Identification of a nematode chemosensory gene family

Abstract

Taking advantage of the recent availability of the whole genome sequence of Caenorhabditis briggsae, a closely related nematode to Caenorhabditis elegans, we have examined the chemosensory gene superfamily by using comparative genomic methods. We have identified a chemosensory gene family, serpentine receptor class ab (srab), which exists in both species with 25 members in C. elegans and 14 members in C. briggsae. More than 20% of these gene models are reannotated. The srab family is similar to, but distinct from, the previously described serpentine receptor class a (sra) family and shows a differential expansion in C. elegans similar to that previously described for sra. The cellular expression patterns for multiple members of the srab family in both phasmid neurons in the tail and amphid neurons in the head supports the conclusion that they are chemosensory genes and suggests that they may play a role in integrating chemosensory inputs from both ends of the organism. The expansion of both the srab and sra gene families in C. elegans relative to C. briggsae is due to multiple rounds of tandem duplication and translocation of individual genes.

Fig. 3.

sra genes. (A) Comparative genomic view of sra genes in C. elegans and C. briggsae. The upper horizontal bars represent C. elegans chromosomes ordered from I to X, and the lower horizontal bars represent C. briggsae supercontigs ordered according to syntenic relationship with the C. elegans genome. Genes were evenly arranged for better view, but the order of the genes was preserved. Orthologous relationships are represented by using lines connecting the orthologous genes. Note that only chromosomes and supercontigs that contained sra-like genes are displayed. (B) Protein sequences for the sra genes from C. elegans and C. briggsae were combined to a gene set before constructing the phylogenetic tree. C. briggsae gene names all contained “CBG” and are coded in blue, and C. elegans gene names are coded in black. Branches representing the expansions are coded in red.

Fig. 4.

sra-like genes. (A) Comparative genomic view of sra-like genes in C. elegans and C. briggsae. The upper horizontal bars represent C. elegans chromosomes ordered from I to X, and the lower horizontal bars represent C. briggsae supercontigs ordered according to syntenic relationship with the C. elegans genome. Genes were evenly distributed for better view, but the order of the genes was preserved. Orthologous relationships were represented by using lines connecting the orthologous genes. Note that only chromosomes and supercontigs that contained sra-like genes are displayed. (B) Protein sequences for the sra-like genes from C. elegans and C. briggsae were combined to a gene set before constructing the phylogenetic tree. C. briggsae gene names all contained with “CBG” and are coded in blue, and C. elegans gene names are coded in black. Branches representing the expansions are coded in red.

Fig. 1.

Phylogenetic analysis of sra and sra-like genes. Spliced nucleotide sequences for sra and sra-like genes for C. elegans and C. briggsae were clearly segregated in the phylogenetic tree. Branches for sra genes are coded in black, and branches for sra-like genes are coded in red.

Fig. 2.

Cellular expression patterns of sra-like genes. Shown is the tail of a C. elegans with expression of T20D4.1 promoter fused with GFP coding region. (A) A pair of PHA GFP-positive neurons. (B) Differential interference contrast view of the tail shown in A. (C and D) Three-dimensional reconstructed views of a pair of PHA neurons in the C. elegans tail with expression of GFP fused with T20D4.1 promoter.