@phdthesis {4363, title = {Genomics and transcriptomics of Antarctic nematodes reveal drivers of life history evolution and genome evolution}, volume = {Ph.D.}, year = {2018}, school = {Brigham Young University}, type = {doctoral}, address = {Provo, UT}, abstract = {

Elemental stoichiometry defines a critical understanding of the relationship between\ nutrient availability and usage throughout different levels of the biological community. We\ found there is a link between available phosphorus (P), cellular phosphorus, and nematode development as postulated by the growth rate hypothesis (GRH). I predicted that in a P-poor environment, cellular RNA concentrations would be lower than they are in P-rich environment, and thus the 18srRNA expression level will have reduced. To most efficiently regulate the\ uptake of limited P, I predicted that nematodes in P-poor environments would decrease the number of copies of the 18s rRNA gene in their genome. I measured life history traits as well as rRNA gene expression and gene copy number. We found that elemental stoichiometry predicts evolutionary changes consistent with the Growth Rate Hypothesis. We sequenced and assembled a draft genome of P. murrayi. Although we expected to find genes responsible for stress tolerance, we hypothesized that in response to strong selection pressure associated with living in\ a simplified ecosystem, over time the genome of P. murrayi should have undergone significant decay (gene loss) relative to species in ecosystems structured more strongly by biotic interactions. We found significantly fewer genes in P. murrayi. To compare patterns of gene expression between two highly divergent Antarctic nematode species, we sequenced and assembled the transcriptomes of S. lindsayae and P. murrayi. Under laboratory conditions at 4\  ̊C, S. lindsayae had significantly lower rates of gene expression but expressed a significantly larger number of genes. We speculate that the differences in gene expression are correlated with life history traits (developmental rates) while the differences in the number of genes expressed can be explained\ by their different genetic systems (S. lindsayae is amphimictic, P. murrayi is parthenogenic) and the soil environments to which they are adapted. Since we previously showed that differences in available P content can influence the evolution of gene expression via gene copy number, and that this ultimately influences growth rate, we wondered how much of this response is driven by genetics versus how strongly these patterns are driven by temperature. To better understand this, we maintained wild type populations of P. murrayi in P-rich and P-poor conditions at 5\  ̊C, 10\  ̊C and 15 ̊C in the laboratory for over 40 generations and sequenced the transcriptomes prepared from each treatment group. We found that nutrient levels played an important role in gene expression when the temperature is optimal for P. murrayi culturing and that temperature is more important in gene expression when the available P is limited. This work underscores the utility of using principles of elemental stoichiometry coupled with genomic and transcriptomics research tools to make and test predictions about life history evolution. The results of my work also\ inform inferences about the ways in which nutrient availability also drives the organization of trophic interactions and ultimately ecosystems.

}, keywords = {LTER-MCM, Antarctic nematodes, Caenorhabditis elegans, genome evolution, growth rate hypothesis, Plectus murrayi, Scottnema lindsayae, transcriptome}, url = {https://search.proquest.com/docview/2081899003}, author = {Xue, Xia and Byron Adams} } @phdthesis {4442, title = {Genomic analysis of nematode-environment interaction}, volume = {Ph.D.}, year = {2010}, month = {08/2010}, school = {Brigham Young University}, type = {doctoral}, address = {Provo, UT}, abstract = {

The natural environments of organisms present a multitude of biotic and abiotic challenges that require both short-term ecological and long-term evolutionary responses. Though most environmental response studies have focused on effects at the ecosystem, community and organismal levels, the ultimate controls of these responses are located in the genome of the organism. Soil nematodes are highly responsive to, and display a wide variety of responses to changing environmental conditions, making them ideal models for the study of organismal interactions with their environment. In an attempt to examine responses to environmental stress (desiccation and freezing), genomic level analyses of gene expression during anhydrobiosis of the Antarctic nematode Plectus murrayi was undertaken. An EST library representative of the desiccation induced transcripts was established and the transcripts differentially expressed during desiccation stress were identified. The expressed genome of P. murrayi showed that desiccation survival in nematodes involves differential expression of a suite of genes from diverse functional areas, and constitutive expression of a number of stress related genes. My study also revealed that exposure to slow desiccation and freezing plays an important role in the transcription of stress related genes, improves desiccation and freezing survival of nematodes. Deterioration of traits essential for biological control has been recognized in diverse biological control agents including insect pathogenic nematodes. I studied the genetic mechanisms behind such deterioration using expression profiling. My results showed that trait deterioration of insect pathogenic nematode induces substantial overall changes in the nematode transcriptome and exhibits a general pattern of metabolic shift causing massive changes in metabolic and other processes. Finally, through field observations and molecular laboratory experiments the validity of the growth rate hypothesis in natural populations of Antarctic nematodes was tested. My results indicated that elemental stoichiometry influences evolutionary adaptations in gene expression and genome evolution. My study, in addition to providing immediate insight into the mechanisms by which multicellular animals respond to their environment, is transformative in its potential to inform other fundamental ecological and evolutionary questions, such as the evolution of life-history patterns and the relationship between community structure and ecological function in ecosystems.

}, keywords = {LTER-MCM, anhydrobiosis, Antarctic nematode, comparative transcriptomics, complementary DNA library, desiccation, functional analysis, Heterorhabditis bacteriophora, McMurdo Dry Valleys, microarray analysis, Plectus murrayi, quantative real-time polymerase chain reaction, Scottnema lindsayae, stoichiometry, stress survival, subtractive hybridization, trait deterioration, transcriptional profiling}, url = {https://scholarsarchive.byu.edu/etd/2578}, author = {Bishwo N. Adhikari and Byron Adams} }