<p> Legume crops are significant agriculturally and environmentally for their ability to form symbiosis with specific soil bacteria capable of nitrogen fixation. Nitrogen fixation for a given legume in a given soil is limited by the availability of the plant&rsquo;s bacterial partners, and by variation in the effectiveness of those symbionts. We used a global-level hierarchical sampling scheme to comprehensively characterize the evolutionary relationships and distributional limitations of nitrogen-fixing bacterial symbionts of the legume crop chickpea. This has been accomplished using culture-dependent and independent approaches to generate over 1,200 draft whole-genome assemblies at the level of bacterial populations, as well as 14 finished-quality genomes using the Pacific Biosciences platform. These strategies reveal that chickpea&rsquo;s symbionts across the globe are confined to the genus <i>Mesorhizobium </i>, but a diversity of taxa within the genus (chapter 1 and 3). Comparative phylogenomic analysis reveals that despite chickpea&rsquo;s symbionts within and across regions coming from different taxa, all share almost identical genes for symbiosis. PacBio genome-assemblies reveal that this is due to the horizontal transfer of a 500 kb chromosomal island known as a symbiosis island, between unrelated strains of the genus <i>Mesorhizobium </i>. Analyzing the symbiosis island at the population level reveals that the symbiosis island spreads repeatedly once introduced to a region, suggesting that strains well-adapted to a particular soil climate continue to dominate once the new host (chickpea) has been introduced, through repeated acquisition of the symbiosis island. This dataset provides additional insights into the functional and taxonomic diversity of other bacteria associated with chickpea nodules (chapter 2).</p><p>

<p> Fusarium wilt of cotton, caused by the soilborne fungus <i>Fusarium oxysporum</i> f. sp. <i>vasinfectum,</i> is a widespread disease occurring in most cotton-growing regions of the world. Fusarium wilt occurs in all domesticated cotton. Currently, six nominal races are recognized: 1, 2, 3, 4, 6, and 8, as well as many un-named genotypes worldwide. Many are widespread in the U.S., but race 4, which is highly virulent, is apparently restricted to California. Race 4 is found in an increasing number of fields in California due in part to seed-borne dissemination. The first aim of this study was to evaluate the efficacy of hot water treatments alone or in conjunction with fungicides and other treatments to reduce the viability of FOV race 4 in infected cotton seed. The second aim was to develop and evaluate a rapid and reliable molecular diagnostic assay, the AmplifyRP^&reg; Acceler8&trade;, for the direct detection of FOV race 4 in cotton tissue. In the seed treatment assay, a 1 hour immersion of seed in water or sterile 30% potato dextrose broth (PDB) at 24&deg;C followed by a 20 minute immersion in a 60&deg;C solution containing four fungicides (azoxystrobin, fludioxonil, thiabendazole, and thiophanate) or thiophanate alone were the most effective pretreatment-treatment combinations in reducing FOV in seed and avoiding loss of seed germination and vigor. The incidence of FOV in the seed was reduced by approximately 86% without reducing seed germination and vigor based on recovery of the fungus on petri plates and greenhouse grow-out assays. FOV was completely eliminated from infected seed when the seed was pretreated in water at 24&deg;C followed by a 20 minute immersion in a solution of thiophanate heated to 70&deg;C. With this treatment, seed germination was reduced by 36% and vigor was reduced by 38%. The AmplifyRP^&reg; Acceler8&trade; diagnostic assay consistently detected FOV race 4 from all infected tissue samples. The test is rapid, simple and more sensitive than conventional PCR. The AmplifyRP^&reg; Acceler8&trade; diagnostic assay detected DNA from FOV race 4 at concentrations of 1 ng/&micro;L and above. In addition, it did not amplify DNA from other known FOV races (races 1, 2, 3, 6, and 8). The whole process from sample preparation to reading the results was completed in as little as 30 minutes. The test detected FOV race 4 in cotton taproots, petioles, and stems.</p>

<p> The ascomycete fungus <i>Magnaporthe oryzae,</i> causative agent of rice blast disease, poses a threat to global food security, destroying enough rice to feed 60 million people each year. Characterization of the host-pathogen interaction between rice and <i>M. oryzae</i> is critical, as better understanding of the system may lead to better disease control strategies. The sequenced genome and repertoire of molecular tools available have made <i> M. oryzae</i> an ideal model system for understanding general plant-pathogen interactions as well. </p><p> The objective of this dissertation was to characterize the <i>M. oryzae</i> homologs of <i>Histoplasma capsulatum RYP</i> (<i><u> R</u>equired for <u>Y</u>east <u>P</u>hase </i>) genes that are required for transition to the parasitic phase. <i> H. capsulatum</i> is a human pathogen that undergoes a dimorphic switch from filamentous to yeast cell growth at 37&deg;C, the host body temperature. Four<i>H. capsulatum RYP</i> genes were identified in a forward genetic screen to identify genes required for entry into the yeast phase. <i> RYP1</i> is a member of the Gti1_Pac2 family, which contains previously characterized regulators of dimorphic switching. <i>RYP2</i> and <i> RYP3</i> are homologs of <i>vosA</i> and <i>velB,</i> members of the Velvet family, best characterized in <i>Aspergillus nidulans, </i> where they coordinate morphological differentiation with secondary metabolism. <i>RYP4</i> is a zinc binuclear cluster protein, a main class in the zinc finger transcription factor family. Deletion of the <i> M. oryzae RYP1</i> homolog, <i>RIG1</i> (<i><u> R</u>equired for <u>I</u>nfectious <u>G</u>rowth </i>), resulted in a non-pathogenic mutant on susceptible rice cultivars, even upon removal of the host penetration barrier. <i>&Delta;rig1</i> was blocked in the transition to infectious hyphal growth, similar to <i> H. capsulatum ryp1,</i> which could not transition to the yeast phase. Deletion mutants of <i>M. oryzae RYP2, RYP3,</i> and <i>RYP4 </i> homologs were similar to the wild type in somatic growth and pathogenicity indicating that although <i>RIG1</i> is a pathogenicity factor conserved in plant and animal pathogens, such conservation does not apply to all of the <i>RYP</i> pathogenicity genes identified in <i>H. capsulatum. </i> </p><p> <i>&Delta;rig1</i> is the first <i>M. oryzae</i> mutant known to be blocked in production of primary infection hyphae. Overall, the study suggests limited parallels exist in phase transition of fungal pathogens of plants and animals.</p>