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Genomics and Molecular Biology in Silkworm
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Genomics and Molecular Biology in Silkworm

A special issue of Insects (ISSN 2075-4450). This special issue belongs to the section "Insect Molecular Biology and Genomics".

Deadline for manuscript submissions: 31 October 2025 | Viewed by 8587

Special Issue Editors

Prof. Dr. Genhong Wang

E-Mail Website
Guest Editor
Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing, China
Interests: nutrient digestion and absorption; insect-plant interaction; artificial selection and domestication
Dr. Zuoming Nie

E-Mail Website
Guest Editor
College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China
Interests: functional genomics and proteomics in silkworm; function of acetylation modification on nutrition-storage protein; preparation and development of active proteins by silkworm bioreactor

Special Issue Information

Dear Colleagues,

Significant progress has been made in research on silkworm molecular biology since the first genomic sequences were publicized 20 years ago. The identification of genes related to development and metamorphosis, immune defense, sex determination, silk synthesis, and nutrition utilization is not only important for the silk industry but also beneficial for the control of lepidopterous pests. In this Special Issue, we welcome manuscripts that report recent discoveries and review key subject areas in the field of “Genomics and Molecular Biology in Silkworm”.

Prof. Dr. Genhong Wang
Dr. Zuoming Nie
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Insects is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • silkworm
  • molecular biology
  • genome
  • development and metamorphosis
  • immune defense
  • silk synthesis
  • nutrition utilization

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Published Papers (10 papers)

