RNA polymerases. In plants, RDR6-dependent secondary siRNAs, including transacting siRNAs (tasiRNAs), arise from transcripts targeted by some microRNAs (miRNAs). In the case of TAS3 tasiRNA formation, ARGONAUTE7 (AGO7)-miR390 complexes interact with primary transcripts at two sites, resulting in recruitment...
Genomic instability underlies diseases of unregulated cell growth that result in
cancers and developmental abnormalities in humans. Similar genome destabilizing
mechanisms are used to create genetic variety in crops for use in breeding and trait
development. Errors that occur during DNA replication may cause mutations if
they are not corrected...
At a time when the biodiversity on Earth is being rapidly lost, new technologies and methods in genomic analysis are fortunately allowing scientists to catalog and explore the diversity that remains more efficiently and precisely. The studies in this dissertation investigate genomic diversity within the milkweed genus, Asclepias, at multiple...