ArticlePloS one2016
Systematic Identification and Characterization of Long Non-Coding RNAs in the Silkworm, Bombyx mori.
Article in PloS one, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 78 papers.
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Who cites it
78 citing papers in PubMed, 160 citations in OpenAlex.
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- Identification and functional prediction of lncRNAs associated with intramuscular lipid deposition in Guangling donkeys.Frontiers in veterinary science · 2024Article
- Genome-Wide Identification and Characterization of Long Non-Coding RNAs in Roots of Rice Seedlings under Nitrogen Deficiency.Plants (Basel, Switzerland) · 2023Article
- Regulatory Roles of Long Non-Coding RNAs Relevant to Antioxidant Enzymes and Immune Responses ofInternational journal of molecular sciences · 2023Article
- Transcriptomic Analysis ofInternational journal of molecular sciences · 2023Article
- Non-coding RNAs identification and regulatory networks in pathogen-host interaction in the microsporidia congenital infection.BMC genomics · 2023Article
- Genome-wide analysis of long noncoding RNAs and their association in regulating the metamorphosis of the Sarcophaga peregrina (Diptera: Sarcophagidae).PLoS neglected tropical diseases · 2023Article
- Systematic Characterization and Regulatory Role of lncRNAs in Asian Honey Bees Responding to Microsporidian Infestation.International journal of molecular sciences · 2023Article
- A Global Survey of the Full-Length Transcriptome ofInternational journal of molecular sciences · 2023Article
18 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
8 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Long noncoding RNAs (lncRNAs) are emerging as important regulators in various biological processes. However, to date, no systematic characterization of lncRNAs has been reported in the silkworm Bombyx mori. In the present study, we generated eighteen RNA-seq datasets with relatively high depth. Using an in-house designed lncRNA identification pipeline, 11,810 lncRNAs were identified for 5,556 loci. Among these lncRNAs, 474 transcripts were intronic lncRNAs (ilncRNAs), 6,250 transcripts were intergenic lncRNAs (lincRNAs), and 5,086 were natural antisense lncRNAs (lncNATs). Compared with protein-coding mRNAs, silkworm lncRNAs are shorter in terms of full length but longer in terms of exon and intron length. In addition, lncRNAs exhibit a lower level of sequence conservation, more repeat sequences overlapped and higher tissue specificity than protein-coding mRNAs in the silkworm. We found that 69 lncRNA transcripts from 33 gene loci may function as miRNA precursors, and 104 lncRNA transcripts from 72 gene loci may act as competing endogenous RNAs (ceRNAs). In total, 49.47% of all gene loci (2,749/5,556) for which lncRNAs were identified showed sex-biased expression. Co-expression network analysis resulted in 19 modules, 12 of which revealed relatively high tissue specificity. The highlighted darkgoldenrod module was specifically associated with middle and posterior silk glands, and the hub lncRNAs within this module were co-expressed with proteins involved in translation, translocation, and secretory processes, suggesting that these hub lncRNAs may function as regulators of the biosynthesis, translocation, and secretion of silk proteins. This study presents the first comprehensive genome-wide analysis of silkworm lncRNAs and provides an invaluable resource for genetic, evolutionary, and genomic studies of B. mori.
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