意大利蜜蜂工蜂中肠的长链非编码 RNA的预测、分析及鉴定
Prediction, analysis and identification of long, non-coding RNA in the midguts of Apis mellifera ligustica workers
熊翠玲** 耿四海** 王心蕊 刘思亚 陈大福 郑燕珍 付中民 杜 宇 王海朋
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DOI：10.7679/j.issn.2095-1353.2018.125
作者单位：福建农林大学蜂学学院，福州 350002
中文关键词：意大利蜜蜂，中肠，lncRNA-seq技术，长链非编码RNA，上下游基因
英文关键词：Apis mellifera ligustica, midgut, lncRNA-seq technology, long non-coding RNA, upstream and downstream genes
中文摘要：【目的】 预测、分析和鉴定意大利蜜蜂Apis mellifera
ligustica工蜂中肠的长链非编码RNA（lncRNA），探究lncRNA的作用。【方法】 结合lncRNA-seq技术和链特异性cDNA建库方法对意大利蜜蜂工蜂中肠进行深度测序；利用Perl脚本对原始数据进行过滤；联用CPC和CNCI软件对测序数据进行lncRNA预测，并比较lncRNA基因与其邻近的蛋白编码基因的结构特征；通过RT-PCR对随机选取的lncRNA进行鉴定；利用相关生物信息学软件对lncRNA、的上下游基因进行GO分类和KEGG代谢通路富集分析。【结果】 意大利蜜蜂工蜂中肠样品的lncRNA-seq共得到1 956 118 858原始读段，经过滤得到1 946 489 304有效读段，共预测出6 353个lncRNA，它们较蛋白编码基因含有较少的外显子数、较短的转录本长度。通过RT-PCR验证了9个lncRNA的表达。lncRNA的上下游基因富集在42个GO条目和256条代谢通路，进一步分析结果表明这些lncRNA参与调控意大利蜜蜂工蜂中肠的新陈代谢和细胞生命活动等生物学过程。【结论】 研究结果丰富了蜜蜂的lncRNA信息，也为阐明lncRNA在意大利蜜蜂工蜂中肠发育及胁迫响应过程中的作用打下了基础。
英文摘要： [Objectives] To predict,
analyze and identify lncRNAs in the midguts of Apis mellifera ligustica workers, and investigate their functions. [Methods] The midguts of A. m. ligustica workers were sequenced
with a combination of lncRNA-seq technology and strand-specific cDNA library
construction method; the raw data was filtered with perl script; lncRNAs were
predicted using CPC and CNCI softwares, and their characteristics were compared
with those of adjacent protein-coding genes; RT-PCR was used to identify
randomly selected lncRNAs; GO classification and KEGG pathway enrichment
analyses of lncRNAs’ upstream and downstream genes were carried out using the
related bioinformatic software. [Results] A total of 1 956 118 858 raw reads were obtained from the deep
sequencing of midgut samples, and 1
946 489 304 clean reads were obtained after filtering. In total, 6 353 lncRNAs
were predicted. Compared with protein-coding genes, these lncRNAs genes had fewer exons and
shorter transcripts. The expression of nine lncRNAs was identified. Further
investigation showed that up- and down-stream genes of A. m. ligustica lncRNAs were enriched in 42 GO terms and 256
pathways. Moreover, these lncRNAs are found to be engaged in the metabolism and
cell-life activity in the midgut of A. m.
ligustica worker. [Conclusion] These results not only enrich the
information of honeybee lncRNAs, but also provide a foundation for revealing
the role of lncRNAs during the development and stress response processes in the A. m. ligustica worker midgut.