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Hassanyar AK, Nie H, Li Z, Lin Y, Huang J, Woldegiorgis ST, Hussain M, Feng W, Zhang Z, Yu K, Su S. Discovery of SNP Molecular Markers and Candidate Genes Associated with Sacbrood Virus Resistance in Apis cerana cerana Larvae by Whole-Genome Resequencing. Int J Mol Sci 2023; 24:ijms24076238. [PMID: 37047210 PMCID: PMC10094193 DOI: 10.3390/ijms24076238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 03/05/2023] [Accepted: 03/07/2023] [Indexed: 03/29/2023] Open
Abstract
Sacbrood virus (SBV) is a significant problem that impedes brood development in both eastern and western honeybees. Whole-genome sequencing has become an important tool in researching population genetic variations. Numerous studies have been conducted using multiple techniques to suppress SBV infection in honeybees, but the genetic markers and molecular mechanisms underlying SBV resistance have not been identified. To explore single nucleotide polymorphisms (SNPs), insertions, deletions (Indels), and genes at the DNA level related to SBV resistance, we conducted whole-genome resequencing on 90 Apis cerana cerana larvae raised in vitro and challenged with SBV. After filtering, a total of 337.47 gigabytes of clean data and 31,000,613 high-quality SNP loci were detected in three populations. We used ten databases to annotate 9359 predicted genes. By combining population differentiation index (FST) and nucleotide polymorphisms (π), we examined genome variants between resistant (R) and susceptible (S) larvae, focusing on site integrity (INT < 0.5) and minor allele frequency (MAF < 0.05). A selective sweep analysis with the top 1% and top 5% was used to identify significant regions. Two SNPs on the 15th chromosome with GenBank KZ288474.1_322717 (Guanine > Cytosine) and KZ288479.1_95621 (Cytosine > Thiamine) were found to be significantly associated with SBV resistance based on their associated allele frequencies after SNP validation. Each SNP was authenticated in 926 and 1022 samples, respectively. The enrichment and functional annotation pathways from significantly predicted genes to SBV resistance revealed immune response processes, signal transduction mechanisms, endocytosis, peroxisomes, phagosomes, and regulation of autophagy, which may be significant in SBV resistance. This study presents novel and useful SNP molecular markers that can be utilized as assisted molecular markers to select honeybees resistant to SBV for breeding and that can be used as a biocontrol technique to protect honeybees from SBV.
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Qin S, Sun L, Zhang S, Sun X, Li M. BmAbl1 Regulates Silk Protein Synthesis via Glutathione Metabolism in Bombyx mori. INSECTS 2022; 13:967. [PMID: 36354792 PMCID: PMC9696079 DOI: 10.3390/insects13110967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 10/19/2022] [Accepted: 10/19/2022] [Indexed: 06/16/2023]
Abstract
Bombyx mori, domesticated from wild silkworms, is an economic insect that feeds on mulberry leaves and produces silk. In the current study, we demonstrated the contribution of BmAbl1 in silk protein synthesis. The inhibition and knockout of BmAbl1 can reduce the larva weight and CSW. The effect on CSW of BmAbl1 is not on the transcriptional level, but on the translational level. RNA-sequencing data suggested that amino acid synthesis and the metabolism process had a great difference between the BmAbl1- and Control strain, particularly glutathione metabolism. An abnormality in glutathione metabolism led to the reduction of free glycine and serine content, which are the main components of fibroin protein. Finally, fibroin protein synthesis has been reduced, including fibroin-heavy chain, fibroin-light chain, and p25 protein. This finding brought to light the role of BmAbl1 in the silk protein synthesis process.
