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Genome-wide analysis of long non-coding RNAs in adult tissues of the melon fly, Zeugodacus cucurbitae (Coquillett)

(2020) BMC GENOMICS. 21(1).
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Abstract
BackgroundLong 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.ResultsWe 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.ConclusionsThis 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.
Keywords
Long non-coding RNA, Zeugodacus cucurbitae, RNA-seq, Transcriptome, Differential expressions, EXPRESSION ANALYSIS, DIAMONDBACK MOTH, GENE-EXPRESSION, IDENTIFICATION, LNCRNAS, ANNOTATION, FEATURES, REVEALS, GENCODE, SEQ

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MLA
Li, Wei-Jun, et al. “Genome-Wide Analysis of Long Non-Coding RNAs in Adult Tissues of the Melon Fly, Zeugodacus Cucurbitae (Coquillett).” BMC GENOMICS, vol. 21, no. 1, 2020, doi:10.1186/s12864-020-07014-x.
APA
Li, W.-J., Song, Y.-J., Han, H.-L., Xu, H.-Q., Wei, D., Smagghe, G., & Wang, J.-J. (2020). Genome-wide analysis of long non-coding RNAs in adult tissues of the melon fly, Zeugodacus cucurbitae (Coquillett). BMC GENOMICS, 21(1). https://doi.org/10.1186/s12864-020-07014-x
Chicago author-date
Li, Wei-Jun, Yu-Jia Song, Hong-Liang Han, Hui-Qian Xu, Dong Wei, Guy Smagghe, and Jin-Jun Wang. 2020. “Genome-Wide Analysis of Long Non-Coding RNAs in Adult Tissues of the Melon Fly, Zeugodacus Cucurbitae (Coquillett).” BMC GENOMICS 21 (1). https://doi.org/10.1186/s12864-020-07014-x.
Chicago author-date (all authors)
Li, Wei-Jun, Yu-Jia Song, Hong-Liang Han, Hui-Qian Xu, Dong Wei, Guy Smagghe, and Jin-Jun Wang. 2020. “Genome-Wide Analysis of Long Non-Coding RNAs in Adult Tissues of the Melon Fly, Zeugodacus Cucurbitae (Coquillett).” BMC GENOMICS 21 (1). doi:10.1186/s12864-020-07014-x.
Vancouver
1.
Li W-J, Song Y-J, Han H-L, Xu H-Q, Wei D, Smagghe G, et al. Genome-wide analysis of long non-coding RNAs in adult tissues of the melon fly, Zeugodacus cucurbitae (Coquillett). BMC GENOMICS. 2020;21(1).
IEEE
[1]
W.-J. Li et al., “Genome-wide analysis of long non-coding RNAs in adult tissues of the melon fly, Zeugodacus cucurbitae (Coquillett),” BMC GENOMICS, vol. 21, no. 1, 2020.
@article{8678518,
  abstract     = {BackgroundLong 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.ResultsWe 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.ConclusionsThis 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.},
  articleno    = {600},
  author       = {Li, Wei-Jun and Song, Yu-Jia and Han, Hong-Liang and Xu, Hui-Qian and Wei, Dong and Smagghe, Guy and Wang, Jin-Jun},
  issn         = {1471-2164},
  journal      = {BMC GENOMICS},
  keywords     = {Long non-coding RNA,Zeugodacus cucurbitae,RNA-seq,Transcriptome,Differential expressions,EXPRESSION ANALYSIS,DIAMONDBACK MOTH,GENE-EXPRESSION,IDENTIFICATION,LNCRNAS,ANNOTATION,FEATURES,REVEALS,GENCODE,SEQ},
  language     = {eng},
  number       = {1},
  pages        = {12},
  title        = {Genome-wide analysis of long non-coding RNAs in adult tissues of the melon fly, Zeugodacus cucurbitae (Coquillett)},
  url          = {http://dx.doi.org/10.1186/s12864-020-07014-x},
  volume       = {21},
  year         = {2020},
}

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