Identification and comparison of long non‐coding RNAs in the silk gland between domestic and wild silkworms

Zhou, Qi; Fang, Shou-Min; Zhang, Qiang; Yu, Qiuhan; Zhang, Ze

doi:10.1111/1744-7917.12443

Cited by 26 publications

(27 citation statements)

References 63 publications

(122 reference statements)

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“…Apart from more "factories" for silk fibroins production, our results revealed that in the late stage of silk gland development, the up-regulated genes in the domestic silkworm are enriched in protein processing in the endoplasmic reticulum and ribosome pathways (Figure 2A and Supplementary Figure S4A), indicating that protein synthesis is more active in the domestic silkworm. These results are consistent with previous studies (Fang et al, 2015;Li J. Y. et al, 2017;Zhou et al, 2018).…”

Section: Discussionsupporting

confidence: 94%

A Comparison of Co-expression Networks in Silk Gland Reveals the Causes of Silk Yield Increase During Silkworm Domestication

Zhou

et al. 2020

Front. Genet.

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Section: Discussionsupporting

confidence: 94%

A Comparison of Co-expression Networks in Silk Gland Reveals the Causes of Silk Yield Increase During Silkworm Domestication

Zhou

et al. 2020

Front. Genet.

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“…indicating that protein synthesis is more active in the domestic silkworm than wild silkworm. These results are consistent with previous studies [18,19,26].…”

Section: Discussionsupporting

confidence: 94%

A comparison of co-expression networks in silk gland reveals the causes of silk yield increase during silkworm domestication

Zhou

et al. 2019

Preprint

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Background Long-term domestication and breeding selection have led to that silk yield of the domestic silkworm (Bombyx mori) have increased several times higher than that of its wild ancestor (B. mandarina). However, little is known about the molecular mechanisms of silk yield increase during silkworm domestication. Results Based on dynamic patterns of functional divergence in silk gland between the domestic and wild silkworms, we found that at early and intermediate stages of silk gland development, the up-regulated genes of the domestic silkworm mainly include DNA integration, nucleic acid binding and transporter activity, which is related to division and growth of cell. This has led to that posterior silk gland (PSG) of the domestic silkworm has significantly more cells (“factories” of fibroin protein synthesis) than that of wild silkworm. At the late stage of silk gland development, the up-regulated genes in the domestic silkworm are enriched in protein processing and ribosome pathways, suggesting that protein synthesis efficiency is greatly improved during silkworm domestication. The synthetic capacity of fibroin proteins of the domestic silkworm has increased, however, the synthetic capacity of sericin proteins has decreased relative to wild silkworm. This reflects that the domestic and wild silkworms have been under different selection pressures. Importantly, we found that the network co-expressed with silk-coding genes for the domestic silkworm is much larger than that for wild silkworm. Furthermore, much more genes co-expressed with silk-coding genes in the domestic silkworm have been subject to artificial selection than those in wild silkworm. Conclusion Our results revealed that increase in silk yield during silkworm domestication is involved in improvement of a biological system which includes not only expansion of “factories” (cells of PSG) of protein synthesis but also high expression of silk-coding genes as well as silk production related genes such as biological energy, transport, and ribosome pathway genes. In addition, a combination of comparative multi-omics and dynamic network biological method used in this study provides a methodology reference for investigation of molecular mechanisms of formation of a complex trait for other domestic animals.

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“…We further explored the potential regulatory functions of lncRNAs on the development of PSGs and the biosynthesis of fibroin. Our current study indicated that the function of the silkworm lncRNAs is not only related to fibroin synthesis and apoptosis of silk glands as stated in the previous studies (Wu et al, 2016;Zhou et al, 2018;Chen et al, 2019), but also promote the degradation of silk proteins by regulating RNA/amino acid degradation, the proteasome and proteolysis. Moreover, lncRNA may participate in nucleotide excision repair, heat shock proteins expression, autophagy activation and endoplasmic reticulum stress response to maintain the homeostasis of the PSG cells.…”

