11 Ybx1 has been demonstrated as a crucial gene in embryogenesis, reproduction as well 12 as development in various vertebrates such as mouse and zebrafish. However, the 13 underlying lncRNA-mediated mechanisms require deep investigation. Particularly, the 14 importance of lncRNA to vertebrate development is controversial and questionable 15 since many studies have yielded contradictory conclusions for the same lncRNAs. In 16 the present study, in order to disclose the lncRNAs implicated in vertebrate 17 development, a systematic transcriptome analysis is conducted based on the RNA 18 sequencing data derived from ybx1 homozygous mutant zebrafish on day5 (day5_ybx1 -19 /-) as well as wild type zebrafish on day5 and day6 (day5_ybx1 +/+ , day6_ybx1 +/+ ). A 20 high-confidence dataset of zebrafish lncRNAs is detected using a stepwise filtering 21 pipeline. Differential expression analysis and co-expression network analysis reveal 22 that several lncRNAs probably act on duox and noxo1a, the genes related to redox 23 (reduction-oxidation reaction) processes which are triggered by ybx1 disruption. 24 Validation by an experimental study on three selected lncRNAs indicates that 25 knockdown of all selected lncRNAs leads to morphological deformation of larvae. In 26 addition, our experiments effectively support the prediction of network analysis in 27 many interaction patterns between the selected lncRNAs and the two redox genes (duox, 28 noxo1a). In short, our study provides new insights into the function and mechanism of 29 lncRNAs implicated in zebrafish embryonic development and demonstrates the 30 importance of lncRNAs in vertebrate development. 31 2 32 Author Summary 33 LncRNAs has been emerged as key regulatory layers because of their multiple 34 functions in diverse biological processes and pathways. However, there is disagreement 35 about the roles of lncRNAs in vertebrate development Some cases demonstrated that 36 lncRNAs was important to development. Others showed that lncRNAs just have feeble 37 functions in development. On the other hand, Ybx1 processing multi-functions has been 38 well demonstrated as a key protein to most vertebrate in development. Hence, aimed at 39 disclosure of key lncRNAs implicated in vertebrate development as well as their 40 possible roles, we performed a systematic transcriptome analysis based on the deep 41 RNA sequencing data of ybx1 homozygous mutant zebrafish and wild type zebrafish. 42 Our analysis successfully revealed several lncRNAs probably target on the redox-43 related genes. Furthermore, our experiments validated the importance of these lncRNAs 44 to zebrafish embryo development. This study is the first to utilize Ybx1 as breakpoint 45 to identify key lncRNA related to vertebrate development and provides new insights 46 into underlying mechanisms of lncRNAs in development. 47 48