Ray Hong et al. (2008) Development & Evolution Meeting "Whole-Genome Sequencing and Analyses of a Pristionchus pacificus "Doppleganger" Strain with Divergent Phenotypes"

Hanh Witte, Simone Kienle, Detlef Weigel, Korbinian Schneeberger, Ralf Sommer, Gilberto Bento, Stephan Ossowski, Christoph Dieterich, Christa Lanz, Ray Hong

[Development & Evolution Meeting, 2008]

Recently diverged wild populations with low genetic differences coupled with strikingly distinct phenotypes offer rare opportunities to thoroughly characterize the genotype-to-phenotype relationships of natural variants. We used the massively parallel sequencing platform, the Solexa Sequence Analyzer (Illumina Inc.), to sequence the entire 169 MB genome of Pristionchus pacificus Poland RS106, a closely related strain to the reference strain California PS312. We identified between 700-6200 candidate SNPs/indels and so far validated 105 of these by traditional Sanger sequencing of PCR products from both strains. The resulting estimated true SNP frequency may be up to 10,000x less than the number of polymorphisms in the P. pacificus mapping strain Washington PS1843 (~1:26) as well as ~160x less frequent than between the C. elegans N2 and CB4858 strains (~1:1500) found in a similar Solexa study(1). Nevertheless, this estimate confirmed our expected low SNP count based on previous Sanger sequencing of randomly chosen ~30 kb genomic regions of the Poland strain. In order to map the loci responsible for the phenotypic variations in mouth dimorphism, vulva induction, egg laying, and chemoattraction to insect pheromones, we genotyped ~1000 Recombinant Inbred Lines from California/Poland crosses using ~100 confirmed SNPs distributed on all six chromosomes. Preliminary findings for loci linked to differences in mouth dimorphisms and egg laying will be discussed. Thus, the combination of the Solexa platform and QTL mapping in genetically similar but phenotypically disparate novel strains offers a rapid, powerful way to compile a nearly complete list of SNPs associated with phenotypic differences among natural variants.

Horner MA et al. (1998) West Coast Worm Meeting "pha-4 ENCODES A fork head/HNF HOMOLOG AND SPECIFIES PHARYNGEAL AND RECTAL ORGAN IDENTITIES"

Labouesse M, Domeier ME, Mango SE, Horner MA, Quintin S

[West Coast Worm Meeting, 1998]

Two regions of the digestive tract, pharynx and rectum, require the activity of the zygotic gene pha-41. In pha-4 mutants, cells that would normally adopt a pharyngeal or rectal fate develop as ectoderm that express the zinc finger protein LIN-26. Recently, we have shown that pha-4 encodes Ce-fkh-1, a member of the HNF-3/ fork head class of transcription factors2. Three lines of evidence suggest that pha-4 specifies organ identity in pharynx and rectal precursors. First, PHA-4 is expressed in cells destined to become the digestive tract. Expression initiates at the 28 cell stage and continues throughout embryogenesis. High levels of PHA-4 are detected in all pharyngeal cells and rectal cells. In addition, PHA-4 is expressed at low levels in the E-derived midgut. Second, pha-4 is required to establish the pharyngeal precursors. Lineage analysis and temperature shift experiments show that pha-4 function is required at a time when the pharynx precursors are born. Third, ectopic PHA-4 can confer pharyngeal and rectal identities. We have expressed PHA-4 throughout the embryo using a heat-inducible promoter. Ectopic PHA-4 is capable of inducing both pharyngeal and rectal cell development in cells not normally destined for these tissue types. Our studies suggest that the compartmentalization of the digestive tract into foregut, midgut, and hindgut relies on evolutionarily conserved molecular mechanisms. In Drosophila, fork head is both expressed in the digestive tract and required for its proper development. Similar to pha-4 mutants, Drosophila fork head mutants exhibit a transformation of foregut and hindgut (analogous to C. elegans pharynx and rectum) into ectoderm3. To test the hypothesis that gut development is phylogenetically conserved, we are attempting to rescue the pha-4 pharyngeal defect with axial and fork head, two pha-4 homologs. These experiments are currently underway. 1. Mango et al., 1994. 2. Azzaria et al., 1996; Horner et al., 1998. 3. Jurgens and Weigel 1988 We thank Carrie Van Doren and Stuart Kim for generously screening the microarray chip.