Meeting Abstract

P3.100  Monday, Jan. 6 15:30  Differential Gene Expression During Early Embryogenesis in the Ctenophore Mnemiopsis leidyi KOCH, BJ*; SCHNITZLER, CE; GILDEA, DE; HENRY, JQ; MARTINDALE, MQ; BAXEVANIS, AD; BROWNE, WE; Natl. Human Genome Res. Inst., NIH; Natl. Human Genome Res. Inst., NIH; Natl. Human Genome Res. Inst., NIH; Univ. of Illinois, Urbana-Champaign; Whitney Lab. for Marine Biosci., Univ. of Florida; Natl. Human Genome Res. Inst., NIH; Univ. of Miami bernard.koch@nih.gov

Mnemiopsis leidyi is a lobate ctenophore found in near-shore waters of the western Atlantic Ocean. Despite being one of the five extant deep metazoan lineages, little is known about many aspects of ctenophore development, including gene expression in the early embryo. To better understand the developmental genetic changes that occur during early Mnemiopsis embryogenesis, we performed RNA-seq experiments comparing gene expression between the zygote and 8-cell stage embryo, when the first asymmetric cell divisions occur. In addition to collecting multiple bioreplicates of these stages, we experimentally isolated E and M blastomeres from 8-cell embryos for a total of four experimental conditions. We pooled RNA-seq reads from all conditions to assemble a de novo reference transcriptome using the Trinity assembler. Our assembly contains 20,424 unique transcripts and rates highly in terms of contiguity, with an N50 of 2,245 bp. It also includes near-full length transcripts for 234 of the 248 CEGMA core eukaryotic genes, suggesting the assembly is not only contiguous, but also complete and accurate. Most importantly, we were able to map an average of 91% of our RNA-seq reads back to this assembly per sample, indicating that it successfully captures the diversity of our conditions. The DESeq and edgeR algorithms were used to assess differential expression among the four conditions. DESeq produced more conservative results than edgeR, detecting fewer differentially expressed genes between the zygote and the 8-cell embryo. This study is one of the first significant attempts to comprehensively characterize developmental gene expression in a ctenophore.