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 May 2024) | Viewed by 1349

Special Issue Editors

College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China
Interests: insect–pathogen/parasite interaction; insect immune response; omics of insects and pathogens/parasites

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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
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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

Published Papers (3 papers)

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Research

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
Viewed by 258
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
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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
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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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