Browsing by Subject "Legumes"
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Item Evolution of highly divergent organellar genomes in two distantly related angiosperm lineages, Eleocharis (Cyperaceae) and papilionoid legumes (Fabaceae)(2021-12-02) Lee, Chaehee; Jansen, Robert K., 1954-; Theriot, Edward C.; Linder, Craig R.; Cannatella, David; Mehdy, MonaThe plastid genomes (plastomes) of most photosynthetic angiosperms are highly conserved in gene content and order in a gene dense unit-genome. Despite low levels of variation across angiosperms, plastomes of several distantly related lineages experienced a dramatic evolutionary history, including extensive genomic rearrangements, gene duplications and losses, repeat accumulation and expansion and contraction of the inverted repeat (IR). Recently, alternative plastome structures were suggested in the angiosperms, Geraniaceae and Medicago. Here plastomes of two Eleocharis species were completed and revealed remarkably divergent features, including large sizes, high rates of sequence rearrangements, low GC content and gene density, gene duplications and losses, and increased repeat content. A novel finding among these aberrant features was the unprecedented level of heteroplasmy with the presence of multiple plastome structural types within a single individual. To better understand structural evolution on a broader phylogenetic scale, plastomes of 31 legumes in the largest subfamily Papilionoideae, along with three non-papilionoideae were completed and combined with 33 publicly available sequences. A number of IR-related and repeat-mediated changes were identified. Like Eleocharis, intraindividual plastome heteroplasmy associated with ycf2 repeats was confirmed in at least four taxa, which is likely present in most 50 kb-inversion clade. Although loss of the inverted repeat has not been reported in legumes outside of the inverted repeat lacking clade (IRLC), one genistoid taxon was found to completely lack the canonical plastome IR. Correlations between plastome rearrangements and substitution rates have been detected in several angiosperms and mitochondrial and plastid genomes tend to evolve in parallel. Given the fact that Eleocharis plastomes were highly rearranged, sequence evolution of Eleocharis organellar genomes was examined by comparing nucleotide substitution rates within and between plastid and mitochondrial genomes in Eleocharis using 31 Eleocharis species and two other Cyperaceae genera. Mitochondrial sequence evolution of Cyperaceae was also investigated with comparison to other angiosperms. Eleocharis experienced extensive gene losses in both genomes and mitochondrial-specific losses of introns. Correlated lineage- and gene-specific accelerations in dN and dS values were identified in both genomes of Eleocharis. Several clades showed higher dS and dN in mitochondrial genes than plastid genes. In addition, the branch leading to Cyperaceae exhibited dramatically elevated substitution rates compared to most angiosperms. Mitochondrial genes of Cyperaceae exhibited dramatic loss of RNA editing sites and a negative correlation between RNA editing and dS values was detected among angiosperms. Therefore, multiple underlying mechanisms for significant rate accelerations in Eleocharis and Cyperaceae are discussedItem Plastid and mitchondrial genome evolution of legumes (Fabaceae)(2016-08) Schwarz, Erika Nicole; Jansen, Robert K., 1954-; Hillis, David M; Linder, Craig R; Roux, Stanley J; Theriot, Edward CPlastid 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.