ASSEMBLY AND CHARACTERIZATION OF THE RAINBOW TROUT EGG TRANSCRIPTOME

Rainbow trout is an important fish species for aquaculture and recreational fisheries. Egg quality is especially important because it is the determining factor for early embryonic development. However, in rainbow trout, the composition of egg transcripts and the identities and functions of egg-specific transcripts are relatively unknown. The present study was undertaken to characterize the transcriptome of rainbow trout egg and identify egg-specific transcripts that play important roles in the development of oocyte and early embryos.

Illumina sequencing yielded 74 million cleaned reads from mature rainbow trout eggs. Tophat2 and cufflinks were used to construct the transcriptome. The assembly yielded a total of 47,458 genes (Table 1). Annotation analysis showed that 30,714 assembled genes have assigned functions, corresponding to 42,362 transcripts. Gene ontology (GO) analysis was conducted to assign GO term to each of the 30,714 genes. A total of 29,408 genes were assigned with at least one GO term.

We also defined a stringent set of 3,315 lincRNAs expressed in rainbow trout egg, including 80 egg-specific lincRNAs. We built co-expression network to associate lincRNAs with mRNAs based on "guilty-by-association" analysis. This analysis identified several groups of lincRNAs associated with distinct functional set of protein-coding genes, such as signaling and development. This study provides a foundation for future studies aimed at understanding the roles of egg-expressed transcripts in controlling egg quality and early embryogenesis in rainbow trout.