Ralf J. Sommer (2006) WormBook "Pristionchus pacificus."

Ralf J. Sommer

[WormBook, 2006]

In the last decade, nematodes other than C. elegans have been studied intensively in evolutionary developmental biology. A few species have been developed as satellite systems for more detailed genetic and molecular studies. One such satellite species is the diplogastrid nematode Pristionchus pacificus. Here, I provide an overview about the biology, phylogeny, ecology, genetics and genomics of P. pacificus.

Ralf J. Sommer (2005) WormBook "Evolution of development in nematodes related to C. elegans."

Ralf J. Sommer

[WormBook, 2005]

The knowledge about C. elegans provides a paradigm for comparative studies. Nematodes are very attractive in evolutionary developmental biology given the species richness of the phylum and the easiness with which several of these species can be cultured under laboratory conditions. Embryonic, gonad, vulva and male tail development were studied and compared in nematodes of five different families, providing a detailed picture of evolutionary changes in development. In particular, vulva development has been studied in great detail and substantial differences in the cellular, genetic and molecular mechanisms have been observed between C. elegans and other nematodes. For example, vulva induction relies on the single anchor cell in C. elegans, whereas a variety of different cellular mechanisms are used in related species. In recent years, a few species have been developed as satellite systems for detailed genetic and molecular studies, such as Oscheius tipulae and Pristionchus pacificus.

Sommer, Ralf J. (2011) International Worm Meeting "Molecular phylogeny and divergence time estimates for beetle-associated Pristionchus nematodes."

Sommer, Ralf J.

[International Worm Meeting, 2011]

Pristionchus pacificus has been established as a model system in evolutionary developmental biology (evo-devo) and for comparison to C. elegans. Recent studies expanded the evo-devo work to ecology and population genetics. P. pacificus and related species have a well-defined association with scarab beetles: Sampling of more than 20,000 scarab beetles from around the world resulted in the isolation of more than 8,000 Pristionchus isogenic female lines. Mating experiments and molecular sequence analysis identified 26 species to date. We provide a molecular phylogenetic framework based on nearly 11,000 characters. Studies on La Reunion, an Island with a unique P. pacificus biodiversity hotspot, provide a case study to link population genetics with ecology and evo-devo. We obtained more than 400 wild isolates of P. pacificus and carried out microsatellite analysis of 21 markers. These studies indicate four major biogeographic clades of P. pacificus. La Reunion represents the only geographic area with P. pacificus strains being present in all four clades. This finding is best explained by P. pacificus invading the island independently with different beetle vectors, such as Oryctes, Amneidus and Maladera (Herrmann et al., 2010). We assessed the molecular phylogeny of P. pacificus and used mutation accumulation line approaches to provide divergence time estimates. Mutation rates were assessed first, by mitochondrial DNA analysis and second, from representative microsatellite markers. Mitochondrial DNA analysis suggests a minimal divergence time for P. pacificus of 105 to 106 generations (Molnar et al., 2011). Similarly, microsatellite markers are used to robustly provide minimal divergence time estimates for closely related strains from La Reunion. This includes a first attempt for a serious analysis of the population size of P. pacificus.

Sommer RJ et al. (1994) Worm Breeder's Gazette "Evolution of Vulva-Formation: Part II: Species With a Central Vulva"

Sommer RJ, Sternberg PW

[Worm Breeder's Gazette, 1994]

Evolution of vulva-formation: Part II: Species with a central vulva Ralf J. Sommer & Paul W. Sternberg, California Institute of Technology, Division of Biology 156-29, Pasadena, CA 91125

Ralf J Sommer et al. (2002) Worm Breeder's Gazette "Towards a Pristionchus genome map- I - P. pacificus BAC Library construction and end sequencing of BAC clones"

Christa Lanz, Taco Jesse, Stephan C Schuster, Heike Keller, Gunther Raddatz, Ralf J Sommer

[Worm Breeder's Gazette, 2002]

In order to facilitate the easier cloning of genes in the satellite model system Pristionchus pacificus , we have initiated a genomic approach by constructing genetic and physical maps of Pristionchus pacificus . An essential prerequisite for a good genomics approach is the availability of a good genomic library with large insert sizes. We constructed a BAC library of Pristionchus pacificus . The library contained 13, 440 clones in total and was a result of 4 different ligations. The average insert size of the clones is 128 kb. Insert sizes ranged between 100-180kb. We estimate the genome coverage of the library to be approximately 8 times. End sequencing of the BAC clones was done at the Genome Centre of the MPI Tubingen. Uptil now 6000 BAC clones have been end sequenced. On an average approximately 600 bp were read from each BAC end. The sequence was checked for quality using the PHRED/PHREP protocol. The total length of the BAC ends sequenced was approximately 10 Mb. The GC content of the sequence was 47%. From the 11271 ends sequenced, 8232 BAC ends gave no hits and 1129 gave hits to the non-redundant NCBI database.

