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Zang H, Guo S, Dong S, Song Y, Li K, Fan X, Qiu J, Zheng Y, Jiang H, Wu Y, Lü Y, Chen D, Guo R. Construction of a Full-Length Transcriptome of Western Honeybee Midgut Tissue and Improved Genome Annotation. Genes (Basel) 2024; 15:728. [PMID: 38927663 DOI: 10.3390/genes15060728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 05/22/2024] [Accepted: 05/26/2024] [Indexed: 06/28/2024] Open
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 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.
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Affiliation(s)
- He Zang
- College of Bee Science and Biomedicine, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- National & Local United Engineering Laboratory of Natural Biotoxin, Fuzhou 350002, China
- Apitherapy Research Institute of Fujian Province, Fuzhou 350002, China
| | - Sijia Guo
- College of Bee Science and Biomedicine, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Shunan Dong
- College of Bee Science and Biomedicine, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yuxuan Song
- College of Bee Science and Biomedicine, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Kunze Li
- College of Bee Science and Biomedicine, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xiaoxue Fan
- College of Bee Science and Biomedicine, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- National & Local United Engineering Laboratory of Natural Biotoxin, Fuzhou 350002, China
- Apitherapy Research Institute of Fujian Province, Fuzhou 350002, China
| | - Jianfeng Qiu
- College of Bee Science and Biomedicine, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- National & Local United Engineering Laboratory of Natural Biotoxin, Fuzhou 350002, China
- Apitherapy Research Institute of Fujian Province, Fuzhou 350002, China
| | - Yidi Zheng
- College of Bee Science and Biomedicine, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Haibin Jiang
- Apiculture Science Institute of Jilin Province, Jilin 132000, China
| | - Ying Wu
- Apiculture Science Institute of Jilin Province, Jilin 132000, China
| | - Yang Lü
- Mudanjiang Branch of Heilongjiang Academy of Agricultural Sciences, Mudanjiang 157000, China
| | - Dafu Chen
- College of Bee Science and Biomedicine, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- National & Local United Engineering Laboratory of Natural Biotoxin, Fuzhou 350002, China
- Apitherapy Research Institute of Fujian Province, Fuzhou 350002, China
| | - Rui Guo
- College of Bee Science and Biomedicine, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- National & Local United Engineering Laboratory of Natural Biotoxin, Fuzhou 350002, China
- Apitherapy Research Institute of Fujian Province, Fuzhou 350002, China
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Yusuf AA, Pirk CWW, Buttstedt A. Expression of honey bee (Apis mellifera) sterol homeostasis genes in food jelly producing glands of workers. JOURNAL OF EXPERIMENTAL ZOOLOGY. PART A, ECOLOGICAL AND INTEGRATIVE PHYSIOLOGY 2024; 341:627-641. [PMID: 38567629 DOI: 10.1002/jez.2813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 03/15/2024] [Accepted: 03/19/2024] [Indexed: 04/04/2024]
Abstract
Adult workers of Western honey bees (Apis mellifera L.) acquire sterols from their pollen diet. These food sterols are transported by the hemolymph to peripheral tissues such as the mandibular and the hypopharyngeal glands in the worker bees' heads that secrete food jelly which is fed to developing larvae. As sterols are obligatory components of biological membranes and essential precursors for molting hormone synthesis in insects, they are indispensable to normal larval development. Thus, the study of sterol delivery to larvae is important for a full understanding of honey bee larval nutrition and development. Whereas hypopharyngeal glands only require sterols for their membrane integrity, mandibular glands add sterols, primarily 24-methylenecholesterol, to its secretion. For this, sterols must be transported through the glandular epithelial cells. We have analyzed for the first time in A. mellifera the expression of genes which are involved in intracellular movement of sterols. Mandibular and hypopharyngeal glands were dissected from newly emerged bees, 6-day-old nurse bees that feed larvae and 26-day-old forager bees. The expression of seven genes involved in intracellular sterol metabolism was measured with quantitative real-time PCR. Relative transcript abundance of sterol metabolism genes was significantly influenced by the age of workers and specific genes but not by gland type. Newly emerged bees had significantly more transcripts for six out of seven genes than older bees indicating that the bulk of the proteins needed for sterol metabolism are produced directly after emergence.
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Affiliation(s)
- Abdullahi A Yusuf
- Social Insects Research Group, Department of Zoology and Entomology, University of Pretoria, Pretoria, South Africa
| | - Christian W W Pirk
- Social Insects Research Group, Department of Zoology and Entomology, University of Pretoria, Pretoria, South Africa
| | - Anja Buttstedt
- Social Insects Research Group, Department of Zoology and Entomology, University of Pretoria, Pretoria, South Africa
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3
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Zhang B, Zhang C, Zhang J, Lu S, Zhao H, Jiang Y, Ma W. Regulatory roles of long non-coding RNAs in short-term heat stress in adult worker bees. BMC Genomics 2024; 25:506. [PMID: 38778290 PMCID: PMC11110378 DOI: 10.1186/s12864-024-10399-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 05/09/2024] [Indexed: 05/25/2024] Open
Abstract
Long non-coding RNAs (lncRNAs) are crucial modulators of post-transcriptional gene expression regulation, cell fate determination, and disease development. However, lncRNA functions during short-term heat stress in adult worker bees are poorly understood. Here, we performed deep sequencing and bioinformatic analyses of honeybee lncRNAs. RNA interference was performed by using siRNA targeting the most highly expressed lncRNA. The silencing effect on lncRNA and the relative expression levels of seven heat shock protein (HSP) genes, were subsequently examined. Overall, 7,842 lncRNAs and 115 differentially expressed lncRNAs (DELs) were identified in adult worker bees following heat stress exposure. Structural analysis revealed that the overall expression abundance, length of transcripts, exon number, and open reading frames of lncRNAs were lower than those of mRNAs. GO analysis revealed that the target genes were mainly involved in "metabolism," "protein folding," "response to stress," and "signal transduction" pathways. KEGG analysis indicated that the "protein processing in endoplasmic reticulum" and "longevity regulating pathway-multiple species" pathways were most enriched. Quantitative real-time polymerase chain reaction (qRT-PCR) detection of the selected DELs confirmed the reliability of the sequencing data. Moreover, the siRNA experiment indicated that feeding siRNA yielded a silencing efficiency of 77.51% for lncRNA MSTRG.9645.5. Upon silencing this lncRNA, the expression levels of three HSP genes were significantly downregulated (p < 0.05), whereas those of three other HSP genes were significantly upregulated (p < 0.05). Our results provide a new perspective for understanding the regulatory mechanisms of lncRNAs in adult worker bees under short-term heat stress.
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Affiliation(s)
- Bing Zhang
- College of Animal Science, Shanxi Agricultural University, Jinzhong, Shanxi, China
| | - Chaoying Zhang
- College of Animal Science, Shanxi Agricultural University, Jinzhong, Shanxi, China
| | - Jiangchao Zhang
- College of Animal Science, Shanxi Agricultural University, Jinzhong, Shanxi, China
| | - Surong Lu
- College of Animal Science, Shanxi Agricultural University, Jinzhong, Shanxi, China
| | - Huiting Zhao
- College of Life Sciences, Shanxi Agricultural University, Jinzhong, Shanxi, China
| | - Yusuo Jiang
- College of Animal Science, Shanxi Agricultural University, Jinzhong, Shanxi, China
| | - Weihua Ma
- College of Horticulture, Shanxi Agricultural University, Taiyuan, Shanxi, China.
