Search for Articles:
Title / Keyword
Author / Affiliation / Email
Journal
Article Type
 
 
Advanced Search
 
Section
Special Issue
Volume
Issue
Number
Page
 
5.6
2.9
Journals
Insects
Special Issues
Insect Transcriptomics
share announcement

Insect Transcriptomics

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

Deadline for manuscript submissions: 30 June 2026 | Viewed by 6479

Special Issue Editor

Prof. Dr. David S. Haymer

E-Mail Website
Guest Editor
Department of Cell and Molecular Biology, School of Medicine, University of Hawaiʻi at Mānoa, Honolulu, HI, USA
Interests: insect molecular biology; insect genomics; invasive species; genetic characterization of mass-reared insect colonies; forensic DNA analysis
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The use of the transcriptome as a research tool has dramatically changed how we approach genetic studies of insect species. A transcriptome may be generated de novo from any species of interest, thereby granting much greater freedom in choosing interesting insect species to characterize. The transcriptome represents only the set of gene products that are expressed at specific times and/or in specific tissues in individuals of a species, and this brings the advantage of being a genome-level study that generates a dataset considerably smaller and more manageable than a complete genome characterization. However, it may also mean that multiple transcriptomes may need to be generated to obtain a complete picture of the genetic composition of a species. Nevertheless, the relative ease with which transcriptomes can be generated and characterized today has revealed fascinating insights into the great diversity of species found in the world of insects. This Special Issue on Insect Transcriptomics will afford researchers an opportunity to publish the most current research on a wide range of topics.

Prof. Dr. David S. Haymer
Guest Editor

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

  • gene expression
  • regulation of gene expression
  • development
  • temporal patterns of expression
  • tissue-specific patterns of expression
  • genome characterization

Benefits of Publishing in a Special Issue

  • Ease of navigation: Grouping papers by topic helps scholars navigate broad scope journals more efficiently.
  • Greater discoverability: Special Issues support the reach and impact of scientific research. Articles in Special Issues are more discoverable and cited more frequently.
  • Expansion of research network: Special Issues facilitate connections among authors, fostering scientific collaborations.
  • External promotion: Articles in Special Issues are often promoted through the journal's social media, increasing their visibility.
  • Reprint: MDPI Books provides the opportunity to republish successful Special Issues in book format, both online and in print.

Further information on MDPI's Special Issue policies can be found here.

Published Papers (8 papers)

Download All Papers
Order results
Result details
Show export options expand_more Show export options expand_less
Select all
Export citation of selected articles as:

Research

15 pages, 2082 KB  
Article
Comparative Transcriptomics Unveils Pathogen-Specific mTOR Pathway Modulation in Monochamus alternatus Infected with Entomopathogenic Fungi
by Haoran Guan, Jinghong He, Chuanyu Zhang, Ruiyang Shan, Haoyuan Chen, Tong Wu, Qin Sun, Liqiong Zeng, Fangfang Zhan, Yu Fang, Gaoping Qu, Chentao Lin, Shouping Cai and Jun Su
Insects 2025, 16(10), 1006; https://doi.org/10.3390/insects16101006 - 28 Sep 2025
Viewed by 636
Abstract
Pine wilt disease (PWD), transmitted by Monochamus alternatus (JPS), poses a severe threat to global pine forests. Although the entomopathogenic fungi Beauveria bassiana (Bb) and Metarhizium anisopliae (Ma) represent environmentally friendly biocontrol alternatives, their practical application is limited by inconsistent field performance and [...] Read more.
Pine wilt disease (PWD), transmitted by Monochamus alternatus (JPS), poses a severe threat to global pine forests. Although the entomopathogenic fungi Beauveria bassiana (Bb) and Metarhizium anisopliae (Ma) represent environmentally friendly biocontrol alternatives, their practical application is limited by inconsistent field performance and an incomplete understanding of host–pathogen interactions. We employed dual RNA-seq at the critical 48 h infection time point to systematically compare the transcriptional responses between JPS and Bb/Ma during infection. Key findings revealed distinct infection strategies: Bb preferentially induced autophagy pathways and modulated host carbohydrate metabolism to facilitate nutrient acquisition, triggering corresponding tissue degradation responses in JPS. In contrast, Ma primarily co-opted host amino acid and sugar metabolic pathways for biosynthetic processes, eliciting a stronger immune defense activation in JPS. Notably, the mTOR signaling pathway was identified as a key regulator of the differential host responses to various entomopathogenic fungi. Further functional validation-specifically, the application of a chemical inhibitor and RNAi targeting mTOR in JPS-confirmed that mTOR inhibition selectively enhanced Bb-induced mortality in JPS without affecting Ma virulence. Our findings reveal the molecular determinants of host–pathogen specificity in PWD biological control and indicate that mTOR regulation could serve as an effective strategy to improve fungal pesticide performance. Full article
(This article belongs to the Special Issue Insect Transcriptomics)
►▼ Show Figures

