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Integration of lncRNA-miRNA-mRNA reveals novel insights into oviposition regulation in honey bees.

ABSTRACT: BACKGROUND:The honey bee (Apis mellifera) is a highly diverse species commonly used for honey production and pollination services. The oviposition of the honey bee queen affects the development and overall performance of the colony. To investigate the ovary activation and oviposition processes on a molecular level, a genome-wide analysis of lncRNAs, miRNAs and mRNA expression in the ovaries of the queens was performed to screen for differentially expressed coding and noncoding RNAs. Further analysis identified relevant candidate genes or RNAs. RESULTS:The analysis of the RNA profiles in different oviposition phase of the queens revealed that 740 lncRNAs, 81 miRNAs and 5,481 mRNAs were differently expressed during the ovary activation; 88 lncRNAs, 13 miRNAs and 338 mRNAs were differently expressed during the oviposition inhibition process; and finally, 100 lncRNAs, four miRNAs and 497 mRNAs were differently expressed during the oviposition recovery process. In addition, functional annotation of differentially expressed RNAs revealed several pathways that are closely related to oviposition, including hippo, MAPK, notch, Wnt, mTOR, TGF-beta and FoxO signaling pathways. Furthermore, in the QTL region for ovary size, 73 differentially expressed genes and 14 differentially expressed lncRNAs were located, which are considered as candidate genes affecting ovary size and oviposition. Moreover, a core set of genes served as bridges among different miRNAs were identified through the integrated analysis of lncRNA-miRNA-mRNA network. CONCLUSION:The observed dramatic expression changes of coding and noncoding RNAs suggest that they may play a critical role in honey bee queens' oviposition. The identified candidate genes for oviposition activation and regulation could serve as a resource for further studies of genetic markers of oviposition in honey bees.

SUBMITTER: Chen X

PROVIDER: S-EPMC5632538 | biostudies-literature | 2017

REPOSITORIES: biostudies-literature

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Integration of lncRNA-miRNA-mRNA reveals novel insights into oviposition regulation in honey bees.

Chen Xiao X Ma Ce C Chen Chao C Lu Qian Q Shi Wei W Liu Zhiguang Z Wang Huihua H Guo Haikun H

PeerJ 20171005

<h4>Background</h4>The honey bee (<i>Apis mellifera</i>) is a highly diverse species commonly used for honey production and pollination services. The oviposition of the honey bee queen affects the development and overall performance of the colony. To investigate the ovary activation and oviposition processes on a molecular level, a genome-wide analysis of lncRNAs, miRNAs and mRNA expression in the ovaries of the queens was performed to screen for differentially expressed coding and noncoding RNA ...[more]

PMID: 29018616

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Project description:MicroRNAs (miRNAs) belong to non-coding small RNAs which have been shown to take a regulatory function at the posttranscriptional level in plant growth development and response to abiotic stress. Hemerocallis fulva is an herbaceous perennial plant with fleshy roots, wide distribution, and strong adaptability. However, salt stress is one of the most serious abiotic stresses to limit the growth and production of Hemerocallis fulva. To identify the miRNAs and their targets involved in the salt stress resistance, the salt-tolerant H. fulva with and without NaCl treatment were used as materials, and the expression differences of miRNAs-mRNAs related to salt-tolerance were explored and the cleavage sites between miRNAs and targets were also identified by using degradome sequencing technology. In this study, twenty and three significantly differential expression miRNAs (p-value < 0.05) were identified in the roots and leaves of H. fulva separately. Additionally, 12,691 and 1538 differentially expressed genes (DEGs) were also obtained, respectively, in roots and leaves. Moreover, 222 target genes of 61 family miRNAs were validated by degradome sequencing. Among the DE miRNAs, 29 pairs of miRNA targets displayed negatively correlated expression profiles. The qRT-PCR results also showed that the trends of miRNA and DEG expression were consistent with those of RNA-seq. A gene ontology (GO) enrichment analysis of these targets revealed that the calcium ion pathway, oxidative defense response, microtubule cytoskeleton organization, and DNA binding transcription factor responded to NaCl stress. Five miRNAs, miR156, miR160, miR393, miR166, and miR396, and several hub genes, squamosa promoter-binding-like protein (SPL), auxin response factor 12 (ARF), transport inhibitor response 1-like protein (TIR1), calmodulin-like proteins (CML), and growth-regulating factor 4 (GRF4), might play central roles in the regulation of NaCl-responsive genes. These results indicate that non-coding small RNAs and their target genes that are related to phytohormone signaling, Ca2+ signaling, and oxidative defense signaling pathways are involved in H. fulva's response to NaCl stress.

Dataset Information

Integration of lncRNA-miRNA-mRNA reveals novel insights into oviposition regulation in honey bees.

Publications

Integration of lncRNA-miRNA-mRNA reveals novel insights into oviposition regulation in honey bees.

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