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Updated: May 4, 2026
Determining Genetic Expression Profiles in C. elegans Using Microarray and Real-time PCR
Published on: July 30, 2011
Relating differential gene expression and genomic analyses to functional adaptation at various developmental stages
Anne Baldino1, Tsvetan Bachvaroff1, J Sook Chung2
1Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, 701 E Pratt St, Baltimore, MD, 21202, USA.
Background:
The blue crab, Callinectes sapidus, exhibits a pelagic, planktonic larval, and benthic post-larval form before molting into a juvenile reminiscent of the adult body plan. This study examined the expression profile and genomic structure for key genes responsible for the adaptive functions involved in the blue crab at different developmental stages. The physiological behavior of each stage reflects unique life history strategies key for the successful recruitment and settlement of a species that supports one of the largest fisheries in the United States.
Results:
The mRNA was sequenced from 5 developmental stages (zoea stage Z3, zoea stage Z5, post-larval stage megalopa, juvenile stage C2/3, and juvenile stage C4/5) from lab-reared animals. The reads were mapped to the current reference genome to determine gene expression patterns. Genes coding for cuticle proteins vary in expression at different life stages and account for a significant portion of the top differentially expressed genes. Opsin genes are significantly upregulated in the megalopa stage, with particularly high expression of opsins sensitive to wavelengths corresponding to blue/green light. The blue-light-sensitive opsin gene family is a set of 7 genes tandemly repeated along the genome with moderate conservation at the amino acid level and large differences in relative expression between gene copies. The 3 highly conserved pseudo-hemocyanin proteins are the most significantly upregulated genes in C4/5-stage juveniles. Phylogeny of decapod pseudo-hemocyanin suggests that duplication of this gene family occurred after species divergence and conservation of introns suggests that duplication within species occurred at the DNA level.
Conclusions:
The orthology analysis provides a deeper context for the gene duplication patterns within decapods. The differential gene expression of specific members of the cuticle, opsin, and pseudo-hemocyanin gene families are strongly tied with the changes in habitat, adaptive behavior, and physiology during blue crab metamorphosis and development.