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Research

Jump to: Review

16 pages, 7129 KiB  
Article
Estrogen-Related Receptor Potential Target Genes in Silkworm (Bombyx mori): Insights into Metabolic Regulation
by Luyu Hou, Jinxin Wu, Die Liu, Haoran Xu, Hongbo Yao, Yiwen Liang, Qingyou Xia, Ping Lin and Guanwang Shen
Insects 2025, 16(5), 469; https://doi.org/10.3390/insects16050469 - 29 Apr 2025
Viewed by 538
Abstract
Estrogen-related receptors (ERRs) are important transcription factors within the nuclear receptor family that regulate cellular energy storage and consumption by binding to estrogen-related receptor response elements (ERREs) on gene promoters. While ERRs’ role in vertebrates is well-studied, their molecular mechanisms in insect metabolism [...] Read more.
Estrogen-related receptors (ERRs) are important transcription factors within the nuclear receptor family that regulate cellular energy storage and consumption by binding to estrogen-related receptor response elements (ERREs) on gene promoters. While ERRs’ role in vertebrates is well-studied, their molecular mechanisms in insect metabolism and development remain unclear. This study systematically summarizes the functions of ERRs in insects, focusing on silkworms by analyzing gene functions and comparing databases. ERRE-like elements were identified in the 2000 bp upstream promoter regions of 69 metabolism-related silkworm genes. Furthermore, electrophoretic mobility shift assays (EMSAs) revealed that ERREs within the promoters of 15 genes related to sugar, fat, and protein metabolism specifically bind to ERR. Notably, an ERRE in the promoter of the trehalose transporter 1 gene (BmTret1), crucial for trehalose homeostasis in insect hemolymph, exhibited significantly enhanced activity in ERR-overexpressing cells. These findings suggest that ERR is a potential regulatory factor in silkworm metabolism and refine its metabolic regulatory network. This study highlights the broader and more critical role of ERR in insects than that previously recognized, contributing to a deeper understanding of insect metabolism and its potential applications in related fields. Full article
(This article belongs to the Special Issue Genomics and Molecular Biology in Silkworm)
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12 pages, 2220 KiB  
Article
BmHR3 Is Essential for Silk Gland Development and Silk Protein Synthesis in Silkworms (Bombyx mori)
by Yao Ou, Qin Luo, Wenhui Zeng, Yiyun Tang, Jie Hu, Chun Liu, Yan Ma and Hanfu Xu
Insects 2025, 16(4), 369; https://doi.org/10.3390/insects16040369 - 1 Apr 2025
Viewed by 473
Abstract
The steroid hormone 20-hydroxyecdysone (20E), which is known to regulate insect molting and metamorphosis, is crucial for the normal development of silk glands (SGs) in the silkworm Bombyx mori. However, how the 20E signaling pathway and its core members function in the [...] Read more.
The steroid hormone 20-hydroxyecdysone (20E), which is known to regulate insect molting and metamorphosis, is crucial for the normal development of silk glands (SGs) in the silkworm Bombyx mori. However, how the 20E signaling pathway and its core members function in the SG remains largely unclear. Here, we report that the orphan nuclear receptor BmHR3, a 20E-response factor, plays an essential role in regulating SG development and silk protein synthesis. First, we showed that tissue-specific BmHR3 overexpression and knockout result in severe developmental defects in posterior silk glands (PSGs). Second, we revealed that BmHR3 dysfunction in PSGs dramatically represses the transcription of silk fibroin protein-coding genes, thereby inhibiting fibroin protein synthesis. Finally, we confirmed that BmHR3 can regulate fibroin protein-coding gene expression via direct and indirect mechanisms. This study elucidates the vital function of BmHR3 in B. mori SG and provides valuable information for thoroughly understanding the regulatory roles of 20E signaling in specialized insect organs. Full article
(This article belongs to the Special Issue Genomics and Molecular Biology in Silkworm)
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14 pages, 5200 KiB  
Article
Comparative Transcriptome Analysis Reveals the Effects of a High-Protein Diet on Silkworm Midgut
by Xinyi Chen, Jiahao Li, Yuxi Shan, Qiaoling Wang, Pingzhen Xu, Heying Qian and Yangchun Wu
Insects 2025, 16(4), 337; https://doi.org/10.3390/insects16040337 - 24 Mar 2025
Viewed by 501
Abstract
The silkworm is a species within the order Lepidoptera and an economic insect. The nutrients are obtained from the leaf and utilized by the silkworm larvae for body growth, development, and cocoon formation. Protein plays a significant functional role in the diet of [...] Read more.
The silkworm is a species within the order Lepidoptera and an economic insect. The nutrients are obtained from the leaf and utilized by the silkworm larvae for body growth, development, and cocoon formation. Protein plays a significant functional role in the diet of silkworms. To investigate the impact of the high-protein diet (HPD 6%) on silkworm growth and development, transcriptomic analysis was conducted on the silkworm midgut, and 1724 differentially expressed genes (DEGs) were identified, comprising 803 up-regulated genes and 921 down-regulated genes. The up-regulated genes exhibited the majority pathway of mitochondrial oxidative phosphorylation, ribosome, and ribosome biogenesis in eukaryotes. The down-regulated genes of DEGs were mostly annotated in ABC transporters, lysosome, endocytosis, and sphingolipid metabolism pathways. The comprehensive analysis of DEGs indicated that substantial modifications were observed in various pathways associated with crucial biological processes. HPD 6% decreased oxidative stress and increased mitochondrial activity, ribosomal activity, and DNA repair capacity. Additionally, the ATP levels were increased in the midgut, malpighian tubule, middle silk gland, and posterior silk gland of the HPD 6% group. Moreover, the activities of SOD and NADH were enhanced in the midgut of the HPD 6% group. Our findings provide valuable insights into the wide-ranging effects of an HPD treatment in insects such as silkworms. Full article
(This article belongs to the Special Issue Genomics and Molecular Biology in Silkworm)
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12 pages, 2588 KiB  
Article
Integrated Genomic Analysis Reveals the Impact of Avermectin on Chromatin Structure and Gene Expression Regulation in Bombyx mori
by Yongkang Guo, Tong Zhang, Wei Lu, Dan Liu, Junjie Lao, Na Zhang, Hao Sun, Ling Jia and Sanyuan Ma
Insects 2025, 16(3), 298; https://doi.org/10.3390/insects16030298 - 12 Mar 2025
Viewed by 631
