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Genomics, Transcriptomics, and Proteomics of Insects
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Genomics, Transcriptomics, and Proteomics of Insects

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Animal Genetics and Genomics".

Deadline for manuscript submissions: closed (15 April 2025) | Viewed by 6959

Special Issue Editors

Dr. Rui Guo

E-Mail Website
Guest Editor
Host–Pathogen Interaction Mechanism and Precision Medicine Team, National & Local United Engineering Laboratory of Natural Biotoxin, Apitherapy Research Institute, College of Bee Science and Biomedicine, Fujian Agriculture and Forestry University, Fuzhou 350002, China
Interests: host–pathogen/parasite interaction; non-coding RNA; epigenetics; transgene; omics
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Dafu Chen

E-Mail Website
Guest Editor
College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China
Interests: bee pathology; bee protection; chalkbrood; bee nosemosis; diagnosis and control of bee diseases
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Insects are distributed worldwide and include numerous and diverse species. Some beneficial insects, such as honeybees and silkworms, play a critical role in maintaining the balance of the ecosystem and producing high-quality products like honey and silk. In contrast, some other insects, such as locusts and mosquitoes, are capable of giving rise to severe losses in food production as well as are a serious threat to human health. In the past two decades, with the continuous revolution and rapid development of sequencing technology and bioinformatics, significant advancements have been made in the field of omics (genomics, transcriptomics, proteomics, etc.) associated with animals, plants, and microorganisms. From the perspective of omics, novel and valuable insights into the biology of bees could be gained, and candidate molecules such as genes, isoforms, and proteins could be screened for further functional dissection. This Special Issue of Genes entitled “Genomics, Transcriptomics, and Proteomics of Insects” will collect high-quality reviews and research articles written by the leading experts in related fields. The scope of this Special Issue includes but is not limited to genomics of insects, transcriptomics of insects, proteomics of insects, third-generation sequencing-based omics of insects, functional genomics of insects, development and application of bioinformatic tools in the study of insects, and insect–biotic factor/abiotic factor interaction from the omics perspective. It is believed that, with our joint efforts, this Special Issue will provide a valuable source and a solid basis for researchers in molecular biology, pathology, protection, physiology, ecology, genetics, epigenetics, and population genetics of insects.

Dr. Rui Guo
Prof. Dr. Dafu Chen
Guest Editors

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Keywords

  • genomics
  • transcriptomics
  • proteomics
  • third-generation sequencing
  • functional genomics
  • bioinformatics
  • mechanisms

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Published Papers (7 papers)