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Stuart SH, Ahmed ACC, Kilikevicius L, Robinson GE. Effects of microRNA-305 knockdown on brain gene expression associated with division of labor in honey bee colonies (Apis mellifera). J Exp Biol 2024; 227:jeb246785. [PMID: 38517067 PMCID: PMC11112348 DOI: 10.1242/jeb.246785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Accepted: 03/13/2024] [Indexed: 03/23/2024]
Abstract
Division of labor in honey bee colonies is based on the behavioral maturation of adult workers that involves a transition from working in the hive to foraging. This behavioral maturation is associated with distinct task-related transcriptomic profiles in the brain and abdominal fat body that are related to multiple regulatory factors including juvenile hormone (JH) and queen mandibular pheromone (QMP). A prominent physiological feature associated with behavioral maturation is a loss of abdominal lipid mass as bees transition to foraging. We used transcriptomic and physiological analyses to study whether microRNAs (miRNAs) are involved in the regulation of division of labor. We first identified two miRNAs that showed patterns of expression associated with behavioral maturation, ame-miR-305-5p and ame-miR-375-3p. We then downregulated the expression of these two miRNAs with sequence-specific antagomirs. Neither ame-miR-305-5p nor ame-miR-375-3p knockdown in the abdomen affected abdominal lipid mass on their own. Similarly, knockdown of ame-miR-305-5p in combination with JH or QMP also did not affect lipid mass. By contrast, ame-miR-305-5p knockdown in the abdomen caused substantial changes in gene expression in the brain. Brain gene expression changes included genes encoding transcription factors previously implicated in behavioral maturation. The results of these functional genomic experiments extend previous correlative associations of microRNAs with honey bee division of labor and point to specific roles for ame-miR-305-5p.
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Affiliation(s)
- Sarai H. Stuart
- Program in Ecology, Evolution, and Conservation Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Amy C. Cash Ahmed
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Laura Kilikevicius
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Gene E. Robinson
- Program in Ecology, Evolution, and Conservation Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
- Neuroscience Program, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
- Department of Entomology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
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5
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Mukogawa B, Nieh JC. The Varroa paradox: infestation levels and hygienic behavior in feral scutellata-hybrid and managed Apis mellifera ligustica honey bees. Sci Rep 2024; 14:1148. [PMID: 38212601 PMCID: PMC10784517 DOI: 10.1038/s41598-023-51071-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 12/30/2023] [Indexed: 01/13/2024] Open
Abstract
The Varroa destructor mite is a parasitic threat to managed and feral honey bee colonies around the world. Beekeepers use miticides to eliminate Varroa in commercial hives, but these chemicals can diminish bee health and increase miticide resistance. In contrast, feral honey bees have developed multiple ways to counteract mites without chemical treatment. We compared mite levels, grooming habits, and mite-biting behavior between feral Africanized honey bees (genomically verified Apis mellifera scutellata hybrids) and managed Italian honey bees (A. mellifera ligustica). Surprisingly, there was no difference in mite infestation levels between scutellata-hybrids and managed bees over one year despite the regular use of miticides in managed colonies. We also found no differences in the social immunity responses of the two groups, as measured by their hygienic habits (through worker brood pin-kill assays), self-grooming, and mite-biting behavior. However, we provide the first report that both scutellata-hybrids and managed honey bees bite off mite chemosensory forelegs, which the mites use to locate brood cells for reproduction, to a significantly greater degree than other legs (a twofold greater reduction in foreleg length relative to the most anterior legs). Such biting may impair mite reproduction.
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Affiliation(s)
- Brandon Mukogawa
- Department of Ecology, Behavior, and Evolution, School of Biological Sciences, University of California San Diego, 9500 Gilman Dr. MC 0116, La Jolla, CA, 92093, USA.
| | - James C Nieh
- Department of Ecology, Behavior, and Evolution, School of Biological Sciences, University of California San Diego, 9500 Gilman Dr. MC 0116, La Jolla, CA, 92093, USA
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Xu Y, Ma L, Liu S, Liang Y, Liu Q, He Z, Tian L, Duan Y, Cai W, Li H, Song F. Chromosome-level genome of the poultry shaft louse Menopon gallinae provides insight into the host-switching and adaptive evolution of parasitic lice. Gigascience 2024; 13:giae004. [PMID: 38372702 PMCID: PMC10904027 DOI: 10.1093/gigascience/giae004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 11/09/2023] [Accepted: 01/16/2024] [Indexed: 02/20/2024] Open
Abstract
BACKGROUND Lice (Psocodea: Phthiraptera) are one important group of parasites that infects birds and mammals. It is believed that the ancestor of parasitic lice originated on the ancient avian host, and ancient mammals acquired these parasites via host-switching from birds. Here we present the first chromosome-level genome of Menopon gallinae in Amblycera (earliest diverging lineage of parasitic lice). We explore the transition of louse host-switching from birds to mammals at the genomic level by identifying numerous idiosyncratic genomic variations. RESULTS The assembled genome is 155 Mb in length, with a contig N50 of 27.42 Mb. Hi-C scaffolding assigned 97% of the bases to 5 chromosomes. The genome of M. gallinae retains a basal insect repertoire of 11,950 protein-coding genes. By comparing the genomes of lice to those of multiple representative insects in other orders, we discovered that gene families of digestion, detoxification, and immunity-related are generally conserved between bird lice and mammal lice, while mammal lice have undergone a significant reduction in genes related to chemosensory systems and temperature. This suggests that mammal lice have lost some of these genes through the adaption to environment and temperatures after host-switching. Furthermore, 7 genes related to hematophagy were positively selected in mammal lice, suggesting their involvement in the hematophagous behavior. CONCLUSIONS Our high-quality genome of M. gallinae provides a valuable resource for comparative genomic research in Phthiraptera and facilitates further studies on adaptive evolution of host-switching within parasitic lice.
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Affiliation(s)
- Ye Xu
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Ling Ma
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Shanlin Liu
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Yanxin Liang
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Qiaoqiao Liu
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Zhixin He
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Li Tian
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Yuange Duan
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Wanzhi Cai
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Hu Li
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Fan Song
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
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Nachtigall PG, Durham AM, Rokyta DR, Junqueira-de-Azevedo ILM. ToxCodAn-Genome: an automated pipeline for toxin-gene annotation in genome assembly of venomous lineages. Gigascience 2024; 13:giad116. [PMID: 38241143 PMCID: PMC10797961 DOI: 10.1093/gigascience/giad116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 10/19/2023] [Accepted: 12/18/2023] [Indexed: 01/21/2024] Open
Abstract
BACKGROUND The rapid development of sequencing technologies resulted in a wide expansion of genomics studies using venomous lineages. This facilitated research focusing on understanding the evolution of adaptive traits and the search for novel compounds that can be applied in agriculture and medicine. However, the toxin annotation of genomes is a laborious and time-consuming task, and no consensus pipeline is currently available. No computational tool currently exists to address the challenges specific to toxin annotation and to ensure the reproducibility of the process. RESULTS Here, we present ToxCodAn-Genome, the first software designed to perform automated toxin annotation in genomes of venomous lineages. This pipeline was designed to retrieve the full-length coding sequences of toxins and to allow the detection of novel truncated paralogs and pseudogenes. We tested ToxCodAn-Genome using 12 genomes of venomous lineages and achieved high performance on recovering their current toxin annotations. This tool can be easily customized to allow improvements in the final toxin annotation set and can be expanded to virtually any venomous lineage. ToxCodAn-Genome is fast, allowing it to run on any personal computer, but it can also be executed in multicore mode, taking advantage of large high-performance servers. In addition, we provide a guide to direct future research in the venomics field to ensure a confident toxin annotation in the genome being studied. As a case study, we sequenced and annotated the toxin repertoire of Bothrops alternatus, which may facilitate future evolutionary and biomedical studies using vipers as models. CONCLUSIONS ToxCodAn-Genome is suitable to perform toxin annotation in the genome of venomous species and may help to improve the reproducibility of further studies. ToxCodAn-Genome and the guide are freely available at https://github.com/pedronachtigall/ToxCodAn-Genome.