Abstract
Avermectin is a widely used insecticide for pest control, such as the Plutella xylostella. Despite its efficacy in pest management, concerns have been raised regarding its effect on non-target species, such as the important economic insect silkworm (Bombyx mori). We [...] Read more.
Avermectin is a widely used insecticide for pest control, such as the Plutella xylostella. Despite its efficacy in pest management, concerns have been raised regarding its effect on non-target species, such as the important economic insect silkworm (Bombyx mori). We aimed to investigate the effects of avermectin application on the 3D genome architecture of silkworm midgut using high-throughput techniques such as high-throughput chromosome conformation capture (Hi-C) coupled with RNA sequencing (RNA-seq) and Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq). Midgut tissue samples, during the fifth instar and three days, were collected from silkworm larvae fed mulberry leaves (control group) and leaves soaked in avermectin solution for 12 h (experimental group). Our findings revealed that avermectin treatment led to significant changes, including 386 differentially expressed genes (252 up-regulated, 134 down-regulated) and increased chromatin accessibility, particularly those involved in immune response, metabolism, and cellular stress pathways. The Hi-C data revealed more intense spatial interactions in the experimental group, leading to increased expression of detoxification proteins like ABC transporter. This study provides important insights into the molecular basis of pesticide resistance and a foundational basis for further research on the genetic and epigenetic mechanisms of insect stress responses. Full article
(This article belongs to the Special Issue Genomics and Molecular Biology in Silkworm)
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15 pages, 3593 KiB  
Article
20-Hydroxyecdysone Regulates the Expression of 30 Genes Specifically Expressed in Larval Digestive Tube of the Silkworm, Bombyx mori
by Jiahao Li, Mulin Xia, Songyao Huang, Guangxie Zhang, Yuncheng Tang, Pingzhen Xu and Meirong Zhang
Insects 2025, 16(3), 291; https://doi.org/10.3390/insects16030291 - 11 Mar 2025
Viewed by 641
Abstract
Nutrients needed to fuel the processes of growth, development, and reproduction, and to form the proteins in the cocoon, are derived from the larval stage. The amount of leaf ingested in the fifth instar silkworm larvae accounted for about 85% of the whole [...] Read more.
Nutrients needed to fuel the processes of growth, development, and reproduction, and to form the proteins in the cocoon, are derived from the larval stage. The amount of leaf ingested in the fifth instar silkworm larvae accounted for about 85% of the whole instars. Nutrients were absorbed following digestion in the digestive tube. We previously reported the successful identification of 227 silkworm larval digestive juice proteins, wherein most of the genes of the identified proteins had high expression features in the midgut, and 30 of them were midgut-specific genes. We chose 30 genes and detected their expression characteristics in the digestive tube, and investigated the developmental expression profiles in the midgut of silkworm larvae from the day-3 fourth instar to the wandering period, as well as the expression dynamics after the 20-hydroxyecdysone (20E) treatment. The genes were specifically expressed in the larval digestive tube. The expression of BMSK0013805 was activated, and that of the other 29 genes were suppressed by 20E. The ecdysteroid ingestion dramatically suppressed the protease activity in the larval midgut, which revealed that 20E may also directly affect digestive activity. The present study is the first to demonstrate that the expression control mechanism of these genes is primarily hormonal regulation, which contributes to furthering our understanding of the mechanism of the genes expressed in the larval digestive tube during development. Full article
(This article belongs to the Special Issue Genomics and Molecular Biology in Silkworm)
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22 pages, 1695 KiB  
Article
Transcriptomic Profiling Provides Insight into the Molecular Basis of Heterosis in Philippine-Reared Bombyx mori Hybrids
by Ma. Ysabella Elaine D. Conde, Jose Planta and Ma. Anita M. Bautista
Insects 2025, 16(3), 243; https://doi.org/10.3390/insects16030243 - 26 Feb 2025
Viewed by 792
Abstract
In the Philippines, Bombyx mori parental strains Lat21 and B221 are crossed to yield NC144 and CN144, which demonstrate hybrid vigor. The molecular basis of the observed vigor in the hybrids is warranted, as it may assist in improving local sericulture programs. This [...] Read more.
In the Philippines, Bombyx mori parental strains Lat21 and B221 are crossed to yield NC144 and CN144, which demonstrate hybrid vigor. The molecular basis of the observed vigor in the hybrids is warranted, as it may assist in improving local sericulture programs. This study, therefore, aims to investigate the basis of hybrid vigor and generate molecular resources through whole-silkworm larvae transcriptome sequencing, assembly, and analysis. Differential gene expression was also conducted among the parental strains and hybrids. Assembly of the pre-processed reads was also performed using de novo and reference-based protocols. As expected, the reference-based assembly was better than de novo, based on E90N50, N50, and BUSCO assembly completeness metrics. The Analysis of the differentially expressed genes (DEGs) revealed 202 upregulated and 182 downregulated genes in the hybrids (with the parents as the reference) and 66 upregulated and 753 downregulated genes in NC144 (with CN144 as the reference). Among these were genes encoding heat shock proteins and antimicrobial peptides, which may serve as markers for marker-assisted breeding. The genes were further validated using quantitative real-time PCR. Moreover, the inducible nature of these genes under stressors like extreme temperature and bacterial exposure suggests their potential as diagnostic tools for stress assessment. Full article
(This article belongs to the Special Issue Genomics and Molecular Biology in Silkworm)
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12 pages, 2680 KiB  
Article
Effects of Novaluron Exposure on the Oviposition and Expression of Ovarian Development Related Genes in Silkworm, Bombyx mori (Lepidoptera: Bombycidae)
by Meng-Jiao Wang, En-Xi Chen, Yi-Lin Ji, Yi-Xuan Qian, Yu-Ming Zhang, Lin Zhu, Guo-Dong Zhao and He-Ying Qian
Insects 2025, 16(1), 9; https://doi.org/10.3390/insects16010009 - 27 Dec 2024
Viewed by 880
Abstract
