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Mangroves represent phylogenetically diverse taxa in tropical coastal terrestrial habitats. They are extremophiles, evolutionarily adapted to tolerate flooding, anoxia, high temperatures, wind, and high and extremely variable salt conditions in typically resource-poor environments. The genetic basis for these adaptations is, however, virtually unknown. The broad objective of my research was to investigate the genetic basis of tolerance strategies in mangroves. As target species, I have selected the mangroves, "Rhizophora mangle" (Rhizophoraceae) and "Heritiera littoralis" (Malvaceae), two ecologically important extremophiles employing markedly different physiological and life history strategies for survival and dominance in this severe environment. For more in depth analysis at the gene level, I have focused my research on "R. mangle" selected gene families of the phenylpropanoid pathway, their differential expression in different tissues and growth conditions, and the putative regulatory mechanisms governed by upstream promoter elements. Mangroves are very poorly represented in the plant molecular literature and remain an untapped resource for understanding and exploiting plant adaptations to extreme environments. Whether the goal is to elucidate the genetic basis for the physiological adaptations to an extreme lifestyle, or to exploit the group's unique genetic resources, much greater genome-level understanding is needed. The choice of sequencing method for my research was 454-GSFLX pyrosequencing. For maximal representation of conditional transcripts, mRNA was isolated from a wide variety of developmental stages, tissues types, and habitats. Sequencing of a normalized cDNA library for each species yielded a combined 537,635 sequences. For the "R. mangle" transcriptome, 225K sequence reads included 40Mbp. These were assembled de novo into 23K contigs with the average size of 785bp. Similarly for "H. littoralis", 300K sequence reads included 50Mbp and were assembled into 26K contigs with the average size of 768bp. Forty five percent of these were annotated using previously reported sequences in GenBank. These are identified with more than 17,000 distinct gene models recorded in the NCBI RefSeq genome database. Convergent evolution has led mangrove species to a common habitat, representative of extreme environmental conditions. A set of -13K gene ontology (GO) annotations in the two mangrove transcriptomes show that both mangroves include 25-35% increased gene models in response to stress, transport, abiotic or biotic stimulus, signal transduction, and cell organization and biogenesis compared to the "Arabidopsis" genome. Based on GO and KEGG Orthology annotations, I have found remarkable similarities in the two transcriptome profiles, and substantial differences from the model plants, "Arabidopsis" and poplar. These similarities suggest evolutionary convergence at the transcriptome level, and a signature pattern, or "lifestyle", which is not apparent in the phylogenetic relationships. To extend the search for unique transcriptome characteristics of the mangrove lifestyle into other mangroves and to do comparative analysis, I have re-annotated all cDNA sequences of mangroves publicly available to date in a searchable database with "R. mangle" and "H. littoralis" transcriptomes. The mangrove transcriptome database, MTDB, is available at: http://mangrove.illinois.edu. To further investigate the tolerance strategy exemplified by "R. mangle", I have chosen to characterize major structural genes in the phenylpropanoid pathway. Apart from the universal functions of phenylpropanoids, in "R. mangle" they play a pivotal role in plant survival in an extreme environment. The phenylpropanoid pathway leading to proanthocyanidins (PA) and other flavonoids provides a carbon sink and a potent mix of defensive compounds that complement the slow growth pattern of these trees in their low nutrient environment. Therefore, this pathway is an appropriate research emphasis and a start for studies of tolerance. I have characterized phenylalanine ammonia-lyase (PAL), chalcone synthase (CHS), and dihydroflavonol reductase (DFR) gene families in "R. mangle", which are at major regulatpry points in the phenylpropanoid pathway. I have identified one DFR, two CHS, and ten PAL genes in "R. mangle". Differential expression patterns within a family as well as co-expression patterns across families were identified in different tissues indicating possible regulatory mechanisms to achieve high concentrations of specific phenylpropanoid end products. [The dissertation citations contained here are published with the permission of ProQuest LLC. Further reproduction is prohibited without permission. Copies of dissertations may be obtained by Telephone (800) 1-800-521-0600. Web page: http://www.proquest.com/en-US/products/dissertations/individuals.shtml.]