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Affiliation(s)
- Pedro G Nachtigall
- Laboratório de Toxinologia Aplicada, CeTICS, Instituto Butantan, São Paulo, 05503-900 SP, Brazil
- Department of Biological Science, Florida State University, Tallahassee, 32306-4295 FL, USA
| | - Alan M Durham
- Departamento de Ciência da Computação, Instituto de Matemática e Estatística, Universidade de São Paulo (USP), São Paulo, 05508-090 SP, Brazil
| | - Darin R Rokyta
- Department of Biological Science, Florida State University, Tallahassee, 32306-4295 FL, USA
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Feldmeyer B, Bornberg-Bauer E, Dohmen E, Fouks B, Heckenhauer J, Huylmans AK, Jones ARC, Stolle E, Harrison MC. Comparative Evolutionary Genomics in Insects. Methods Mol Biol 2024; 2802:473-514. [PMID: 38819569 DOI: 10.1007/978-1-0716-3838-5_16] [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] [Indexed: 06/01/2024]
Abstract
Genome sequencing quality, in terms of both read length and accuracy, is constantly improving. By combining long-read sequencing technologies with various scaffolding techniques, chromosome-level genome assemblies are now achievable at an affordable price for non-model organisms. Insects represent an exciting taxon for studying the genomic underpinnings of evolutionary innovations, due to ancient origins, immense species-richness, and broad phenotypic diversity. Here we summarize some of the most important methods for carrying out a comparative genomics study on insects. We describe available tools and offer concrete tips on all stages of such an endeavor from DNA extraction through genome sequencing, annotation, and several evolutionary analyses. Along the way we describe important insect-specific aspects, such as DNA extraction difficulties or gene families that are particularly difficult to annotate, and offer solutions. We describe results from several examples of comparative genomics analyses on insects to illustrate the fascinating questions that can now be addressed in this new age of genomics research.
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Affiliation(s)
- Barbara Feldmeyer
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Molecular Ecology, Frankfurt, Germany
| | - Erich Bornberg-Bauer
- Institute for Evolution and Biodiversity, University of Münster, Münster, Germany
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Elias Dohmen
- Institute for Evolution and Biodiversity, University of Münster, Münster, Germany
| | - Bertrand Fouks
- Institute for Evolution and Biodiversity, University of Münster, Münster, Germany
| | - Jacqueline Heckenhauer
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt, Germany
- Department of Terrestrial Zoology, Senckenberg Research Institute and Natural History Museum Frankfurt, Frankfurt, Germany
| | - Ann Kathrin Huylmans
- Institute of Organismic and Molecular Evolution, Johannes Gutenberg University, Mainz, Germany
| | - Alun R C Jones
- Institute for Evolution and Biodiversity, University of Münster, Münster, Germany
| | - Eckart Stolle
- Museum Koenig, Leibniz Institute for the Analysis of Biodiversity Change (LIB), Bonn, Germany
| | - Mark C Harrison
- Institute for Evolution and Biodiversity, University of Münster, Münster, Germany.
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9
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Salvatore G, Chibani Bahi Amar A, Canale-Tabet K, Fridi R, Tabet Aoul N, Saci S, Labarthe E, Palombo V, D'Andrea M, Vignal A, Faux P. Natural clines and human management impact the genetic structure of Algerian honey bee populations. Genet Sel Evol 2023; 55:94. [PMID: 38114899 PMCID: PMC10729559 DOI: 10.1186/s12711-023-00864-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 12/04/2023] [Indexed: 12/21/2023] Open
Abstract
BACKGROUND The Algerian honey bee population is composed of two described subspecies A. m. intermissa and A. m. sahariensis, of which little is known regarding population genomics, both in terms of genetic differentiation and of possible contamination by exogenous stock. Moreover, the phenotypic differences between the two subspecies are expected to translate into genetic differences and possible adaptation to heat and drought in A. m. sahariensis. To shed light on the structure of this population and to integrate these two subspecies in the growing dataset of available haploid drone sequences, we performed whole-genome sequencing of 151 haploid drones. RESULTS Integrated analysis of our drone sequences with a similar dataset of European reference populations did not detect any significant admixture in the Algerian honey bees. Interestingly, most of the genetic variation was not found between the A. m. intermissa and A. m. sahariensis subspecies; instead, two main genetic clusters were found along an East-West axis. We found that the correlation between genetic and geographic distances was higher in the Western cluster and that close-family relationships were mostly detected in the Eastern cluster, sometimes at long distances. In addition, we selected a panel of 96 ancestry-informative markers to decide whether a sampled bee is Algerian or not, and tested this panel in simulated cases of admixture. CONCLUSIONS The differences between the two main genetic clusters suggest differential breeding management between eastern and western Algeria, with greater exchange of genetic material over long distances in the east. The lack of detected admixture events suggests that, unlike what is seen in many places worldwide, imports of queens from foreign countries do not seem to have occurred on a large scale in Algeria, a finding that is relevant for conservation purposes. In addition, the proposed panel of 96 markers was found effective to distinguish Algerian from European honey bees. Therefore, we conclude that applying this approach to other taxa is promising, in particular when genetic differentiation is difficult to capture.
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Affiliation(s)
- Giovanna Salvatore
- Department of Agricultural, Environmental and Food Sciences, University of Molise, Via De Sanctis Snc, 86100, Campobasso, Italy.
- GenPhySE, Université de Toulouse, INRAE, INPT, INP-ENVT, 31326, Castanet-Tolosan, France.
| | - Amira Chibani Bahi Amar
- Laboratoire de Génétique Moléculaire et Cellulaire (LGMC), Département de Génétique Moléculaire Appliquée, Université des Sciences et de la Technologie d'Oran Mohamed Boudiaf, USTOMB, BP 1505, El M'naouer, 31000, Oran, Algeria
| | - Kamila Canale-Tabet
- GenPhySE, Université de Toulouse, INRAE, INPT, INP-ENVT, 31326, Castanet-Tolosan, France
| | - Riad Fridi
- Laboratoire de Génétique Moléculaire et Cellulaire (LGMC), Département de Génétique Moléculaire Appliquée, Université des Sciences et de la Technologie d'Oran Mohamed Boudiaf, USTOMB, BP 1505, El M'naouer, 31000, Oran, Algeria
| | - Nacera Tabet Aoul
- Laboratoire de Génétique Moléculaire et Cellulaire (LGMC), Département de Génétique Moléculaire Appliquée, Université des Sciences et de la Technologie d'Oran Mohamed Boudiaf, USTOMB, BP 1505, El M'naouer, 31000, Oran, Algeria
- Department of Biotechnology, Faculty SNV, University of Oran1 Ahmed Ben Bella, Oran, Algeria
| | - Soumia Saci
- National Institute of Agronomic Research of Algeria (INRAA), El Harrach, Alger, Algeria
| | - Emmanuelle Labarthe
- GenPhySE, Université de Toulouse, INRAE, INPT, INP-ENVT, 31326, Castanet-Tolosan, France
| | - Valentino Palombo
- Department of Agricultural, Environmental and Food Sciences, University of Molise, Via De Sanctis Snc, 86100, Campobasso, Italy
| | - Mariasilvia D'Andrea
- Department of Agricultural, Environmental and Food Sciences, University of Molise, Via De Sanctis Snc, 86100, Campobasso, Italy
| | - Alain Vignal
- GenPhySE, Université de Toulouse, INRAE, INPT, INP-ENVT, 31326, Castanet-Tolosan, France
| | - Pierre Faux
- GenPhySE, Université de Toulouse, INRAE, INPT, INP-ENVT, 31326, Castanet-Tolosan, France.
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10
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Lu RX, Bhatia S, Simone-Finstrom M, Rueppell O. Quantitative trait loci mapping for survival of virus infection and virus levels in honey bees. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2023; 116:105534. [PMID: 38036199 DOI: 10.1016/j.meegid.2023.105534] [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: 09/22/2023] [Revised: 11/22/2023] [Accepted: 11/25/2023] [Indexed: 12/02/2023]
Abstract
Israeli acute paralysis virus (IAPV) is a highly virulent, Varroa-vectored virus that is of global concern for honey bee health. Little is known about the genetic basis of honey bees to withstand infection with IAPV or other viruses. We set up and analyzed a backcross between preselected honey bee colonies of low and high IAPV susceptibility to identify quantitative trait loci (QTL) associated with IAPV susceptibility. Experimentally inoculated adult worker bees were surveyed for survival and selectively sampled for QTL analysis based on SNPs identified by whole-genome resequencing and composite interval mapping. Additionally, natural titers of other viruses were quantified in the abdomen of these workers via qPCR and also used for QTL mapping. In addition to the full dataset, we analyzed distinct subpopulations of susceptible and non-susceptible workers separately. These subpopulations are distinguished by a single, suggestive QTL on chromosome 6, but we identified numerous other QTL for different abdominal virus titers, particularly in the subpopulation that was not susceptible to IAPV. The pronounced QTL differences between the susceptible and non-susceptible subpopulations indicate either an interaction between IAPV infection and the bees' interaction with other viruses or heterogeneity among workers of a single cohort that manifests itself as IAPV susceptibility and results in distinct subgroups that differ in their interaction with other viruses. Furthermore, our results indicate that low susceptibility of honey bees to viruses can be caused by both, virus tolerance and virus resistance. QTL were partially overlapping among different viruses, indicating a mixture of shared and specific processes that control viruses. Some functional candidate genes are located in the QTL intervals, but their genomic co-localization with numerous genes of unknown function delegates any definite characterization of the underlying molecular mechanisms to future studies.
