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Song J, Li Z, Zhou L, Chen X, Sew WQG, Herranz H, Ye Z, Olsen JV, Li Y, Nygaard M, Christensen K, Tong X, Bohr VA, Rasmussen LJ, Dai F. FOXO-regulated OSER1 reduces oxidative stress and extends lifespan in multiple species. Nat Commun 2024; 15:7144. [PMID: 39164296 PMCID: PMC11336091 DOI: 10.1038/s41467-024-51542-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Accepted: 08/12/2024] [Indexed: 08/22/2024] Open
Abstract
FOXO transcription factors modulate aging-related pathways and influence longevity in multiple species, but the transcriptional targets that mediate these effects remain largely unknown. Here, we identify an evolutionarily conserved FOXO target gene, Oxidative stress-responsive serine-rich protein 1 (OSER1), whose overexpression extends lifespan in silkworms, nematodes, and flies, while its depletion correspondingly shortens lifespan. In flies, overexpression of OSER1 increases resistance to oxidative stress, starvation, and heat shock, while OSER1-depleted flies are more vulnerable to these stressors. In silkworms, hydrogen peroxide both induces and is scavenged by OSER1 in vitro and in vivo. Knockdown of OSER1 in Caenorhabditis elegans leads to increased ROS production and shorter lifespan, mitochondrial fragmentation, decreased ATP production, and altered transcription of mitochondrial genes. Human proteomic analysis suggests that OSER1 plays roles in oxidative stress response, cellular senescence, and reproduction, which is consistent with the data and suggests that OSER1 could play a role in fertility in silkworms and nematodes. Human studies demonstrate that polymorphic variants in OSER1 are associated with human longevity. In summary, OSER1 is an evolutionarily conserved FOXO-regulated protein that improves resistance to oxidative stress, maintains mitochondrial functional integrity, and increases lifespan in multiple species. Additional studies will clarify the role of OSER1 as a critical effector of healthy aging.
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Affiliation(s)
- Jiangbo Song
- State Key Laboratory of Resource Insects, Key Laboratory for Sericulture Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing, 400715, China
| | - Zhiquan Li
- Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Lei Zhou
- State Key Laboratory of Resource Insects, Key Laboratory for Sericulture Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing, 400715, China
| | - Xin Chen
- State Key Laboratory of Resource Insects, Key Laboratory for Sericulture Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing, 400715, China
| | - Wei Qi Guinevere Sew
- Department of Cellular and Molecular Medicine, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Héctor Herranz
- Department of Cellular and Molecular Medicine, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Zilu Ye
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200, Copenhagen, Denmark
- Key Laboratory of Common Mechanism Research for Major Diseases, Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Suzhou, China
| | - Jesper Velgaard Olsen
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Yuan Li
- Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Marianne Nygaard
- Epidemiology, Biostatistics and Biodemography, Department of Public Health, University of Southern Denmark, Odense, Denmark
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
| | - Kaare Christensen
- Epidemiology, Biostatistics and Biodemography, Department of Public Health, University of Southern Denmark, Odense, Denmark
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
- Department of Clinical Biochemistry, Odense University Hospital, Odense, Denmark
| | - Xiaoling Tong
- State Key Laboratory of Resource Insects, Key Laboratory for Sericulture Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing, 400715, China
| | - Vilhelm A Bohr
- Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, 2200, Copenhagen, Denmark
- Section on DNA repair, National Institute on Aging, National Institutes of Health, Baltimore, MD, 21224, USA
| | - Lene Juel Rasmussen
- Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, 2200, Copenhagen, Denmark.
| | - Fangyin Dai
- State Key Laboratory of Resource Insects, Key Laboratory for Sericulture Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing, 400715, China.
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Kakino K, Mon H, Ebihara T, Hino M, Masuda A, Lee JM, Kusakabe T. Comprehensive Transcriptome Analysis in the Testis of the Silkworm, Bombyx mori. INSECTS 2023; 14:684. [PMID: 37623394 PMCID: PMC10455414 DOI: 10.3390/insects14080684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 07/26/2023] [Accepted: 08/01/2023] [Indexed: 08/26/2023]
Abstract
Spermatogenesis is an important process in reproduction and is conserved across species, but in Bombyx mori, it shows peculiarities, such as the maintenance of spermatogonia by apical cells and fertilization by dimorphic spermatozoa. In this study, we attempted to characterize the genes expressed in the testis of B. mori, focusing on aspects of expression patterns and gene function by transcriptome comparisons between different tissues, internal testis regions, and Drosophila melanogaster. The transcriptome analysis of 12 tissues of B. mori, including those of testis, revealed the widespread gene expression of 20,962 genes and 1705 testis-specific genes. A comparative analysis of the stem region (SR) and differentiated regions (DR) of the testis revealed 4554 and 3980 specific-enriched genes, respectively. In addition, comparisons with D. melanogaster testis transcriptome revealed homologs of 1204 SR and 389 DR specific-enriched genes that were similarly expressed in equivalent regions of Drosophila testis. Moreover, gene ontology (GO) enrichment analysis was performed for SR-specific enriched genes and DR-specific enriched genes, and the GO terms of several biological processes were enriched, confirming previous findings. This study advances our understanding of spermatogenesis in B. mori and provides an important basis for future research, filling a knowledge gap between fly and mammalian studies.
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Affiliation(s)
- Kohei Kakino
- Laboratory of Insect Genome Science, Kyushu University Graduate School of Bioresource and Bioenvironmental Sciences, Motooka 744, Nishi-ku, Fukuoka 819-0395, Japan; (K.K.); (H.M.); (T.E.)
| | - Hiroaki Mon
- Laboratory of Insect Genome Science, Kyushu University Graduate School of Bioresource and Bioenvironmental Sciences, Motooka 744, Nishi-ku, Fukuoka 819-0395, Japan; (K.K.); (H.M.); (T.E.)
| | - Takeru Ebihara
- Laboratory of Insect Genome Science, Kyushu University Graduate School of Bioresource and Bioenvironmental Sciences, Motooka 744, Nishi-ku, Fukuoka 819-0395, Japan; (K.K.); (H.M.); (T.E.)
| | - Masato Hino
- Laboratory of Sanitary Entomology, Kyushu University Graduate School of Bioresource and Bioenvironmental Sciences, Motooka 744, Nishi-ku, Fukuoka 819-0395, Japan;
| | - Akitsu Masuda
- Laboratory of Creative Science for Insect Industries, Kyushu University Graduate School of Bioresource and Bioenvironmental Sciences, Motooka 744, Nishi-ku, Fukuoka 819-0395, Japan; (A.M.); (J.M.L.)
| | - Jae Man Lee
- Laboratory of Creative Science for Insect Industries, Kyushu University Graduate School of Bioresource and Bioenvironmental Sciences, Motooka 744, Nishi-ku, Fukuoka 819-0395, Japan; (A.M.); (J.M.L.)
| | - Takahiro Kusakabe
- Laboratory of Insect Genome Science, Kyushu University Graduate School of Bioresource and Bioenvironmental Sciences, Motooka 744, Nishi-ku, Fukuoka 819-0395, Japan; (K.K.); (H.M.); (T.E.)
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3
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Feng P, Wang Y, Zou H, Zhu Q, Ren Y, Shu Q, Su W, Liu W, Hu Y, Li B. The effects of glyphosate exposure on gene transcription and immune function of the silkworm, Bombyx mori. ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY 2023; 112:e21990. [PMID: 36537163 DOI: 10.1002/arch.21990] [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: 10/26/2022] [Revised: 11/17/2022] [Accepted: 12/09/2022] [Indexed: 06/17/2023]
Abstract
Glyphosate is a widely used herbicide and crop desiccant. However, whether its extensive use has any effect on the species diversity of nontarget organisms is still unclear. In this study, we used the silkworm, Bombyx mori, as the research subject, and performed RNA sequencing to analyze the transcriptional profile of silkworm midgut after exposure to glyphosate at 2975.20 mg/L (a concentration commonly used at mulberry fields). A total of 125 significantly differentially expressed genes (DEGs) were detected in the midgut of glyphosate-exposed silkworm (q < 0.05), of which 53 were upregulated and 72 were downregulated. Gene ontology enrichment analysis showed that the DEGs were mainly enriched in biological process, cellular component, and molecular function. Kyoto encyclopedia of genes and genomes analysis showed that the differential genes were mainly related to oxidative stress, nutrient metabolism, and immune defense pathways, including oxidative stress-related Cat and Jafrac1, nutrient metabolism-related Fatp and Scpx, and immune-related CYP6AN2, UGT40B4, CTL11, serpin-2, and so forth. Experimental verification showed that glyphosate exposure led to a 4.35-fold increase in the mortality of silkworm after Beauveria bassiana infection, which might be caused by the decreased PO (phenoloxidase) activity and impaired immunity. These results provide evidence for the potential effects of residue glyphosate on the physiological functions of silkworm, and also provide a reference for the biosafety evaluation of glyphosate.
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Affiliation(s)
- Piao Feng
- School of Basic Medicine and Biological Sciences, Soochow University, Suzhou, Jiangsu, P.R. China
| | - Yuanfei Wang
- School of Basic Medicine and Biological Sciences, Soochow University, Suzhou, Jiangsu, P.R. China
| | - Hongbin Zou
- School of Basic Medicine and Biological Sciences, Soochow University, Suzhou, Jiangsu, P.R. China
| | - Qingyu Zhu
- School of Basic Medicine and Biological Sciences, Soochow University, Suzhou, Jiangsu, P.R. China
| | - Yuying Ren
- School of Basic Medicine and Biological Sciences, Soochow University, Suzhou, Jiangsu, P.R. China
| | - Qilong Shu
- School of Basic Medicine and Biological Sciences, Soochow University, Suzhou, Jiangsu, P.R. China
| | - Wujie Su
- School of Basic Medicine and Biological Sciences, Soochow University, Suzhou, Jiangsu, P.R. China
| | - Wei Liu
- Suzhou Taihu snow silk Co., Ltd, Suzhou, Jiangsu, P.R. China
| | - Yufang Hu
- Suzhou Taihu snow silk Co., Ltd, Suzhou, Jiangsu, P.R. China
| | - Bing Li
- School of Basic Medicine and Biological Sciences, Soochow University, Suzhou, Jiangsu, P.R. China
- Sericulture Institute of Soochow University, Suzhou, Jiangsu, P.R. China
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4
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Lu Y, Luo J, An E, Lu B, Wei Y, Chen X, Lu K, Liang S, Hu H, Han M, He S, Shen J, Guo D, Bu N, Yang L, Xu W, Lu C, Xiang Z, Tong X, Dai F. Deciphering the Genetic Basis of Silkworm Cocoon Colors Provides New Insights into Biological Coloration and Phenotypic Diversification. Mol Biol Evol 2023; 40:7013732. [PMID: 36718535 PMCID: PMC9937047 DOI: 10.1093/molbev/msad017] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 01/09/2023] [Accepted: 01/18/2023] [Indexed: 02/01/2023] Open
Abstract
The genetic basis of phenotypic variation is a long-standing concern of evolutionary biology. Coloration has proven to be a visual, easily quantifiable, and highly tractable system for genetic analysis and is an ever-evolving focus of biological research. Compared with the homogenized brown-yellow cocoons of wild silkworms, the cocoons of domestic silkworms are spectacularly diverse in color, such as white, green, and yellow-red; this provides an outstanding model for exploring the phenotypic diversification and biological coloration. Herein, the molecular mechanism underlying silkworm green cocoon formation was investigated, which was not fully understood. We demonstrated that five of the seven members of a sugar transporter gene cluster were specifically duplicated in the Bombycidae and evolved new spatial expression patterns predominantly expressed in silk glands, accompanying complementary temporal expression; they synergistically facilitate the uptake of flavonoids, thus determining the green cocoon. Subsequently, polymorphic cocoon coloring landscape involving multiple loci and the evolution of cocoon color from wild to domestic silkworms were analyzed based on the pan-genome sequencing data. It was found that cocoon coloration involved epistatic interaction between loci; all the identified cocoon color-related loci existed in wild silkworms; the genetic segregation, recombination, and variation of these loci shaped the multicolored cocoons of domestic silkworms. This study revealed a new mechanism for flavonoids-based biological coloration that highlights the crucial role of gene duplication followed by functional diversification in acquiring new genetic functions; furthermore, the results in this work provide insight into phenotypic innovation during domestication.