Sommer RJ et al. (1994) Worm Breeder's Gazette "Evolution of Vulva Formation: Part IV: Variation in AC Position Can Cause a Shift of Vulva Formation Towards P(4-6).p."

Sternberg PW, Sommer RJ

[Worm Breeder's Gazette, 1994]

Evolution of vulva formation: Part IV: Variation in AC position can cause a shift of vulva formation towards p(4- 6).p Ralf J. Sommer & Paul W. Sternberg, HHMI & California Institute of Technology, Division of Biology 156-29, Pasadena, CA

Pires da Silva A et al. (2000) European Worm Meeting "Novel mutants defective in vulva induction in Pristionchus pacificus"

Sommer RJ, Pires da Silva A

[European Worm Meeting, 2000]

More than 50 genes involved in vulva development have been characterized in the rhabditid C. elegans. The extensive characterization of this model system provides a framework for studying the genetic basis of evolutionary modifications. Cell fate specification during vulva formation differs significantly between C. elegansand the diplogasterid nematode Pristionchus pacificus. Cell ablation experiments in P. pacificus demonstrate the existence of several novel cell-cell interactions (Sigrist and Sommer, 1999; Sommer and Sternberg, 1996). To understand the molecular mechanisms underlying vulval pattern formation in P. pacificus, we performed several TMP/UV and EMS mutagenesis screens. The mutants isolated in these screens fall into two categories: I) "generation-vulvaless" mutants do not generate Pn.p cells; II) "induction-vulvaless" mutants generate Pn.p cells, but these fail to differentiate. We have isolated and characterized a new class of induction vulvaless mutants, in which P6.p differentiates as a normal 1 cell, but P5.p and P7.p adopt a non-vulval fate (3). In wild type P. pacificus, as in C. elegans, P6.p adopts the 1 fate, whereas P5.p and P7.p generate the 2 lineage. Four mutants, tu114(TMP/UV), tu132(EMS), tu48(EMS) and tu51 (EMS), display this defect to different extents. Complementation test among these mutants are in progress. We are using a PCR-based genomic substraction strategy (RDA) to identify the deletion associated with the tu114 mutant. The identification of the genes involved in the induction of the vulva in P. pacificus may help us understand how molecular mechanisms change during evolution. Sigrist, C. B., and Sommer, R. J. (1999). Vulva formation in Pristionchus pacificus relies on continuous gonadal induction. Dev Genes Evol 209, 451-9. Sommer, R. J., and Sternberg, P. W. (1996). Apoptosis and change of competence limit the size of the vulva equivalence group in Pristionchus pacificus: a genetic analysis. Curr Biol 6, 52-9.

Sommer RJ et al. (2000) European Worm Meeting "Novel mutants defective in vulva induction in Pristionchus pacificus"

Pires da Silva A, Sommer RJ

[European Worm Meeting, 2000]

More than 50 genes involved in vulva development have been characterized in the rhabditid C. elegans. The extensive characterization of this model system provides a framework for studying the genetic basis of evolutionary modifications. Cell fate specification during vulva formation differs significantly between C. elegansand the diplogasterid nematode Pristionchus pacificus. Cell ablation experiments in P. pacificus demonstrate the existence of several novel cell-cell interactions (Sigrist and Sommer, 1999; Sommer and Sternberg, 1996). To understand the molecular mechanisms underlying vulval pattern formation in P. pacificus, we performed several TMP/UV and EMS mutagenesis screens. The mutants isolated in these screens fall into two categories: I) "generation-vulvaless" mutants do not generate Pn.p cells; II) "induction-vulvaless" mutants generate Pn.p cells, but these fail to differentiate. We have isolated and characterized a new class of induction vulvaless mutants, in which P6.p differentiates as a normal 1 cell, but P5.p and P7.p adopt a non-vulval fate (3). In wild type P. pacificus, as in C. elegans, P6.p adopts the 1 fate, whereas P5.p and P7.p generate the 2 lineage. Four mutants, tu114 (TMP/UV), tu132 (EMS), tu48 (EMS) and tu51 (EMS), display this defect to different extents. Complementation test among these mutants are in progress. We are using a PCR-based genomic substraction strategy (RDA) to identify the deletion associated with the tu114 mutant. The identification of the genes involved in the induction of the vulva in P. pacificus may help us understand how molecular mechanisms change during evolution. Sigrist, C. B., and Sommer, R. J. (1999). Vulva formation in Pristionchus pacificus relies on continuous gonadal induction. Dev Genes Evol 209, 451-9. Sommer, R. J., and Sternberg, P. W. (1996). Apoptosis and change of competence limit the size of the vulva equivalence group in Pristionchus pacificus: a genetic analysis. Curr Biol 6, 52-9.