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Affiliation(s)
- Robert X Lu
- Department of Biological Sciences, University of Alberta, 116 Street & 85 Avenue, Edmonton, Alberta, T6G 2E9, Canada
| | - Shilpi Bhatia
- Department of Biology, North Carolina Agricultural and Technical State University, 1601 E Market Street, Greensboro, NC 27411, USA
| | - Michael Simone-Finstrom
- USDA-ARS Honey Bee Breeding, Genetics and Physiology Research Laboratory, 1157 Ben Hur Road, Baton Rouge, LA 70820, USA
| | - Olav Rueppell
- Department of Biological Sciences, University of Alberta, 116 Street & 85 Avenue, Edmonton, Alberta, T6G 2E9, Canada; Department of Biology, University of North Carolina at Greensboro, 321 McIver Street, Greensboro, NC 27412, USA.
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Xiao X, Haas J, Nauen R. Functional orthologs of honeybee CYP6AQ1 in stingless bees degrade the butenolide insecticide flupyradifurone. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 268:115719. [PMID: 37992638 DOI: 10.1016/j.ecoenv.2023.115719] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 11/15/2023] [Accepted: 11/19/2023] [Indexed: 11/24/2023]
Abstract
Flupyradifurone (FPF), a novel butenolide insecticide binding to nicotinic acetylcholine receptors (nAChRs), has been shown to be less acutely toxic to western honey bees (Apis mellifera) than other insecticides such as neonicotinoids sharing the same target-site. A previous study revealed that this is due to enhanced oxidative metabolism of FPF, mediated by three cytochrome P450 monooxygenases (P450s), including CYP6AQ1. Therefore, we followed a toxicogenomics approach and investigated the potential role of functional CYP6AQ1 orthologs in FPF metabolism from eight different bee species, including stingless bees (Tribe: Meliponini). We conducted a phylogenetic analysis on four stingless bee species, including Frieseomelitta varia, Heterotrigona itama, Melipona quadrifasciata and Tetragonula carbonaria to identify CYP6AQ1-like functional orthologs. Three non-Meliponini, but tropical bee species, i.e., Ammobates syriacus, Euglossa dilemma and Megalopta genalis were analyzed as well. We identified candidate P450s in all (neo)tropical species with greater than 61% and 67% predicted protein sequence identities when compared to A. mellifera CYP6AQ1 and Bombus terrestris CYP6AQ26, respectively. Heterologous expression in High Five insect cells of these functional orthologs revealed a common coumarin substrate profile and a preference for the O-debenzylation of bulkier substrates. Competition assays using the fluorescent probe substrate 7-benzyloxymethoxy-4-trifluoromethylcoumarin (BOMFC) with these enzymes indicated inhibition of BOMFC metabolism by increasing concentrations of FPF. Furthermore, UPLC-MS/MS analysis revealed the capacity of all CYP6AQ1-like orthologs to metabolize FPF by hydroxylation in vitro at various levels, indicating a conserved FPF detoxification potential in different (neo)tropical bee species including Meliponini. This research, employing a toxicogenomics approach, provides important insights into the potential of stingless and other tropical bee species to detoxify FPF, and highlights the significance of investigating the detoxification mechanisms of insecticides in non-Apis bee species by molecular tools to inform risk assessment and conservation efforts.
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Affiliation(s)
- Xingzhi Xiao
- Institute of Crop Science and Resource Conservation, University of Bonn, 53115 Bonn, Germany; Bayer AG, Crop Science Division, R&D, D-40789 Monheim, Germany
| | - Julian Haas
- Bayer AG, Crop Science Division, R&D, D-40789 Monheim, Germany
| | - Ralf Nauen
- Bayer AG, Crop Science Division, R&D, D-40789 Monheim, Germany.
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12
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Zhang Y, Fan X, Zang H, Liu X, Feng P, Ye D, Zhu L, Wu Y, Jiang H, Chen D, Guo R. Novel Insights into the circRNA-Modulated Developmental Mechanism of Western Honey Bee Larval Guts. INSECTS 2023; 14:897. [PMID: 37999096 PMCID: PMC10671861 DOI: 10.3390/insects14110897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 11/10/2023] [Accepted: 11/18/2023] [Indexed: 11/25/2023]
Abstract
Circular RNAs (circRNAs) are a class of novel non-coding RNAs (ncRNAs) that play essential roles in the development and growth of vertebrates through multiple manners. However, the mechanism by which circRNAs modulate the honey bee gut development is currently poorly understood. Utilizing the transcriptome data we obtained earlier, the highly expressed circRNAs in the Apis mellifera worker 4-, 5-, and 6-day-old larval guts were analyzed, which was followed by an in-depth investigation of the expression pattern of circRNAs during the process of larval guts development and the potential regulatory roles of differentially expressed circRNAs (DEcircRNAs). In total, 1728 expressed circRNAs were detected in the A. mellifera larval guts. Among the most highly expressed 10 circRNAs, seven (novel_circ_000069, novel_circ_000027, novel_circ_000438, etc.) were shared by the 4-, 5-, and 6-day-old larval guts. In addition, 21 (46) up-regulated and 22 (27) down-regulated circRNAs were, respectively, screened in the Am4 vs. Am5 (Am5 vs. Am6) comparison groups. Additionally, nine DEcircRNAs, such as novel_circ_000340, novel_circ_000758 and novel_circ_001116, were shared by these two comparison groups. These DEcircRNAs were predicted to be transcribed from 14 and 29 parental genes; these were respectively annotated to 15 and 22 GO terms such as biological regulation and catalytic activity as well as 16 and 21 KEGG pathways such as dorsoventral axis formation and apoptosis. Moreover, a complicated competing endogenous RNA (ceRNA) network was observed; novel_circ_000838 in the Am4 vs. Am5 comparison group potentially targeted ame-miR-6000a-3p, further targeting 518 mRNAs engaged in several developmental signaling pathways (e.g., TGF-beta, hedgehog, and wnt signaling pathway) and immune pathways (e.g., phagosome, lysosome, and MAPK signaling pathway). The results demonstrated that the novel_circ_000838-ame-miR-6000a-3p axis may plays a critical regulatory part in the larval gut development and immunity. Furthermore, back-splicing sites of six randomly selected DEcircRNAs were amplified and verified by PCR; an RT-qPCR assay of these six DEcircRNAs confirmed the reliability of the used high-throughput sequencing data. Our findings provide a novel insight into the honey bee gut development and pave a way for illustration of the circRNA-modulated developmental mechanisms underlying the A. mellifera worker larval guts.
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Affiliation(s)
- Yiqiong Zhang
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.Z.); (X.F.); (H.Z.); (X.L.); (P.F.); (D.Y.); (L.Z.); (D.C.)
| | - Xiaoxue Fan
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.Z.); (X.F.); (H.Z.); (X.L.); (P.F.); (D.Y.); (L.Z.); (D.C.)
- National & Local United Engineering Laboratory of Natural Biotoxin, Fuzhou 350002, China
- Apitherapy Research Institute of Fujian Province, Fuzhou 350002, China
| | - He Zang
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.Z.); (X.F.); (H.Z.); (X.L.); (P.F.); (D.Y.); (L.Z.); (D.C.)