Bombyx mori (Lepidoptera: Bombycidae) is an important economic insect, which mainly feeds on mulberry leaves and is widely used in many research fields. The growth and development of silkworm larvae are easily affected by the use of chemical insecticides such as novaluron, a [...] Read more.
Bombyx mori (Lepidoptera: Bombycidae) is an important economic insect, which mainly feeds on mulberry leaves and is widely used in many research fields. The growth and development of silkworm larvae are easily affected by the use of chemical insecticides such as novaluron, a benzoylurea insecticide. However, the effect of novaluron exposure on the reproduction of silkworms has not yet been studied. In this study, the effect of trace novaluron on the oviposition of silkworms and histopathological changes were first evaluated, and then the gene expression level changes after novaluron exposure were also determined by employing qRT-PCR. It was found that the number of eggs and the hatching rate of eggs in silkworms decreased significantly after feeding on leaves with a trace amount of novaluron (p ≤ 0.01). Furthermore, novaluron exposure could affect the development of ovary tissue by reducing the number of oocytes and oogonia in the ovaries of silkworms fed with novaluron. In addition, the transcription levels of genes related to ovary development (Vg, Ovo, Otu, Sxl-S and Sxl-L) and hormone regulation (EcR and JHBP2) showed varying degrees of downregulation at 24 h, 48 h, and 72 h after novaluron treatment (p ≤ 0.05). Therefore, we speculated that novaluron can affect the energy metabolism, ovary development, and egg formation of silkworms, thus leading to reproductive disorders of silkworms after novaluron exposure. Full article
(This article belongs to the Special Issue Genomics and Molecular Biology in Silkworm)
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11 pages, 2061 KiB  
Article
Genetic Diversity and Differentiation of Silkworm (Bombyx mori) Local Germplasm Resources in China and Uzbekistan
by Xia Xu, Xin Du, Jine Chen, Lusong Yao, Xiuling He, Linbao Zhu, Shaofang Yu, Valiev Sayfiddin Tojiddinovich, Baxtiyar Ubaydullayevich Nasirillayev, Ismatullaeva Diloram Adilovna, Khudjamatov Safarali Khasanboy ugl and Yongqiang Wang
Insects 2024, 15(12), 1020; https://doi.org/10.3390/insects15121020 - 23 Dec 2024
Cited by 1 | Viewed by 1106
Abstract
Silkworm (Bombyx mori) is an economically significant insect that produces silk and makes important contributions to the development of silk-producing countries. The genetic diversity and unique adaptive traits of silkworm germplasm resources form the foundation for breeding efforts. In various geographical [...] Read more.
Silkworm (Bombyx mori) is an economically significant insect that produces silk and makes important contributions to the development of silk-producing countries. The genetic diversity and unique adaptive traits of silkworm germplasm resources form the foundation for breeding efforts. In various geographical regions, silkworm have developed distinct traits through long-term adaptive selection. In this study, we focused on identifying and evaluating representative silkworm germplasm resources from both China and Uzbekistan. We discovered notable differences in the morphology and production traits of local silkworm strains, likely influenced by differing geographical environments. It is also possible that China has a long history of silkworm rearing and after a long time of breeding selection, the diversity of silkworm morphology is less than that of Uzbekistan, but the production characteristics are more suitable for silk utilization. Phylogenetic analysis based on genomic comparisons revealed that Uzbekistan’s local silkworm strains are positioned between China’s local and improved strains. This suggests that Uzbekistan silkworms primarily originated from China. The further analysis of genetic diversity and strain differentiation highlights the unique differences of each country’s silkworms, especially in terms of genetic diversity on chromosome 1 (sex chromosome). By identifying and evaluating these germplasm resources and linking them to unique advantageous traits, it provides a scientific basis for improving cocoon silk quality and optimizing sericulture productivity. Full article
(This article belongs to the Special Issue Genomics and Molecular Biology in Silkworm)
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16 pages, 7130 KiB  
Article
Genomic Analysis Reveals Novel Genes and Adaptive Mechanisms for Artificial Diet Utilization in the Silkworm Strain Guican No.5
by Lei Xin, Delong Guan, Nan Wei, Xiaoyan Zhang, Weian Deng, Xiaodong Li and Jing Song
Insects 2024, 15(12), 1010; https://doi.org/10.3390/insects15121010 - 20 Dec 2024
Viewed by 915
Abstract
The transition from traditional mulberry leaf feeding to artificial diet cultivation represents a major advancement in modern sericulture, yet the genetic mechanisms driving this adaptation remain largely unexplored. This study investigates the genomic basis of artificial diet adaptation in the silkworm strain Guican [...] Read more.
The transition from traditional mulberry leaf feeding to artificial diet cultivation represents a major advancement in modern sericulture, yet the genetic mechanisms driving this adaptation remain largely unexplored. This study investigates the genomic basis of artificial diet adaptation in the silkworm strain Guican No.5 through whole-genome resequencing and transcriptome analysis. We identified 8,935,179 single-nucleotide polymorphisms (SNPs) across all chromosomes, accounting for 2.01% of the genome, with particularly high densities observed in chromosomes 23, 26, and 28. Our analysis also revealed 879 novel transcripts, many of which are involved in digestion, detoxification, and stress response pathways. Key novel genes, including three carboxylesterases, two cytochrome P450s, one heat shock protein, and one copper/zinc superoxide dismutase, exhibited varying degrees of sequence similarity to known proteins, suggesting modifications to existing genetic frameworks. Notably, one novel P450 gene displayed only 74.07% sequence identity with its closest homolog, indicating the emergence of a new protein sequence. Additionally, several key genes showed high similarity to wild silkworm (Bombyx mandarina) proteins, underscoring their evolutionary origins. These findings provide valuable insights into the molecular mechanisms underpinning artificial diet adaptation in silkworms and offer genomic resources to enhance artificial diet formulations and breeding programs in sericulture. Full article
(This article belongs to the Special Issue Genomics and Molecular Biology in Silkworm)
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Review

