Plastid and mitchondrial genome evolution of legumes (Fabaceae)

Plastid genome (plastome) organization is highly conserved across seed plants with a quadripartite structure including the small single copy (SSC), the large single copy (LSC) and two copies of an inverted repeat (IR). There are several unrelated lineages that have experienced extensive structural rearrangements such as inversions and gene/intron losses and indels. Fabaceae is typically recognized as having three subfamilies: Caesalpinioideae, Mimosoideae and Papilionoideae. Publicly available plastid genomes of legumes have for the most part been limited to the subfamily Papilionoideae due to their economic importance and known structural rearrangements. In several other angiosperm lineages, correlations between accelerated rates of genomic rearrangements and nucleotide substitition rates in the plastome have been identified. Additionally, increased frequency of plastome structural changes and accelerated nucleotide substitutions have been shown to be correlated with increased evolutionary rates in the mitochondrial genome (mitogenome). To date, few legume mitochondrial genomes (7) are publicly available. My dissertation research uses Fabaceae to investigate 1) plastid genomic changes and rearrangements across all three subfamilies and 2) correlations between biological features and nucleotide substitution rates of both plastid and mitochondrial genes. Chapter two focuses on plastid structural evolution across three subfamilies of Fabaceae and shows papilionoids have smaller genomes with varying degrees of genomic rearrangements, and they have experienced multiple, independent gene/intron losses and inversions that limit the phylogenetic utility of these changes. Chapter three finds accelerated substitution rates in protein coding plastome genes among papilionoid taxa, especially those lacking one copy of the inverted repeat (IR), decreased rates in genes previously contained in the IR, and faster rates in herbaceous versus woody taxa. Chapter four focuses on substitution rates of mitochondrial genes and shows a correlation between plastid and mitochondrial substitution rates in addition to an acceleration in the papilionoid taxa, where, again, the herbaceous habit is correlated with higher rates.