The roles of long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) in embryonic development remain unclear. We performed a comprehensive analysis of lncRNA and circRNA profiles in rabbit embryos at different stages by whole transcriptome sequencing. We identified 719 lncRNAs and 744 circRNAs that were differentially expressed between stages S1, S2 and S3. A total of 241 differentially expressed lncRNAs and 166 differentially expressed circRNAs were significantly involved in embryonic morphogenesis and development. An RNA network was established and of the embryonic development-associated RNAs, the lncRNAs TCONS_00009253 and TCONS_00010436 were persistently downregulated, while circRNA_07129, circRNA_15209, and circRNA_12526 were persistently upregulated, and their co-expressed mRNAs TBX1, WNT3 and FGFR2 were persistently downregulated during embryonic development. These candidate RNAs were mainly involved in the Wnt, PI3K-Akt, and calcium signaling pathways. This study reports candidate lncRNAs and circRNAs that may be indispensable for the morphogenesis and development of rabbit embryos.

长的非编码RNA（lncRNA）和环状RNA（circRNA）在胚胎发育中的作用尚不清楚。我们通过全转录组测序对兔子胚胎在不同阶段的lncRNA和circRNA谱进行了全面分析。我们鉴定了在阶段S1，S2和S3之间差异表达的719个lncRNA和744个circRNA。共有241个差异表达的lncRNA和166个差异表达的circRNA显着参与了胚胎的形态发生和发展。建立了一个RNA网络，与胚胎发育相关的RNA中，lncRNA TCONS_00009253和TCONS_00010436被持续下调，而circRNA_07129，circRNA_15209和circRNA_12526被持续上调，并且它们共表达的mRNA TBX1，WNT3和FGFR2在胚胎发育过程中持续下调。这些候选RNA主要参与Wnt，PI3K-Akt和钙信号通路。这项研究报告了可能是兔胚胎的形态发生和发育必不可少的候选lncRNA和circRNA。