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Affiliation(s)
- Sheng Qin
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212100, China
- Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, Sericultural Research Institute, Chinese Academy of Agricultural Science, Zhenjiang 212100, China
| | - Lingling Sun
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212100, China
| | - Shu Zhang
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212100, China
| | - Xia Sun
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212100, China
- Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, Sericultural Research Institute, Chinese Academy of Agricultural Science, Zhenjiang 212100, China
| | - Muwang Li
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212100, China
- Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, Sericultural Research Institute, Chinese Academy of Agricultural Science, Zhenjiang 212100, China
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Xiao R, Yuan Y, Xia H, Ge Q, Chen L, Zhu F, Xu J, Wang X, Fan Y, Wang Q, Yang Y, Chen K. Comparative transcriptome and proteome reveal synergistic functions of differentially expressed genes and proteins implicated in an over-dominant silkworm heterosis of increased silk yield. INSECT MOLECULAR BIOLOGY 2022; 31:551-567. [PMID: 35445454 DOI: 10.1111/imb.12779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 03/09/2022] [Accepted: 04/14/2022] [Indexed: 06/14/2023]
Abstract
We previously observed an over-dominant silkworm heterosis of increased yield in a cross of Bombyx mori nuclear polyhydrosis virus-resistant strain NB with a susceptible strain 306. In the present study, we found that heterosis also exists in crosses of NB with other susceptible strains, indicating it is a more general phenomenon. We performed comparative transcriptome and proteome and identified 1624 differentially expressed genes (DEGs) and 298 differentially expressed proteins (DEPs) in silk glands between parents and F1 hybrids, of which 24 DEGs/DEPs showed consistent expression at mRNA and protein levels revealed by Venn joint analysis. Their expressions are completely non-additive, mainly transgressive and under low-parent, suggesting recombination of parental genomes may be the major genetic mechanism for the heterosis. GO and KEGG analyses revealed that they may function in generally similar but distinctive aspects of metabolisms and processes with signal transduction and translation being most affected. Notably, they may not only up-regulate biosynthesis and transport of silk proteins but also down-regulate other unrelated processes, synergistically and globally remodelling the silk gland to increase yield and cause the heterosis. Our findings contribute insights into the understanding of silkworm heterosis and silk gland development and provide targets for transgenic manipulation to further increase the silk yield.
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Affiliation(s)
- Rui Xiao
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Yi Yuan
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Hengchuan Xia
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Qi Ge
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Liang Chen
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Feifei Zhu
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Jia Xu
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Xueqi Wang
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Yixuan Fan
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Qiang Wang
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Yanhua Yang
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Keping Chen
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu, China
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4
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Luan Y, Li C, Zuo W, Hu H, Gao R, Zhang B, Tong X, Lu C, Dai F. Gene mapping reveals the association between tyrosine protein kinase Abl1 and the silk yield of Bombyx mori. Anim Genet 2021; 52:342-350. [PMID: 33683721 DOI: 10.1111/age.13052] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/14/2021] [Indexed: 11/29/2022]
Abstract
The Z chromosome of the silkworm contains a major gene that influences silk yield. This major locus on chromosome Z accounts for 35.10% of the phenotypic variance. The location and identification of the gene have been a focus of silkworm genetics research. Unfortunately, identification of this gene has been difficult. We used extreme phenotype subpopulations and selected from a backcross population, BC1 M, which was obtained using the high-yield strain 872B and the low-yield strain IS-Dazao as parents, for mapping the gene on the chromosome Z. The candidate region was narrowed down to 134 kb at the tip of the chromosome. BmAbl1 in this region correlated with silk gland development by spatiotemporal expression analysis. This gene was differentially expressed in the posterior silk glands of the high- and low-yield strains. In BmAbl1, an insertion-deletion (indel) within the 10th exonic region and an SNP within the 6th intronic region were detected and shown to be associated with cocoon shell weight in 84 Bombyx mori strains with different yields. Nucleotide diversity analysis of BmAbl1 and its 50 kb flanking regions indicated that BmAbl1 has experienced strong artificial selection during silkworm domestication. This study is the first to identify the genes controlling silk yield in the major QTL of the Z chromosome using forward genetics.