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Affiliation(s)
| | | | - Erxia An
- State Key Laboratory of Silkworm Genome Biology, Institute of Sericulture and Systems Biology, Southwest University, Chongqing, China
| | - Bo Lu
- State Key Laboratory of Silkworm Genome Biology, Institute of Sericulture and Systems Biology, Southwest University, Chongqing, China,Key Laboratory of Sericulture Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing, China
| | - Yinqiu Wei
- State Key Laboratory of Silkworm Genome Biology, Institute of Sericulture and Systems Biology, Southwest University, Chongqing, China
| | - Xiang Chen
- State Key Laboratory of Silkworm Genome Biology, Institute of Sericulture and Systems Biology, Southwest University, Chongqing, China,Key Laboratory of Sericulture Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing, China
| | - Kunpeng Lu
- State Key Laboratory of Silkworm Genome Biology, Institute of Sericulture and Systems Biology, Southwest University, Chongqing, China
| | - Shubo Liang
- State Key Laboratory of Silkworm Genome Biology, Institute of Sericulture and Systems Biology, Southwest University, Chongqing, China
| | - Hai Hu
- State Key Laboratory of Silkworm Genome Biology, Institute of Sericulture and Systems Biology, Southwest University, Chongqing, China
| | - Minjin Han
- State Key Laboratory of Silkworm Genome Biology, Institute of Sericulture and Systems Biology, Southwest University, Chongqing, China,Key Laboratory of Sericulture Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing, China
| | - Songzhen He
- State Key Laboratory of Silkworm Genome Biology, Institute of Sericulture and Systems Biology, Southwest University, Chongqing, China
| | - Jianghong Shen
- State Key Laboratory of Silkworm Genome Biology, Institute of Sericulture and Systems Biology, Southwest University, Chongqing, China
| | - Dongyang Guo
- State Key Laboratory of Silkworm Genome Biology, Institute of Sericulture and Systems Biology, Southwest University, Chongqing, China
| | - Nvping Bu
- State Key Laboratory of Silkworm Genome Biology, Institute of Sericulture and Systems Biology, Southwest University, Chongqing, China
| | - Ling Yang
- State Key Laboratory of Silkworm Genome Biology, Institute of Sericulture and Systems Biology, Southwest University, Chongqing, China
| | - Wenya Xu
- State Key Laboratory of Silkworm Genome Biology, Institute of Sericulture and Systems Biology, Southwest University, Chongqing, China
| | - Cheng Lu
- State Key Laboratory of Silkworm Genome Biology, Institute of Sericulture and Systems Biology, Southwest University, Chongqing, China
| | - Zhonghuai Xiang
- State Key Laboratory of Silkworm Genome Biology, Institute of Sericulture and Systems Biology, Southwest University, Chongqing, China
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Global Profiling of Genes Expressed in the Silk Glands of Philippine-Reared Mulberry Silkworms (Bombyx mori). INSECTS 2022; 13:insects13080669. [PMID: 35893024 PMCID: PMC9329738 DOI: 10.3390/insects13080669] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 07/13/2022] [Accepted: 07/20/2022] [Indexed: 02/04/2023]
Abstract
RNA sequencing was used to assemble transcriptome data for Philippine-reared silkworm and compare gene expression profiles of strains reared in high- and low-temperature environments. RNA was isolated from the silk glands of fifth instar larvae and mRNA-enriched libraries were sequenced using Illumina NextSeq 500. Transcriptome reads were assembled using reference-based and de novo assemblers, and assemblies were evaluated using different metrics for transcriptome quality, including the read mapping rate, E90N50, RSEM-eval, and the presence of single-copy orthologs. All transcriptome assemblies were able to reconstruct >40,000 transcripts. Differential expression analysis found 476 differentially expressed genes (DEGs; 222 upregulated, 254 downregulated) in strains reared in different temperatures. Among the top DEGs were myrosinase, heat shock proteins, serine protease inhibitors, dehydrogenases, and regulators of the juvenile hormone. Validation of some of the top DEGs using qPCR supported the findings of the in silico analysis. GO term enrichment analysis reveals an overrepresentation of GO terms related to nucleotide metabolism and biosynthesis, lipid and carbohydrate metabolic processes, regulation of transcription, nucleotide binding, protein binding, metal binding, catalytic activity, oxidoreductase activity, and hydrolase activity. The data provided here will serve as a resource for improving local strains and increasing silk production of Philippine-reared B. mori strains.
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Guo X, Xuan N, Liu G, Xie H, Lou Q, Arnaud P, Offmann B, Picimbon JF. An Expanded Survey of the Moth PBP/GOBP Clade in Bombyx mori: New Insight into Expression and Functional Roles. Front Physiol 2021; 12:712593. [PMID: 34776998 PMCID: PMC8582636 DOI: 10.3389/fphys.2021.712593] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 09/13/2021] [Indexed: 02/01/2023] Open
Abstract
We studied the expression profile and ontogeny (from the egg stage through the larval stages and pupal stages, to the elderly adult age) of four OBPs from the silkworm moth Bombyx mori. We first showed that male responsiveness to female sex pheromone in the silkworm moth B. mori does not depend on age variation; whereas the expression of BmorPBP1, BmorPBP2, BmorGOBP1, and BmorGOBP2 varies with age. The expression profile analysis revealed that the studied OBPs are expressed in non-olfactory tissues at different developmental stages. In addition, we tested the effect of insecticide exposure on the expression of the four OBPs studied. Exposure to a toxic macrolide insecticide endectocide molecule (abamectin) led to the modulated expression of all four genes in different tissues. The higher expression of OBPs was detected in metabolic tissues, such as the thorax, gut, and fat body. All these data strongly suggest some alternative functions for these proteins other than olfaction. Finally, we carried out ligand docking studies and reported that PBP1 and GOBP2 have the capacity of binding vitamin K1 and multiple different vitamins.
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Affiliation(s)
- Xia Guo
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Ning Xuan
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Guoxia Liu
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Hongyan Xie
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Qinian Lou
- Shandong Silkworm Institute, Shandong Academy of Agricultural Sciences, Yantai, China
| | - Philippe Arnaud
- Protein Engineering and Functionality Unit, UMR CNRS 6286, University of Nantes, Nantes, France
| | - Bernard Offmann
- Protein Engineering and Functionality Unit, UMR CNRS 6286, University of Nantes, Nantes, France
| | - Jean-François Picimbon
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Jinan, China.,School of Bioengineering, QILU University of Technology, Jinan, China
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Comparative Transcriptome Analysis Revealed Genes Involved in Sexual and Polyploid Growth Dimorphisms in Loach ( Misgurnus anguillicaudatus). BIOLOGY 2021; 10:biology10090935. [PMID: 34571812 PMCID: PMC8468957 DOI: 10.3390/biology10090935] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 09/05/2021] [Accepted: 09/13/2021] [Indexed: 11/16/2022]
Abstract
Simple Summary Misgurnus anguillicaudatus not only exhibits sexual size dimorphism, but also shows polyploid size dimorphism. Here, we performed comparative transcriptome integration analysis of multiple tissues of diploid and tetraploid M. anguillicaudatus of both sexes. We found that differences in energy metabolism and steroid hormone synthesis levels may be the main causes of sexual and polyploidy growth dimorphisms of M. anguillicaudatus. Fast-growing M. anguillicaudatus (tetraploids, females) have higher levels of energy metabolism and lower steroid hormone synthesis and fatty acid degradation abilities than slow-growing M. anguillicaudatus (diploids, males). Abstract Sexual and polyploidy size dimorphisms are widespread phenomena in fish, but the molecular mechanisms remain unclear. Loach (Misgurnus anguillicaudatus) displays both sexual and polyploid growth dimorphism phenomena, and are therefore ideal models to study these two phenomena. In this study, RNA-seq was used for the first time to explore the differentially expressed genes (DEGs) between both sexes of diploid and tetraploid loaches in four tissues (brain, gonad, liver, and muscle). Results showed that 21,003, 17, and 1 DEGs were identified in gonad, liver, and muscle tissues, respectively, between females and males in both diploids and tetraploids. Regarding the ploidy levels, 4956, 1496, 2187, and 1726 DEGs were identified in the brain, gonad, liver, and muscle tissues, respectively, between tetraploids and diploids of the same sex. When both sexual and polyploid size dimorphisms were considered simultaneously in the four tissues, only 424 DEGs were found in the gonads, indicating that these gonadal DEGs may play an important regulatory role in regulating sexual and polyploid size dimorphisms. Regardless of the sex or ploidy comparison, the significant DEGs involved in glycolysis/gluconeogenesis and oxidative phosphorylation pathways were upregulated in faster-growing individuals, while steroid hormone biosynthesis-related genes and fatty acid degradation and elongation-related genes were downregulated. This suggests that fast-growing loaches (tetraploids, females) have higher energy metabolism levels and lower steroid hormone synthesis and fatty acid degradation abilities than slow-growing loaches (diploids, males). Our findings provide an archive for future systematic research on fish sexual and polyploid dimorphisms.