McGhee JD (1987) Biochemistry "Purification and characterization of a carboxylesterase from the intestine of the nematode Caenorhabditis elegans."

McGhee JD

[Biochemistry, 1987]

The major intestinal esterase from the nematode Caenorhabditis elegans has been purified to essential homogeneity. Starting from whole worms, the overall purification is 9000-fold with a 10% recovery of activity. The esterase is a single polypeptide chain of Mr 60,000 and is stoichiometrically inhibited by organophosphates. Substrate preferences and inhibition patterns classify the enzyme as a carboxylesterase (EC 3.1.1.1), but the physiological function is unknown. The sequence of 13 amino acid residues at the esterase N- terminus has been determined. This partial sequence shows a surprisingly high degree of similarity to the N-terminal sequence of two carboxylesterases recently isolated from Drosophila mojavensis [Pen, J., van Beeumen, J., & Beintema, J. J. (1986) Biochem. J. 238, 691-699].

Anderton SM et al. (1996) East Coast Worm Meeting "Comparisons of serotonin containing neurons in freeliving nematodes: correlation (or not) of ventral cord neurons with vulval precursor cell patterns."

Anderton SM, Loer CM

[East Coast Worm Meeting, 1996]

We are interested in how patterns of serotonergic neurons are specified in the nematode. In C. elegans, six hypodermal cells (P38.p) are competent to produce vulva in the central body of the hermaphrodite. In this same body region in the ventral nerve cord (VNC) of the male, P38.aap normally divide to produce two neurons, one of which contains serotonin (CP neurons, P38.aapp). We wondered whether related species of worms that have a different number of vulval precursor cells than C. elegans might also alter the pattern of serotonergic neurons in the male. We first examined Pristionchus pactficus which in the hermaphrodite has only 4 Pn.p ectoblasts, P58.p; anterior and posterior Pn.p cells undergo programmed cell death (R. Sommer, personal communication). We found four serotonin-immunoreactive (JR) CP-like neurons in male Pristionchus VNC, correctly positioned to be P58.aapp. In the hermaphrodite VNC, we saw four cells, two anterior and two posterior to the vulva, and appearing to innervate the vulval region. These are likely to be 7C cells, only four of which (P58.aap) survive in Pristionchus (R. Sommer, pers. comm.). VC cells in C. elegans occasionally stain with serotonin antisera. With this simple picture in mind of a correlation between Pn.p cell fates in the hermaphrodite and Pn.aapp fate in the male, we examined several other species of worms with varying numbers of Pn.p cells (Sommer & Sternberg, 1995, Dev. Biol. 167: 61; Sommer & Sternberg, 1994, Science 265: 114). The simple-minded hypothesis did not hold up beyond Pristionchus. Panagrolaimus, also with P58.p cells in the hermaphrodite, had 8 CP-like somas in the male VNC (4 faint in the anterior, 4 bright in the posterior). Essentially the same pattern was seen in the male Rhabditella, in which the hermaphrodite has 5 Pn.p cells (P48.p). Both Pelodera and Teratorhabditis (each with P48.p in the hermaphrodite), looked like C. elegans, with 6 CP-like cells in the male VNC. Each of these species sometimes showed other faintly staining somas, paired with the CP-like neurons. Similar cells are sometimes seen in C. elegans and are believed to be CA neurons (Pn.aapa). We will present a complete pattern of serotoninIR cells in males and hermaphrodites for each of these species. We wish to thank Ralf Sommer for providing the non-C. elegans strains used and sharing unpublished information about them. Another undergraduate, Nicole Hinson, did the first staining with Pristionchus during a summer HHMI fellowship.