title: A new dataset of spermatogenic vs. oogenic transcriptomes in the nematode Caenorhabditis elegans.
abstract: 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, we use RNA-Seq to identify genes expressed in isolated XX gonads, which are approximately 95% germline and 5% somatic gonadal tissue. We generate data from mutants making either sperm [fem-3(q96)] or oocytes [fog-2(q71)], both grown at 22°. Our dataset identifies a total of 10,754 mRNAs in the polyadenylated transcriptome of XX gonads, with 2748 enriched in spermatogenic gonads, 1732 enriched in oogenic gonads, and the remaining 6274 not enriched in either. These spermatogenic, oogenic, and gender-neutral gene datasets compare well with those of previous studies, but double the number of genes identified. A comparison of the additional genes found in our study with in situ hybridization patterns in the Kohara database suggests that most are expressed in the germline. We also query our RNA-Seq data for differential exon usage and find 351 mRNAs with sex-enriched isoforms. We suggest that this new dataset will prove useful for studies focusing on C. elegans germ cell biology.
authors: Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706.
authors: Marco A
authors: MA
authors: Ortiz
authors: Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706.
authors: Daniel
authors: D
authors: Noble
authors: Graduate Program in Cellular and Molecular Biology, University of Wisconsin-Madison, Madison, Wisconsin 53706.
authors: Elena P
authors: EP
authors: Sorokin
authors: Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706 Graduate Program in Cellular and Molecular Biology, University of Wisconsin-Madison, Madison, Wisconsin 53706 Howard Hughes Medical Institute, University of Wisconsin-Madison, Madison, Wisconsin 53706 jekimble@wisc.edu.
authors: Judith
authors: J
authors: Kimble
mesh_terms: D017398:Alternative Splicing; D000818:Animals; D001483:Base Sequence; D017173:Caenorhabditis elegans / Q000235:genetics* / Q000378:metabolism; D030561:Databases, Nucleic Acid; D006066:Gonads / Q000378:metabolism; D008297:Male; D008969:Molecular Sequence Data; D009865:Oocytes / Q000378:metabolism*; D018510:RNA, Helminth / Q000235:genetics; D017423:Sequence Analysis, RNA; D013094:Spermatozoa / Q000378:metabolism*; D059467:Transcriptome
chemical_list: D018510:RNA, Helminth
keywords: C. elegans; Genetics of Sex; RNA-Seq; germline sex; splicing