6 results on '"Zou, Bangxing"'
Search Results
2. The Spatio-Temporal Expression Profiles of Silkworm Pseudogenes Provide Valuable Insights into Their Biological Roles.
- Author
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Wan, Linrong, Su, Siyuan, Liu, Jinyun, Zou, Bangxing, Jiang, Yaming, Jiao, Beibei, Tang, Shaokuan, Zhang, Youhong, Deng, Cao, and Xiao, Wenfu
- Subjects
PSEUDOGENES ,SILKWORMS ,GENE regulatory networks ,OLFACTORY receptors ,DOMESTICATION of animals ,AMINO acid sequence - Abstract
Background: Pseudogenes are sequences that have lost the ability to transcribe RNA molecules or encode truncated but possibly functional proteins. While they were once considered to be meaningless remnants of evolution, recent researches have shown that pseudogenes play important roles in various biological processes. However, the studies of pseudogenes in the silkworm, an important model organism, are limited and have focused on single or only a few specific genes. Objective: To fill these gaps, we present a systematic genome-wide studies of pseudogenes in the silkworm. Methods: We identified the pseudogenes in the silkworm using the silkworm genome assemblies, transcriptome, protein sequences from silkworm and its related species. Then we used transcriptome datasets from 832 RNA-seq analyses to construct spatio-temporal expression profiles for these pseudogenes. Additionally, we identified tissue-specifically expressed and differentially expressed pseudogenes to further understand their characteristics. Finally, the functional roles of pseudogenes as lncRNAs were systematically analyzed. Results: We identified a total of 4410 pseudogenes, which were grouped into 4 groups, including duplications (DUPs), unitary pseudogenes (Unitary), processed pseudogenes (retropseudogenes, RETs), and fragments (FRAGs). The most of pseudogenes in the domestic silkworm were generated before the divergence of wild and domestic silkworm, however, the domestication may also involve in the accumulation of pseudogenes. These pseudogenes were clearly divided into 2 cluster, a highly expressed and a lowly expressed, and the posterior silk gland was the tissue with the most tissue-specific pseudogenes (199), implying these pseudogenes may be involved in the development and function of silkgland. We identified 3299 lncRNAs in these pseudogenes, and the target genes of these lncRNAs in silkworm pseudogenes were enriched in the egg formation and olfactory function. Conclusions: This study replenishes the genome annotations for silkworm, provide valuable insights into the biological roles of pseudogenes. It will also contribute to our understanding of the complex gene regulatory networks in the silkworm and will potentially have implications for other organisms as well. [ABSTRACT FROM AUTHOR]
- Published
- 2024
- Full Text
- View/download PDF
3. Systematic identification of smORFs in domestic silkworm (Bombyx mori)
- Author
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Wan, Linrong, primary, Xiao, Wenfu, additional, Huang, Ziyan, additional, Zhou, Anlian, additional, Jiang, Yaming, additional, Zou, Bangxing, additional, Liu, Binbin, additional, Deng, Cao, additional, and Zhang, Youhong, additional
- Published
- 2023
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4. Cytochrome P450 monooxygenase genes in the wild silkworm, Bombyx mandarina
- Author
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Xiao Jinshu, Meng-jia Liu, Zhang Youhong, Ya-Ming Jiang, Cao Deng, Linrong Wan, Xiao Wenfu, Zou Bangxing, and Zhou Anlian
- Subjects
Cytochrome ,Bioinformatics ,lcsh:Medicine ,Cytochrome P450 ,Genome ,General Biochemistry, Genetics and Molecular Biology ,03 medical and health sciences ,0302 clinical medicine ,Bombyx mandarina ,Gene family ,KEGG ,Agricultural Science ,Gene ,030304 developmental biology ,Genetics ,0303 health sciences ,biology ,General Neuroscience ,fungi ,lcsh:R ,General Medicine ,Mandarina ,Genomics ,biology.organism_classification ,Wild silkworm ,biology.protein ,General Agricultural and Biological Sciences ,Entomology ,Zoology ,030217 neurology & neurosurgery - Abstract
Wild (Bombyx mandarina) and domestic silkworms (B. mori) are good models for investigating insect domestication, as 5000 years of artificial breeding and selection have resulted in significant differences between B. mandarina and B. mori. In this study, we improved the genome assemblies to the chromosome level and updated the protein-coding gene annotations for B. mandarina. Based on this updated genome, we identified 68 cytochrome P450 genes in B. mandarina. The cytochrome P450 repository in B. mandarina is smaller than in B. mori. Certain currently unknown key genes, rather than gene number, are critical for insecticide resistance in B. mandarina, which shows greater resistance to insecticides than B. mori. Based on the physical maps of B. mandarina, we located 66 cytochrome P450s on 18 different chromosomes, and 27 of the cytochrome P450 genes were concentrated into seven clusters. KEGG enrichment analysis of the P450 genes revealed the involvement of cytochrome P450 genes in hormone biosynthesis. Analyses of the silk gland transcriptome identified candidate cytochrome P450 genes (CYP306A) involved in ecdysteroidogenesis and insecticide metabolism in B. mandarina.