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Research

13 pages, 2042 KiB  
Article
Transcriptomic Characterization of miRNAs in Pyrrhalta aenescens Fairmaire in Response to 20-Hydroxyecdysone Treatment
by Jie Liu, Li Gao, Chao Du, Tianfeng Duan and Li Liu
Genes 2025, 16(4), 435; https://doi.org/10.3390/genes16040435 - 5 Apr 2025
Viewed by 344
Abstract
Background/Objectives: Pyrrhalta aenescens, a major pest of elm trees, causes extensive ecological and economic damage through rapid population growth and defoliation. Existing research mainly focuses on its biological traits and chemical control, with little knowledge about its reproductive development mechanisms, a key [...] Read more.
Background/Objectives: Pyrrhalta aenescens, a major pest of elm trees, causes extensive ecological and economic damage through rapid population growth and defoliation. Existing research mainly focuses on its biological traits and chemical control, with little knowledge about its reproductive development mechanisms, a key factor in population expansion. In other insects, the steroid hormone 20-hydroxyecdysone (20E) regulates development and reproduction via microRNA (miRNA)-mediated pathways, but this has not been studied in P. aenescens. This study aimed to systematically identify miRNAs responsive to 20E in P. aenescens and unravel their roles in regulating reproduction and metabolic pathways, providing foundational insights into hormone–miRNA crosstalk in this ecologically significant pest. Methods: Adult beetles (collected from Baotou, Inner Mongolia) were injected with 1.0 μg/μL 20E or control. Total RNA from three biological replicates (10 adults each) was sequenced, followed by miRNA identification, differential expression analysis, target prediction, and functional enrichment. Results: Small RNA sequencing identified 205 miRNAs (162 conserved, 43 novel), with 12 DEMs post-20E treatment. Target prediction linked these miRNAs to 7270 genes, including key regulators of the FoxO signaling pathway and MAPK signaling pathway. KEGG analysis highlighted lipid metabolism and stress response pathways. Conclusions: This study revealed that 20E modulates miRNA networks to regulate FoxO and MAPK pathways in P. aenescens, suggesting hormonal control of lipid metabolism and developmental processes. As the first miRNA resource for this pest, our findings provide mechanistic insights into 20E–miRNA crosstalk and identify potential molecular targets for disrupting its reproductive biology, laying a foundation for eco-friendly pest control. Full article
(This article belongs to the Special Issue Genomics, Transcriptomics, and Proteomics of Insects)
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15 pages, 4972 KiB  
Article
Developmental Expression Patterns of miRNA in Mythimna separata Walker (Lepidotera: Noctuidae)
by Yuhan Liu, Huiman Tian, Shaoqiu Ren, Xiulin Chen, Kun Luo, Guangwei Li and Boliao Li
Genes 2025, 16(2), 234; https://doi.org/10.3390/genes16020234 - 19 Feb 2025
Viewed by 471
Abstract
Background/Objectives: miRNAs are a family of single-stranded non-coding RNAs that regulate gene expression by targeting messenger RNAs (mRNAs) for suppression, with an average length of 22 nt. The oriental armyworm, Mythimna separata Walker, is a pest insect with long-distance migratory capability, which causes [...] Read more.
Background/Objectives: miRNAs are a family of single-stranded non-coding RNAs that regulate gene expression by targeting messenger RNAs (mRNAs) for suppression, with an average length of 22 nt. The oriental armyworm, Mythimna separata Walker, is a pest insect with long-distance migratory capability, which causes severe loss of grains and pastures in Eastern Asia, Southeastern Asia, and Oceania. This study aims to elucidate the post-transcriptional regulatory mechanisms of miRNAs in the development of this pest. Methods: We carried out small RNA sequencing on samples from eggs, third instar larvae, pre-pupae, pupae, and adults. Results: A total of 400 miRNAs were identified, among which 40 were known and 360 were novel miRNAs. Dynamic trend analysis of miRNAs revealed that 199 miRNAs were highly expressed in eggs (profile 12), while 173 miRNAs were highly expressed in both eggs and pupae (profile 13). The results of differential expression analysis of miRNAs (DEmiR) revealed that 75 miRNAs were significantly more abundant in eggs compared to other developmental stages. Furthermore, more up-regulated miRNAs were observed than down-regulated miRNAs in adults relative to 3rd instar larvae, pre-pupae, and pupae. The core genes for miRNA biosynthesis—Pasha, Dicer1, and Ago1—were highly expressed in eggs but poorly expressed in 3rd instar larvae. KEGG enrichment analyses indicated that several genes in the pentose and glucuronate interconversion pathway, as well as the fructose and mannose metabolism pathway, were regulated by DEmiRs. Conclusions: DEmiRNAs targeted most genes of M. separata, resulting in a complex miRNA–mRNA regulation mode. Full article
(This article belongs to the Special Issue Genomics, Transcriptomics, and Proteomics of Insects)
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17 pages, 7574 KiB  
Article
Identification of Retrocopies in Lepidoptera and Impact on Domestication of Silkworm
by Lingzi Bie, Jiahe Sun, Yi Wang and Chunfang Wang
Genes 2024, 15(12), 1641; https://doi.org/10.3390/genes15121641 - 21 Dec 2024
Viewed by 538
Abstract
Background: During the domestication of silkworm, an economic insect, its physiological characteristics have changed greatly. RNA-based gene duplication, known as retrocopy, plays an important role in the formation of new genes and genome evolution, but the retrocopies of lepidopteran insects have not been [...] Read more.
