Corals are critical to marine biodiversity and human welfare. Coral reefs cover <1% of the seafloor but support ~1/3 of all marine species. Approximately 1.5 billion people live within 100 km of coral reefs, relying upon them for food, income from tourism, and protection from storms. Their economic value has been estimated at $375 billion annually. The foundation of coral reefs is the intracellular symbiosis between corals and photosynthetic dinoflagellates of the family Symbiodiniaceae. Tropical corals satisfy up to 95% of their nutritional requirements through photosynthesis, and their ability to construct reefs is biochemically coupled to photosynthesis. While permitting corals to thrive, photosymbiosis also increases their exposure to environmental stressors and vulnerability to climate change. Reliance on photosynthesis restricts reef-building corals to shallow, clear, tropical waters, where they experience higher temperatures and UV exposure. The generation of reactive oxygen species by the symbiont also exposes corals to greater oxidative stress. The symbiosis is particularly sensitive to climate change: all of the mass coral bleaching events have occurred since 1982, driven by elevated ocean temperatures. Molecular cross-talk between host and symbiont impacts resilience of the coral holobiont and resistance to bleaching. Unfortunately, we know little about how photosymbiosis impacts expression or activity of coral genes. Tropical corals engage in an obligate symbiosis with Symbiodiniaceae, so we cannot study their gene expression in a stable aposymbiotic state. However, the northern star coral, Astrangia poculata, engages in a facultative symbiosis with Symbiodiniaceae. I used RNA sequencing to investigate how symbiosis impacts gene expression in A. poculata, focusing on genes implicated in photosymbiosis: antioxidant enzymes (specifically superoxide dismutases) and the NF-κB signaling pathway. From an improved transcriptome assembly, I recovered core elements of a primitively simple NF-κB signaling pathway and a rich complement of SOD proteins. 273 coral transcripts—many associated with protein metabolism and vesicle-mediated transport— were differentially expressed in symbiotic versus aposymbiotic corals. Unlike in the facultatively symbiotic sea anemone Exaiptasia, symbiosis was not associated with depressed NF-κB transcript levels. IKKε, a potential positive regulator of NF-κB activity, was strongly up-regulated, as was one particular superoxide dismutase.

京都大学 / 0048 / 新制・課程博士 / 博士(理学) / 甲第20211号 / 理博第4296号 / 新制||理||1617(附属図書館) / 京都大学大学院理学研究科生物科学専攻 / (主査)教授 工藤 洋, 教授 髙林 純示, 教授 田村 実 / 学位規則第4条第1項該当 / Doctor of Science / Kyoto University / DGAM

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Catfish, the "king" of the U.S. aquaculture, is threatened by a severe, systemic bacterial disease known as enteric septicemia of catfish (ESC). This disease causes high mortality and massive economic losses in cultured channel catfish (Ictalurus punctatus) in the United States. E. ictaluri penetrates catfish intestinal epithelia quickly and establishes a systemic infection rapidly. However, our knowledge on catfish intestine and E. ictaluri interaction is very limited. In Particular, catfish intestinal immune responses and virulence genes needed by E. ictaluri to evade host defenses are not well understood. Hence, our long-term goal is to identify the molecular mechanisms of E. ictaluri-host interactions. The overall objectives of this study were to understand catfish immune responses to E. ictaluri infection and determine essential genes of E. ictaluri during the intestinal invasion. To accomplish the overall objectives of this research, intestinal ligated loops were constructed surgically in live catfish and loops were injected with wild-type E. ictaluri and two live attenuated E. ictaluri vaccine strains developed recently by our research group. We first determined catfish intestinal immune responses against E. ictaluri wild-type and live attenuated vaccine strains. Then, we analyzed the global gene expression patterns of wild-type E. ictaluri and vaccine strains during catfish intestinal invasion using high throughput RNA-Seq technology. Results showed a moderate level of neutrophil and B cell infiltration correlated with significantly lower expression of TNF-α, CD4-1, and CD8-α in the vaccine injected intestinal tissue compared to that of wild-type injected intestinal tissue. Further, RNA-Seq data analysis showed the prominent expression of genes related to bacterial secretion systems, ATP production processes, and multidrug resistance (MDR) efflux pumps in wild-type E. ictaluri. In contrast, the prominently expressed genes in vaccine strains were related to the phosphotransferase system and sugar metabolism processes. All these data suggest that our live attenuated vaccines are capable of triggering effective immune responses in catfish without causing damage to the host.

The genetic mechanisms by which natural populations maintain abundant phenotypic variation and adapt to their local environments remains a controversial topic in evolutionary biology. An intriguing mechanism involving highly mutable microsatellites follows the “tuning knob” model which proposes that stepwise changes in microsatellite allele lengths reciprocally generate phenotypic variation in a stepwise manner. In this study, I explored the predictions of the tuning knob model focusing specifically on transcribed microsatellites within and among natural populations of common sunflower (Helianthus annuus L.) transecting a latitudinal cline. An RNA-Seq experiment was conducted on 95 individuals from Kansas and Oklahoma grown in a common garden. To explore the potential role that microsatellites play in gene expression divergence in common sunflower, enrichment of microsatellites within differentially expressed (DE) genes was assessed. The results showed that A and AG repeat-containing microsatellites are enriched within DE genes and that 83.5% of these microsatellites are located within untranslated regions (UTRs). This finding is consistent with a role for transcribed microsatellites in gene expression divergence. RNA-Seq data were then used to assess microsatellite allele length effects on gene expression. Of all the microsatellites characterized in a reference transcriptome, 3,325 were consistently genotyped. The study identified 479 microsatellites at which allele length significantly correlated with gene expression (eSTRs). When irregular allele sizes were removed from the analysis, the number of eSTRs rose to 2379. eSTRs were most abundant within UTRs (70.4%) which suggests that they are well-positioned as cis-regulatory elements. A population genetic study conducted with 672 individuals across 17 sunflower populations from Saskatchewan to Oklahoma revealed strong signatures of directional selection acting on 13 eSTRs compared to 19 anonymous microsatellites assumed to evolve in a neutral fashion. This demonstrates that longer or shorter alleles may be favored in more extreme environments to that considered in the focal study. A second common garden experiment conducted with populations further north and south of focal populations revealed consistent patterns of correlation between microsatellite allele length and gene expression at some eSTRs. This study provides evidence that a substantial number of transcribed microsatellites function as “tuning knobs” of adaptation in common sunflower by modulating gene expression in a stepwise manner. These findings imply that the genomes of natural populations may include hundreds of active tuning knobs that can facilitate rapid evolution.