Operons are clusters of genes that are co-regulated from a common promoter. 
Operons are typically associated with prokaryotes, although a small number of 
eukaryotes have been shown to possess them. Among metazoans, operons have been 
extensively characterized in the nematode Caenorhabditis elegans in which ∼15% 
of the total genes are organized into operons. The most recent genome assembly 
for the ascidian Ciona intestinalis placed ∼20% of the genes (2909 total) into 
1310 operons. The majority of these operons are composed of two genes, while the 
largest are composed of six. Here is reported a computational analysis of the 
genes that comprise the Ciona operons. Gene ontology (GO) terms were identified 
for about two-thirds of the operon-encoded genes. Using the extensive collection 
of public EST libraries, estimates of temporal patterns of gene expression were 
generated for the operon-encoded genes. Lastly, conservation of operons was 
analyzed by determining how many operon-encoded genes were present in the 
ascidian Ciona savignyi and whether these genes were organized in orthologous 
operons. Over 68% of the operon-encoded genes could be assigned one or more GO 
terms and 697 of the 1310 operons contained genes in which all genes had at 
least one GO term. Of these 697 operons, GO terms were shared by all of the 
genes within 146 individual operons, suggesting that most operons encode genes 
with unrelated functions. An analysis of operon gene expression from nine 
different EST libraries indicated that for 587 operons, all of the genes that 
comprise an individual operon were expressed together in at least one EST 
library, suggesting that these genes may be co-regulated. About 50% (74/146) of 
the operons with shared GO terms also showed evidence of gene co-regulation. 
Comparisons with the C. savignyi genome identified orthologs for 1907 of 2909 
operon genes. About 38% (504/1310) of the operons are conserved between the two 
Ciona species. These results suggest that like C. elegans, operons in Ciona are 
comprised of a variety of genes that are not necessarily related in function. 
The genes in only 50% of the operons appear to be co-regulated, suggesting that 
more complex gene regulatory mechanisms are likely operating.