Figure 1

19 pages, 5781 KB  
Article
Transcriptome Analysis and Identification of Chemosensory Genes in the Galleria mellonella Larvae
by Jiaoxin Xie, Huiman Zhang, Chenyang Li, Lele Sun, Peng Wang and Yuan Guo
Insects 2025, 16(10), 1004; https://doi.org/10.3390/insects16101004 - 27 Sep 2025
Viewed by 548
Abstract
The greater wax moth Galleria mellonella (Lepidoptera: Galleriinae) represents a ubiquitous apicultural pest that poses significant threats to global beekeeping industries. The larvae damage honeybee colonies by consuming wax combs and tunneling through brood frames, consequently destroying critical hive infrastructure including brood-rearing areas, [...] Read more.
The greater wax moth Galleria mellonella (Lepidoptera: Galleriinae) represents a ubiquitous apicultural pest that poses significant threats to global beekeeping industries. The larvae damage honeybee colonies by consuming wax combs and tunneling through brood frames, consequently destroying critical hive infrastructure including brood-rearing areas, honey storage cells, and pollen reserves. Larval feeding behavior is critically dependent on chemosensory input for host recognition and food selection. In this study, we conducted a transcriptome analysis of larval heads and bodies in G. mellonella. We identified a total of 25 chemosensory genes: 9 odorant binding proteins (OBPs), 1 chemosensory protein (CSP), 5 odorant receptors (ORs), 4 gustatory receptors (GRs), 4 ionotropic receptors (IRs) and 2 sensory neuron membrane proteins (SNMPs). TPM normalization was employed to assess differential expression patterns of chemosensory genes between heads and bodies. Nine putative chemosensory genes were detected as differentially expressed, suggesting their potential functional roles. Subsequently, we quantified expression dynamics via reverse transcription quantitative PCR in major chemosensory tissues (larval heads, adult male and female antennae), revealing adult antennal-biased expression for most chemosensory genes in G. mellonella. Notably, two novel candidates (GmelOBP22 and GmelSNMP3) exhibited particularly high expression in larval heads, suggesting their crucial functional roles in larval development and survival. These findings enhance our understanding of the chemosensory mechanisms in G. mellonella larvae and establish a critical foundation for future functional investigations into its olfactory mechanisms. Full article
(This article belongs to the Special Issue Insect Transcriptomics)
►▼ Show Figures

Figure 1

26 pages, 4388 KB  
Article
Recurrent Duplication, Testis-Biased Expression, and Functional Diversification of Esf2/ABT1 Family Genes in Drosophila
by Elizaveta D. Davydova, Alexei A. Kotov, Alina V. Chernizova, Ekaterina Yu. Yakovleva and Ludmila V. Olenina
Insects 2025, 16(9), 956; https://doi.org/10.3390/insects16090956 - 11 Sep 2025
Viewed by 773
Abstract
Gene duplications are considered to be the major evolutionary resource of novel functions. The gene family Esf2/ABP1 is conserved in metazoan organisms from yeast to humans. Here we performed a search and characterization of Esf2/ABP1 homologs in the Drosophila genus. Whereas in the [...] Read more.
Gene duplications are considered to be the major evolutionary resource of novel functions. The gene family Esf2/ABP1 is conserved in metazoan organisms from yeast to humans. Here we performed a search and characterization of Esf2/ABP1 homologs in the Drosophila genus. Whereas in the majority of Drosophila species this gene family is represented by only a single gene, in the melanogaster and suzukii subgroups recurrent gene duplications arose, providing 47 homologous genes located on the X chromosome. To study the evolutionary history of duplicates, we performed phylogenetic, functional domain, and tissue-specific expression analyses. We revealed a male-specific and testis-biased transcription pattern of duplicated copies in Drosophila melanogaster and Drosophila sechellia compared to ubiquitous expression of the parental gene. The amplification of 21 repeated paralogs within the heterochromatic piRNA cluster resulted in the ovarian-specific transformation of these repeats into piRNAs in D. melanogaster. In three species of the suzukii subgroup, Esf2/ABP1 genes evolved with domain diversification: in addition to RNA-binding ABT1-like domain preservation, all homologous proteins acquired expanded intrinsically disordered regions. By studying the duplicated copies of the Esf2/ABP1 family in Drosophila, we offer insight into how novel gene functions emerge and are maintained, contributing to life’s diversity and complexity. Full article
(This article belongs to the Special Issue Insect Transcriptomics)
►▼ Show Figures

