02256nas a2200217 4500008004100000245008600041210006900127260001200196520154900208653001401757653002401771653002001795653001701815653002001832100001301852700001901865700002201884700002201906700001701928856009301945 2021 eng d00aGenome analysis of Plectus murrayi, a nematode from continental Antarctica0 aGenome analysis of IPlectus murrayiI a nematode from continental c01/20213 a

Plectus murrayi is one of the most common and locally abundant invertebrates of continental Antarctic ecosystems. Because it is readily cultured on artificial medium in the laboratory and highly tolerant to an extremely harsh environment, Plectus murrayi is emerging as a model organism for understanding the evolutionary origin and maintenance of adaptive responses to multiple environmental stressors, including freezing and desiccation. The de novo assembled genome of Plectus murrayi contains 225.741 million base pairs and a total of 14,689 predicted genes. Compared to Caenorhabditis elegans, the architectural components of Plectus murrayi are characterized by a lower number of protein-coding genes, fewer transposable elements, but more exons, than closely related taxa from less harsh environments. We compared the transcriptomes of lab-reared Plectus murrayi with wild-caught Plectus murrayi and found genes involved in growth and cellular processing were up-regulated in lab-cultured Plectus murrayi, while a few genes associated with cellular metabolism and freeze tolerance were expressed at relatively lower levels. Preliminary comparative genomic and transcriptomic analyses suggest that the observed constraints on P. murrayi genome architecture and functional gene expression, including genome decay and intron retention, may be an adaptive response to persisting in a biotically simplified, yet consistently physically harsh environment.

10agene loss10agenome architecture10agenome assembly10agenome decay10aPlectus murrayi1 aXue, Xia1 aSuvorov, Anton1 aFujimoto, Stanley1 aDilman, Adler, R.1 aAdams, Byron uhttps://academic.oup.com/g3journal/advance-article/doi/10.1093/g3journal/jkaa045/604418904018nas a2200217 4500008004100000245011800041210006900159260004000228490001000268520328000278653002403558653002703582653002103609653002703630653002003657653002403677653001803701100001303719700001703732856005103749 2018 eng d00aGenomics and transcriptomics of Antarctic nematodes reveal drivers of life history evolution and genome evolution0 aGenomics and transcriptomics of Antarctic nematodes reveal drive aProvo, UTbBrigham Young University0 vPh.D.3 a

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.

10aAntarctic nematodes10aCaenorhabditis elegans10agenome evolution10agrowth rate hypothesis10aPlectus murrayi10aScottnema lindsayae10atranscriptome1 aXue, Xia1 aAdams, Byron uhttps://search.proquest.com/docview/2081899003