Section: Introductionsupporting

confidence: 77%

“…The scoring thresholds for the three software programs were as follows: CPC, 0 (transcripts with a value >0 were considered mRNAs, and those with a value <0 were considered lncRNAs); CNCI, 0 (transcripts with a value >0 were considered mRNAs, and those with a value <0 were considered lncRNAs); and txCdsPredict, 500 (transcripts with a value >500 were considered mRNAs, while those with a value <500 were considered lncRNAs). All predicted lncRNAs were aligned to lncRNAs collected in BmncRNAdb and previous study (Wu et al, 2016;Zhou et al, 2018). We introduced NCBI Blast tool for the comparison which was based on sequence similarity (Parameters: blastall -e 1e-5 -p blastn -a 8 -d xx.fa -i xx.fa -o blast).…”

Section: Sequence Analysis and Lncrna Identificationmentioning

confidence: 99%

“…A total of 11,810 lncRNAs were identified using RNA-seq, and coexpression network analysis revealed that hub lncRNAs associated with the middle silk gland (MSG) and posterior silk gland (PSG) may function as regulators of the biosynthesis, translocation, and secretion of silk proteins (Wu et al, 2016). The differentially expressed lncRNAs (DELs) in the silk gland are mainly associated with processes related to silk protein translation, which indicates that lncRNAs may participate in the regulation of silk protein production between domestic and wild silkworms (Zhou et al, 2018). Furthermore, lncRNAs play an important role in silk gland-related apoptosis by interacting with other RNAs (Chen et al, 2019).…”

Section: Introductionmentioning

confidence: 99%

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Comparative mRNA and LncRNA Analysis of the Molecular Mechanisms Associated With Low Silk Production in Bombyx mori

Ruan

et al. 2021

Front. Genet.

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Naked pupa sericin and Naked pupa are two mutant strains of Bombyx mori with extremely low or no fibroin production compared to the Qiufeng and Baiyu strains, both of which exhibit very high silk fibroin production. However, the molecular mechanisms by which long non-coding RNAs regulate fibroin synthesis need further study. In this study, we performed high-throughput RNA-seq to investigate lncRNA and mRNA expression profiles in the posterior silk gland of Qiufeng, Baiyu, Nd-sD, and Nd silkworms at the third day of the 5th instar. Our efforts yielded 26,767 novel lncRNAs and 6,009 novel mRNAs, the expression levels of silk protein genes and silk gland transcription factors were decreased in Qiufeng vs. Nd-sD and Qiufeng vs. Nd, while those of many genes related to autophagy, apoptosis, RNA degradation, ubiquitin-mediated proteolysis and heat shock proteins were increased. Moreover, the expression of a large number of genes responsible for protein synthesis and secretion was significantly decreased in Nd. GO and KEGG analysis results showed that nucleotide excision repair, mRNA surveillance pathways, amino acid degradation, protein digestion and absorption, ER-associated degradation and proteasome pathways were significantly enriched for the Qiufeng vs. Nd-sD and Qiufeng vs. Nd comparisons. In conclusion, our findings contribute to the lncRNA and mRNA database of Bombyx mori, and the identified differentially expressed mRNAs and lncRNAs help to reveal the molecular mechanisms of low silk production in Nd-sD and Nd, providing new insights for improvement of silk yield and elucidation of silk mechanical properties.

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Identification and comparison of long non‐coding RNAs in the silk gland between domestic and wild silkworms

Cited by 26 publications

References 63 publications

A Comparison of Co-expression Networks in Silk Gland Reveals the Causes of Silk Yield Increase During Silkworm Domestication

A Comparison of Co-expression Networks in Silk Gland Reveals the Causes of Silk Yield Increase During Silkworm Domestication

A comparison of co-expression networks in silk gland reveals the causes of silk yield increase during silkworm domestication

Comparative mRNA and LncRNA Analysis of the Molecular Mechanisms Associated With Low Silk Production in Bombyx mori

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