Chongqing Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, 400715, China.
International Joint Laboratory of China-Belgium on Sustainable Crop Pest Control, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China.
BMC Genomics. 2020 Aug 31;21(1):600. doi: 10.1186/s12864-020-07014-x.
Long non-coding RNAs (lncRNAs) are involved in many fundamental biological processes, such as transcription regulation, protein degradation, and cell differentiation. Information on lncRNA in the melon fly, Zeugodacus cucurbitae (Coquillett) is currently limited.
We constructed 24 RNA-seq libraries from eight tissues (midgut, Malpighian tubules, fat body, ovary, and testis) of Z. cucurbitae adults. A total of 3124 lncRNA transcripts were identified. Among those, 1464 were lincRNAs, 1037 were intronic lncRNAs, 301 were anti-sense lncRNAs, and 322 were sense lncRNAs. The majority of lncRNAs contained two exons and one isoform. Differentially expressed lncRNAs were analyzed between tissues, and Malpighian tubules versus testis had the largest number. Some lncRNAs exhibited strong tissue specificity. Specifically expressed lncRNAs were identified and filtered in tissues of female and male Z. cucurbitae based on their expression levels. Four midgut-specific lncRNAs were validated by quantitative real-time polymerase chain reaction (RT-qPCR), and the data were consistent with RNA-seq data. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses of targets of midgut-specific lncRNAs indicated an enrichment of the metabolic process.
This was the first systematic identification of lncRNA in the melon fly. Expressions of lncRNAs in multiple adult tissues were evaluated by quantitative transcriptomic analysis. These qualitative and quantitative analyses of lncRNAs, especially the tissue-specific lncRNAs in Z. cucurbitae, provide useful data for further functional studies.
长非编码 RNA（lncRNA）参与许多基本的生物学过程，如转录调控、蛋白质降解和细胞分化。目前关于瓜实蝇 Zeugodacus cucurbitae（Coquillett）的 lncRNA 信息有限。
我们从 8 种成年瓜实蝇组织（中肠、马氏管、脂肪体、卵巢和睾丸）构建了 24 个 RNA-seq 文库。共鉴定出 3124 个 lncRNA 转录本。其中，1464 个为 lincRNA，1037 个为内含子 lncRNA，301 个为反义 lncRNA，322 个为正义 lncRNA。大多数 lncRNA 含有两个外显子和一个亚型。分析了组织间差异表达的 lncRNA，马氏管与睾丸之间的差异表达 lncRNA 数量最多。一些 lncRNA 表现出强烈的组织特异性。根据表达水平，在雌雄瓜实蝇的组织中鉴定和筛选了特异表达的 lncRNA。通过定量实时聚合酶链反应（RT-qPCR）验证了 4 个中肠特异性 lncRNA，数据与 RNA-seq 数据一致。中肠特异性 lncRNA 靶基因的基因本体（GO）和京都基因与基因组百科全书（KEGG）通路分析表明代谢过程富集。
这是首次在瓜实蝇中系统地鉴定 lncRNA。通过定量转录组分析评估了 lncRNA 在多种成年组织中的表达。这些瓜实蝇 lncRNA 的定性和定量分析，特别是组织特异性 lncRNA，为进一步的功能研究提供了有用的数据。
Zotero 插件