We have identified Conserved Non-coding Elements (CNEs) in the regulatory region 
of Caenorhabditis elegans and Caenorhabditis briggsae mab-9, a T-box gene known 
to be important for cell fate specification in the developing C. elegans 
hindgut. Two adjacent CNEs (a region 78 bp in length) are both necessary and 
sufficient to drive reporter gene expression in posterior hypodermal cells. The 
failure of a genomic mab-9::gfp construct lacking this region to express in 
posterior hypodermis correlates with the inability of this construct to 
completely rescue the mab-9 mutant phenotype. Transgenic males carrying this 
construct in a mab-9 mutant background exhibit tail abnormalities including 
morphogenetic defects, altered tail autofluorescence and abnormal lectin-binding 
properties. Hermaphrodites display reduced susceptibility to the C. elegans 
pathogen Microbacterium nematophilum. This comparative genomics approach has 
therefore revealed a previously unknown role for mab-9 in hypodermal function 
and we suggest that MAB-9 is required for the secretion and/or modification of 
posterior cuticle.