Doctor of Philosophy, Case Western Reserve University, 2023, Biology

Tylosema esculentum (marama bean) is an underutilized legume, long considered as a local potential crop due to its rich nutritional value. The reference plastome and mitogenome were assembled using a hybrid method with both Illumina and PacBio data. The diversity was explored with the WGS data of 84 samples from various geographic locations in Namibia and Pretoria. Phylogenetic analysis revealed two cytotypes with distinct plastomes and mitogenomes with differing levels of variability. Deep sequencing has identified heteroplasmy with both types of organellar genomes present, albeit one at a very low frequency. The inheritance of this complex of organellar genomes appears to be fairly constant, providing a conundrum of how the two genomes co-exist and are propagated through generations. The type 1 mitogenome has two autonomous rings with a total length of 399,572 bp, which can be restructured into five smaller circular molecules through recombination on 3 pairs of long direct repeats. The type 2 mitogenome contains a unique 2,108 bp sequence, which connects distant segments to form a new structure consisting of three circular molecules and one linear chromosome. This increased the copy number of nad9, rrns, rrn5, trnC, and trnfM. The two mitogenomes differed at another 230 loci, with only one nonsynonymous substitution in matR. cpDNA insertions were concentrated in one subgenomic ring of the mitogenome, including a 9,798 bp long fragment that contains potential psbC, rps14, psaA, and psaB pseudogenes. The two types of plastomes range in length from 161,537 bp to 161,580 bp, differing at 122 loci and at a 230 bp inversion. The chloroplast genes rpoC2, rpoB, and ndhD were found to be more diverse than other genes in marama plastome. 21.6 Gb PacBio HiFi data was assembled using Canu v2.2 into an unphased assembly of 1.24 Gb. k-mer analysis indicated that marama may be ancient tetraploid with an estimated genome size of only 277 Mb. The generated assembly has an N50 v (open full item for complete abstract)

Committee: Christopher Cullis (Advisor); Hillel Chiel (Committee Chair); Peter Zimmerman (Committee Member); Jean Burns (Committee Member); Sarah Bagby (Committee Member) Subjects: Bioinformatics; Genetics; Plant Biology

BS, Kent State University, 2012, College of Arts and Sciences / Department of Biological Sciences

In plants and animals, offspring typically inherit half of their nuclear genes from each parent, and all of their mitochondrial and chloroplast genes from only one parent (usually from their mothers). However, recent studies have shown evidence of paternal inheritance and bi-parental inheritance of extra-nuclear genes in several species. I investigated patterns of chloroplast inheritance in a native flowering plant, Lobelia siphilitica (Lobeliaceae). Dams from six populations were crossed with sires from twelve populations to track inheritance patterns in the offspring. Fifty-five crosses were examined by sequencing the rps16-psbK region of the chloroplast genome of each individual parent and offspring. I found that offspring matched their mothers 98% of the time (80% of the crosses), suggesting that strict maternal inheritance is predominant in this species. However, I found evidence of heteroplasmy (multiple chloroplast types within individuals) in several parents and offspring, and in one cross, paternal inheritance was observed in one third of the offspring. Instances of heteroplasmy and paternal inheritance in offspring were restricted to four crosses, all of them having mothers from a single L. siphilitica population from southern Indiana, and two involving the same mother plant. Understanding the mechanisms and frequency of deviation from strict maternal inheritance is important for interpreting patterns of evolution in natural populations.

Committee: Andrea Case PhD (Advisor); Soumitra Basu PhD (Committee Member); Helen Piontkivska PhD (Committee Member); Gail Fraizer PhD (Committee Member) Subjects: Biology; Botany; Genetics; Molecular Biology; Plant Biology; Plant Sciences

MS, Kent State University, 2011, College of Arts and Sciences / Department of Biological Sciences

Eukaryotic organisms have two distinct genomes—the nuclear genome and the cytoplasmic genome. Eukaryotic organisms are commonly thought to transmit their cytoplasmic genomes uniparentally, usually from the maternal parent. This form of inheritance should result in only one unique cytoplasmic genome in each individual. However, recent studies have found evidence of more than one unique genome within individuals (referred to as heteroplasmy) in several taxonomic lineages. Heteroplasmy could arise if mutation or recombination create unique subsets of cytoplasmic genomes within cells, or if bi-parental inheritance of the cytoplasmic genome, via paternal leakage, introduces multiple unique cytoplasmic genomes to a zygote. Once heteroplasmy is present, it could be passed to offspring via normal maternal inheritance, or could be lost between generations. Regardless of how it occurs, heteroplasmy warrants study, particularly determining the extent to which heteroplasmy provides evidence of non-maternal inheritance in eukaryotes. This thesis documents the causes and consequences of mitochondrial heteroplasmy in Mimulus guttatus (Phrymaceae), a flowering plant. I used a single PCR-based genetic marker that can distinguish two known unique mitotypes of M. guttatus. I quantified variation in heteroplasmy using quantitative PCR to estimate the ratio of these two mitotypes, both within and among populations and within individuals. I screened open-pollinated seed offspring and the offspring of controlled crosses to look for evidence of paternal leakage, and compared individual mitotype ratios to a series of fitness-related phenotypic traits to assess whether heteroplasmy could be subject to natural selection. First, I found that the occurrence and extent of mitochondrial heteroplasmy varies substantially within and among M. guttatus populations. Second, I also found evidence of within-individual variation in mitotype ratios, where different tissues exhibited different levels of h (open full item for complete abstract)

Committee: Andrea L. Case PhD (Advisor) Subjects: Biology; Evolution and Development; Genetics; Plant Biology