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17 pages, 790 KiB  
Review
Towards a Rational Basis for the Selection of Probiotics to Improve Silkworm Health and Performance
by Siripuk Suraporn, Jisheng Liu, Feifei Ren, Luoluo Wang, Min Feng, Olle Terenius and Luc Swevers
Insects 2025, 16(2), 162; https://doi.org/10.3390/insects16020162 - 4 Feb 2025
Cited by 2 | Viewed by 1272
Abstract
Pathogenic infections of silkworms constitute the greatest threat to sericulture. An attractive approach to the improvement in silkworm health and performance comprises the use of probiotics, i.e., microorganisms that confer beneficial properties such as an increased growth rate and resistance against pathogens. While [...] Read more.
Pathogenic infections of silkworms constitute the greatest threat to sericulture. An attractive approach to the improvement in silkworm health and performance comprises the use of probiotics, i.e., microorganisms that confer beneficial properties such as an increased growth rate and resistance against pathogens. While this method has already resulted in promising results, generally, there is a lack of a rational basis for guidance on the selection of probiotics. This review attempts to organize useful information that needs to be considered for the successful application of probiotics: the constitution of the microbiota in silkworms and its origins; the interaction of the major silkworm pathogens with the microbiota; and the microorganisms that have been used so far as silkworm probiotics. Our analysis points to two major issues that seem of vital importance: (1) the absence of a “core microbiota” in silkworms which necessitates continuous supply of beneficial microorganisms according to environmental conditions and (2) the apparent negative impact that some other microorganisms can have on resistance against baculovirus infections. Recent findings have reported the beneficial effects of lactic acid bacteria (Lactobacillus sp.) when applied as probiotics in improving silkworm health and performance. Full article
(This article belongs to the Special Issue Genomics and Molecular Biology in Silkworm)
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