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Yi Y, Li J, Zong Z, Liu X, Song H, Wang H, Zhang Z, Zhang H, Li Y. Cloning, expression, and characteristic analysis of the novel β-galactosidase from silkworm, Bombyx mori. Genesis 2021; 59:e23446. [PMID: 34449115 DOI: 10.1002/dvg.23446] [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] [Received: 06/23/2021] [Revised: 08/16/2021] [Accepted: 08/18/2021] [Indexed: 01/22/2023]
Abstract
β-Galactosidase is a critical exoglycosidase involved in the hydrolysis of lactose, the modification and degradation of glycoprotein in vivo. In this study, the β-galactosidase gene of silkworm (BmGal), whose cDNA comprises 11 exons and contains an intact ORF of 1,821 bp, was cloned. The protein sequence of BmGal showed high similarity with other known insect β-galactosidases. No activity of the BmGal expressed in Escherichia coli or Pichia pastoris was detected while it was successfully expressed with high enzyme activity in baculovirus expression system in silkworm, and the electrophoresis result revealed that the BmGal showed activity in oligomer mode. Enzyme activity assay showed that its optimum pH was 8.4 and its optimum temperature was 40 °C. What is more, we found that iron ions can stimulate the activity of the enzyme while cobalt, nickel, or lead ions can inhibit its activity significantly. Besides, the temporal-spatial transcription pattern of the BmGal mRNA level was analyzed, which showed that BmGal was transcribed at the highest level in the fifth larval instar but relatively low level in the pupal and adult stage, and the highest transcriptional level of BmGal was found in testis among all the tissues concerned.
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Affiliation(s)
- Yongzhu Yi
- College of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
| | - Jialei Li
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhipeng Zong
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xingjian Liu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Haozhi Song
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Haining Wang
- College of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
| | - Zhifang Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Huan Zhang
- Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Yinü Li
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
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Xu Y, Li Y, Wang Q, Zheng C, Zhao D, Shi F, Liu X, Tao J, Zong S. Identification of key genes associated with overwintering in Anoplophora glabripennis larva using gene co-expression network analysis. PEST MANAGEMENT SCIENCE 2021; 77:805-816. [PMID: 32909651 DOI: 10.1002/ps.6082] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 09/06/2020] [Accepted: 09/10/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND Anoplophora glabripennis (Coleoptera: Cerambycidae) is a major quarantine pest in forestry. It is widely distributed throughout many regions such as Asia, Europe, and North America, and has enormous destructive potential for forests. The larvae of A. glabripennis overwinter in a dormant state with strong cold tolerance, and whether the larvae survive winter determines the population density in the following year. However, the molecular mechanisms of this process are not clear. RESULTS RNA sequencing (RNA-Seq) analysis of A. glabripennis larvae at five overwintering stages identified 6876 differentially expressed genes (DEGs). Among these, 46 functional genes that might respond to low temperature were identified. Weighted gene co-expression network analysis revealed that the MEturquoise module was correlated with the overwintering process. The STPK, PP2A, DGAT, and HSF genes were identified as hub genes using visualization of gene network. In addition, four genes related to sugar transport, gluconeogenesis and glycosylation were screened, which may be involved in the metabolic regulation of overwintering larvae. The protein-protein interaction network indicated that ribosomal protein and ATP synthase may play an important role in connecting with other proteins. The expression levels of fifteen hub genes were further validated by quantitative RT-PCR, and the results were consistent with RNA-Seq. CONCLUSION This study demonstrates key genes that may reveal the molecular mechanism of overwintering in A. glabripennis larvae. The genes may be the potential targets to prevent larvae from surviving the cold winter by developing new biological agents using genetic engineering.
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Affiliation(s)
- Yabei Xu
- Key Laboratory of Beijing for the Control of Forest Pests, Beijing Forestry University, Beijing, China
| | - Yurong Li
- Key Laboratory of Beijing for the Control of Forest Pests, Beijing Forestry University, Beijing, China
| | - Qianqian Wang
- Key Laboratory of Beijing for the Control of Forest Pests, Beijing Forestry University, Beijing, China
| | - Chunchun Zheng
- Key Laboratory of Beijing for the Control of Forest Pests, Beijing Forestry University, Beijing, China
| | - Dongfang Zhao
- Key Laboratory of Beijing for the Control of Forest Pests, Beijing Forestry University, Beijing, China
| | - Fengming Shi
- Key Laboratory of Beijing for the Control of Forest Pests, Beijing Forestry University, Beijing, China
| | - Xinhai Liu
- Ulanqab Municipal Bureau of Parks, Ulanqab, China
| | - Jing Tao
- Key Laboratory of Beijing for the Control of Forest Pests, Beijing Forestry University, Beijing, China
| | - Shixiang Zong
- Key Laboratory of Beijing for the Control of Forest Pests, Beijing Forestry University, Beijing, China
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10
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Hu Q, Xiao H, Wang Q, Tian H, Meng Y. Identification and expression of forkhead box genes in the Chinese giant salamander Andrias davidianus. Reprod Fertil Dev 2019; 30:634-642. [PMID: 28945985 DOI: 10.1071/rd17049] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 09/07/2017] [Indexed: 11/23/2022] Open
Abstract
In the present study, 21 forkhead box (Fox) genes were identified in Andrias davidianus, including 13 full-length genes and eight partial sequences. Phylogenetic analysis showed that most were conserved in other investigated amphibians, whereas the Foxk1 gene was found exclusively in A. davidianus. Molecular evolution analysis indicated that most Fox genes underwent purifying selection, whereas two sites of the adFoxp4 gene showed positive selection and were located on the adFoxp4 protein surface. Expression profiles of all Fox genes identified were analysed in the hypothalamic-pituitary-gonad axis by reverse transcription-quantitative polymerase chain reaction. Eighteen genes exhibited sexually dimorphic expression (15 ovary-biased and three testis-biased genes), whereas two genes showed no difference between ovary and testis. Further investigation of 12 selected sexually dimorphic Fox genes showed changes in the expression profile of 11 genes in the ovary of larvae reared at high temperatures (28°C). The results of the present study provide information on Fox genes in an amphibian and suggest that they play key roles in sexual development and reproduction in A. davidianus.
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Affiliation(s)
- Qiaomu Hu
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, Hubei, 430223, China
| | - Hanbing Xiao
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, Hubei, 430223, China
| | - Qilong Wang
- Tengzhou Fisheries Center, Tengzhou, Shandong, 277500, China
| | - Haifeng Tian
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, Hubei, 430223, China
| | - Yan Meng
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, Hubei, 430223, China
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11
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Kerkvliet J, de Fouchier A, van Wijk M, Groot AT. The Bellerophon pipeline, improving de novo transcriptomes and removing chimeras. Ecol Evol 2019; 9:10513-10521. [PMID: 31624564 PMCID: PMC6787812 DOI: 10.1002/ece3.5571] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 07/22/2019] [Accepted: 07/28/2019] [Indexed: 12/31/2022] Open
Abstract
Transcriptome quality control is an important step in RNA-Seq experiments. However, the quality of de novo assembled transcriptomes is difficult to assess, due to the lack of reference genome to compare the assembly to. We developed a method to assess and improve the quality of de novo assembled transcriptomes by focusing on the removal of chimeric sequences. These chimeric sequences can be the result of faulty assembled contigs, merging two transcripts into one. The developed method is incorporated into a pipeline, which we named Bellerophon, that is broadly applicable and easy to use. Bellerophon first uses the quality assessment tool TransRate to indicate the quality, after which it uses a transcripts per million (TPM) filter to remove lowly expressed contigs and CD-HIT-EST to remove highly identical contigs. To validate the quality of this method, we performed three benchmark experiments: (1) a computational creation of chimeras, (2) identification of chimeric contigs in a transcriptome assembly, (3) a simulated RNA-Seq experiment using a known reference transcriptome. Overall, the Bellerophon pipeline was able to remove between 40% and 91.9% of the chimeras in transcriptome assemblies and removed more chimeric than nonchimeric contigs. Thus, the Bellerophon sequence of filtration steps is a broadly applicable solution to improve transcriptome assemblies.
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Affiliation(s)
- Jesse Kerkvliet
- Institute for Biodiversity and Ecosystem DynamicsUniversity of AmsterdamAmsterdamThe Netherlands
| | - Arthur de Fouchier
- Institute for Biodiversity and Ecosystem DynamicsUniversity of AmsterdamAmsterdamThe Netherlands
- Departement of EntomolgyMax Planck Institute for Chemical EcologyJenaGermany
- Present address:
Laboratory of Experimental and Comparative Ethology, Université Paris 13Sorbonne Paris CitéVilletaneuseFrance
| | - Michiel van Wijk
- Institute for Biodiversity and Ecosystem DynamicsUniversity of AmsterdamAmsterdamThe Netherlands
| | - Astrid Tatjana Groot
- Institute for Biodiversity and Ecosystem DynamicsUniversity of AmsterdamAmsterdamThe Netherlands
- Departement of EntomolgyMax Planck Institute for Chemical EcologyJenaGermany
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12
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Activity and inactivity of moth sex chromosomes in somatic and meiotic cells. Chromosoma 2019; 128:533-545. [PMID: 31410566 DOI: 10.1007/s00412-019-00722-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 07/17/2019] [Accepted: 08/06/2019] [Indexed: 10/26/2022]
Abstract
Moths and butterflies (Lepidoptera) are the most species-rich group of animals with female heterogamety, females mostly having a WZ, males a ZZ sex chromosome constitution. We studied chromatin conformation, activity, and inactivity of the sex chromosomes in the flour moth Ephestia kuehniella and the silkworm Bombyx mori, using immunostaining with anti-H3K9me2/3, anti-RNA polymerase II, and fluoro-uridine (FU) labelling of nascent transcripts, with conventional widefield fluorescence microscopy and 'spatial structured illumination microscopy' (3D-SIM). The Z chromosome is euchromatic in somatic cells and throughout meiosis. It is transcriptionally active in somatic cells and in the postpachaytene stage of meiosis. The W chromosome in contrast is heterochromatic in somatic cells as well as in meiotic cells at pachytene, but euchromatic and transcriptionally active like all other chromosomes at postpachytene. As the W chromosomes are apparently devoid of protein-coding genes, their transcripts must be non-coding. We found no indication of 'meiotic sex chromosome inactivation' (MSCI) in the two species.
