(Featured image on main blog page: Rhincalanus gigas, by Miram Gleiber)
We recently produced of a high-quality transcriptome for the Antarctic copepod Rhincalanus gigas and described changes in gene expression during the transition between the last juvenile stage and adult female stage. The work is available here:
Berger CA, Steinberg DK, Copley NJ, and Tarrant AM. (In press). De novo transcriptome assembly of the Southern Ocean copepod Rhincalanus gigas sheds light on developmental changes in gene expression. Marine Genomics, p.100835. https://doi.org/10.1016/j.margen.2021.100835. Open access, pdf of corrected proof available here
This is part of an NSF-funded project to investigate the physiological ecology of lipid-storing Antarctic copepods in an evolutionary context. I collected the samples in 2019 along the West Antarctic Peninsula as part of the Palmer Long-Term Ecological Research Program assessment cruise. The analysis was led by MIT-WHOI Joint Program PhD candidate Cory Berger.
In discussing the changes in gene expression, we focused largely on genes related to lipid storage and metabolism. This is because Rhincalanus is part of a group of copepods that store lipids in a specialized organ called the oil sac. This mode of energy storage helps copepods survive periods of low food availability and fuel egg production in adults. Not surprisingly, we found genes related to lipid synthesis to be highly expressed in the lipid-storing juvenile copepods. Some of these genes are similar to lipid storage genes we have previously identified in another lipid-storing copepod, Calanus finmarchicus, but we’ve also identified some differences. For example, different forms of long-chain fatty acid elongases and delta-9 desaturases are up-regulated in both species. We are broadly interested in how these gene families have evolved and diversified within copepod lineages and how those patterns may relate to different patterns of lipid synthesis and storage.
To analyze these broader evolutionary patterns, we will need access to more data. We are working on similar analyses within two other Antarctic species, Calanus propinquus and Calanoides acutus. We also plan to compare the data we have collected with analyses done by other researchers in a wider range of species. We are particularly interested in trying out CrustyBase, a new crustacean community database developed by Cameron Hyde and Tomer Ventura at the University of the Sunshine Coast. The database provides a convenient online format to compare expression patterns of homologous genes across crustacean species. We’ve added a couple copepod datasets (transcriptomes and gene expression information) to the database and are hoping to recruit some other copepod researchers to contribute their work.