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Affiliation(s)
- Y Luan
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, College of Biotechnology, Southwest University, Chongqing, 400715, China
| | - C Li
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, College of Biotechnology, Southwest University, Chongqing, 400715, China
| | - W Zuo
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, College of Biotechnology, Southwest University, Chongqing, 400715, China
| | - H Hu
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, College of Biotechnology, Southwest University, Chongqing, 400715, China
| | - R Gao
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, College of Biotechnology, Southwest University, Chongqing, 400715, China
| | - B Zhang
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, College of Biotechnology, Southwest University, Chongqing, 400715, China
| | - X Tong
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, College of Biotechnology, Southwest University, Chongqing, 400715, China
| | - C Lu
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, College of Biotechnology, Southwest University, Chongqing, 400715, China
| | - F Dai
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, College of Biotechnology, Southwest University, Chongqing, 400715, China
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Wang D, Li S, Wei L, Li Z, Liu B, Cao D. Transcriptome analysis identifies key genes involved in carotenoid biosynthesis in the flesh of red pummelo (Citrus maxima). BIOTECHNOL BIOTEC EQ 2020. [DOI: 10.1080/13102818.2020.1792341] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Affiliation(s)
- Dongxia Wang
- Department of Agriculture and Forestry, College of Agriculture and Animal Husbandry, Qinghai University, Qinghai, Xining, PR China
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Qinghai, Xining, PR China
| | - Shiming Li
- Qinghai Province Key Laboratory of Crop Molecular Breeding, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai, PR China
| | - Le Wei
- Department of Life Sciences, College of Biologic and Geographic Sciences, Qinghai Normal University, Qinghai, Xining, PR China
| | - Zongren Li
- Department of Agriculture and Forestry, College of Agriculture and Animal Husbandry, Qinghai University, Qinghai, Xining, PR China
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Qinghai, Xining, PR China
| | - Baolong Liu
- Qinghai Province Key Laboratory of Crop Molecular Breeding, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai, PR China
- Laboratory of Wheat Quality Improvement, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Xining, Qinghai, PR China
| | - Dong Cao
- Department of Agriculture and Forestry, College of Agriculture and Animal Husbandry, Qinghai University, Qinghai, Xining, PR China
- Qinghai Province Key Laboratory of Crop Molecular Breeding, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai, PR China
- Laboratory of Wheat Quality Improvement, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Xining, Qinghai, PR China
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6
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Chen T, Sun Q, Ma Y, Zeng W, Liu R, Qu D, Huang L, Xu H. A transcriptome atlas of silkworm silk glands revealed by PacBio single-molecule long-read sequencing. Mol Genet Genomics 2020; 295:1227-1237. [PMID: 32524299 DOI: 10.1007/s00438-020-01691-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Accepted: 05/25/2020] [Indexed: 02/05/2023]
Abstract
The silk gland of the silkworm Bombyx mori is a specialized organ where silk proteins are efficiently synthesized under precise regulation that largely determines the properties of silk fibers. To understand the genes involved in the regulation of silk protein synthesis, considerable research has focused on the transcripts expressed in silk glands; however, the complete transcriptome profile of this organ has yet to be elucidated. Here, we report a full-length silk gland transcriptome obtained by PacBio single-molecule long-read sequencing technology. In total, 11,697 non-redundant transcripts were identified in mixed samples of silk glands dissected from larvae at five developmental stages. When compared with the published reference, the full-length transcripts optimized the structures of 3002 known genes, and a total of 9061 novel transcripts with an average length of 2171 bp were detected. Among these, 1403 (15.5%) novel transcripts were computationally revealed to be lncRNAs, 8135 (89.8%) novel transcripts were annotated to different protein and nucleotide databases, and 5655 (62.4%) novel transcripts were predicted to have complete ORFs. Furthermore, we found 1867 alternative splicing events, 2529 alternative polyadenylation events, 784 fusion events and 6596 SSRs. This study provides a comprehensive set of reference transcripts and greatly revises and expands the available silkworm transcript data. In addition, these data will be very useful for studying the regulatory mechanisms of silk protein synthesis.
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Affiliation(s)
- Tao Chen
- College of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, 212003, Jiangsu, China
- The Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Nanjing, 212018, Jiangsu, China
| | - Qiwei Sun
- International Bioinformatics Center, BGI Genomics Co., Ltd, Shenzhen, 518083, Guangdong, China
| | - Yan Ma
- State Key Laboratory of Silkworm Genome Biology, College of Biotechnology, Southwest University, Chongqing, 400715, China
| | - Wenhui Zeng
- State Key Laboratory of Silkworm Genome Biology, College of Biotechnology, Southwest University, Chongqing, 400715, China
| | - Rongpeng Liu
- State Key Laboratory of Silkworm Genome Biology, College of Biotechnology, Southwest University, Chongqing, 400715, China
| | - Dawei Qu
- State Key Laboratory of Silkworm Genome Biology, College of Biotechnology, Southwest University, Chongqing, 400715, China
| | - Lihua Huang
- International Bioinformatics Center, BGI Genomics Co., Ltd, Shenzhen, 518083, Guangdong, China
| | - Hanfu Xu
- State Key Laboratory of Silkworm Genome Biology, College of Biotechnology, Southwest University, Chongqing, 400715, China.