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13
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Ye X, Tang X, Wang X, Che J, Wu M, Liang J, Ye L, Qian Q, Li J, You Z, Zhang Y, Wang S, Zhong B. Improving Silkworm Genome Annotation Using a Proteogenomics Approach. J Proteome Res 2019; 18:3009-3019. [PMID: 31250652 DOI: 10.1021/acs.jproteome.8b00965] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The silkworm genome has been deeply sequenced and assembled, but accurate genome annotation, which is important for modern biological research, remains far from complete. To improve silkworm genome annotation, we carried out a proteogenomics analysis using 9.8 million mass spectra collected from different tissues and developmental stages of the silkworm. The results confirmed the translational products of 4307 existing gene models and identified 1701 novel genome search-specific peptides (GSSPs). Using these GSSPs, 74 novel gene-coding sequences were identified, and 121 existing gene models were corrected. We also identified 1182 novel junction peptides based on an exon-skipping database that resulted in the identification of 973 alternative splicing sites. Furthermore, we performed RNA-seq analysis to improve silkworm genome annotation at the transcriptional level. A total of 1704 new transcripts and 1136 new exons were identified, 2581 untranslated regions (UTRs) were revised, and 1301 alternative splicing (AS) genes were identified. The transcriptomics results were integrated with the proteomics data to further complement and verify the new annotations. In addition, 14 incorrect genes and 10 skipped exons were verified using the two analysis methods. Altogether, we identified 1838 new transcripts and 1593 AS genes and revised 5074 existing genes using proteogenomics and transcriptome analyses. Data are available via ProteomeXchange with identifier PXD009672. The large-scale proteogenomics and transcriptome analyses in this study will greatly improve silkworm genome annotation and contribute to future studies.
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Affiliation(s)
- Xiaogang Ye
- College of Animal Sciences , Zhejiang University , Hangzhou , P. R. China
| | - Xiaoli Tang
- College of Animal Sciences , Zhejiang University , Hangzhou , P. R. China
| | - Xiaoxiao Wang
- College of Animal Sciences , Zhejiang University , Hangzhou , P. R. China
| | - Jiaqian Che
- College of Animal Sciences , Zhejiang University , Hangzhou , P. R. China
| | - Meiyu Wu
- College of Animal Sciences , Zhejiang University , Hangzhou , P. R. China
| | - Jianshe Liang
- College of Animal Sciences , Zhejiang University , Hangzhou , P. R. China
| | - Lupeng Ye
- College of Animal Sciences , Zhejiang University , Hangzhou , P. R. China
| | - Qiujie Qian
- College of Animal Sciences , Zhejiang University , Hangzhou , P. R. China
| | - Jianying Li
- College of Animal Sciences , Zhejiang University , Hangzhou , P. R. China
| | - Zhengying You
- College of Animal Sciences , Zhejiang University , Hangzhou , P. R. China
| | - Yuyu Zhang
- College of Animal Sciences , Zhejiang University , Hangzhou , P. R. China
| | - Shaohua Wang
- College of Animal Sciences , Zhejiang University , Hangzhou , P. R. China
| | - Boxiong Zhong
- College of Animal Sciences , Zhejiang University , Hangzhou , P. R. China
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14
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Wang RX, Tong XL, Gai TT, Li CL, Qiao L, Hu H, Han MJ, Xiang ZH, Lu C, Dai FY. A serine protease homologue Bombyx mori scarface induces a short and fat body shape in silkworm. INSECT MOLECULAR BIOLOGY 2018; 27:319-332. [PMID: 29441628 DOI: 10.1111/imb.12373] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Body shape is one of the most prominent and basic characteristics of any organism. In insects, abundant variations in body shape can be observed both within and amongst species. However, the molecular mechanism underlying body shape fine-tuning is very complex and has been largely unknown until now. In the silkworm Bombyx mori, the tubby (tub) mutant has an abnormal short fat body shape and the abdomen of tub larvae expands to form a fusiform body shape. Morphological investigation revealed that the body length was shorter and the body width was wider than that of the Dazao strain. Thus, this mutant is a good model for studying the molecular mechanisms of body shape fine-tuning. Using positional cloning, we identified a gene encoding the serine protease homologue, B. mori scarface (Bmscarface), which is associated with the tub phenotype. Sequence analysis revealed a specific 312-bp deletion from an exon of Bmscarface in the tub strain. In addition, recombination was not observed between the tub and Bmscarface loci. Moreover, RNA interference of Bmscarface resulted in the tub-like phenotype. These results indicate that Bmscarface is responsible for the tub mutant phenotype. This is the first study to report that mutation of a serine protease homologue can induce an abnormal body shape in insects.
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Affiliation(s)
- R-X Wang
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture, Southwest University, Chongqing, China
| | - X-L Tong
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture, Southwest University, Chongqing, China
| | - T-T Gai
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture, Southwest University, Chongqing, China
| | - C-L Li
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture, Southwest University, Chongqing, China
| | - L Qiao
- Institute of Entomology and Molecular Biology, College of Life Sciences, Chongqing Normal University, Chongqing, China
| | - H Hu
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture, Southwest University, Chongqing, China
| | - M-J Han
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture, Southwest University, Chongqing, China
| | - Z-H Xiang
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture, Southwest University, Chongqing, China
| | - C Lu
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture, Southwest University, Chongqing, China
| | - F-Y Dai
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture, Southwest University, Chongqing, China
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15
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Xiao W, Chen P, Xiao J, Wang L, Liu T, Wu Y, Dong F, Jiang Y, Pan M, Zhang Y, Lu C. Comparative transcriptome profiling of a thermal resistant vs. sensitive silkworm strain in response to high temperature under stressful humidity condition. PLoS One 2017; 12:e0177641. [PMID: 28542312 PMCID: PMC5436693 DOI: 10.1371/journal.pone.0177641] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2017] [Accepted: 05/01/2017] [Indexed: 11/25/2022] Open
Abstract
Thermotolerance is important particularly for poikilotherms such as insects. Understanding the mechanisms by which insects respond to high temperatures can provide insights into their adaptation to the environment. Therefore, in this study, we performed a transcriptome analysis of two silkworm strains with significantly different resistance to heat as well as humidity; the thermo-resistant strain 7532 and the thermos-sensitive strain Knobbed. We identified in total 4,944 differentially expressed genes (DEGs) using RNA-Seq. Among these, 4,390 were annotated and 554 were novel. Gene Ontology (GO) analysis of 747 DEGs identified between RT_48h (Resistant strain with high-temperature Treatment for 48 hours) and ST_48h (Sensitive strain with high-temperature Treatment for 48 hours) showed significant enrichment of 12 GO terms including metabolic process, extracellular region and serine-type peptidase activity. Moreover, we discovered 12 DEGs that may contribute to the heat-humidity stress response in the silkworm. Our data clearly showed that 48h post-exposure may be a critical time point for silkworm to respond to high temperature and humidity. These results provide insights into the genes and biological processes involved in high temperature and humidity tolerance in the silkworm, and advance our understanding of thermal tolerance in insects.
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Affiliation(s)
- Wenfu Xiao
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture, Southwest University, Chongqing, China
- Sericultural Research Institute Sichuan Academy of Agricultural Sciences, Sichuan Nanchong, China
| | - Peng Chen
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture, Southwest University, Chongqing, China
| | - Jinshu Xiao
- Sericultural Research Institute Sichuan Academy of Agricultural Sciences, Sichuan Nanchong, China
| | - La Wang
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture, Southwest University, Chongqing, China
| | - Taihang Liu
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture, Southwest University, Chongqing, China
| | - Yunfei Wu
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture, Southwest University, Chongqing, China
| | - Feifan Dong
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture, Southwest University, Chongqing, China
| | - Yaming Jiang
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture, Southwest University, Chongqing, China
| | - Minhui Pan
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture, Southwest University, Chongqing, China
| | - Youhong Zhang
- Sericultural Research Institute Sichuan Academy of Agricultural Sciences, Sichuan Nanchong, China
- * E-mail: (CL); (YZ)
| | - Cheng Lu
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture, Southwest University, Chongqing, China
- * E-mail: (CL); (YZ)
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16
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Tang PA, Wu HJ, Xue H, Ju XR, Song W, Zhang QL, Yuan ML. Characterization of transcriptome in the Indian meal moth Plodia interpunctella (Lepidoptera: Pyralidae) and gene expression analysis during developmental stages. Gene 2017; 622:29-41. [PMID: 28412460 DOI: 10.1016/j.gene.2017.04.018] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Revised: 12/01/2016] [Accepted: 04/12/2017] [Indexed: 12/18/2022]
Abstract
The Indian meal moth Plodia interpunctella (Lepidoptera: Pyralidae) is a worldwide pest that causes serious damage to stored foods. Although many efforts have been conducted on this species due to its economic importance, the study of genetic basis of development, behavior and insecticide resistance has been greatly hampered due to lack of genomic information. In this study, we used high throughput sequencing platform to perform a de novo transcriptome assembly and tag-based digital gene expression profiling (DGE) analyses across four different developmental stages of P. interpunctella (egg, third-instar larvae, pupae and adult). We obtained approximate 9gigabyte (GB) of clean data and recovered 84,938 unigenes, including 37,602 clusters and 47,336 singletons. These unigenes were annotated using BLAST against the non-redundant protein databases and then functionally classified based on Gene Ontology (GO), Clusters of Orthologous Groups (COG), and Kyoto Encyclopedia of Genes and Genomes databases (KEGG). A large number of differentially expressed genes were identified by pairwise comparisons among different developmental stages. Gene expression profiles dramatically changed between developmental stage transitions. Some of these differentially expressed genes were related to digestion and cuticularization. Quantitative real-time PCR results of six randomly selected genes conformed the findings in the DGEs. Furthermore, we identified over 8000 microsatellite markers and 97,648 single nucleotide polymorphisms which will be useful for population genetics studies of P. interpunctella. This transcriptomic information provided insight into the developmental basis of P. interpunctella and will be helpful for establishing integrated management strategies and developing new targets of insecticides for this serious pest.
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Affiliation(s)
- Pei-An Tang
- Collaborative Innovation Center for Modern Grain Circulation and Safety, College of Food Science and Engineering, Nanjing University of Finance and Economics, Nanjing 210023, China.
| | - Hai-Jing Wu
- Collaborative Innovation Center for Modern Grain Circulation and Safety, College of Food Science and Engineering, Nanjing University of Finance and Economics, Nanjing 210023, China
| | - Hao Xue
- Collaborative Innovation Center for Modern Grain Circulation and Safety, College of Food Science and Engineering, Nanjing University of Finance and Economics, Nanjing 210023, China
| | - Xing-Rong Ju
- Collaborative Innovation Center for Modern Grain Circulation and Safety, College of Food Science and Engineering, Nanjing University of Finance and Economics, Nanjing 210023, China
| | - Wei Song
- Collaborative Innovation Center for Modern Grain Circulation and Safety, College of Food Science and Engineering, Nanjing University of Finance and Economics, Nanjing 210023, China
| | - Qi-Lin Zhang
- Evo-devo Institute, School of Life Sciences, Nanjing University, Nanjing 210008, China
| | - Ming-Long Yuan
- State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou 730020, China.
