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Conserved transcriptional responses to cyanobacterial stressors are mediated by alternate regulation, of paralogous genes in Daphnia

(2015) MOLECULAR ECOLOGY. 24(8). p.1844-1855
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Abstract
Despite a significant increase in genomic data, our knowledge of gene functions and their transcriptional responses to environmental stimuli remains limited. Here, we use the model keystone species Daphnia pulex to study environmental responses of genes in the context of their gene family history to better understand the relationship between genome structure and gene function in response to environmental stimuli. Daphnia were exposed to five different treatments, each consisting of a diet supplemented with one of five cyanobacterial species, and a control treatment consisting of a diet of only green algae. Differential gene expression profiles of Daphnia exposed to each of these five cyanobacterial species showed that genes with known functions are more likely to be shared by different expression profiles, whereas genes specific to the lineage of Daphnia are more likely to be unique to a given expression profile. Furthermore, while only a small number of nonlineage-specific genes were conserved across treatment type, there was a high degree of overlap in expression profiles at the functional level. The conservation of functional responses across the different cyanobacterial treatments can be attributed to the treatment-specific expression of different paralogous genes within the same gene family. Comparison with available gene expression data in the literature suggests differences in nutritional composition in diets with cyanobacterial species compared to diets of green algae as a primary driver for cyanobacterial effects on Daphnia. We conclude that conserved functional responses in Daphnia across different cyanobacterial treatments are mediated through alternate regulation of paralogous gene families.
Keywords
molecular evolution, gene structure and function, transcriptomics, FATTY-ACID-COMPOSITION, crustaceans, MICROCYSTIS-AERUGINOSA, POPULATION-GROWTH, GENOME, PULEX, ZOOPLANKTON, PATHWAYS, ANABAENA, MAGNA, WATER

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MLA
Asselman, Jana et al. “Conserved Transcriptional Responses to Cyanobacterial Stressors Are Mediated by Alternate Regulation, of Paralogous Genes in Daphnia.” MOLECULAR ECOLOGY 24.8 (2015): 1844–1855. Print.
APA
Asselman, J., Pfrender, M. E., Lopez, J. A., De Coninck, D., Janssen, C., Shaw, J. R., & De Schamphelaere, K. (2015). Conserved transcriptional responses to cyanobacterial stressors are mediated by alternate regulation, of paralogous genes in Daphnia. MOLECULAR ECOLOGY, 24(8), 1844–1855.
Chicago author-date
Asselman, Jana, Michael E Pfrender, Jacqueline A Lopez, Dieter De Coninck, Colin Janssen, Joseph R Shaw, and Karel De Schamphelaere. 2015. “Conserved Transcriptional Responses to Cyanobacterial Stressors Are Mediated by Alternate Regulation, of Paralogous Genes in Daphnia.” Molecular Ecology 24 (8): 1844–1855.
Chicago author-date (all authors)
Asselman, Jana, Michael E Pfrender, Jacqueline A Lopez, Dieter De Coninck, Colin Janssen, Joseph R Shaw, and Karel De Schamphelaere. 2015. “Conserved Transcriptional Responses to Cyanobacterial Stressors Are Mediated by Alternate Regulation, of Paralogous Genes in Daphnia.” Molecular Ecology 24 (8): 1844–1855.
Vancouver
1.
Asselman J, Pfrender ME, Lopez JA, De Coninck D, Janssen C, Shaw JR, et al. Conserved transcriptional responses to cyanobacterial stressors are mediated by alternate regulation, of paralogous genes in Daphnia. MOLECULAR ECOLOGY. 2015;24(8):1844–55.
IEEE
[1]
J. Asselman et al., “Conserved transcriptional responses to cyanobacterial stressors are mediated by alternate regulation, of paralogous genes in Daphnia,” MOLECULAR ECOLOGY, vol. 24, no. 8, pp. 1844–1855, 2015.
@article{5889627,
  abstract     = {Despite a significant increase in genomic data, our knowledge of gene functions and their transcriptional responses to environmental stimuli remains limited. Here, we use the model keystone species Daphnia pulex to study environmental responses of genes in the context of their gene family history to better understand the relationship between genome structure and gene function in response to environmental stimuli. Daphnia were exposed to five different treatments, each consisting of a diet supplemented with one of five cyanobacterial species, and a control treatment consisting of a diet of only green algae. Differential gene expression profiles of Daphnia exposed to each of these five cyanobacterial species showed that genes with known functions are more likely to be shared by different expression profiles, whereas genes specific to the lineage of Daphnia are more likely to be unique to a given expression profile. Furthermore, while only a small number of nonlineage-specific genes were conserved across treatment type, there was a high degree of overlap in expression profiles at the functional level. The conservation of functional responses across the different cyanobacterial treatments can be attributed to the treatment-specific expression of different paralogous genes within the same gene family. Comparison with available gene expression data in the literature suggests differences in nutritional composition in diets with cyanobacterial species compared to diets of green algae as a primary driver for cyanobacterial effects on Daphnia. We conclude that conserved functional responses in Daphnia across different cyanobacterial treatments are mediated through alternate regulation of paralogous gene families.},
  author       = {Asselman, Jana and Pfrender, Michael E and Lopez, Jacqueline A and De Coninck, Dieter and Janssen, Colin and Shaw, Joseph R and De Schamphelaere, Karel},
  issn         = {0962-1083},
  journal      = {MOLECULAR ECOLOGY},
  keywords     = {molecular evolution,gene structure and function,transcriptomics,FATTY-ACID-COMPOSITION,crustaceans,MICROCYSTIS-AERUGINOSA,POPULATION-GROWTH,GENOME,PULEX,ZOOPLANKTON,PATHWAYS,ANABAENA,MAGNA,WATER},
  language     = {eng},
  number       = {8},
  pages        = {1844--1855},
  title        = {Conserved transcriptional responses to cyanobacterial stressors are mediated by alternate regulation, of paralogous genes in Daphnia},
  url          = {http://dx.doi.org/10.1111/mec.13148},
  volume       = {24},
  year         = {2015},
}

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