A New Transcriptomes Dataset for C elegans

The nematode Caenorhabditis elegans is an important model for studies of germ cell biology, including the meiotic cell cycle, gamete specification as sperm or oocyte and gamete development. Fundamental to those studies is a genome-level knowledge of the germline transcriptome.

Here researchers at the University  of  Wisconsin-­‐Madison, use RNA-Seq to identify genes expressed in isolated XX gonads, which are roughly 95% germline and 5% somatic gonadal tissue. They generate data from mutants making either sperm [fem-3(q96)] or oocytes [fog-2(q71)], both grown at 22°. Their dataset identifies a total of 10,754 mRNAs in the polyadenylated transcriptome of XX gonads, with 2,748 enriched in spermatogenic gonads, 1,732 enriched in oogenic gonads and the remaining 6,274 not enriched in either. These spermatogenic, oogenic and gender-neutral gene datasets compare well with those of earlier studies, but double the number of genes identified. A comparison of the additional genes found in this study with in situ hybridization patterns in the Kohara database suggests that most are expressed in the germline. The researchers also query the RNA-Seq data for differential exon usage and find 351 mRNAs with sex-enriched isoforms. They suggest that this new dataset will prove useful for studies focusing on C. elegans germ cell biology.


Ortiz MA, Noble D, Sorokin EP, Kimble J. (2014) A New Dataset of Spermatogenic vs. Oogenic Transcriptomes in the Nematode Caenorhabditis elegans. G3 (Bethesda) [Epub ahead of print]. [article]