Abstract
Many arthropods undergo a seasonal dormancy termed “diapause” to optimize timing of reproduction in highly seasonal environments. In the North Atlantic, the copepod Calanus finmarchicus completes one to three generations annually with some individuals maturing into adults, while others interrupt their development to enter diapause. It is unknown which, why and when individuals enter the diapause program. Transcriptomic data from copepods on known programs were analyzed using dimensionality reduction of gene expression and functional analyses to identify program-specific genes and biological processes. These analyses elucidated physiological differences and established protocols that distinguish between programs. Differences in gene expression were associated with maturation of individuals on the reproductive program, while those on the diapause program showed little change over time. Only two of six filters effectively separated copepods by developmental program. The first one included all genes annotated to RNA metabolism and this was confirmed using differential gene expression analysis. The second filter identified 54 differentially expressed genes that were consistently up-regulated in individuals on the diapause program in comparison with those on the reproductive program. Annotated to oogenesis, RNA metabolism and fatty acid biosynthesis, these genes are both indicators for diapause preparation and good candidates for functional studies.
Highlights
The more specific filter of ‘fatty acid biosynthesis’ separated the samples into four clusters, with the early and late field samples placed into distinct transcriptional phenotypes (Fig. 5C)
differentially expressed genes (DEGs) were identified using a generalized linear model followed by downstream pairwise likelihood ratio tests
An existing RNA-Seq dataset was analyzed to develop a workflow for environmental transcriptomics that can classify pre-adult CV C. finmarchicus individuals by developmental program
Summary
The more specific filter of ‘fatty acid biosynthesis’ separated the samples into four clusters, with the early and late field samples placed into distinct transcriptional phenotypes (Fig. 5C). Such a pattern could be explained by the regulation of fatty acid metabolism along the CV’s progression towards diapause in the field, and/or it could reflect responses to environmental differences between the two sampling times. The 23 DEGs annotated to ‘fatty acid biosynthesis process’ (GO:0006633) show a general upregulation of genes associated with lipid synthesis i
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