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Ma L, Li K, Guo Y, Sun X, Deng H, Li K, Feng Q, Li S. Ras-Raf-MAPK signaling promotes nuclear localization of FOXA transcription factor SGF1 via Ser91 phosphorylation. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2018; 1865:560-571. [PMID: 29355586 DOI: 10.1016/j.bbamcr.2018.01.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 01/11/2018] [Accepted: 01/14/2018] [Indexed: 01/27/2023]
Abstract
Ras-Raf-MAPK signaling promotes cell proliferation and cell survival. We previously reported that Ras1CA overexpression, specifically in the posterior silk glands (PSGs) of the silkworm Bombyx mori, increased fibroin synthesis and cell size, resulting in improved silk yields. In this study, we compared the iTRAQ-based phosphoproteomic profiles of PSGs from wild-type and Ras1CA-overexpressing silkworms. Silk gland factor 1 (SGF1), a FOXA transcription factor that plays a critical role in activating fibroin gene expression, was identified as a phosphoprotein harboring Ser91 as a potential MAPK phosphorylation site. Ser91 phosphorylation of SGF1 was enhanced by Ras1CA overexpression, and this finding was verified by selected reaction monitoring. Consistently, MAPK activity is well correlated with Ser91 phosphorylation of SGF1 and its nuclear localization in PSG cells during silkworm development. Ras1CA overexpression and treatment with inhibitors of Ras signaling promoted or inhibited SGF1 nuclear localization, respectively; mutation of Ser91 to Ala91 eliminated SGF1 nuclear localization. Moreover, MAPK binds to SGF1 and directly phosphorylates Ser91, demonstrating Ser91 as a MAPK phosphorylation site in SGF1. In conclusion, Ras-Raf-MAPK signaling promotes SGF1 nuclear localization for transactivation via Ser91 phosphorylation in silkworms, showing that FOXA transcription factors are regulated via MAPK phosphorylation in animals.
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Affiliation(s)
- Li Ma
- Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology & School of Life Sciences, South China Normal University, Guangzhou 510631, China; Department of Neonatology, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai 200062, China; Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Kang Li
- Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology & School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Yaxin Guo
- Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China; School of Life Science, East China Normal University, Shanghai 200241, China
| | - Xiang Sun
- Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology & School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Huimin Deng
- Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology & School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Kai Li
- School of Life Science, East China Normal University, Shanghai 200241, China
| | - Qili Feng
- Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology & School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Sheng Li
- Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology & School of Life Sciences, South China Normal University, Guangzhou 510631, China; Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China.
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8
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Zhang P, Liu S, Song HS, Zhang G, Jia Q, Li S. Yorkie CA overexpression in the posterior silk gland improves silk yield in Bombyx mori. JOURNAL OF INSECT PHYSIOLOGY 2017; 100:93-99. [PMID: 28583832 DOI: 10.1016/j.jinsphys.2017.06.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Revised: 06/01/2017] [Accepted: 06/01/2017] [Indexed: 06/07/2023]
Abstract
The traditional hybrid breeding techniques can no longer meet the increasing demands for silk production by the silkworm, Bombyx mori, and further improvement of the silk yield will depend on modern molecular breeding techniques. Here, we report improved silk yield in transgenic silkworms overexpressing the oncogene YorkieCA specifically in the posterior silk gland (PSG). The YorkieCA cDNA was ligated downstream of the hr3 enhancer and the fibroin L-chain (Fil) promoter, then inserted into a piggyBac vector for transgene. Overexpression of YorkieCA in the PSG significantly increased the weight of the PSG, and also increased the weight of the cocoon, larval body, and pupal body to decreasing degrees. Overexpression of YorkieCA up-regulated the Yorkie target genes resulting in increased cell size, endomitosis, the number of protein synthesis organelles, the expression of fibroin genes in the PSG, and eventually silk yield. Additionally, as we reported previously using the binary GAL4/UAS system, transgenic silkworms overexpressing Ras1CA with the hr3 enhancer and the Fil promoter also showed improved silk yield. Unfortunately, the hybrid progeny of YorkieCA-overexpressing silkworms and Ras1CA-overexpressing silkworms did not show overlapping improved silk yield due to the failure to increase expression of both Yorkie and Ras1.