- Published
- 2021
5. Comparative genome-wide DNA methylation analysis reveals epigenomic differences in response to heat-humidity stress in Bombyx mori
- Author
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Yu-Jie Feng, Min-Hui Pan, Xiao Jinshu, Zhan-Qi Dong, Cheng Lu, Xiao Wenfu, Zou Bangxing, Li Zhou, Zhang Youhong, and Peng Chen
- Subjects
Hot Temperature ,Bisulfite sequencing ,Genome, Insect ,02 engineering and technology ,Biology ,Biochemistry ,Epigenesis, Genetic ,03 medical and health sciences ,Structural Biology ,Stress, Physiological ,Cellular metabolic process ,Animals ,Sulfites ,Epigenetics ,KEGG ,Molecular Biology ,Gene ,030304 developmental biology ,Epigenomics ,Genetics ,0303 health sciences ,Whole Genome Sequencing ,fungi ,Humidity ,General Medicine ,DNA Methylation ,021001 nanoscience & nanotechnology ,Bombyx ,Differentially methylated regions ,DNA methylation ,0210 nano-technology ,Heat-Shock Response - Abstract
DNA methylation is an important epigenetic modification and has been shown to be involved in the response to abiotic stress. However, there are few studies on DNA methylation in insect response to environmental signals. In this study, we conducted a comprehensive comparative analysis of DNA methylation profiles between two silkworm strains with significantly different resistance to heat and humidity by whole-genome bisulfite sequencing (WGBS). We identified, in total, 2934 differentially methylated regions (DMRs) between RT_48h (resistant strain with high-temperature/humidity treatment for 48 h) and ST_48h (sensitive strain with high-temperature/humidity treatment for 48 h) under cytosine context (CG), which corresponded to 1230 DMR-related genes (DMGs), and the DMRs were primarily located in the gene body (exon and intron) region. Gene ontology (GO) and KEGG analysis showed that these DMGs were most significantly enriched in binding, cellular metabolic process, and RNA transport pathways. Moreover, 10 DMGs have been revealed to be involved in the heat-humidity stress response in the silkworm. The results of this study indicated that DNA methylation plays crucial roles in silkworm response to environmental stressors and provides important clues to identify key resistance genes in silkworm under high-temperature/humidity stress response.
- Published
- 2020
6. Cytochrome P450 monooxygenase genes in the wild silkworm, Bombyx mandarina .
- Author
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Wan L, Zhou A, Xiao W, Zou B, Jiang Y, Xiao J, Deng C, and Zhang Y
- Abstract
Wild ( Bombyx mandarina) and domestic silkworms ( B. mori ) are good models for investigating insect domestication, as 5000 years of artificial breeding and selection have resulted in significant differences between B. mandarina and B. mori . In this study, we improved the genome assemblies to the chromosome level and updated the protein-coding gene annotations for B. mandarina . Based on this updated genome, we identified 68 cytochrome P450 genes in B. mandarina . The cytochrome P450 repository in B. mandarina is smaller than in B. mori . Certain currently unknown key genes, rather than gene number, are critical for insecticide resistance in B. mandarina, which shows greater resistance to insecticides than B. mori . Based on the physical maps of B. mandarina, we located 66 cytochrome P450s on 18 different chromosomes, and 27 of the cytochrome P450 genes were concentrated into seven clusters. KEGG enrichment analysis of the P450 genes revealed the involvement of cytochrome P450 genes in hormone biosynthesis. Analyses of the silk gland transcriptome identified candidate cytochrome P450 genes ( CYP306A ) involved in ecdysteroidogenesis and insecticide metabolism in B. mandarina ., Competing Interests: Cao Deng is employed by Genefang and DNA Stories Bioinformatics Center. The members of Genefang Research Team are employed by Genefang. The authors declare there are no competing interests., (©2021 Wan et al.)
- Published
- 2021
- Full Text
- View/download PDF
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