Background: During the domestication of silkworm, an economic insect, its physiological characteristics have changed greatly. RNA-based gene duplication, known as retrocopy, plays an important role in the formation of new genes and genome evolution, but the retrocopies of lepidopteran insects have not been fully identified and analyzed, which not only severely limits researchers from exploring the effects of retrocopies on lepidopteran insects but also affects the studies on the domestication of silkworm. Methods: We compared the genomes and proteomes of eight lepidopteran insects and used a series of screening criteria for auxiliary screening to obtain the retrocopies in lepidopteran insects and explored their characteristics. In addition, based on the silkworm transcriptome data from the SilkDB3.0 website, we explored the functions of the retrocopies on the domestication of the silkworm. Results: A total of 1993 retrocopies and 1208 parental genes in lepidopteran insects were obtained. We revealed that the retrocopies in Lepidoptera do not conform to the “out of X” hypothesis but fit the “out of testis” hypothesis. These retrocopies were subject to strong functional constraints and performed important functions in growth and development. Transcriptome analysis revealed that the expression pattern of the retrocopies and their parental genes were irrelevant. Through the analysis of the retrocopies in silkworm generated after domestication and located in the candidate domestication regions, the possible universal connection between the retrocopies and the domestication of silkworm were found. Conclusions: Our study pioneered the exploration of retrocopies in multiple Lepidoptera species and found the potential association between the retrocopies and the domestication of silkworm. Full article
(This article belongs to the Special Issue Genomics, Transcriptomics, and Proteomics of Insects)
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13 pages, 5282 KiB  
Article
The ebony Gene in Silkworm Black Pupae Significantly Affects 30 K Proteins During the Pupal Stage
by Runhuan Yang, Huiduo Guo, Juan Sun, Tao Gui, Xinyu Li, Heying Qian and Anli Chen
Genes 2024, 15(12), 1560; https://doi.org/10.3390/genes15121560 - 29 Nov 2024
Viewed by 799
Abstract
Background/Objectives: The body color and patterns of insects play important roles in foraging, evading predators, mating, thermoregulation, and environmental adaptation. During the rearing of the QiufengN silkworm strain, a mutant with black pupal cuticle (QiufengNBP) was discovered. Preliminary map-based cloning and sequence [...] Read more.
Background/Objectives: The body color and patterns of insects play important roles in foraging, evading predators, mating, thermoregulation, and environmental adaptation. During the rearing of the QiufengN silkworm strain, a mutant with black pupal cuticle (QiufengNBP) was discovered. Preliminary map-based cloning and sequence analysis indicated that the ebony gene might significantly influence the formation of the black pupa mutant and the expression of 30K proteins. This study aims to determine the function of the ebony gene and its effect on the expression of the 30K protein during the pupal stage; Methods and Results: We employed CRISPR/Cas9 gene-editing technology to knock out the ebony gene in the Nistari strain, resulting in individuals with black pupae, named Nistari Black Pupa (NisBP). This confirmed that the ebony gene plays a crucial role in black pupa formation. Two-dimensional electrophoresis (2-DE) analysis of the pupal cuticle of NisBP and its wild-type Nistari found that the ebony gene has a significant impact on the expression of 30K proteins, which are vital for embryonic development and serve as key storage proteins; Conclusions: This study is the first to demonstrate that the ebony gene affects the expression of 30K proteins, laying the foundation for further research on their functions and providing insights into the developmental mechanisms of silkworms. Full article
(This article belongs to the Special Issue Genomics, Transcriptomics, and Proteomics of Insects)
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15 pages, 2647 KiB  
Article
Comparison of Brain Gene Expression Profiles Associated with Auto-Grooming Behavior between Apis cerana and Apis mellifera Infested by Varroa destructor
by Jiali Liao, Kunlin Wan, Yang Lü, Wenyao Ouyang, Jingnan Huang, Liyuan Zheng, Liuchang Miao, Songkun Su and Zhiguo Li
Genes 2024, 15(6), 763; https://doi.org/10.3390/genes15060763 - 11 Jun 2024
Cited by 1 | Viewed by 1290
Abstract
The grooming behavior of honeybees serves as a crucial auto-protective mechanism against Varroa mite infestations. Compared to Apis mellifera, Apis cerana demonstrates more effective grooming behavior in removing Varroa mites from the bodies of infested bees. However, the underlying mechanisms regulating grooming [...] Read more.
The grooming behavior of honeybees serves as a crucial auto-protective mechanism against Varroa mite infestations. Compared to Apis mellifera, Apis cerana demonstrates more effective grooming behavior in removing Varroa mites from the bodies of infested bees. However, the underlying mechanisms regulating grooming behavior remain elusive. In this study, we evaluated the efficacy of the auto-grooming behavior between A. cerana and A. mellifera and employed RNA-sequencing technology to identify differentially expressed genes (DEGs) in bee brains with varying degrees of grooming behavior intensity. We observed that A. cerana exhibited a higher frequency of mite removal between day 5 and day 15 compared to A. mellifera, with day-9 bees showing the highest frequency of mite removal in A. cerana. RNA-sequencing results revealed the differential expression of the HTR2A and SLC17A8 genes in A. cerana and the CCKAR and TpnC47D genes in A. mellifera. Subsequent homology analysis identified the HTR2A gene and SLC17A8 gene of A. cerana as homologous to the HTR2A gene and SLC17A7 gene of A. mellifera. These DEGs are annotated in the neuroactive ligand–receptor interaction pathway, the glutamatergic synaptic pathway, and the calcium signaling pathway. Moreover, CCKAR, TpnC47D, HTR2A, and SLC17A7 may be closely related to the auto-grooming behavior of A. mellifera, conferring resistance against Varroa infestation. Our results further explain the relationship between honeybee grooming behavior and brain function at the molecular level and provide a reference basis for further studies of the mechanism of honeybee grooming behavior. Full article