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Affiliation(s)
- Panli Zhang
- College of Life Sciences, Shanghai University, Shanghai 200444, China
| | - Shumin Liu
- Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Hong-Sheng Song
- College of Life Sciences, Shanghai University, Shanghai 200444, China
| | - Guozheng Zhang
- College of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu 212018, China
| | - Qiangqiang Jia
- Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Sciences and School of Life Sciences, South China Normal University, Guangzhou 510631, China.
| | - Sheng Li
- Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Sciences and School of Life Sciences, South China Normal University, Guangzhou 510631, China.
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Zhou QZ, Zhang B, Yu QY, Zhang Z. BmncRNAdb: a comprehensive database of non-coding RNAs in the silkworm, Bombyx mori. BMC Bioinformatics 2016; 17:370. [PMID: 27623959 PMCID: PMC5022206 DOI: 10.1186/s12859-016-1251-y] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Accepted: 09/08/2016] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Long non-coding RNAs (lncRNAs) may play critical roles in a wide range of developmental processes of higher organisms. Recently, lncRNAs have been widely identified across eukaryotes and many databases of lncRNAs have been developed for human, mouse, fruit fly, etc. However, there is rare information about them in the only completely domesticated insect, silkworm (Bombyx mori). DESCRIPTION In this study, we systematically scanned lncRNAs using the available silkworm RNA-seq data and public unigenes. Finally, we identified and collected 6281 lncRNAs in the silkworm. Besides, we also collected 1986 microRNAs (miRNAs) from previous studies. Then, we organized them into a comprehensive and web-based database, BmncRNAdb. This database offers a user-friendly interface for data browse and online analysis as well as the three online tools for users to predict the target genes of lncRNA or miRNA. CONCLUSIONS We have systematically identified and collected the silkworm lncRNAs and constructed a comprehensive database of the silkworm lncRNAs and miRNAs. This work gives a glimpse into lncRNAs of the silkworm and lays foundations for the ncRNAs study of the silkworm and other insects in the future. The BmncRNAdb is freely available at http://gene.cqu.edu.cn/BmncRNAdb/index.php .
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Affiliation(s)
- Qiu-Zhong Zhou
- Laboratory of Evolutionary and Functional Genomics, School of Life Sciences, Chongqing University, Huxi Campus, No. 55 Daxuecheng South Rd., Shapingba, Chongqing, 401331 China
| | - Bindan Zhang
- School of Economics and Business Administration, Chongqing University, Campus A, No. 174 Shazheng Rd., Shapingba, Chongqing, 400044 China
| | - Quan-You Yu
- Laboratory of Evolutionary and Functional Genomics, School of Life Sciences, Chongqing University, Huxi Campus, No. 55 Daxuecheng South Rd., Shapingba, Chongqing, 401331 China
| | - Ze Zhang
- Laboratory of Evolutionary and Functional Genomics, School of Life Sciences, Chongqing University, Huxi Campus, No. 55 Daxuecheng South Rd., Shapingba, Chongqing, 401331 China
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10
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Liu S, Zhang P, Song HS, Qi HS, Wei ZJ, Zhang G, Zhan S, Liu Z, Li S. Yorkie Facilitates Organ Growth and Metamorphosis in Bombyx. Int J Biol Sci 2016; 12:917-30. [PMID: 27489496 PMCID: PMC4971731 DOI: 10.7150/ijbs.14872] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2016] [Accepted: 05/06/2016] [Indexed: 01/15/2023] Open
Abstract
The Hippo pathway, which was identified from genetic screens in the fruit fly, Drosophila melanogaster, has a major size-control function in animals. All key components of the Hippo pathway, including the transcriptional coactivator Yorkie that is the most critical substrate and downstream effector of the Hippo kinase cassette, are found in the silkworm, Bombyx mori. As revealed by microarray and quantitative real-time PCR, expression of Hippo pathway genes is particularly enriched in several mitotic tissues, including the ovary, testis, and wing disc. Developmental profiles of Hippo pathway genes are generally similar (with the exception of Yorkie) within each organ, but vary greatly in different tissues showing nearly opposing expression patterns in the wing disc and the posterior silk gland (PSG) on day 2 of the prepupal stage. Importantly, the reduction of Yorkie expression by RNAi downregulated Yorkie target genes in the ovary, decreased egg number, and delayed larval-pupal-adult metamorphosis. In contrast, baculovirus-mediated Yorkie(CA) overexpression upregulated Yorkie target genes in the PSG, increased PSG size, and accelerated larval-pupal metamorphosis. Together the results show that Yorkie potentially facilitates organ growth and metamorphosis, and suggest that the evolutionarily conserved Hippo pathway is critical for size control, particularly for PSG growth, in the silkworm.