- National & Local United Engineering Laboratory of Natural Biotoxin, Fuzhou 350002, China
- Apitherapy Research Institute of Fujian Province, Fuzhou 350002, China
| | - Xiaoyu Liu
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.Z.); (X.F.); (H.Z.); (X.L.); (P.F.); (D.Y.); (L.Z.); (D.C.)
| | - Peilin Feng
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.Z.); (X.F.); (H.Z.); (X.L.); (P.F.); (D.Y.); (L.Z.); (D.C.)
| | - Daoyou Ye
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.Z.); (X.F.); (H.Z.); (X.L.); (P.F.); (D.Y.); (L.Z.); (D.C.)
| | - Leran Zhu
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.Z.); (X.F.); (H.Z.); (X.L.); (P.F.); (D.Y.); (L.Z.); (D.C.)
| | - Ying Wu
- Jilin Institute of Apicultural Research, Jilin 132013, China; (Y.W.); (H.J.)
| | - Haibin Jiang
- Jilin Institute of Apicultural Research, Jilin 132013, China; (Y.W.); (H.J.)
| | - Dafu Chen
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.Z.); (X.F.); (H.Z.); (X.L.); (P.F.); (D.Y.); (L.Z.); (D.C.)
- National & Local United Engineering Laboratory of Natural Biotoxin, Fuzhou 350002, China
- Apitherapy Research Institute of Fujian Province, Fuzhou 350002, China
| | - Rui Guo
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.Z.); (X.F.); (H.Z.); (X.L.); (P.F.); (D.Y.); (L.Z.); (D.C.)
- National & Local United Engineering Laboratory of Natural Biotoxin, Fuzhou 350002, China
- Apitherapy Research Institute of Fujian Province, Fuzhou 350002, China
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13
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Cornman RS. Data mining reveals tissue-specific expression and host lineage-associated forms of Apis mellifera filamentous virus. PeerJ 2023; 11:e16455. [PMID: 38025724 PMCID: PMC10655722 DOI: 10.7717/peerj.16455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 10/23/2023] [Indexed: 12/01/2023] Open
Abstract
Background Apis mellifera filamentous virus (AmFV) is a large double-stranded DNA virus of uncertain phylogenetic position that infects honey bees (Apis mellifera). Little is known about AmFV evolution or molecular aspects of infection. Accurate annotation of open-reading frames (ORFs) is challenged by weak homology to other known viruses. This study was undertaken to evaluate ORFs (including coding-frame conservation, codon bias, and purifying selection), quantify genetic variation within AmFV, identify host characteristics that covary with infection rate, and examine viral expression patterns in different tissues. Methods Short-read data were accessed from the Sequence Read Archive (SRA) of the National Center for Biotechnology Information (NCBI). Sequence reads were downloaded from accessions meeting search criteria and scanned for kmers representative of AmFV genomic sequence. Samples with kmer counts above specified thresholds were downloaded in full for mapping to reference sequences and de novo assembly. Results At least three distinct evolutionary lineages of AmFV exist. Clade 1 predominates in Europe but in the Americas and Africa it is replaced by the other clades as infection level increases in hosts. Only clade 3 was found at high relative abundance in hosts with African ancestry, whereas all clades achieved high relative abundance in bees of non-African ancestry. In Europe and Africa, clade 2 was generally detected only in low-level infections but was locally dominant in some North American samples. The geographic distribution of clade 3 was consistent with an introduction to the Americas with 'Africanized' honey bees in the 1950s. Localized genomic regions of very high nucleotide divergence in individual isolates suggest recombination with additional, as-yet unidentified AmFV lineages. A set of 155 high-confidence ORFs was annotated based on evolutionary conservation in six AmFV genome sequences representative of the three clades. Pairwise protein-level identity averaged 94.6% across ORFs (range 77.1-100%), which generally exhibited low evolutionary rates and moderate to strong codon bias. However, no robust example of positive diversifying selection on coding sequence was found in these alignments. Most of the genome was detected in RNA short-read alignments. Transcriptome assembly often yielded contigs in excess of 50 kb and containing ORFs in both orientations, and the termini of long transcripts were associated with tandem repeats. Lower levels of AmFV RNA were detected in brain tissue compared to abdominal tissue, and a distinct set of ORFs had minimal to no detectable expression in brain tissue. A scan of DNA accessions from the parasitic mite Varroa destructor was inconclusive with respect to replication in that species. Discussion Collectively, these results expand our understanding of this enigmatic virus, revealing transcriptional complexity and co-evolutionary associations with host lineage.
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14
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Yang J, Liu Y, Zhong D, Xu L, Gao H, Keasling JD, Luo X, Chou HH. Combinatorial optimization and spatial remodeling of CYPs to control product profile. Metab Eng 2023; 80:119-129. [PMID: 37703999 DOI: 10.1016/j.ymben.2023.09.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 09/07/2023] [Accepted: 09/08/2023] [Indexed: 09/15/2023]
Abstract
Activating inert substrates is a challenge in nature and synthetic chemistry, but essential for creating functionally active molecules. In this work, we used a combinatorial optimization approach to assemble cytochrome P450 monooxygenases (CYPs) and reductases (CPRs) to achieve a target product profile. By creating 110 CYP-CPR pairs and iteratively screening different pairing libraries, we demonstrated a framework for establishing a CYP network that catalyzes six oxidation reactions at three different positions of a chemical scaffold. Target product titer was improved by remodeling endoplasmic reticulum (ER) size and spatially controlling the CYPs' configuration on the ER. Out of 47 potential products that could be synthesized, 86% of the products synthesized by the optimized network was our target compound quillaic acid (QA), the aglycone backbone of many pharmaceutically important saponins, and fermentation achieved QA titer 2.23 g/L.
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Affiliation(s)
- Jiazeng Yang
- Shenzhen Key Laboratory for the Intelligent Microbial Manufacturing of Medicines, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China; CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China; Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, 518055, China
| | - Yuguang Liu
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China; Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, 518055, China
| | - Dacai Zhong
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China; Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, 518055, China
| | - Linlin Xu
- Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, 518055, China
| | - Haixin Gao
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China; Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, 518055, China
| | - Jay D Keasling
- Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, 518055, China; Joint BioEnergy Institute, Emeryville, CA, 94608, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA; Department of Chemical and Biomolecular Engineering & Department of Bioengineering, University of California, Berkeley, CA, 94720, USA; Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
| | - Xiaozhou Luo
- Shenzhen Key Laboratory for the Intelligent Microbial Manufacturing of Medicines, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China; CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China; Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, 518055, China
| | - Howard H Chou
- Shenzhen Key Laboratory for the Intelligent Microbial Manufacturing of Medicines, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China; CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China; Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, 518055, China.
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15
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Bresnahan ST, Galbraith D, Ma R, Anton K, Rangel J, Grozinger CM. Beyond conflict: Kinship theory of intragenomic conflict predicts individual variation in altruistic behaviour. Mol Ecol 2023; 32:5823-5837. [PMID: 37746895 DOI: 10.1111/mec.17145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 09/08/2023] [Accepted: 09/11/2023] [Indexed: 09/26/2023]
Abstract
Behavioural variation is essential for animals to adapt to different social and environmental conditions. The Kinship Theory of Intragenomic Conflict (KTIC) predicts that parent-specific alleles can support different behavioural strategies to maximize allele fitness. Previous studies, including in honey bees (Apis mellifera), supported predictions of the KTIC for parent-specific alleles to promote selfish behaviour. Here, we test the KTIC prediction that for altruism-promoting genes (i.e. those that promote behaviours that support the reproductive fitness of kin), the allele with the higher altruism optimum should be selected to be expressed while the other is silenced. In honey bee colonies, workers act altruistically when tending to the queen by performing a 'retinue' behaviour, distributing the queen's mandibular pheromone (QMP) throughout the hive. Workers exposed to QMP do not activate their ovaries, ensuring they care for the queen's brood instead of competing to lay unfertilized eggs. Due to the haplodiploid genetics of honey bees, the KTIC predicts that response to QMP is favoured by the maternal genome. We report evidence for parent-of-origin effects on the retinue response behaviour, ovarian development and gene expression in brains of worker honey bees exposed to QMP, consistent with the KTIC. Additionally, we show enrichment for genes with parent-of-origin expression bias within gene regulatory networks associated with variation in bees' response to QMP. Our study demonstrates that intragenomic conflict can shape diverse social behaviours and influence expression patterns of single genes as well as gene networks.
