The Pristionchus pacificus genome provides a unique perspective on nematode lifestyle and parasitism

Here we present a draft genome sequence of the nematode Pristionchus pacificus, a species that is associated with beetles and is used as a model system in evolutionary biology. With 169 Mb and 23,500 predicted protein-coding genes, the P. pacificus genome is larger than those of Caenorhabditis elegans and the human parasite Brugia malayi. Compared to C. elegans, the P. pacificus genome has more genes encoding cytochrome P450 enzymes, glucosyltransferases, sulfotransferases and ABC transporters, many of which were experimentally validated. The P. pacificus genome contains genes encoding cellulase and diapausin, and cellulase activity is found in P. pacificus secretions, indicating that cellulases can be found in nematodes beyond plant parasites. The relatively higher number of detoxification and degradation enzymes in P. pacificus is consistent with its necromenic lifestyle and might represent a preadaptation for parasitism. Thus, comparative genomics analysis of three ecologically distinct nematodes offers a unique opportunity to investigate the association between genome structure and lifestyle.

[1]  R. Sommer,et al.  Morphological, genetic and molecular description of Pristionchus pacificus sp. n. (Nematoda : Neodiplogastridae ) , 1996 .

[2]  Michael J. Sanderson,et al.  A Nonparametric Approach to Estimating Divergence Times in the Absence of Rate Constancy , 1997 .

[3]  R. Poulin.  Evolutionary Ecology of Parasites , 1997 .

[4]  Mark L. Blaxter,et al.  A molecular evolutionary framework for the phylum Nematoda , 1998, Nature.

[5]  J. Berg.  Genome sequence of the nematode C. elegans: a platform for investigating biology. , 1998, Science.

[6]  Andrew Smith.  Genome sequence of the nematode C-elegans: A platform for investigating biology , 1998 .

[7]  B. Henrissat,et al.  Endogenous cellulases in animals: isolation of beta-1, 4-endoglucanase genes from two species of plant-parasitic cyst nematodes. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[8]  P. Roberts,et al.  Plant parasitic nematodes: digesting a page from the microbe book. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[9]  Franz Oesch,et al.  Chapter 4 – Xenobiotic Metabolism , 1999 .

[10]  X. Huang,et al.  CAP3: A DNA sequence assembly program. , 1999, Genome research.

[11]  Christian E. V. Storm,et al.  Automatic clustering of orthologs and in-paralogs from pairwise species comparisons. , 2001, Journal of molecular biology.

[12]  S. Eddy,et al.  Automated de novo identification of repeat sequence families in sequenced genomes. , 2002, Genome research.

[13]  Hanh Witte,et al.  A bacterial artificial chromosome-based genetic linkage map of the nematode Pristionchus pacificus. , 2002, Genetics.

[14]  Anton J. Enright,et al.  An efficient algorithm for large-scale detection of protein families. , 2002, Nucleic acids research.

[15]  R. Durbin,et al.  The Genome Sequence of Caenorhabditis briggsae: A Platform for Comparative Genomics , 2003, PLoS biology.

[16]  Mario Stanke,et al.  Gene prediction with a hidden Markov model and a new intron submodel , 2003, ECCB.

[17]  T. Yamashita,et al.  Insect diapause-specific peptide from the leaf beetle has consensus with a putative iridovirus peptide , 2003, Peptides.

[18]  Ian Korf,et al.  Gene finding in novel genomes , 2004, BMC Bioinformatics.

[19]  Steven Salzberg,et al.  TigrScan and GlimmerHMM: two open source ab initio eukaryotic gene-finders , 2004, Bioinform..

[20]  Ewan Birney,et al.  Automated generation of heuristics for biological sequence comparison , 2005, BMC Bioinformatics.

[21]  John T Jones,et al.  A family of glycosyl hydrolase family 45 cellulases from the pine wood nematode Bursaphelenchus xylophilus , 2004, FEBS letters.

[22]  R. Sommer,et al.  Conservation and diversification of Wnt signaling function during the evolution of nematode vulva development , 2005, Nature Genetics.

[23]  Jonathan E. Allen,et al.  JIGSAW, GeneZilla, and GlimmerHMM: puzzling out the features of human genes in the ENCODE regions , 2006, Genome Biology.

[24]  Elaine R. Mardis,et al.  Application of a superword array in genome assembly , 2006, Nucleic acids research.

[25]  Gang Liu,et al.  Automatic clustering of orthologs and inparalogs shared by multiple proteomes , 2006, ISMB.

[26]  K. Kiontke,et al.  Ecology of Caenorhabditis species. , 2006, WormBook : the online review of C. elegans biology.

[27]  R. Sommer,et al.  HAIRY-like Transcription Factors and the Evolution of the Nematode Vulva Equivalence Group , 2006, Current Biology.

[28]  R. Sommer,et al.  Pristionchus pacificus: a well-rounded nematode. , 2006, BioEssays : news and reviews in molecular, cellular and developmental biology.

[29]  M. Blaxter.  Symbiont genes in host genomes: fragments with a future? , 2007, Cell host & microbe.

[30]  S. Richards,et al.  Widespread Lateral Gene Transfer from Intracellular Bacteria to Multicellular Eukaryotes , 2007, Science.

[31]  R. Sommer,et al.  The pax-3 gene is involved in vulva formation in Pristionchus pacificus and is a target of the Hox gene lin-39 , 2007, Development.

[32]  Jonathan E. Allen,et al.  Draft Genome of the Filarial Nematode Parasite Brugia malayi , 2007, Science.

[33]  R. Sommer,et al.  Phylogeny of the nematode genus Pristionchus and implications for biodiversity, biogeography and the evolution of hermaphroditism , 2007, BMC Evolutionary Biology.

[34]  R. Sommer,et al.  The Nematode Pristionchus pacificus (Nematoda: Diplogastridae) Is Associated with the Oriental Beetle Exomala orientalis (Coleoptera: Scarabaeidae) in Japan , 2007, Zoological science.

[35]  Yoshihiro Yamanishi,et al.  KEGG for linking genomes to life and the environment , 2007, Nucleic Acids Res..

[36]  R. Sommer,et al.  Wnt Signaling Induces Vulva Development in the Nematode Pristionchus pacificus , 2008, Current Biology.

[37]  L. Holm,et al.  The Pfam protein families database , 2005, Nucleic Acids Res..