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Affiliation(s)
- Shumin Liu
- 1. Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Panli Zhang
- 1. Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China; 2. College of Life Sciences, Shanghai University, Shanghai 200444, China
| | - Hong-Sheng Song
- 2. College of Life Sciences, Shanghai University, Shanghai 200444, China
| | - Hai-Sheng Qi
- 3. School of Biotechnology and Food Engineering, Hefei University of Technology, Hefei 230009, China
| | - Zhao-Jun Wei
- 3. School of Biotechnology and Food Engineering, Hefei University of Technology, Hefei 230009, China
| | - Guozheng Zhang
- 4. College of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang Jiangsu 212018, China
| | - Shuai Zhan
- 1. Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Zhihong Liu
- 5. Epartment of Urology, Shanghai General Hospital, Medical School of Shanghai Jiao Tong University, Shanghai 200080, China
| | - Sheng Li
- 1. Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
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Chang H, Cheng T, Wu Y, Hu W, Long R, Liu C, Zhao P, Xia Q. Transcriptomic Analysis of the Anterior Silk Gland in the Domestic Silkworm (Bombyx mori) - Insight into the Mechanism of Silk Formation and Spinning. PLoS One 2015; 10:e0139424. [PMID: 26418001 PMCID: PMC4587926 DOI: 10.1371/journal.pone.0139424] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Accepted: 09/14/2015] [Indexed: 01/08/2023] Open
Abstract
Silk proteins are synthesized in the middle and posterior silk glands of silkworms, then transit into the anterior of the silk gland, where the silk fibers are produced, stored and processed. The mechanism of formation and spinning of the silk fibers has not been fully elucidated, and transcriptome analyses specific to the anterior silk gland have not been reported. In the present study, we explored gene expression profiles in five regions of silk gland samples using the RNA-Seq method. As a result, there were 959,979,570 raw reads obtained, of which 583,068,172 reads were mapped to the silkworm genome. A total of 7419 genes were found to be expressed in terms of reads per kilobase of exon model per million mapped reads ≥ 5 in at least one sample. The gene numbers and expression levels of the expressed genes differed between these regions. The differentially expressed genes were analyzed, and 282 genes were detected as up-regulated in the anterior silk gland, compared with the other parts. Functions of these genes were addressed using the gene ontology and Kyoto Encyclopedia of Genes and Genomes databases, and seven key pathways were enriched. It suggested that the ion transportation, energy metabolism, protease inhibitors and cuticle proteins played essential roles in the process of silk formation and spinning in the anterior silk gland. In addition, 210 genes were found differently expressed between males and females, which should help to elucidate the mechanism of the quality difference in silk fibers from male and female silkworms.
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Affiliation(s)
- Huaipu Chang
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Beibei, Chongqing, China
- College of Biotechnology, Southwest University, Beibei, Chongqing, China
| | - Tingcai Cheng
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Beibei, Chongqing, China
| | - Yuqian Wu
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Beibei, Chongqing, China
| | - Wenbo Hu
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Beibei, Chongqing, China
| | - Renwen Long
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Beibei, Chongqing, China
| | - Chun Liu
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Beibei, Chongqing, China
| | - Ping Zhao
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Beibei, Chongqing, China
| | - Qingyou Xia
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Beibei, Chongqing, China
- * E-mail:
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Liu ZQ, Lin S, Baker PJ, Wu LF, Wang XR, Wu H, Xu F, Wang HY, Brathwaite ME, Zheng YG. Transcriptome sequencing and analysis of the entomopathogenic fungus Hirsutella sinensis isolated from Ophiocordyceps sinensis. BMC Genomics 2015; 16:106. [PMID: 25765329 PMCID: PMC4342880 DOI: 10.1186/s12864-015-1269-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Accepted: 01/22/2015] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND Ophiocordyceps sinensis, a worm and fungus combined mixture which Hirsutella sinensis is parasitic on the caterpillar body, has been used as a traditional medicine or healthy food in China for thousands of years. H. sinensis is reported as the only correct anamorph of O. sinensis and its main active ingredients are similar to the natural O. sinensis. RESULTS H. sinensis L0106, asexual strain of O. sinensis, was isolated and identified in this study. Three transcriptomes of H. sinensis at different cultivation periods (growth period 3d, pre-stable period 6d and stable period 9d) were sequenced for the first time by RNA-Seq method, and 25,511 unigenes (3d), 25,214 unigenes (6d) and 16,245 unigenes (9d) were assembled and obtained, respectively. These unigenes of the three samples were further assembled into 20,822 unigenes (All), and 62.3 percent of unigenes (All) could be annotated based on protein databases. Subsequently, the genes and enzymes involved in the biosynthesis of the active ingredients according to the sequencing and annotation results were predicted. Based on the predictions, we further investigated the interaction of different pathway networks and the corresponding enzymes. Furthermore, the differentially expressed genes (DEGs) of H. sinensis grown during different developmental stages (3d-VS-6d, 3d-VS-9d and 6d-VS-9d) were globally detected and analyzed based on the data from RNA-Seq, and 764 DEGs between 3d and 6d, 1,869 DEGs between 3d and 9d, and 770 DEGs between 6d and 9d were found, respectively. CONCLUSIONS This work presented here would aid in understanding and carrying out future studies on the genetic basis of H. sinensis and contribute to the further artificial production and application of this organism. This study provided a substantial contribution and basis to further characterize the gene expression profiles of H. sinensis in the metabolic pathways of active ingredients.
