The Hox and ParaHox genes of bilateria share a similar expression pattern along the body axis and are known to be associated with anterior-posterior patterning. In vertebrates, the Hox genes are also expressed in presomitic mesoderm and gut endoderm and the ParaHox genes show a restricted expression pattern in the gut-related derivatives. Regional expression patterns in the embryonic central nervous system of the basal chordates amphioxus and ascidian have been reported; however, little is known about their endodermal expression in the alimentary canal. We focus on the Hox and ParaHox genes in the ascidian Ciona intestinalis and investigate the gene expression patterns in the juvenile, which shows morphological regionality in the alimentary canal. Gene expression analyses by using whole-mount in situ hybridization reveal that all Hox genes have a regional expression pattern along the alimentary canal. Expression of Hox1 to Hox4 is restricted to the posterior region of pharyngeal derivatives. Hox5 to Hox13 show an ordered expression pattern correlated with each Hox gene number along the postpharyngeal digestive tract. This expression pattern along the anterior-posterior axis has also been observed in Ciona ParaHox genes. Our observations suggest that ascidian Hox and ParaHox clusters are dispersed; however, the ordered expression patterns along the alimentary canal appear to be conserved among chordates.

Fatty-acid-binding proteins (FABPs) are small intracellular proteins associated with the transportation of fatty acids. Members of the FABPs share similar amino acid sequences and tertiary structures and form, together with a member of the cellular retinol-binding proteins (CRBPs), the intracellular-lipid-binding protein (iLBP) family. In vertebrates, several types of FABP have been isolated and classified into three subfamilies: 2-4. In invertebrates, several FABP-related proteins have been reported in protostomes and amphioxus; however, little is known about the relationship between their phylogenetic positions and expression patterns. We have performed a genome-wide survey of FABP-related genes in protochordates: amphioxus Branchiostoma belcheri and the ascidian Ciona intestinalis. Comprehensive BLAST searches in NCBI and the Ciona Ghost Database by using amino acid sequences of all FABPs have revealed that the ascidian C. intestinalis and amphioxus B. belcheri contain six and seven FABP-related genes in their haploid genomes, respectively. Expression pattern analyses by whole-mount in situ hybridization in Ciona transparent juveniles and serial-section in situ hybridizations in adult amphioxus have revealed that all genes are mainly expressed in the postpharyngeal digestive tract. In particular, the expression of FABP-related genes of subfamily-2 (liver/ileum type) and subfamily-3 (intestinal type) in the ascidian pyloric gland and amphioxus hepatic cecum provides insight into the evolution of hepatic-related structures of chordates and FABP-related genes.