Pristionchus.org: a genome-centric database of the nematode satellite species Pristionchus pacificus

Abstract

Comparative studies have been of invaluable importance to the understanding of evolutionary biology. The evolution of developmental programs can be studied in nematodes at a single cell resolution given their fixed cell lineage. We have established Pristionchus pacificus as a major satellite organism for evolutionary developmental biology relative to Caenorhabditis elegans, the model nematode. Online genomic information to support studies in this satellite system can be accessed at http://www.pristionchus.org. Our web resource offers diverse content covering genome browsing, genetic and physical maps, similarity searches, a community platform and assembly details. Content will be continuously improved as we annotate the P.pacificus genome, and will be an indispensable resource for P.pacificus genomics.

Figure 1

Overview of web portal division. The Navigation bar is placed to the top of the web page. There is a news board to the left and the main content below the navigation bar. The welcome page is shown, which features an introductory text as to the concepts of comparative evolutionary studies.

Figure 2

Graphical display of Pristionchus genome annotation. We employ the highly customizable Generic Genome Browser framework for viewing, analyzing and exporting local sequence annotation.

Figure 3

ContigGraphViewer—a JAVA applet for graphically representing long-distance relations in the Pristionchus genome assembly. BAC and Fosmid end mappings onto contigs are shown as a graph where vertices constitute contigs and arcs carry BAC or Fosmid labels.

Figure 4

Comparative map view—genetic map of Chromosome I is shown in conjunction with all contigs of the physical map that have a corresponding SSCP marker.