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Affiliation(s)
- Sean T Bresnahan
- Department of Entomology, Center for Pollinator Research, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
- Intercollege Graduate Degree Program in Molecular, Cellular, and Integrative Biosciences, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
| | - David Galbraith
- Department of Entomology, Center for Pollinator Research, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Rong Ma
- Department of Entomology, Center for Pollinator Research, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Kate Anton
- Department of Entomology, Center for Pollinator Research, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Juliana Rangel
- Department of Entomology, Texas A&M University, College Station, Texas, USA
| | - Christina M Grozinger
- Department of Entomology, Center for Pollinator Research, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
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Koludarov I, Velasque M, Senoner T, Timm T, Greve C, Hamadou AB, Gupta DK, Lochnit G, Heinzinger M, Vilcinskas A, Gloag R, Harpur BA, Podsiadlowski L, Rost B, Jackson TNW, Dutertre S, Stolle E, von Reumont BM. Prevalent bee venom genes evolved before the aculeate stinger and eusociality. BMC Biol 2023; 21:229. [PMID: 37867198 PMCID: PMC10591384 DOI: 10.1186/s12915-023-01656-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 06/29/2023] [Indexed: 10/24/2023] Open
Abstract
BACKGROUND Venoms, which have evolved numerous times in animals, are ideal models of convergent trait evolution. However, detailed genomic studies of toxin-encoding genes exist for only a few animal groups. The hyper-diverse hymenopteran insects are the most speciose venomous clade, but investigation of the origin of their venom genes has been largely neglected. RESULTS Utilizing a combination of genomic and proteo-transcriptomic data, we investigated the origin of 11 toxin genes in 29 published and 3 new hymenopteran genomes and compiled an up-to-date list of prevalent bee venom proteins. Observed patterns indicate that bee venom genes predominantly originate through single gene co-option with gene duplication contributing to subsequent diversification. CONCLUSIONS Most Hymenoptera venom genes are shared by all members of the clade and only melittin and the new venom protein family anthophilin1 appear unique to the bee lineage. Most venom proteins thus predate the mega-radiation of hymenopterans and the evolution of the aculeate stinger.
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Affiliation(s)
- Ivan Koludarov
- Justus Liebig University of Gießen, Institute for Insect Biotechnology, Heinrich-Buff-Ring 58, 35392, Giessen, Germany.
- Department of Informatics, Bioinformatics and Computational Biology, i12, Technical University of Munich, Boltzmannstr. 3, Garching, 85748, Munich, Germany.
| | - Mariana Velasque
- Genomics & Regulatory Systems Unit, Okinawa Institute of Science & Technology, Tancha, Okinawa, 1919, Japan
| | - Tobias Senoner
- Department of Informatics, Bioinformatics and Computational Biology, i12, Technical University of Munich, Boltzmannstr. 3, Garching, 85748, Munich, Germany
| | - Thomas Timm
- Protein Analytics, Institute of Biochemistry, Justus Liebig University, Friedrichstrasse 24, 35392, Giessen, Germany
| | - Carola Greve
- LOEWE Centre for Translational Biodiversity Genomics (TBG), Senckenberganlage 25, 60325, Frankfurt, Germany
| | - Alexander Ben Hamadou
- LOEWE Centre for Translational Biodiversity Genomics (TBG), Senckenberganlage 25, 60325, Frankfurt, Germany
| | - Deepak Kumar Gupta
- LOEWE Centre for Translational Biodiversity Genomics (TBG), Senckenberganlage 25, 60325, Frankfurt, Germany
| | - Günter Lochnit
- Protein Analytics, Institute of Biochemistry, Justus Liebig University, Friedrichstrasse 24, 35392, Giessen, Germany
| | - Michael Heinzinger
- Department of Informatics, Bioinformatics and Computational Biology, i12, Technical University of Munich, Boltzmannstr. 3, Garching, 85748, Munich, Germany
| | - Andreas Vilcinskas
- Justus Liebig University of Gießen, Institute for Insect Biotechnology, Heinrich-Buff-Ring 58, 35392, Giessen, Germany
- Fraunhofer Institute for Molecular Biology and Applied Ecology, Department of Bioresources, Ohlebergsweg 12, 35392, Giessen, Germany
| | - Rosalyn Gloag
- Rosalyn Gloag - School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Brock A Harpur
- Brock A. Harpur - Department of Entomology, Purdue University, 901 W. State Street, West Lafayette, IN, 47907, USA
| | - Lars Podsiadlowski
- Leibniz Institute for the Analysis of Biodiversity Change, Zoological Research Museum Alexander Koenig, Centre of Molecular Biodiversity Research, Adenauerallee 160, 53113, Bonn, Germany
| | - Burkhard Rost
- Department of Informatics, Bioinformatics and Computational Biology, i12, Technical University of Munich, Boltzmannstr. 3, Garching, 85748, Munich, Germany
| | - Timothy N W Jackson
- Australian Venom Research Unit, Department of Biochemistry and Pharmacology, University of Melbourne, Grattan Street, Parkville, Viktoria, 3010, Australia
| | | | - Eckart Stolle
- Leibniz Institute for the Analysis of Biodiversity Change, Zoological Research Museum Alexander Koenig, Centre of Molecular Biodiversity Research, Adenauerallee 160, 53113, Bonn, Germany
| | - Björn M von Reumont
- LOEWE Centre for Translational Biodiversity Genomics (TBG), Senckenberganlage 25, 60325, Frankfurt, Germany.
- Faculty of Biological Sciences, Group of Applied Bioinformatics, Goethe University Frankfurt, Max-Von-Laue Str. 13, 60438, Frankfurt, Germany.
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17
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Vertacnik KL, Herrig DK, Godfrey RK, Hill T, Geib SM, Unckless RL, Nelson DR, Linnen CR. Evolution of five environmentally responsive gene families in a pine-feeding sawfly, Neodiprion lecontei (Hymenoptera: Diprionidae). Ecol Evol 2023; 13:e10506. [PMID: 37791292 PMCID: PMC10542623 DOI: 10.1002/ece3.10506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Revised: 07/17/2023] [Accepted: 07/21/2023] [Indexed: 10/05/2023] Open
Abstract
A central goal in evolutionary biology is to determine the predictability of adaptive genetic changes. Despite many documented cases of convergent evolution at individual loci, little is known about the repeatability of gene family expansions and contractions. To address this void, we examined gene family evolution in the redheaded pine sawfly Neodiprion lecontei, a noneusocial hymenopteran and exemplar of a pine-specialized lineage evolved from angiosperm-feeding ancestors. After assembling and annotating a draft genome, we manually annotated multiple gene families with chemosensory, detoxification, or immunity functions before characterizing their genomic distributions and molecular evolution. We find evidence of recent expansions of bitter gustatory receptor, clan 3 cytochrome P450, olfactory receptor, and antimicrobial peptide subfamilies, with strong evidence of positive selection among paralogs in a clade of gustatory receptors possibly involved in the detection of bitter compounds. In contrast, these gene families had little evidence of recent contraction via pseudogenization. Overall, our results are consistent with the hypothesis that in response to novel selection pressures, gene families that mediate ecological interactions may expand and contract predictably. Testing this hypothesis will require the comparative analysis of high-quality annotation data from phylogenetically and ecologically diverse insect species and functionally diverse gene families. To this end, increasing sampling in under-sampled hymenopteran lineages and environmentally responsive gene families and standardizing manual annotation methods should be prioritized.
