Genome-wide identification of long non-coding RNAs reveals potential association with asexual and sexual development.

UNLABELLED

Long non-coding RNAs (lncRNAs) play pivotal roles in regulating diverse biological processes across plants, mammals, and fungi. However, the information on lncRNAs in oomycete asexual and sexual reproduction, which are two pivotal processes in the pathogenic cycle, has not been elucidated. In this present study, strand-specific RNA sequencing data of with asexual development and sexual reproduction were reanalyzed, and a total of 4,399 lncRNAs were systematically identified. Compared to messenger RNAs (mRNAs), lncRNAs had a higher proportion of transcripts containing more than one exon, shorter nucleotide lengths, and lower expression levels. Target analysis showed that although only 280 lncRNA-mRNA pairs were shared, the functional pathways in which and targets participated were similar. Weighted gene co-expression network analysis of differentially expressed lncRNAs (DElncRs) and differentially expressed mRNAs (DEmRs) of asexual development stages indicated that lncRNAs might participate in different asexual stages and transformation of the growth stages via regulating functional genes. Expression trend analysis of DElncRs and DEmRs showed that lncRNAs may promote asexual development via upregulating mRNAs encoding development- and invasion-related proteins, such as INF6, triosephosphate isomerase, and glycoprotein elicitor. Co-expression analysis of DElncRs and DEmRs of sexual reproduction showed that lncRNAs could increase the level of mRNAs related to mating, such as M96 mating-specific protein and Crinkler family protein, which meant that lncRNAs might participate in sexual reproduction by regulating mating-related genes. Our study conducted a comprehensive analysis of lncRNAs in and suggested a potential function of lncRNAs in asexual and sexual development.

IMPORTANCE

This study systematically analyzed lncRNAs in , revealing the associations between lncRNAs and functional genes. The potential regulatory roles of lncRNAs in the asexual and sexual reproduction stages were clarified, providing a new perspective for in-depth understanding of the reproductive regulatory network of oomycetes. This not only expands the understanding of the functions of non-coding RNAs in different biological groups but also provides potential targets for the development of new disease prevention and control strategies, promoting related research in the fields of agriculture and biology.