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Affiliation(s)
- Zhi-Qiang Liu
- Institute of Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, Zhejiang, P R China.
| | - Shan Lin
- Institute of Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, Zhejiang, P R China.
| | - Peter James Baker
- Institute of Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, Zhejiang, P R China.
| | - Ling-Fang Wu
- Institute of Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, Zhejiang, P R China.
| | - Xiao-Rui Wang
- Institute of Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, Zhejiang, P R China.
| | - Hui Wu
- East China Pharmaceutical Group Limited Co., Ltd, Hangzhou, 311000, Zhejiang, P R China.
| | - Feng Xu
- East China Pharmaceutical Group Limited Co., Ltd, Hangzhou, 311000, Zhejiang, P R China.
| | - Hong-Yan Wang
- East China Pharmaceutical Group Limited Co., Ltd, Hangzhou, 311000, Zhejiang, P R China.
| | - Mgavi Elombe Brathwaite
- Polytechnic School of Engineering, New York University, 6 MetroTech Center, Brooklyn, NY, 11201, USA.
| | - Yu-Guo Zheng
- Institute of Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, Zhejiang, P R China.
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Jin S, Cheng T, Jiang L, Lin P, Yang Q, Xiao Y, Kusakabe T, Xia Q. Identification of a new Sprouty protein responsible for the inhibition of the Bombyx mori nucleopolyhedrovirus reproduction. PLoS One 2014; 9:e99200. [PMID: 24915434 PMCID: PMC4051654 DOI: 10.1371/journal.pone.0099200] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2014] [Accepted: 05/12/2014] [Indexed: 11/18/2022] Open
Abstract
The rat sarcoma-extracellular signal regulated kinase mitogen-activated protein kinases pathway, one of the most ancient signaling pathways, is crucial for the defense against Bombyx mori nucleopolyhedrovirus (BmNPV) infection. Sprouty (Spry) proteins can inhibit the activity of this pathway by receptor tyrosine kinases. We cloned and identified a new B. mori gene with a Spry domain similar to the Spry proteins of other organisms, such as fruitfly, mouse, human, chicken, Xenopus and zebrafish, and named it BmSpry. The gene expression analysis showed that BmSpry was transcribed in all of the examined tissues and in all developmental stages from embryo to adult. BmSpry also induced expression of BmNPV in the cells. Our results indicated: (1) the knock-down of BmSpry led to increased BmNPV replication and silkworm larvae mortality; (2) over-expression of BmSpry led to reduced BmNPV replication; and (3) BmSpry regulated the activation of ERK and inhibited BmNPV replication. These results showed that BmSpry plays a crucial role in the antiviral defense of the silkworm both in vitro and in vivo.
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Affiliation(s)
- Shengkai Jin
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China
| | - Tingcai Cheng
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China
| | - Liang Jiang
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China
| | - Ping Lin
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China
| | - Qiong Yang
- Sericulture and Farm Product Processing Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Yang Xiao
- Sericulture and Farm Product Processing Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Takahiro Kusakabe
- Laboratory of Silkworm Science, Kyushu University Graduate School of Bioresource and Bioenvironmental Sciences, Fukuoka, Japan
| | - Qingyou Xia
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China
- * E-mail:
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