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Affiliation(s)
- Kim L. Vertacnik
- Department of EntomologyUniversity of KentuckyLexingtonKentuckyUSA
| | | | - R. Keating Godfrey
- McGuire Center for Lepidoptera and Biodiversity, University of FloridaGainesvilleFloridaUSA
| | - Tom Hill
- National Institute of Allergy and Infectious DiseasesBethesdaMarylandUSA
| | - Scott M. Geib
- Tropical Crop and Commodity Protection Research UnitUnited States Department of Agriculture: Agriculture Research Service Pacific Basin Agricultural Research CenterHiloHawaiiUSA
| | - Robert L. Unckless
- Department of Molecular BiosciencesUniversity of KansasLawrenceKansasUSA
| | - David R. Nelson
- Department of Microbiology, Immunology and BiochemistryUniversity of Tennessee Health Science CenterMemphisTennesseeUSA
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18
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Saarman NP, Son JH, Zhao H, Cosme LV, Kong Y, Li M, Wang S, Weiss BL, Echodu R, Opiro R, Aksoy S, Caccone A. Genomic evidence of sex chromosome aneuploidy and infection-associated genotypes in the tsetse fly Glossina fuscipes, the major vector of African trypanosomiasis in Uganda. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2023; 114:105501. [PMID: 37709241 PMCID: PMC10593118 DOI: 10.1016/j.meegid.2023.105501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 09/07/2023] [Accepted: 09/11/2023] [Indexed: 09/16/2023]
Abstract
The primary vector of the trypanosome parasite causing human and animal African trypanosomiasis in Uganda is the riverine tsetse fly Glossina fuscipes fuscipes (Gff). Our study improved the Gff genome assembly with whole genome 10× Chromium sequencing of a lab reared pupae, identified autosomal versus sex-chromosomal regions of the genome with ddRAD-seq data from 627 field caught Gff, and identified SNPs associated with trypanosome infection with genome-wide association (GWA) analysis in a subset of 351 flies. Results from 10× Chromium sequencing greatly improved Gff genome assembly metrics and assigned a full third of the genome to the sex chromosome. Results from ddRAD-seq suggested possible sex-chromosome aneuploidy in Gff and identified a single autosomal SNP to be highly associated with trypanosome infection. The top associated SNP was ∼1100 bp upstream of the gene lecithin cholesterol acyltransferase (LCAT), an important component of the molecular pathway that initiates trypanosome lysis and protection in mammals. Results suggest that there may be naturally occurring genetic variation in Gff in genomic regions in linkage disequilibrium with LCAT that can protect against trypanosome infection, thereby paving the way for targeted research into novel vector control strategies that can promote parasite resistance in natural populations.
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Affiliation(s)
| | - Jae Hak Son
- Rutgers, The State University of New Jersey, Piscataway, NJ, USA.
| | - Hongyu Zhao
- Yale School of Public Health, New Haven, CT, USA.
| | | | - Yong Kong
- Yale School of Public Health, New Haven, CT, USA.
| | - Mo Li
- Yale School of Public Health, New Haven, CT, USA
| | | | | | | | | | - Serap Aksoy
- Yale School of Public Health, New Haven, CT, USA.
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19
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Patir A, Raper A, Fleming R, Henderson BEP, Murphy L, Henderson NC, Clark EL, Freeman TC, Barnett MW. Cellular heterogeneity of the developing worker honey bee (Apis mellifera) pupa: a single cell transcriptomics analysis. G3 (BETHESDA, MD.) 2023; 13:jkad178. [PMID: 37548242 PMCID: PMC10542211 DOI: 10.1093/g3journal/jkad178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 06/30/2023] [Accepted: 07/24/2023] [Indexed: 08/08/2023]
Abstract
It is estimated that animals pollinate 87.5% of flowering plants worldwide and that managed honey bees (Apis mellifera) account for 30-50% of this ecosystem service to agriculture. In addition to their important role as pollinators, honey bees are well-established insect models for studying learning and memory, behavior, caste differentiation, epigenetic mechanisms, olfactory biology, sex determination, and eusociality. Despite their importance to agriculture, knowledge of honey bee biology lags behind many other livestock species. In this study, we have used scRNA-Seq to map cell types to different developmental stages of the worker honey bee (prepupa at day 11 and pupa at day 15) and sought to determine their gene expression signatures. To identify cell-type populations, we examined the cell-to-cell network based on the similarity of the single-cells transcriptomic profiles. Grouping similar cells together we identified 63 different cell clusters of which 17 clusters were identifiable at both stages. To determine genes associated with specific cell populations or with a particular biological process involved in honey bee development, we used gene coexpression analysis. We combined this analysis with literature mining, the honey bee protein atlas, and gene ontology analysis to determine cell cluster identity. Of the cell clusters identified, 17 were related to the nervous system and sensory organs, 7 to the fat body, 19 to the cuticle, 5 to muscle, 4 to compound eye, 2 to midgut, 2 to hemocytes, and 1 to malpighian tubule/pericardial nephrocyte. To our knowledge, this is the first whole single-cell atlas of honey bees at any stage of development and demonstrates the potential for further work to investigate their biology at the cellular level.
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Affiliation(s)
- Anirudh Patir
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK
| | - Anna Raper
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK
| | - Robert Fleming
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK
| | - Beth E P Henderson
- The Queen's Medical Research Institute, Centre for Inflammation Research, University of Edinburgh,Edinburgh BioQuarter, Edinburgh EH16 4TJ, UK
| | - Lee Murphy
- Edinburgh Clinical Research Facility, Western General Hospital, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Neil C Henderson
- The Queen's Medical Research Institute, Centre for Inflammation Research, University of Edinburgh,Edinburgh BioQuarter, Edinburgh EH16 4TJ, UK
- Institute of Genetics and Cancer, Western General Hospital, University of Edinburgh,Edinburgh EH4 2XU, UK
| | - Emily L Clark
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK
| | - Tom C Freeman
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK
| | - Mark W Barnett
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK
- Beebytes Analytics CIC, The Roslin Innovation Centre, University of Edinburgh, The Charnock Bradley Building, Easter Bush, Midlothian EH25 9RG, UK
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20
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Sumner JT, Andrasz CL, Johnson CA, Wax S, Anderson P, Keeling EL, Davidson JM. De novo genome assembly and comparative genomics for the colonial ascidian Botrylloides violaceus. G3 (BETHESDA, MD.) 2023; 13:jkad181. [PMID: 37555394 PMCID: PMC10542563 DOI: 10.1093/g3journal/jkad181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 01/25/2023] [Accepted: 07/12/2023] [Indexed: 08/10/2023]
Abstract
Ascidians have the potential to reveal fundamental biological insights related to coloniality, regeneration, immune function, and the evolution of these traits. This study implements a hybrid assembly technique to produce a genome assembly and annotation for the botryllid ascidian, Botrylloides violaceus. A hybrid genome assembly was produced using Illumina, Inc. short and Oxford Nanopore Technologies long-read sequencing technologies. The resulting assembly is comprised of 831 contigs, has a total length of 121 Mbp, N50 of 1 Mbp, and a BUSCO score of 96.1%. Genome annotation identified 13 K protein-coding genes. Comparative genomic analysis with other tunicates reveals patterns of conservation and divergence within orthologous gene families even among closely related species. Characterization of the Wnt gene family, encoding signaling ligands involved in development and regeneration, reveals conserved patterns of subfamily presence and gene copy number among botryllids. This supports the use of genomic data from nonmodel organisms in the investigation of biological phenomena.
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Affiliation(s)
- Jack T Sumner
- Department of Biological Sciences, California Polytechnic State University, San Luis Obispo, CA 93407, USA
| | - Cassidy L Andrasz
- Department of Biological Sciences, California Polytechnic State University, San Luis Obispo, CA 93407, USA
| | - Christine A Johnson
- Department of Biological Sciences, California Polytechnic State University, San Luis Obispo, CA 93407, USA
| | - Sarah Wax
- Department of Biological Sciences, California Polytechnic State University, San Luis Obispo, CA 93407, USA
| | - Paul Anderson
- Department of Computer Science and Software Engineering, California Polytechnic State University, San Luis Obispo, CA 93407, USA
| | - Elena L Keeling
- Department of Biological Sciences, California Polytechnic State University, San Luis Obispo, CA 93407, USA
| | - Jean M Davidson
- Department of Biological Sciences, California Polytechnic State University, San Luis Obispo, CA 93407, USA
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21
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Everitt T, Wallberg A, Christmas MJ, Olsson A, Hoffmann W, Neumann P, Webster MT. The Genomic Basis of Adaptation to High Elevations in Africanized Honey Bees. Genome Biol Evol 2023; 15:evad157. [PMID: 37625795 PMCID: PMC10484329 DOI: 10.1093/gbe/evad157] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 08/11/2023] [Accepted: 08/18/2023] [Indexed: 08/27/2023] Open
Abstract
A range of different genetic architectures underpin local adaptation in nature. Honey bees (Apis mellifera) in the Eastern African Mountains harbor high frequencies of two chromosomal inversions that likely govern adaptation to this high-elevation habitat. In the Americas, honey bees are hybrids of European and African ancestries and adaptation to latitudinal variation in climate correlates with the proportion of these ancestries across the genome. It is unknown which, if either, of these forms of genetic variation governs adaptation in honey bees living at high elevations in the Americas. Here, we performed whole-genome sequencing of 29 honey bees from both high- and low-elevation populations in Colombia. Analysis of genetic ancestry indicated that both populations were predominantly of African ancestry, but the East African inversions were not detected. However, individuals in the higher elevation population had significantly higher proportions of European ancestry, likely reflecting local adaptation. Several genomic regions exhibited particularly high differentiation between highland and lowland bees, containing candidate loci for local adaptation. Genes that were highly differentiated between highland and lowland populations were enriched for functions related to reproduction and sperm competition. Furthermore, variation in levels of European ancestry across the genome was correlated between populations of honey bees in the highland population and populations at higher latitudes in South America. The results are consistent with the hypothesis that adaptation to both latitude and elevation in these hybrid honey bees are mediated by variation in ancestry at many loci across the genome.