Graphical abstract

16 pages, 2861 KB  
Article
Comparative Transcriptome Analysis Reveals Epithelial Growth Factor Receptor (EGFR) Pathway and Secreted C-Type Lectins as Essential Drivers of Leg Regeneration in Periplaneta americana
by Xiaoxuan Liu, Nan Sun, Xiaojuan Wu, Jiajia Wu, Shuqi Xian, Dayong Wang and Yechun Pei
Insects 2025, 16(9), 934; https://doi.org/10.3390/insects16090934 - 5 Sep 2025
Viewed by 758
Abstract
The American cockroach (Periplaneta americana) serves as an exemplary model for regeneration research due to its exceptional regenerative capabilities, particularly in appendage regeneration. In this study, regenerated coxa tissue underwent histological analysis through H & E straining. Microscopic examination revealed the [...] Read more.
The American cockroach (Periplaneta americana) serves as an exemplary model for regeneration research due to its exceptional regenerative capabilities, particularly in appendage regeneration. In this study, regenerated coxa tissue underwent histological analysis through H & E straining. Microscopic examination revealed the progression of regeneration. To elucidate the underlying mechanisms, a comparative transcriptomic analysis was conducted between regenerating legs and non-amputated control legs. This analysis identified 2343 differentially expressed genes (DEGs) between 0 days post-amputation (0 dpa) and 7 dpa, 2963 DEGs between 14 dpa and 0 dpa, and 3135 DEGs between 14 dpa and 7 dpa. Significantly, several DEGs are associated with growth- or regeneration-related processes, including extracellular matrix (different collagen, Pro-resilin isoforms, integrin beta (itgb) and matrix metalloproteinase (mmp)), immune-related genes (Toll-like receptor 13 (tlr13), defensin (def), drosomycin-like defensin (dld), Polyphenoloxidases2 (ppo2), cytochrome P450 (p450), peptidoglycan recognition protein (pgrp) and secreted C-type lectin (sClec)), insulin-like growth factor (IGF) and Epidermal Growth Factor Receptor (EGFR). Functional validation through RNA interference (RNAi) further suggested that EGFR and a specific C-type lectin (Regenectin) regulate leg regeneration in Periplaneta americana. These findings enhance our understanding of the molecular mechanisms governing regeneration in this species. Full article
(This article belongs to the Special Issue Insect Transcriptomics)
►▼ Show Figures