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17
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Tong XL, Fu MY, Chen P, Chen L, Xiang ZH, Lu C, Dai FY. Ultrabithorax and abdominal-A specify the abdominal appendage in a dosage-dependent manner in silkworm, Bombyx mori. Heredity (Edinb) 2017; 118:578-584. [PMID: 28121309 DOI: 10.1038/hdy.2016.131] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Revised: 10/21/2016] [Accepted: 12/05/2016] [Indexed: 11/09/2022] Open
Abstract
In insects, there is a considerable diversity in leg distribution on the body, including number, segmental arrangement, morphological identity and consequent function, but the genetic basis for these differences is not well understood. Here by positional cloning, we showed that a ~355 kb region, including Bombyx mori Ultrabithorax (BmUbx) and abdominal-A (Bmabd-A), was responsible for the silkworm mutant Kh-extra-crescents-like (EKh-l) that displayed additional thoracic limb-like legs on the first abdominal segment (A1) and occasionally on the second abdominal segment (A2). We found that BmUbx gene was downregulated at both messenger RNA level and protein level in EKh-l embryo, while its expression domain in the EKh-l embryo was almost the same as that in the wild type. Whereas Bmabd-A was upregulated at both levels and was ectopically overexpressed on the supernumerary leg-bearing segments in EKh-l. Compared with the previously reported Ecs-l mutant in which increased expression of both BmUbx and Bmabd-A gave rise to ectopic proleg-like appendages on the same segments, we propose that overexpressed Bmabd-A gene is capable to promote the outgrowth of extra leg appendages on A1 and A2 segments, whereas BmUbx gene is required to specify accurate morphologies of the ectopic legs in a dosage-dependent manner in silkworm. These results provide insights into how these hox genes regulate the leg morphologic diversity on the same segments.
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Affiliation(s)
- X L Tong
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China.,Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture, Southwest University, Chongqing, China
| | - M Y Fu
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China.,Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture, Southwest University, Chongqing, China
| | - P Chen
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China
| | - L Chen
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China
| | - Z H Xiang
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China.,Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture, Southwest University, Chongqing, China
| | - C Lu
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China.,Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture, Southwest University, Chongqing, China
| | - F Y Dai
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China.,Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture, Southwest University, Chongqing, China
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18
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Singh D, Chetia H, Kabiraj D, Sharma S, Kumar A, Sharma P, Deka M, Bora U. A comprehensive view of the web-resources related to sericulture. Database (Oxford) 2016; 2016:baw086. [PMID: 27307138 PMCID: PMC4909305 DOI: 10.1093/database/baw086] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Revised: 04/25/2016] [Accepted: 05/02/2016] [Indexed: 12/03/2022]
Abstract
Recent progress in the field of sequencing and analysis has led to a tremendous spike in data and the development of data science tools. One of the outcomes of this scientific progress is development of numerous databases which are gaining popularity in all disciplines of biology including sericulture. As economically important organism, silkworms are studied extensively for their numerous applications in the field of textiles, biomaterials, biomimetics, etc. Similarly, host plants, pests, pathogens, etc. are also being probed to understand the seri-resources more efficiently. These studies have led to the generation of numerous seri-related databases which are extremely helpful for the scientific community. In this article, we have reviewed all the available online resources on silkworm and its related organisms, including databases as well as informative websites. We have studied their basic features and impact on research through citation count analysis, finally discussing the role of emerging sequencing and analysis technologies in the field of seri-data science. As an outcome of this review, a web portal named SeriPort, has been created which will act as an index for the various sericulture-related databases and web resources available in cyberspace.Database URL: http://www.seriport.in/.
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Affiliation(s)
- Deepika Singh
- Bioengineering Research Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam 781039, India
| | - Hasnahana Chetia
- Bioengineering Research Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam 781039, India
| | - Debajyoti Kabiraj
- Bioengineering Research Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam 781039, India
| | - Swagata Sharma
- Bioengineering Research Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam 781039, India
| | - Anil Kumar
- Centre for Biological Sciences (Bioinformatics), Central University of South Bihar (CUSB), Patna 800014, India
| | - Pragya Sharma
- Department of Bioengineering & Technology, Gauhati University Institute of Science & Technology, Gauhati University, Guwahati, Assam 781014, India
| | - Manab Deka
- Department of Bioengineering & Technology, Gauhati University Institute of Science & Technology, Gauhati University, Guwahati, Assam 781014, India
| | - Utpal Bora
- Bioengineering Research Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam 781039, India Centre for the Environment, Indian Institute of Technology Guwahati, Guwahati, Assam 781039, India Mugagen Laboratories Pvt. Ltd, Technology Incubation Centre, Indian Institute of Technology Guwahati, Guwahati, Assam 781039, India
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19
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Comparative analysis of the integument transcriptomes of the black dilute mutant and the wild-type silkworm Bombyx mori. Sci Rep 2016; 6:26114. [PMID: 27193628 PMCID: PMC4872147 DOI: 10.1038/srep26114] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Accepted: 04/27/2016] [Indexed: 11/21/2022] Open
Abstract
The insect cuticle is a critical protective shell that is composed predominantly of chitin and various cuticular proteins and pigments. Indeed, insects often change their surface pigment patterns in response to selective pressures, such as threats from predators, sexual selection and environmental changes. However, the molecular mechanisms underlying the construction of the epidermis and its pigmentation patterns are not fully understood. Among Lepidoptera, the silkworm is a favorable model for color pattern research. The black dilute (bd) mutant of silkworm is the result of a spontaneous mutation; the larval body color is notably melanized. We performed integument transcriptome sequencing of the wild-type strain Dazao and the mutant strains +/bd and bd/bd. In these experiments, during an early stage of the fourth molt, a stage at which approximately 51% of genes were expressed genome wide (RPKM ≥1) in each strain. A total of 254 novel transcripts were characterized using Cuffcompare and BLAST analyses. Comparison of the transcriptome data revealed 28 differentially expressed genes (DEGs) that may contribute to bd larval melanism, including 15 cuticular protein genes that were remarkably highly expressed in the bd/bd mutant. We suggest that these significantly up-regulated cuticular proteins may promote melanism in silkworm larvae.
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20
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Transcriptomic Analysis of Resistant and Susceptible Bombyx mori Strains Following BmNPV Infection Provides Insights into the Antiviral Mechanisms. Int J Genomics 2016; 2016:2086346. [PMID: 27195279 PMCID: PMC4852350 DOI: 10.1155/2016/2086346] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Accepted: 03/06/2016] [Indexed: 11/30/2022] Open
Abstract
Purpose. To decipher transcriptomic changes and related genes with potential functions against Bombyx mori nucleopolyhedrovirus infection and to increase the understanding of the enhanced virus resistance of silkworm on the transcriptomic level. Methods. We assembled and annotated transcriptomes of the Qiufeng (susceptible to infection) and QiufengN (resistant to infection) strains and performed comparative analysis in order to decipher transcriptomic changes and related genes with potential functions against BmNPV infection. Results. A total of 78,408 SNPs were identified in the Qiufeng strain of silkworm and 56,786 SNPs were identified in QiufengN strain. Besides, novel AS events were found in these 2 strains. In addition, 1,728 DEGs were identified in the QiufengN strain compared with Qiufeng strain. These DEGs were involved in GO terms related to membrane, metabolism, binding and catalytic activity, cellular processes, and organismal systems. The highest levels of gene representation were found in oxidative phosphorylation, phagosome, TCA cycle, arginine and proline metabolism, and pyruvate metabolism. Additionally, COG analysis indicated that DEGs were involved in “amino acid transport and metabolism” and “carbohydrate transport and metabolism.” Conclusion. We identified a series of major pathological changes in silkworm following infection and several functions were related to the antiviral mechanisms of silkworm.
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Reassessing ecdysteroidogenic cells from the cell membrane receptors' perspective. Sci Rep 2016; 6:20229. [PMID: 26847502 PMCID: PMC4742824 DOI: 10.1038/srep20229] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Accepted: 12/23/2015] [Indexed: 02/06/2023] Open
Abstract
Ecdysteroids secreted by the prothoracic gland (PG) cells of insects control the
developmental timing of their immature life stages. These cells have been
historically considered as carrying out a single function in insects, namely the
biochemical conversion of cholesterol to ecdysteroids and their secretion. A growing
body of evidence shows that PG cells receive multiple cues during insect development
so we tested the hypothesis that they carry out more than just one function in
insects. We characterised the molecular nature and developmental profiles of cell
membrane receptors in PG cells of Bombyx mori during the final larval stage
and determined what receptors decode nutritional, developmental and physiological
signals. Through iterative approaches we identified a complex repertoire of cell
membrane receptors that are expressed in intricate patterns and activate previously
unidentified signal transduction cascades in PG cells. The expression patterns of
some of these receptors explain precisely the mechanisms that are known to control
ecdysteroidogenesis. However, the presence of receptors for the notch, hedgehog and
wingless signalling pathways and the expression of innate immunity-related receptors
such as phagocytosis receptors, receptors for microbial ligands and Toll-like
receptors call for a re-evaluation of the role these cells play in insects.
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Li Y, Bu C, Li T, Wang S, Jiang F, Yi Y, Yang H, Zhang Z. Cloning and analysis of DnaJ family members in the silkworm, Bombyx mori. Gene 2015; 576:88-98. [PMID: 26434795 DOI: 10.1016/j.gene.2015.09.079] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Revised: 09/24/2015] [Accepted: 09/28/2015] [Indexed: 02/03/2023]
Abstract
Heat shock proteins (Hsps) are involved in a variety of critical biological functions, including protein folding, degradation, and translocation and macromolecule assembly, act as molecular chaperones during periods of stress by binding to other proteins. Using expressed sequence tag (EST) and silkworm (Bombyx mori) transcriptome databases, we identified 27 cDNA sequences encoding the conserved J domain, which is found in DnaJ-type Hsps. Of the 27 J domain-containing sequences, 25 were complete cDNA sequences. We divided them into three types according to the number and presence of conserved domains. By analyzing the gene structures, intron numbers, and conserved domains and constructing a phylogenetic tree, we found that the DnaJ family had undergone convergent evolution, obtaining new domains to expand the diversity of its family members. The acquisition of the new DnaJ domains most likely occurred prior to the evolutionary divergence of prokaryotes and eukaryotes. The expression of DnaJ genes in the silkworm was generally higher in the fat body. The tissue distribution of DnaJ1 proteins was detected by western blotting, demonstrating that in the fifth-instar larvae, the DnaJ1 proteins were expressed at their highest levels in hemocytes, followed by the fat body and head. We also found that the DnaJ1 transcripts were likely differentially translated in different tissues. Using immunofluorescence cytochemistry, we revealed that in the blood cells, DnaJ1 was mainly localized in the cytoplasm.
