ARS | Publication request: Identification and characterization of long non-coding RNAs in rainbow trout eggs

Submitted to: Annual International Plant & Animal Genome Conference
Publication Type: Abstract Only
Publication Acceptance Date: January 12, 2013
Publication Date: January 14, 2013
Citation: Wang, J., Ma, H., Rexroad III, C.E., Yao, J. 2013. Identification and characterization of long non-coding RNAs in rainbow trout eggs. Annual International Plant & Animal Genome Conference. P0509.

Technical Abstract: Long non-coding RNAs (lncRNAs) are in general considered as a diverse class of transcripts longer than 200 nucleotides that structurally resemble mRNAs but do not encode proteins. Recent advances in RNA sequencing (RNA-Seq) and bioinformatics methods have provided an opportunity to indentify and analyze such transcripts. Here we report the identification and characterization of lncRNAs in rainbow trout eggs. A total of 527 non-coding transcripts were identified from 18,330 ESTs derived from rainbow trout eggs. The average size of these transcripts was 508 bp. Of these lncRNAs, 89 appear to be specifically expressed in eggs. We characterized each lncRNA by a panorama of properties, including sequence, structural, transcriptional and orthology features. Comparisons of the rainbow trout lncRNAs with the lncRNAs from zebrafish embryos revealed that the identified lncRNAs are not conserved between the 2 species. Computational analysis also showed that individual lncRNAs are related to specific pathways and functions from cell cycle regulation to morphogenesis. This study represents the first attempt to identify lncRNAs in rainbow trout. Further analysis of expression signatures of the egg expressed lncRNAs and understanding their roles in controlling early embryogenesis may ultimately lead to the development of molecular markers for egg quality and embryonic development potential in rainbow trout.