Figure 1

13 pages, 1866 KB  
Article
Transcriptomic Analysis of Chilo suppressalis (Walker) (Lepidoptera: Pyralidae) Reveals Cold Tolerance Mechanisms Under Parasitism Stress
by Chuan-Lei Dong, Elyar Abil, Rong Ji, Yu-Zhou Du and Ming-Xing Lu
Insects 2025, 16(9), 907; https://doi.org/10.3390/insects16090907 - 1 Sep 2025
Viewed by 655
Abstract
Parasitoids exhibit remarkable abilities to manipulate host physiology, ensuring offspring survival and development. This study investigated the molecular mechanisms underlying how the parasitoid Cotesia chilonis modulates cold tolerance in its host, the rice stem borer Chilo suppressalis, using transcriptome sequencing. We found [...] Read more.
Parasitoids exhibit remarkable abilities to manipulate host physiology, ensuring offspring survival and development. This study investigated the molecular mechanisms underlying how the parasitoid Cotesia chilonis modulates cold tolerance in its host, the rice stem borer Chilo suppressalis, using transcriptome sequencing. We found that the host larvae’s supercooling point was lowest at 3 days post-parasitism but increased significantly by day 4. Transcriptome analysis identified 507 differentially expressed genes (DEGs), including 235 up-regulated by parasitism. Functional enrichment revealed that these DEGs were primarily associated with ribosome biogenesis, protein processing in the endoplasmic reticulum (ER), and oxidative phosphorylation under parasitism stress. Notably, 24 DEGs linked to temperature tolerance were predominantly heat shock proteins (HSPs) and calcium signaling-related genes. The reliability of transcriptome data was confirmed via RT-qPCR for eight randomly selected DEGs. Functional assays demonstrated that parasitism stress significantly inhibited ER activity. However, HSP expression did not significantly affect ER activity or cytosolic Ca2+ concentration in the hemolymph cells of C. suppressalis larvae. This research provides insights into the complex physiological and molecular mechanisms through which C. suppressalis responds to parasitism stress, particularly concerning cold tolerance modulation. Full article
(This article belongs to the Special Issue Insect Transcriptomics)
►▼ Show Figures

Graphical abstract

12 pages, 1251 KB  
Article
Alternative Characterizations of Methyl Lucidone-Responsive Differentially Expressed Genes in Drosophila melanogaster Using DEG-by-Index Ratio Transformation
by Sang Woon Shin, Ji Ae Kim, Jun Hyoung Jeon, Kunhyang Park, SooJin Lee and Hyun-Woo Oh
Insects 2025, 16(9), 898; https://doi.org/10.3390/insects16090898 - 27 Aug 2025
Viewed by 639
Abstract
Identifying robust differentially expressed genes (DEGs) in RNA-Seq data remains challenging under variable experimental conditions. To address this, we performed five independent RNA-Seq experiments using Drosophila melanogaster larvae treated with methyl lucidone—a putative juvenile hormone disruptor—and compared conventional normalization methods (relative log expression [...] Read more.
Identifying robust differentially expressed genes (DEGs) in RNA-Seq data remains challenging under variable experimental conditions. To address this, we performed five independent RNA-Seq experiments using Drosophila melanogaster larvae treated with methyl lucidone—a putative juvenile hormone disruptor—and compared conventional normalization methods (relative log expression [RLE] via DESeq2 and trimmed mean of M-values [TMM] via edgeR) against our novel DEG-by-index ratio transformation (DiRT). DESeq2 identified two significant DEGs, while edgeR detected none; both methods showed limited validation across four additional independent experiments. In contrast, DiRT identified a distinct set of numerous DEGs with improved reproducibility and reliable validation. KEGG pathway analysis revealed that DiRT-derived DEGs were functionally enriched in pathways related to methyl lucidone detoxification, including the proteasome, drug metabolism, and xenobiotic metabolism mediated by cytochrome P450 and other enzymes. Although DESeq2 and edgeR remain widely used standard methods, DiRT offers a novel complementary approach to enhance DEG characterization in RNA-Seq studies affected by experimental variability. Full article
(This article belongs to the Special Issue Insect Transcriptomics)
►▼ Show Figures