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Affiliation(s)
- Yinü Li
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China.
| | - Cuiyu Bu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China.
| | - Tiantian Li
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China.
| | - Shibao Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China.
| | - Feng Jiang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China.
| | - Yongzhu Yi
- The Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, China.
| | - Huipeng Yang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China.
| | - Zhifang Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China.
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Shi XF, Li YN, Yi YZ, Xiao XG, Zhang ZF. Identification and Characterization of 30 K Protein Genes Found in Bombyx mori (Lepidoptera: Bombycidae) Transcriptome. JOURNAL OF INSECT SCIENCE (ONLINE) 2015; 15:iev057. [PMID: 26078299 PMCID: PMC4535582 DOI: 10.1093/jisesa/iev057] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Accepted: 04/23/2015] [Indexed: 06/04/2023]
Abstract
The 30 K proteins, the major group of hemolymph proteins in the silkworm, Bombyx mori (Lepidoptera: Bombycidae), are structurally related with molecular masses of ∼30 kDa and are involved in various physiological processes, e.g., energy storage, embryonic development, and immune responses. For this report, known 30 K protein gene sequences were used as Blastn queries against sequences in the B. mori transcriptome (SilkTransDB). Twenty-nine cDNAs (Bm30K-1-29) were retrieved, including four being previously unidentified in the Lipoprotein_11 family. The genomic structures of the 29 genes were analyzed and they were mapped to their corresponding chromosomes. Furthermore, phylogenetic analysis revealed that the 29 genes encode three types of 30 K proteins. The members increased in each type is mainly a result of gene duplication with the appearance of each type preceding the differentiation of each species included in the tree. Real-Time Quantitative Polymerase Chain Reaction (Q-PCR) confirmed that the genes could be expressed, and that the three types have different temporal expression patterns. Proteins from the hemolymph was separated by SDS-PAGE, and those with molecular mass of ∼30 kDa were isolated and identified by mass spectrometry sequencing in combination with searches of various databases containing B. mori 30K protein sequences. Of the 34 proteins identified, 13 are members of the 30 K protein family, with one that had not been found in the SilkTransDB, although it had been found in the B. mori genome. Taken together, our results indicate that the 30 K protein family contains many members with various functions. Other methods will be required to find more members of the family.
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Affiliation(s)
- Xiao-Feng Shi
- The Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street Beijing, 100081, China The College of Biological Sciences, China Agricultural University, Beijing, 100094, China
| | - Yi-Nü Li
- The Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street Beijing, 100081, China
| | - Yong-Zhu Yi
- The Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, Jiangsu Province, 212018, China
| | - Xing-Guo Xiao
- The College of Biological Sciences, China Agricultural University, Beijing, 100094, China
| | - Zhi-Fang Zhang
- The Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street Beijing, 100081, China
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Transcriptome analysis of the brain of the silkworm Bombyx mori infected with Bombyx mori nucleopolyhedrovirus: A new insight into the molecular mechanism of enhanced locomotor activity induced by viral infection. J Invertebr Pathol 2015; 128:37-43. [DOI: 10.1016/j.jip.2015.04.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Revised: 04/02/2015] [Accepted: 04/08/2015] [Indexed: 12/24/2022]
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25
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Zhou L, Li H, Hao F, Li N, Liu X, Wang G, Wang Y, Tang H. Developmental Changes for the Hemolymph Metabolome of Silkworm (Bombyx mori L.). J Proteome Res 2015; 14:2331-47. [PMID: 25825269 DOI: 10.1021/acs.jproteome.5b00159] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Silkworm (Bombyx mori) is a lepidopteran-holometabolic model organism. To understand its developmental biochemistry, we characterized the larval hemolymph metabonome from the third instar to prepupa stage using (1)H NMR spectroscopy whilst hemolymph fatty acid composition using GC-FID/MS. We unambiguously assigned more than 60 metabolites, among which tyrosine-o-β-glucuronide, mesaconate, homocarnosine, and picolinate were reported for the first time from the silkworm hemolymph. Phosphorylcholine was the most abundant metabolite in all developmental stages with exception for the periods before the third and fourth molting. We also found obvious developmental dependence for the hemolymph metabonome involving multiple pathways including protein biosyntheses, glycolysis, TCA cycle, the metabolisms of choline amino acids, fatty acids, purines, and pyrimidines. Most hemolymph amino acids had two elevations during the feeding period of the fourth instar and prepupa stage. Trehalose was the major blood sugar before day 8 of the fifth instar, whereas glucose became the major blood sugar after spinning. C16:0, C18:0 and its unsaturated forms were dominant fatty acids in hemolymph. The developmental changes of hemolymph metabonome were associated with dietary nutrient intakes, biosyntheses of cell membrane, pigments, proteins, and energy metabolism. These findings offered essential biochemistry information in terms of the dynamic metabolic changes during silkworm development.
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Affiliation(s)
- Lihong Zhou
- †College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China.,‡Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, China.,¶College of Life Sciences, Jianghan University, Wuhan 430056, China
| | - Huihui Li
- ‡Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, China
| | - Fuhua Hao
- ‡Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, China
| | - Ning Li
- ‡Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, China
| | - Xin Liu
- †College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Guoliang Wang
- ¶College of Life Sciences, Jianghan University, Wuhan 430056, China
| | - Yulan Wang
- ‡Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, China.,⊥Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, Hangzhou 310058, China
| | - Huiru Tang
- ‡Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, China.,§State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, Metabonomics and Systems Biology Laboratory, School of Life Sciences, Fudan University, Shanghai 200433, China
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26
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Dong Y, Dai F, Ren Y, Liu H, Chen L, Yang P, Liu Y, Li X, Wang W, Xiang H. Comparative transcriptome analyses on silk glands of six silkmoths imply the genetic basis of silk structure and coloration. BMC Genomics 2015; 16:203. [PMID: 25886738 PMCID: PMC4372302 DOI: 10.1186/s12864-015-1420-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Accepted: 02/28/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Silk has numerous unique properties that make it a staple of textile manufacturing for several thousand years. However, wider applications of silk in modern have been stalled due to limitations of traditional silk produced by Bombyx mori. While silk is commonly produced by B. mori, several wild non-mulberry silkmoths--especially members of family Saturniidae--produce silk with superior properties that may be useful for wider applications. Further utilization of such silks is hampered by the non-domestication status or limited culturing population of wild silkworms. To date there is insufficient basic genomic or transcriptomic data on these organisms or their silk production. RESULTS We sequenced and compared the transcriptomes of silk glands of six Saturniidae wild silkmoth species through next-generation sequencing technology, identifying 37758 ~ 51734 silkmoth unigenes, at least 36.3% of which are annotated with an e-value less than 10(-5). Sequence analyses of these unigenes identified a batch of genes specific to Saturniidae that are enriched in growth and development. Analyses of silk proteins including fibroin and sericin indicate intra-genus conservation and inter-genus diversification of silk protein features among the wild silkmoths, e.g., isoelectric points, hydrophilicity profile and amino acid composition in motifs of silk H-fibroin. Interestingly, we identified p25 in two of the silkmoths, which were previously predicted to be absent in Saturniidae. There are rapid evolutionary changes in sericin proteins, which might account for the highly heterogeneity of sericin in Saturniidae silkmoths. Within the six sikmoths, both colored-cocoon silkmoth specific transcripts and differentially expressed genes between the colored-cocoon and non-colored-cocoon silkmoths are significantly enriched in catalytic activity, especially transferase activity, suggesting potentially viable targets for future gene mining or genetic manipulation. CONCLUSIONS Our results characterize novel and potentially valuable gene resources of saturniid silkmoths that may facilitate future genetic improvement and modification of mulberry silkworms. Our results suggest that the disparate features of silk--coloration, retention, strength, etc. --are likely not only due to silk proteins, but also to the environment of silk assembly, and more specifically, that stable silk coloration exhibited by some Saturniidae silkmoths may be attributable to active catalytic progress in pigmentation.
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Affiliation(s)
- Yang Dong
- Kunming University of Science and Technology, 727 South Jingming Road, Chenggong District, Kunming, Yunnan Province, 650500, China.,State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 32 East Jiaochang Road, Kunming, Yunnan Province, 650223, China
| | - Fangyin Dai
- State Key Laboratory of Silkworm Genome Biology, Key Sericultural Laboratory of Agricultural Ministry, Institute of Sericulture and Systems Biology, Southwest University, 2 Tiansheng Road, Beibei District, Chongqing, 400715, China
| | - Yandong Ren
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 32 East Jiaochang Road, Kunming, Yunnan Province, 650223, China
| | - Hui Liu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 32 East Jiaochang Road, Kunming, Yunnan Province, 650223, China
| | - Lei Chen
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 32 East Jiaochang Road, Kunming, Yunnan Province, 650223, China
| | - Pengcheng Yang
- Institute of Zoology, Chinese Academy of Sciences, 69 East Beichen Road, Chaoyang District, Beijing, 100101, China
| | - Yanqun Liu
- Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang Province, 110866, China
| | - Xin Li
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, Maryland, 21205, USA
| | - Wen Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 32 East Jiaochang Road, Kunming, Yunnan Province, 650223, China.
| | - Hui Xiang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 32 East Jiaochang Road, Kunming, Yunnan Province, 650223, China.
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27
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Fang SM, Hu BL, Zhou QZ, Yu QY, Zhang Z. Comparative analysis of the silk gland transcriptomes between the domestic and wild silkworms. BMC Genomics 2015; 16:60. [PMID: 25887670 PMCID: PMC4328555 DOI: 10.1186/s12864-015-1287-9] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Accepted: 01/26/2015] [Indexed: 12/21/2022] Open
Abstract
Background Bombyx mori was domesticated from the Chinese wild silkworm, Bombyx mandarina. Wild and domestic silkworms are good models in which to investigate genes related to silk protein synthesis that may be differentially expressed in silk glands, because their silk productions are very different. Here we used the mRNA deep sequencing (RNA-seq) approach to identify the differentially expressed genes (DEGs) in the transcriptomes of the median/posterior silk glands of two domestic and two wild silkworms. Results The results indicated that about 58% of the total genes were expressed (reads per kilo bases per million reads (RPKM) ≥ 1) in each silkworm. Comparisons of the domestic and wild silkworm transcriptomes revealed 32 DEGs, of which 16 were up-regulated in the domestic silkworms compared with in the wild silkworms, and the other 16 were up-regulated in the wild silkworms compared with in the domestic silkworms. Quantitative real-time polymerase chain reaction (qPCR) was performed for 15 randomly selected DEGs in domestic versus wild silkworms. The qPCR results were mostly consistent with the expression levels determined from the RNA-seq data. Based on a Gene Ontology (GO) enrichment analysis and manual annotation, five of the up-regulated DEGs in the wild silkworms were predicted to be involved in immune response, and seven of the up-regulated DEGs were related to the GO term “oxidoreductase activity”, which is associated with antioxidant systems. In the domestic silkworms, the up-regulated DEGs were related mainly to tissue development, secretion of proteins and metabolism. Conclusions The up-regulated DEGs in the two domestic silkworms may be involved mainly in the highly efficient biosynthesis and secretion of silk proteins, while the up-regulated DEGs in the two wild silkworms may play more important roles in tolerance to pathogens and environment adaptation. Our results provide a foundation for understanding the molecular mechanisms of the silk production difference between domestic and wild silkworms. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1287-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Shou-Min Fang
- School of Life Sciences, Chongqing University, Chongqing, 400044, China. .,College of Life Science, China West Normal University, Nanchong, 637002, China.
| | - Bi-Li Hu
- Key Sericultural Laboratory of Shaanxi, Ankang University, Ankang, 725000, China.
| | - Qiu-Zhong Zhou
- School of Life Sciences, Chongqing University, Chongqing, 400044, China.
| | - Quan-You Yu
- School of Life Sciences, Chongqing University, Chongqing, 400044, China.
| | - Ze Zhang
- School of Life Sciences, Chongqing University, Chongqing, 400044, China.