(This article belongs to the Special Issue Genomics, Transcriptomics, and Proteomics of Insects)
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17 pages, 4566 KiB  
Article
Construction of a Full-Length Transcriptome of Western Honeybee Midgut Tissue and Improved Genome Annotation
by He Zang, Sijia Guo, Shunan Dong, Yuxuan Song, Kunze Li, Xiaoxue Fan, Jianfeng Qiu, Yidi Zheng, Haibin Jiang, Ying Wu, Yang Lü, Dafu Chen and Rui Guo
Genes 2024, 15(6), 728; https://doi.org/10.3390/genes15060728 - 1 Jun 2024
Cited by 1 | Viewed by 1585
Abstract
Honeybees are an indispensable pollinator in nature with pivotal ecological, economic, and scientific value. However, a full-length transcriptome for Apis mellifera, assembled with the advanced third-generation nanopore sequencing technology, has yet to be reported. Here, nanopore sequencing of the midgut tissues of [...] Read more.
Honeybees are an indispensable pollinator in nature with pivotal ecological, economic, and scientific value. However, a full-length transcriptome for Apis mellifera, assembled with the advanced third-generation nanopore sequencing technology, has yet to be reported. Here, nanopore sequencing of the midgut tissues of uninoculated and Nosema ceranae-inoculated A. mellifera workers was conducted, and the full-length transcriptome was then constructed and annotated based on high-quality long reads. Next followed improvement of sequences and annotations of the current reference genome of A. mellifera. A total of 5,942,745 and 6,664,923 raw reads were produced from midguts of workers at 7 days post-inoculation (dpi) with N. ceranae and 10 dpi, while 7,100,161 and 6,506,665 raw reads were generated from the midguts of corresponding uninoculated workers. After strict quality control, 6,928,170, 6,353,066, 5,745,048, and 6,416,987 clean reads were obtained, with a length distribution ranging from 1 kb to 10 kb. Additionally, 16,824, 17,708, 15,744, and 18,246 full-length transcripts were respectively detected, including 28,019 nonredundant ones. Among these, 43,666, 30,945, 41,771, 26,442, and 24,532 full-length transcripts could be annotated to the Nr, KOG, eggNOG, GO, and KEGG databases, respectively. Additionally, 501 novel genes (20,326 novel transcripts) were identified for the first time, among which 401 (20,255), 193 (13,365), 414 (19,186), 228 (12,093), and 202 (11,703) were respectively annotated to each of the aforementioned five databases. The expression and sequences of three randomly selected novel transcripts were confirmed by RT-PCR and Sanger sequencing. The 5′ UTR of 2082 genes, the 3′ UTR of 2029 genes, and both the 5′ and 3′ UTRs of 730 genes were extended. Moreover, 17,345 SSRs, 14,789 complete ORFs, 1224 long non-coding RNAs (lncRNAs), and 650 transcription factors (TFs) from 37 families were detected. Findings from this work not only refine the annotation of the A. mellifera reference genome, but also provide a valuable resource and basis for relevant molecular and -omics studies. Full article
(This article belongs to the Special Issue Genomics, Transcriptomics, and Proteomics of Insects)
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12 pages, 2663 KiB  
Article
Preliminary Study on the Pathogenic Mechanism of Jujube Flower Disease in Honeybees (Apis mellifera ligustica) Based on Midgut Transcriptomics
by Yali Du, Kai Xu, Huiting Zhao, Ying Wu, Haibin Jiang, Jinming He and Yusuo Jiang
Genes 2024, 15(5), 533; https://doi.org/10.3390/genes15050533 - 24 Apr 2024
Cited by 1 | Viewed by 1173
Abstract
Honeybees are prone to poisoning, also known as jujube flower disease, after collecting nectar from jujube flowers, resulting in the tumultuous demise of foragers. The prevalence of jujube flower disease has become one of the main factors affecting the development of the jujube [...] Read more.
Honeybees are prone to poisoning, also known as jujube flower disease, after collecting nectar from jujube flowers, resulting in the tumultuous demise of foragers. The prevalence of jujube flower disease has become one of the main factors affecting the development of the jujube and beekeeping industries in Northern China. However, the pathogenic mechanisms underlying jujube flower disease in honeybees are poorly understood. Herein, we first conducted morphological observations of the midgut using HE-staining and found that jujube flower disease-affected honeybees displayed midgut damage with peritrophic membrane detachment. Jujube flower disease was found to increase the activity of chitinase and carboxylesterase (CarE) and decrease the activity of superoxide dismutase (SOD), catalase (CAT), glutathione S-transferase (GST), and the content of CYP450 in the honeybee midgut. Transcriptomic data identified 119 differentially expressed genes in the midgut of diseased and healthy honeybees, including CYP6a13, CYP6a17, CYP304a1, CYP6a14, AADC, and AGXT2, which are associated with oxidoreductase activity and vitamin binding. In summary, collecting jujube flower nectar could reduce antioxidant and detoxification capacities of the honeybee midgut and, in more severe cases, damage the intestinal structure, suggesting that intestinal damage might be the main cause of honeybee death due to jujube nectar. This study provides new insights into the pathogenesis of jujube flower disease in honeybees. Full article
(This article belongs to the Special Issue Genomics, Transcriptomics, and Proteomics of Insects)
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