Divergent gene expression in the conserved dauer stage of the nematodes Pristionchus pacificus and Caenorhabditis elegans

Abstract

Background: An organism can respond to changing environmental conditions by adjusting gene regulation and by forming alternative phenotypes. In nematodes, these mechanisms are coupled because many species will form dauer larvae, a stress-resistant and non-aging developmental stage, when exposed to unfavorable environmental conditions, and execute gene expression programs that have been selected for the survival of the animal in the wild. These dauer larvae represent an environmentally induced, homologous developmental stage across many nematode species, sharing conserved morphological and physiological properties. Hence it can be expected that some core components of the associated transcriptional program would be conserved across species, while others might diverge over the course of evolution. However, transcriptional and metabolic analysis of dauer development has been largely restricted to Caenorhabditis elegans. Here, we use a transcriptomic approach to compare the dauer stage in the evolutionary model system Pristionchus pacificus with the dauer stage in C. elegans.

Results: We have employed Agilent microarrays, which represent 20,446 P. pacificus and 20,143 C. elegans genes to show an unexpected divergence in the expression profiles of these two nematodes in dauer and dauer exit samples. P. pacificus and C. elegans differ in the dynamics and function of genes that are differentially expressed. We find that only a small number of orthologous gene pairs show similar expression pattern in the dauers of the two species, while the non-orthologous fraction of genes is a major contributor to the active transcriptome in dauers. Interestingly, many of the genes acquired by horizontal gene transfer and orphan genes in P. pacificus, are differentially expressed suggesting that these genes are of evolutionary and functional importance.

Conclusion: Our data set provides a catalog for future functional investigations and indicates novel insight into evolutionary mechanisms. We discuss the limited conservation of core developmental and transcriptional programs as a common aspect of animal evolution.

Figure 1

Limited conservation in the dauer related transcriptomes of the two species. (a) Overlap between genes differentially expressed in P. pacificus (green) and C. elegans dauers versus dauer-exit (12 hours) samples. The rectangular boxes represent the entire transcriptome on the array and their area of overlap represents the 1:1 orthologs between the two species, which are represented on both microarrays. The ovals represent the set of differentially expressed genes in each species. 184 orthologous gene pairs are called significantly differentially expressed in both the species, indicating limited conservation (Fisher's exact test p-value = 0.029). A substantial number of non-orthologous, species-specific genes are also differentially expressed in both the species. These gene sets are further analyzed by dividing them into distinct classes which are indicated in blue text (see main text for details) (b) Comparison of log2 expression fold changes for the set of 6,126 1:1 orthologs for the dauer versus dauer-exit comparison. Pearson's correlation coefficient over the entire set of 6,126 orthologs is r = 0.12, and increases to r = 0.29 for the 184 orthologs, which are significantly differentially expressed in both species (FDR corrected p-value < =0 0.05; purple boxes mark the significant orthologs, number per quadrant I - IV: 51 + 51 + 65 + 17 = 184).

Figure 2

Log2 fold changes of median PFAM gene expression levels inP. pacificusandC. elegans. All genes on the microarrays were stratified by PFAM domain annotation into partially overlapping gene families with at least 5 members. A positive log2 fold change indicates that the corresponding genes were up-regulated in the dauer stages in comparison to the dauer exit time point.

Figure 3

Differences in regulation of metabolism related genes during the dauer exit time course inC. elegansandP. pacificus. Gene-to-pathway assignments were retrieved for C. elegans from the KEGG database. Pathway assignments were transferred to P. pacificus by mapping 1:1 orthologs. All tables show genes that are up, down or at a similar expression level in a dauer vs. dauer exit (12 hours post induction) comparison.