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Papantonis A, Swevers L, Iatrou K. Chorion genes: a landscape of their evolution, structure, and regulation. ANNUAL REVIEW OF ENTOMOLOGY 2015; 60:177-194. [PMID: 25341099 DOI: 10.1146/annurev-ento-010814-020810] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Differential regulation at the level of transcription provides a means for controlling gene expression in eukaryotes, especially during development. Insect model systems have been extensively used to decipher the molecular basis of such regulatory cascades, and one of the oldest such model systems is the regulation of chorion gene expression during ovarian follicle maturation. Recent experimental and technological advances have shed new light onto the system, allowing us to revisit it. Thus, in this review we try to summarize almost 40 years' worth of studies on chorion gene regulation while-by comparing Bombyx mori and Drosophila melanogaster models-attempting to present a comprehensive, unified model of the various regulatory aspects of choriogenesis that takes into account the evolutionary conservation and divergence of the underlying mechanisms.
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Affiliation(s)
- Argyris Papantonis
- Research Group for Systems Biology of Chromatin, Center for Molecular Medicine, University of Cologne, 50931 Cologne, Germany;
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Kong F, Li H, Sun P, Zhou Y, Mao Y. De novo assembly and characterization of the transcriptome of seagrass Zostera marina using Illumina paired-end sequencing. PLoS One 2014; 9:e112245. [PMID: 25423588 PMCID: PMC4244107 DOI: 10.1371/journal.pone.0112245] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Accepted: 10/10/2014] [Indexed: 01/15/2023] Open
Abstract
Background The seagrass Zostera marina is a monocotyledonous angiosperm belonging to a polyphyletic group of plants that can live submerged in marine habitats. Zostera marina L. is one of the most common seagrasses and is considered a cornerstone of marine plant molecular ecology research and comparative studies. However, the mechanisms underlying its adaptation to the marine environment still remain poorly understood due to limited transcriptomic and genomic data. Principal Findings Here we explored the transcriptome of Z. marina leaves under different environmental conditions using Illumina paired-end sequencing. Approximately 55 million sequencing reads were obtained, representing 58,457 transcripts that correspond to 24,216 unigenes. A total of 14,389 (59.41%) unigenes were annotated by blast searches against the NCBI non-redundant protein database. 45.18% and 46.91% of the unigenes had significant similarity with proteins in the Swiss-Prot database and Pfam database, respectively. Among these, 13,897 unigenes were assigned to 57 Gene Ontology (GO) terms and 4,745 unigenes were identified and mapped to 233 pathways via functional annotation against the Kyoto Encyclopedia of Genes and Genomes pathway database (KEGG). We compared the orthologous gene family of the Z. marina transcriptome to Oryza sativa and Pyropia yezoensis and 11,667 orthologous gene families are specific to Z. marina. Furthermore, we identified the photoreceptors sensing red/far-red light and blue light. Also, we identified a large number of genes that are involved in ion transporters and channels including Na+ efflux, K+ uptake, Cl− channels, and H+ pumping. Conclusions Our study contains an extensive sequencing and gene-annotation analysis of Z. marina. This information represents a genetic resource for the discovery of genes related to light sensing and salt tolerance in this species. Our transcriptome can be further utilized in future studies on molecular adaptation to abiotic stress in Z. marina.
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Affiliation(s)
- Fanna Kong
- Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- * E-mail:
| | - Hong Li
- Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Peipei Sun
- Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Yang Zhou
- Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Yunxiang Mao
- Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
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30
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Ou J, Deng HM, Zheng SC, Huang LH, Feng QL, Liu L. Transcriptomic analysis of developmental features of Bombyx mori wing disc during metamorphosis. BMC Genomics 2014; 15:820. [PMID: 25261999 PMCID: PMC4196006 DOI: 10.1186/1471-2164-15-820] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Accepted: 09/17/2014] [Indexed: 12/27/2022] Open
Abstract
Background Wing discs of B. mori are transformed to pupal wings during the larva-to-pupa metamorphosis with dramatic morphological and structural changes. To understand these changes at a transcriptional level, RNA-seq of the wing discs from 6-day-old fifth instar larvae (L5D6), prepupae (PP) and pupae (P0) was performed. Results In total, 12,254 transcripts were obtained from the wing disc, out of which 5,287 were identified to be differentially expressed from L5D6 to PP and from PP to P0. The results of comprehensive analysis of RNA-seq data showed that during larvae-to-pupae metamorphosis, many genes of 20E signaling pathway were up-regulated and those of JH signaling pathway were down-regulated. Seventeen transcription factors were significantly up-regulated. Cuticle protein genes (especially wing cuticle protein genes), were most abundant and significantly up-regulated at P0 stage. Genes responsible for the degradation and de novo synthesis of chitin were significantly up-regulated. There were A and B two types of chitin synthases in B. mori, whereas only chitin synthase A was up-regulated. Both trehalose and D-fructose, which are precursors of chitin synthesis, were detected in the hemolymph of L5D6, PP and P0, suggesting de novo synthesis of chitin. However, most of the genes that are related to early wing disc differentiation were down-regulated. Conclusions Extensive transcriptome and DGE profiling data of wing disc during metamorphosis of silkworm have been generated, which provided comprehensive gene expression information at the transcriptional level. These results implied that during the larva-to-pupa metamorphosis, pupal wing development and transition might be mainly controlled by 20E signaling in B. mori. The 17 up-regulated transcription factors might be involved in wing development. Chitin required for pupal wing development might be generated from both degradation of componential chitin and de novo synthesis. Chitin synthase A might be responsible for the chitin synthesis in the pupal wing, while both trehalose and D-fructose might contribute to the de novo synthesis of chitin during the formation of pupal wing. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-820) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | - Qi-Li Feng
- Laboratory of Molecular and Developmental Entomology, Guangdong Provincial Key Lab of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou 510631, China.
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31
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Ma L, Ma Q, Li X, Cheng L, Li K, Li S. Transcriptomic analysis of differentially expressed genes in the Ras1(CA)-overexpressed and wildtype posterior silk glands. BMC Genomics 2014; 15:182. [PMID: 24606580 PMCID: PMC4029079 DOI: 10.1186/1471-2164-15-182] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2013] [Accepted: 02/27/2014] [Indexed: 11/24/2022] Open
Abstract
Background Using the piggyBac-mediated GAL4/UAS transgenic system established in the silkworm, Bombyx mori, we have previously reported that overexpression of the Ras1CA oncogene specifically in the posterior silk gland (PSG) improved cell growth, fibroin synthesis, and thus silk yield. However, the detailed molecular mechanism remains to be fully elucidated. To achieve this goal, Illumina sequencing was used in the present study to compare the transcriptomes of the Ras1CA-overexpressed and wildtype PSGs. Results The transcriptomic sequencing results in 56 million reads following filtering steps. Most of the reads (~70%) are successfully mapped to the Bombyx genome. The mapped reads are situated within at least 9,133 predicted genes, covering 62.46% genes of the Bombyx genome. GO annotation shows that 2512 of the 2,636 differentially expressed genes (DEGs) are mostly distributed in metabolic process, cell and cell part, and binding, and KEGG annotation shows that 1,941 DEGs are mapped into 277 pathways. Importantly, Ras1CA overexpression in the PSG upregulated many DEGs distributed in “pathways in cancer”, “insulin signaling pathway”, and “MAPK signaling pathway” as well as “purine metabolism” and “pyrimidine metabolism”. Transcriptional regulation of these DEGs was verified by quantitative real-time PCR. Moreover, injection of small-molecule chemical inhibitors of the Ras1 downstream effectors into the Ras1CA-overexpressed silkworms revealed that both Raf-MAPK and PI3K-TORC1 pathways are required for the Ras1-induced DEG expression. Conclusion The transcriptomic analysis illustrates that, apart from phosphorylational regulation, Ras1 activates its downstream Raf-MAPK and PI3K-TORC1 pathways at the transcriptional level. Meanwhile, Ras1 increases DNA content and induces endoreplication, at least in part, by upregulating genes in “nucleotide metabolism” and “cell cycle”. This study provides further insights into the molecular mechanism of how Ras1CA overexpression in the PSG improves silk yield. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-182) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | - Leilei Cheng
- Key Laboratory of 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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Gschloessl B, Vogel H, Burban C, Heckel D, Streiff R, Kerdelhué C. Comparative analysis of two phenologically divergent populations of the pine processionary moth (Thaumetopoea pityocampa) by de novo transcriptome sequencing. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2014; 46:31-42. [PMID: 24468684 DOI: 10.1016/j.ibmb.2014.01.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2013] [Revised: 01/11/2014] [Accepted: 01/13/2014] [Indexed: 06/03/2023]
Abstract
The pine processionary moth Thaumetopoea pityocampa is a Mediterranean lepidopteran defoliator that experiences a rapid range expansion towards higher latitudes and altitudes due to the current climate warming. Its phenology - the time of sexual reproduction - is certainly a key trait for the local adaptation of the processionary moth to climatic conditions. Moreover, an exceptional case of allochronic differentiation was discovered ca. 15 years ago in this species. A population with a shifted phenology (the summer population, SP) co-exists near Leiria, Portugal, with a population following the classical cycle (the winter population, WP). The existence of this population is an outstanding opportunity to decipher the genetic bases of phenology. No genomic resources were so far available for T. pityocampa. We developed a high-throughput sequencing approach to build a first reference transcriptome, and to proceed with comparative analyses of the sympatric SP and WP. We pooled RNA extracted from whole individuals of various developmental stages, and performed a transcriptome characterisation for both populations combining Roche 454-FLX and traditional Sanger data. The obtained sequences were clustered into ca. 12,000 transcripts corresponding to 9265 unigenes. The mean transcript coverage was 21.9 reads per bp. Almost 70% of the de novo assembled transcripts displayed significant similarity to previously published proteins and around 50% of the transcripts contained a full-length coding region. Comparative analyses of the population transcriptomes allowed to investigate genes specifically expressed in one of the studied populations only, and to identify the most divergent homologous SP/WP transcripts. The most divergent pairs of transcripts did not correspond to obvious phenology-related candidate genes, and 43% could not be functionally annotated. This study provides the first comprehensive genome-wide resource for the target species T. pityocampa. Many of the assembled genes are orthologs of published Lepidoptera genes, which allows carrying out gene-specific re-sequencing. Data mining has allowed the identification of SNP loci that will be useful for population genomic approaches and genome-wide scans of population differentiation to identify signatures of selection.
