Chen Dafu, Chen Huazhi, Du Yu, Zhou Dingding, Geng Sihai, Wang Haipeng, Wan Jieqi, Xiong Cuiling, Zheng Yanzhen, Guo Rui
College of Bee Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
Insects. 2019 Aug 9;10(8):245. doi: 10.3390/insects10080245.
Long non-coding RNAs (lncRNAs) are a diverse class of transcripts that structurally resemble mRNAs but do not encode proteins, and lncRNAs have been proven to play pivotal roles in a wide range of biological processes in animals and plants. However, knowledge of expression patterns and potential roles of honeybee lncRNA response to infection is completely unknown. Here, we performed whole transcriptome strand-specific RNA sequencing of normal midguts of workers (Am7CK, Am10CK) and -inoculated midguts (Am7T, Am10T), followed by comprehensive analyses using bioinformatic and molecular approaches. A total of 6353 lncRNAs were identified, including 4749 conserved lncRNAs and 1604 novel lncRNAs. These lncRNAs had minimal sequence similarities with other known lncRNAs in other species; however, their structural features were similar to counterparts in mammals and plants, including shorter exon and intron length, lower exon number, and lower expression level, compared with protein-coding transcripts. Further, 111 and 146 -responsive lncRNAs were identified from midguts at 7-days post-inoculation (dpi) and 10 dpi compared with control midguts. Twelve differentially expressed lncRNAs (DElncRNAs) were shared by Am7CK vs. Am7T and Am10CK vs. Am10T comparison groups, while the numbers of unique DElncRNAs were 99 and 134, respectively. Functional annotation and pathway analysis showed that the DElncRNAs may regulate the expression of neighboring genes by acting in and fashion. Moreover, we discovered 27 lncRNAs harboring eight known miRNA precursors and 513 lncRNAs harboring 2257 novel miRNA precursors. Additionally, hundreds of DElncRNAs and their target miRNAs were found to form complex competitive endogenous RNA (ceRNA) networks, suggesting that these DElncRNAs may act as miRNA sponges. Furthermore, DElncRNA-miRNA-mRNA networks were constructed and investigated, the results demonstrated that a portion of the DElncRNAs were likely to participate in regulating the host material and energy metabolism as well as cellular and humoral immune host responses to invasion. Our findings revealed here offer not only a rich genetic resource for further investigation of the functional roles of lncRNAs involved in the response to infection, but also a novel insight into understanding the host-pathogen interaction during honeybee microsporidiosis.
长链非编码RNA（lncRNAs）是一类多样的转录本，其结构与mRNA相似但不编码蛋白质，并且lncRNAs已被证明在动植物的广泛生物过程中发挥关键作用。然而，蜜蜂lncRNA对感染的表达模式和潜在作用却完全未知。在此，我们对工蜂正常中肠（Am7CK、Am10CK）和接种后的中肠（Am7T、Am10T）进行了全转录组链特异性RNA测序，随后使用生物信息学和分子方法进行了综合分析。共鉴定出6353个lncRNAs，包括4749个保守lncRNAs和1604个新的lncRNAs。这些lncRNAs与其他物种中其他已知lncRNAs的序列相似性极小；然而，它们的结构特征与哺乳动物和植物中的对应物相似，与蛋白质编码转录本相比，其外显子和内含子长度较短、外显子数量较少且表达水平较低。此外，与对照中肠相比，在接种后7天（dpi）和10 dpi的中肠中分别鉴定出111个和146个响应lncRNAs。Am7CK与Am7T以及Am10CK与Am10T比较组共有12个差异表达lncRNAs（DElncRNAs），而独特的DElncRNAs数量分别为99个和134个。功能注释和通路分析表明，DElncRNAs可能通过顺式和反式作用调节邻近基因的表达。此外，我们发现27个lncRNAs含有8个已知的miRNA前体，513个lncRNAs含有2257个新的miRNA前体。此外，发现数百个DElncRNAs及其靶标miRNA形成复杂的竞争性内源RNA（ceRNA）网络，表明这些DElncRNAs可能充当miRNA海绵。此外，构建并研究了DElncRNA-miRNA-mRNA网络，结果表明一部分DElncRNAs可能参与调节宿主物质和能量代谢以及宿主对微孢子虫入侵的细胞和体液免疫反应。我们在此揭示的发现不仅为进一步研究参与蜜蜂对微孢子虫感染反应的lncRNAs的功能作用提供了丰富的遗传资源，也为理解蜜蜂微孢子虫病期间宿主-病原体相互作用提供了新的见解。
