As two species diverge, much of their genomes begin to differentiate. In many lineages, however, the genomic structure remains remarkably intact, with orthologous gene content maintained across millions of years and significant changes to their biological characteristics. The maintenance of gene content is defined as conserved synteny while the preservation of gene order is defined as conserved linkage; the conservation of both can be incredibly informative when interrogating and comparing two genomes. In non-model organisms, linkage conservation to a well-developed model allows informed, cost-effective and rapid answers to fundamental biological questions without generation of equivalent resources. With the development of new model organisms, we can begin to discuss more fundamental evolutionary concepts, such as the maintenance of chromosomal gene content across larger evolutionary time-scales, or the reorganization that occurs in chromosomes following major genomic events such as whole-genome duplications. In this work, I utilized the rapid development of primary genomic resources in the non-model teleost sablefish (Anoplopoma fimbria) to demonstrate that conserved linkage to a model genomic reference can identify the gene most likely responsible for genetic sex-control. I then assembled the first genome for a non-duplicated member of the teleost lineage Protacanthopterygii, the northern pike (Esox lucius), and demonstrated the conservation of synteny between three major lineages of teleosts, the Protacanthopterygii, the Acanthopterygii and the Ostariophysi. I further showed that the genome of northern pike retains an ancestral teleost organization and pre-duplicated genome in comparison to the economically important Salmoniformes. Finally, with continued improvements of the genome to the chromosome level, I demonstrated the degree of conserved linkage maintained between Atlantic salmon and northern pike and explained how conserved linkage through both genomes could be used to improve the genome assembly of the other, even with over 125 million years of separation. As genomic technology continues to advance and new genomic resources become available, the continued refinement of genome re-organization post duplication will be revealed, and this pre-duplication outgroup will continue to push our understanding of the effects of genome duplication, as we transition from genome organization to functional modifications of gene duplicates following duplication. / Graduate / 2018-12-01

Leaf rust caused by Puccinia hordei is an important disease of barley (Hordeum vulgare) in many regions of the world. Yield losses up to 62% have been reported in susceptible cultivars. The Rph5 gene confers resistance to the most prevalent races (8 and 30) of barley leaf rust in the United States. Therefore, the molecular mapping of Rph5 is of great interest. Genetic studies were performed by analysis of 93 and 91 F2 plants derived from the crosses 'Bowman' (rph5) x 'Magnif 102' (Rph5) and 'Moore' (rph5) x Virginia 92-42-46 (Rph5), respectively. Linkage analysis positioned the Rph5 locus to the extreme telomeric region of the short arm of barley chromosome 3H at 0.2 cM proximal to RFLP marker VT1 and 0.5 cM distal from RFLP marker C970 in the Bowman x Magnif 102 population. Synteny between rice chromosome 1 and barley chromosome 3 was employed to saturate the region within the sub-centimorgan region around Rph5 using sequence-tagged site (STS) markers that were developed based on barley expressed sequence tags (ESTs) syntenic to the phage (P1)-derived artificial chromosome (PAC) clones comprising distal region of the rice chromosome 1S. Five rice PAC clones were used as queries to blastn 370,258 barley ESTs. Ninety four non-redundant EST sequences were identified from the EST database and used as templates to design 174 pairs of primer combinations. As a result, 10 EST-based STS markers were incorporated into the 'Bowman' x 'Magnif 102' high-resolution map of the Rph5 region. More importantly, six markers, including five EST-derived STS sequences, co-segregate with Rph5. Genes, represented by these markers, are putative candidates for Rph5. Results of this study demonstrate the usefulness of rice genomic resources for efficient deployment of barley EST resources for marker saturation of targeted barley genomic region. / Ph. D.