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Affiliation(s)
- Bernhard Gschloessl
- INRA, UMR CBGP (INRA/IRD/CIRAD/Montpellier Supagro), Campus International de Baillarguet, CS30016, F-34988 Montferrier-sur-Lez Cedex, France.
| | - Heiko Vogel
- Max Planck Institute for Chemical Ecology, Department of Entomology, 07745 Jena, Germany
| | - Christian Burban
- INRA, UMR1202 BIOGECO, 69 Route d'Arcachon, F-33612 Cestas Cedex, France
| | - David Heckel
- Max Planck Institute for Chemical Ecology, Department of Entomology, 07745 Jena, Germany
| | - Réjane Streiff
- INRA, UMR CBGP (INRA/IRD/CIRAD/Montpellier Supagro), Campus International de Baillarguet, CS30016, F-34988 Montferrier-sur-Lez Cedex, France
| | - Carole Kerdelhué
- INRA, UMR CBGP (INRA/IRD/CIRAD/Montpellier Supagro), Campus International de Baillarguet, CS30016, F-34988 Montferrier-sur-Lez Cedex, France
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Wang SH, You ZY, Ye LP, Che J, Qian Q, Nanjo Y, Komatsu S, Zhong BX. Quantitative Proteomic and Transcriptomic Analyses of Molecular Mechanisms Associated with Low Silk Production in Silkworm Bombyx mori. J Proteome Res 2014; 13:735-51. [DOI: 10.1021/pr4008333] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Shao-hua Wang
- College
of Animal Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, P.R. China
| | - Zheng-ying You
- College
of Animal Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, P.R. China
| | - Lu-peng Ye
- College
of Animal Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, P.R. China
| | - Jiaqian Che
- College
of Animal Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, P.R. China
| | - Qiujie Qian
- College
of Animal Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, P.R. China
| | - Yohei Nanjo
- National
Institute of Crop Science, NARO, Kannondai 2-1-18, Tsukuba 305-8518, Japan
| | - Setsuko Komatsu
- National
Institute of Crop Science, NARO, Kannondai 2-1-18, Tsukuba 305-8518, Japan
| | - Bo-xiong Zhong
- College
of Animal Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, P.R. China
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Nandety RS, Kamita SG, Hammock BD, Falk BW. Sequencing and de novo assembly of the transcriptome of the glassy-winged sharpshooter (Homalodisca vitripennis). PLoS One 2013; 8:e81681. [PMID: 24339955 PMCID: PMC3858241 DOI: 10.1371/journal.pone.0081681] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2013] [Accepted: 10/15/2013] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND The glassy-winged sharpshooter Homalodisca vitripennis (Hemiptera: Cicadellidae), is a xylem-feeding leafhopper and important vector of the bacterium Xylella fastidiosa; the causal agent of Pierce's disease of grapevines. The functional complexity of the transcriptome of H. vitripennis has not been elucidated thus far. It is a necessary blueprint for an understanding of the development of H. vitripennis and for designing efficient biorational control strategies including those based on RNA interference. RESULTS Here we elucidate and explore the transcriptome of adult H. vitripennis using high-throughput paired end deep sequencing and de novo assembly. A total of 32,803,656 paired-end reads were obtained with an average transcript length of 624 nucleotides. We assembled 32.9 Mb of the transcriptome of H. vitripennis that spanned across 47,265 loci and 52,708 transcripts. Comparison of our non-redundant database showed that 45% of the deduced proteins of H. vitripennis exhibit identity (e-value ≤1(-5)) with known proteins. We assigned Gene Ontology (GO) terms, Kyoto Encyclopedia of Genes and Genomes (KEGG) annotations, and potential Pfam domains to each transcript isoform. In order to gain insight into the molecular basis of key regulatory genes of H. vitripennis, we characterized predicted proteins involved in the metabolism of juvenile hormone, and biogenesis of small RNAs (Dicer and Piwi sequences) from the transcriptomic sequences. Analysis of transposable element sequences of H. vitripennis indicated that the genome is less expanded in comparison to many other insects with approximately 1% of the transcriptome carrying transposable elements. CONCLUSIONS Our data significantly enhance the molecular resources available for future study and control of this economically important hemipteran. This transcriptional information not only provides a more nuanced understanding of the underlying biological and physiological mechanisms that govern H. vitripennis, but may also lead to the identification of novel targets for biorationally designed control strategies.
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Affiliation(s)
- Raja Sekhar Nandety
- Department of Plant Pathology, University of California Davis, Davis, California, United States of America
| | - Shizuo G. Kamita
- Department of Entomology and UC Davis Comprehensive Cancer Research Center, University of California Davis, Davis, California, United States of America
| | - Bruce D. Hammock
- Department of Entomology and UC Davis Comprehensive Cancer Research Center, University of California Davis, Davis, California, United States of America
| | - Bryce W. Falk
- Department of Plant Pathology, University of California Davis, Davis, California, United States of America
- * E-mail:
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Bazinet AL, Cummings MP, Mitter KT, Mitter CW. Can RNA-Seq resolve the rapid radiation of advanced moths and butterflies (Hexapoda: Lepidoptera: Apoditrysia)? An exploratory study. PLoS One 2013; 8:e82615. [PMID: 24324810 PMCID: PMC3853519 DOI: 10.1371/journal.pone.0082615] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2013] [Accepted: 10/23/2013] [Indexed: 11/19/2022] Open
Abstract
Recent molecular phylogenetic studies of the insect order Lepidoptera have robustly resolved family-level divergences within most superfamilies, and most divergences among the relatively species-poor early-arising superfamilies. In sharp contrast, relationships among the superfamilies of more advanced moths and butterflies that comprise the mega-diverse clade Apoditrysia (ca. 145,000 spp.) remain mostly poorly supported. This uncertainty, in turn, limits our ability to discern the origins, ages and evolutionary consequences of traits hypothesized to promote the spectacular diversification of Apoditrysia. Low support along the apoditrysian "backbone" probably reflects rapid diversification. If so, it may be feasible to strengthen resolution by radically increasing the gene sample, but case studies have been few. We explored the potential of next-generation sequencing to conclusively resolve apoditrysian relationships. We used transcriptome RNA-Seq to generate 1579 putatively orthologous gene sequences across a broad sample of 40 apoditrysians plus four outgroups, to which we added two taxa from previously published data. Phylogenetic analysis of a 46-taxon, 741-gene matrix, resulting from a strict filter that eliminated ortholog groups containing any apparent paralogs, yielded dramatic overall increase in bootstrap support for deeper nodes within Apoditrysia as compared to results from previous and concurrent 19-gene analyses. High support was restricted mainly to the huge subclade Obtectomera broadly defined, in which 11 of 12 nodes subtending multiple superfamilies had bootstrap support of 100%. The strongly supported nodes showed little conflict with groupings from previous studies, and were little affected by changes in taxon sampling, suggesting that they reflect true signal rather than artifacts of massive gene sampling. In contrast, strong support was seen at only 2 of 11 deeper nodes among the "lower", non-obtectomeran apoditrysians. These represent a much harder phylogenetic problem, for which one path to resolution might include further increase in gene sampling, together with improved orthology assignments.
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Affiliation(s)
- Adam L. Bazinet
- Laboratory of Molecular Evolution, Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, United States of America
| | - Michael P. Cummings
- Laboratory of Molecular Evolution, Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, United States of America
| | - Kim T. Mitter
- Department of Entomology, University of Maryland, College Park, Maryland, United States of America
| | - Charles W. Mitter
- Department of Entomology, University of Maryland, College Park, Maryland, United States of America
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Xia Q, Li S, Feng Q. Advances in silkworm studies accelerated by the genome sequencing of Bombyx mori. ANNUAL REVIEW OF ENTOMOLOGY 2013; 59:513-536. [PMID: 24160415 DOI: 10.1146/annurev-ento-011613-161940] [Citation(s) in RCA: 193] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Significant progress has been achieved in silkworm (Bombyx mori) research since the last review on this insect was published in this journal in 2005. In this article, we review the new and exciting progress and discoveries that have been made in B. mori during the past 10 years, which include the construction of a fine genome sequence and a genetic variation map, the evolution of genomes, the advent of functional genomics, the genetic basis of silk production, metamorphic development, immune response, and the advances in genetic manipulation. These advances, which were accelerated by the genome sequencing project, have promoted B. mori as a model organism not only for lepidopterans but also for general biology.
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Affiliation(s)
- Qingyou Xia
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400715, China;
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Shi XF, Bin Han, Li YN, Yi YZ, Li XM, Shen XJ, Zhang ZF. Proteomic analysis of the phenotype of the scaleless wings mutant in the silkworm, Bombyx mori. J Proteomics 2012; 78:15-25. [PMID: 23174119 DOI: 10.1016/j.jprot.2012.11.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2012] [Revised: 10/20/2012] [Accepted: 11/04/2012] [Indexed: 10/27/2022]
Abstract
A scaleless wing mutant of silkworm, Bombyx mori, has much fewer scales than wild type (WT). The scaleless phenotype was associated with tracheal system developmental deficiency and excessive apoptosis of scale cells. In this study, the wing discs proteins of WT and scaleless during pupation were studied using 2-DE and mass spectrometry. Of the 99 identified protein spots, four critical differentially expressed proteins between WT and scaleless were further verified using Q-PCR. At the first day of pupation (P0) in WT, imaginal disk growth factor (IDGF) was upregulated, whereas actin-depolymerizing factor 1 (ADF1) and profilin (PFN), which associated with cellular motility and cytoplasmic extension, were downregulated. We speculated their coaction counteracts the correct organization of the tracheal system in wing disc. Thiol peroxiredoxin (TPx) was upregulated in scaleless at P0, but its mRNA higher expression occurred in the day before pupation (S4). TPx could inhibit the formation of hydrogen peroxide, preventing the release of cytochrome C and activation of the caspase family protease. Its higher expression in scaleless was responsible for the apoptosis of scale cells delayed. The results provide further evidence that the scaleless phenotype was related to the tracheal system developmental deficiency and excessive apoptosis of scale cells.
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Affiliation(s)
- Xiao-Feng Shi
- The Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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