Genomic sequencing has become ubiquitous within the discipline of Biology. Here I use
two case studies in which whole genomic DNA facilitates answers to foundational biological
questions for organisms that do not have assembled genomes and have benefited little, if at all,
from any sequencing in the past. Eleusine indica (L.) Gaertn. (Poaceae) is a prolific weed that is
also a known genome donor for E. coracana (L.) Gaertn., a subsistence crop used in west Africa
and east India. The genus Marshallia Schreb. (Asteraceae) comprises eight species, occurs
throughout the southeast and is notable for inflorescences with a pink or white puffball
appearance. In Chapter 1 general context and background is provided regarding both E. indica
and Marshallia and the aims of the study are provided. Chapter 2 is an assembly of the
mitochondrial genome of Eleusine indica and a survey of the mitochondrial gene content of
Poaceae. Plant mitochondrial genomes are challenging to assemble because of large
recombinogenic regions, this in turn makes surveys of mitochondrial gene content hard to
accomplish without the use of extensive assembly efforts or laborious wet lab techniques. A new
in silico approach is described and applied to determine mitochondrial gene content within
publicly available datasets. The results are confirmed by past studies, but also expand sampling
within Poaceae and provide new insight into the specific timing of mitochondrial gene loss in
Poaceae. In Chapter 3 a repetitive element is assembled and characterized as a proof of concept
for the usefulness of whole genomic low coverage sequence data within Marshallia. In Chapter 4
several facets of these data are employed to determine interspecies relationships within
Marshallia. Seventeen datasets are used in phylogenetic analysis of assemble plastid genomes,
entire ribosomal cistrons and mitochondrial sequences. Additionally the abundance of the
repetitive element Marobo is characterized in Chapter 3 along with the relative abundance of
several repetitive element superfamilies. Finally, a reduced set of transcriptomes is assembled
and used for phylogenetic analysis. The results of all assemblies are compared and this yields the
first in-depth exploration of the phylogenetic history of the species within Marshallia.
Relationships within the Marshallia show species-specific divergence of the ribosomal DNA,
which are in contrast to the interspecific sharing of cytotypes, this pattern is indicative of past
introgression events