Figure 1

20 pages, 4119 KB  
Article
Insights into Lead Toxicity and Detoxification Mechanisms in the Silkworm, Bombyx mori
by Dan-Dan Bian, Yan-Xia Shi, Kai-Wen Shi, Hui-Cong Du, Bo-Ping Tang and Qiu-Ning Liu
Insects 2025, 16(7), 699; https://doi.org/10.3390/insects16070699 - 7 Jul 2025
Cited by 1 | Viewed by 1164
Abstract
Bombyx mori, a key lepidopteran model with economic importance, is highly susceptible to environmental heavy metal pollution. This study investigated the mechanisms of Pb toxicity and the associated detoxification and metabolic defense responses in silkworms, employing transcriptome sequencing, enzyme activity assays, and [...] Read more.
Bombyx mori, a key lepidopteran model with economic importance, is highly susceptible to environmental heavy metal pollution. This study investigated the mechanisms of Pb toxicity and the associated detoxification and metabolic defense responses in silkworms, employing transcriptome sequencing, enzyme activity assays, and histopathological analysis. Pb exposure caused significant histopathological changes and apoptosis in the fat body, marked by structural disorganization, swollen adipocytes, and degraded extracellular matrix. Molecular analysis showed activation of antioxidant defenses, with superoxide dismutase (SOD) and catalase (CAT) activities significantly elevated (p < 0.05), while peroxidase (POD) activity declined (p < 0.05). Levels of malondialdehyde (MDA) and glutathione (GSH) also decreased. In detoxification responses, carboxylesterase (CarE) activity was reduced, whereas cytochrome P450 (P450) and glutathione S-transferase (GST) activities increased (p < 0.05). Transcriptome sequencing revealed 1,418 differentially expressed genes (DEGs), with notable upregulation of key detoxification genes (p < 0.05), including six cytochrome P450s (CYPs), five uridine diphosphate-glycosyltransferases (UGTs), three glutathione S-transferases (GSTs), and six ATP-binding cassette transporters (ABCs). KEGG enrichment analysis highlighted the involvement of these DEGs in drug metabolism, glutathione metabolism, and ABC transporter pathways (p < 0.05). Functional validation showed that knocking down Cap ‘n’ Collar C (CncC) significantly suppressed key detoxification genes (CYP18A1, CYP332A1, GSTd3, GSTt1, UGT33D8; p < 0.05). qRT-PCR and Western blot analyses confirmed that the Caspase-3 pathway mediates Pb-induced apoptosis, with increased cleaved Caspase-3 and Caspase-4 levels following CncC silencing. Overall, our findings elucidate the mechanisms of Pb toxicity in silkworms and identify CncC as a critical regulator of detoxification and defense against heavy metal stress in lepidopteran insects. Full article
(This article belongs to the Special Issue Insect Transcriptomics)
►▼ Show Figures

Figure 1

16 pages, 7509 KB  
Article
Transcriptomic Analysis of Venom Secretion in Achelura yunnanensis: Lipid Metabolism, Redox Reactions, and Structural Adaptations
by Ping Liu, Hui-Qin Zhu, Si-Ming Wang, Yu-Qian Wang, Zhen-Yuan Ruan, Lu Qiao, Xing-Xing Wu, Qing-Hua Yan, Ya-Ping Lu, Bing Bai and Wei-Feng Ding
Insects 2025, 16(6), 588; https://doi.org/10.3390/insects16060588 - 3 Jun 2025
Viewed by 737
Abstract
As a key pest damaging urban greenery in Yunnan, China, Achelura yunnanensis larvae secrete venom for defense, yet the molecular basis of this process remains poorly understood. This study aimed to uncover the molecular mechanisms of venom secretion by comparing the dorsal epidermis [...] Read more.
As a key pest damaging urban greenery in Yunnan, China, Achelura yunnanensis larvae secrete venom for defense, yet the molecular basis of this process remains poorly understood. This study aimed to uncover the molecular mechanisms of venom secretion by comparing the dorsal epidermis tissue (LDET) with the larval proleg tissue (LP). We performed transcriptomic analysis using RNA sequencing to identify differentially expressed genes between LDET and LP (10 biological replicates per tissue type), followed by functional enrichment and gene expression correlation analyses to explore tissue-specific characteristics. LDET exhibited significant upregulation of pathways related to lipid metabolism, redox reactions, and surface protective structure formation, suggesting their roles in venom stabilization, activation, and safe secretion. Conversely, genes linked to non-venom-related functions, such as extracellular matrix organization and epidermal development, were downregulated in LDET, indicating resource reallocation toward venom production. These findings reveal a multi-component mechanism in LDET that supports venom secretion through metabolic and structural adaptations, with lipid metabolism genes constituting 18.3% of total differentially expressed genes, highlighting evolutionary trade-offs in insect defense. This study provides new insights into insect venom secretion and offers potential targets for pest control strategies. Full article
(This article belongs to the Special Issue Insect Transcriptomics)
►▼ Show Figures

Figure 1

Show export options expand_more Show export options expand_less
Select all
Export citation of selected articles as:
 
Displaying articles 1-8
Back to TopTop