Nematoda. Nematoda

Pristionchus pacificus is a nematode model whose genome has recently been sequenced. To refine the genome annotation we performed transcriptome and proteome analysis and gathered comprehensive experimental information on gene expression. Transcriptome analysis on a 454 FLX platform generated >700,000 expressed sequence tags from two normalized EST libraries, whereas proteome analysis on a LTQ-Orbitrap mass spectrometer detected >27,000 non-redundant peptide sequences from >4000 proteins at ppb mass accuracy and FDR50 % of all pioneer genes are transcribed under standard culture conditions and that pioneer proteins significantly contribute to the unimodal distribution of predicted protein sizes in P. pacificus, which has an unusually low median size of 240 amino acids (26.8 kDa). In contrast, the predicted proteome of the Caenorhabditis elegans follows a distinct bimodal distribution, with significant functional differences between small and large protein populations. Combined, these results provide the first catalogue of the expressed genome of P. pacificus, refinement of its genome annotation and the first comparison of related nematode models at the proteome level.