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Affiliation(s)
- Turid Everitt
- Department Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Andreas Wallberg
- Department Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Matthew J Christmas
- Department Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Anna Olsson
- Department Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Wolfgang Hoffmann
- Grupo de Biocalorimetría, Universidad de Pamplona, Pamplona, Colombia
| | - Peter Neumann
- Institute of Bee Health, Vetsuisse Faculty, University of Bern and Agroscope, Bern, Switzerland
| | - Matthew T Webster
- Department Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
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22
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Brůna T, Li H, Guhlin J, Honsel D, Herbold S, Stanke M, Nenasheva N, Ebel M, Gabriel L, Hoff KJ. Galba: genome annotation with miniprot and AUGUSTUS. BMC Bioinformatics 2023; 24:327. [PMID: 37653395 PMCID: PMC10472564 DOI: 10.1186/s12859-023-05449-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 08/21/2023] [Indexed: 09/02/2023] Open
Abstract
BACKGROUND The Earth Biogenome Project has rapidly increased the number of available eukaryotic genomes, but most released genomes continue to lack annotation of protein-coding genes. In addition, no transcriptome data is available for some genomes. RESULTS Various gene annotation tools have been developed but each has its limitations. Here, we introduce GALBA, a fully automated pipeline that utilizes miniprot, a rapid protein-to-genome aligner, in combination with AUGUSTUS to predict genes with high accuracy. Accuracy results indicate that GALBA is particularly strong in the annotation of large vertebrate genomes. We also present use cases in insects, vertebrates, and a land plant. GALBA is fully open source and available as a docker image for easy execution with Singularity in high-performance computing environments. CONCLUSIONS Our pipeline addresses the critical need for accurate gene annotation in newly sequenced genomes, and we believe that GALBA will greatly facilitate genome annotation for diverse organisms.
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Affiliation(s)
- Tomáš Brůna
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Heng Li
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, 02215 MA USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, 02215 MA USA
| | - Joseph Guhlin
- Genomics Aotearoa and Laboratory for Evolution and Development, Department of Biochemistry, University of Otago, Dunedin, 9016 New Zealand
| | - Daniel Honsel
- Institute of Computer Science, University of Göttingen, 37077 Göttingen, Germany
| | - Steffen Herbold
- Faculty for Computer Science and Mathematics, University of Passau, 94032 Passau, Germany
| | - Mario Stanke
- Institute of Mathematics and Computer Science, and Center for Functional Genomics of Microbes, University of Greifswald, 17489 Greifswald, Germany
| | - Natalia Nenasheva
- Institute of Mathematics and Computer Science, and Center for Functional Genomics of Microbes, University of Greifswald, 17489 Greifswald, Germany
| | - Matthis Ebel
- Institute of Mathematics and Computer Science, and Center for Functional Genomics of Microbes, University of Greifswald, 17489 Greifswald, Germany
| | - Lars Gabriel
- Institute of Mathematics and Computer Science, and Center for Functional Genomics of Microbes, University of Greifswald, 17489 Greifswald, Germany
| | - Katharina J. Hoff
- Institute of Mathematics and Computer Science, and Center for Functional Genomics of Microbes, University of Greifswald, 17489 Greifswald, Germany
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23
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Zarate D, Mukogawa B, Kohn J, Nieh JC. Seasonal variation in defense behavior in European and scutellata-hybrid honey bees (Apis mellifera) in Southern California. Sci Rep 2023; 13:12790. [PMID: 37550348 PMCID: PMC10406949 DOI: 10.1038/s41598-023-38153-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 07/04/2023] [Indexed: 08/09/2023] Open
Abstract
Nest defense in the honey bee (Apis mellifera) is a complex collective behavior modulated by various interacting social, environmental, and genetic factors. Scutellata-hybrid ("Africanized") honey bees are usually considered to be far more defensive than European honey bees which are therefore preferred for commercial and hobbyist beekeeping. In the most recent zone of scutellata hybridization, the southern USA, the degree to which this defensiveness differs among current strains, and the extent to which defensiveness varies across a season has not been measured. We quantified the levels of A. m. scutellata ancestry in colonies and conducted a seasonal assessment (May through November) of colony nest defensiveness in feral scutellata-hybrid and a popular lineage of European honey bee commonly used in managed environments (sold as A. mellifera ligustica) hives at two apiaries in Southern California. Standard measures of defensiveness were low in both scutellata-hybrid and European colonies during May. Defensiveness increased during the later months of the study in scutellata-hybrid colonies. Most measures of defensiveness did not increase in managed colonies. Defensiveness in the scutellata-hybrids appears lower than what has been previously documented in Brazil and Mexico, possibly due to their lower proportion of A. m. scutellata ancestry.
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Affiliation(s)
- Daniela Zarate
- Department of Ecology, Behavior, and Evolution, School of Biological Sciences, University of California San Diego, 9500 Gilman Dr., MC 0116, La Jolla, CA, 92093-0116, USA.
| | - Brandon Mukogawa
- Department of Ecology, Behavior, and Evolution, School of Biological Sciences, University of California San Diego, 9500 Gilman Dr., MC 0116, La Jolla, CA, 92093-0116, USA
| | - Joshua Kohn
- Department of Ecology, Behavior, and Evolution, School of Biological Sciences, University of California San Diego, 9500 Gilman Dr., MC 0116, La Jolla, CA, 92093-0116, USA
| | - James C Nieh
- Department of Ecology, Behavior, and Evolution, School of Biological Sciences, University of California San Diego, 9500 Gilman Dr., MC 0116, La Jolla, CA, 92093-0116, USA
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24
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Inwood SN, Skelly J, Guhlin JG, Harrop TWR, Goldson SL, Dearden PK. Chromosome-level genome assemblies of two parasitoid biocontrol wasps reveal the parthenogenesis mechanism and an associated novel virus. BMC Genomics 2023; 24:440. [PMID: 37543591 PMCID: PMC10403939 DOI: 10.1186/s12864-023-09538-4] [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: 05/22/2023] [Accepted: 07/27/2023] [Indexed: 08/07/2023] Open
Abstract
BACKGROUND Biocontrol is a key technology for the control of pest species. Microctonus parasitoid wasps (Hymenoptera: Braconidae) have been released in Aotearoa New Zealand as biocontrol agents, targeting three different pest weevil species. Despite their value as biocontrol agents, no genome assemblies are currently available for these Microctonus wasps, limiting investigations into key biological differences between the different species and strains. METHODS AND FINDINGS Here we present high-quality genomes for Microctonus hyperodae and Microctonus aethiopoides, assembled with short read sequencing and Hi-C scaffolding. These assemblies have total lengths of 106.7 Mb for M. hyperodae and 129.2 Mb for M. aethiopoides, with scaffold N50 values of 9 Mb and 23 Mb respectively. With these assemblies we investigated differences in reproductive mechanisms, and association with viruses between Microctonus wasps. Meiosis-specific genes are conserved in asexual Microctonus, with in-situ hybridisation validating expression of one of these genes in the ovaries of asexual Microctonus aethiopoides. This implies asexual reproduction in these Microctonus wasps involves meiosis, with the potential for sexual reproduction maintained. Investigation of viral gene content revealed candidate genes that may be involved in virus-like particle production in M. aethiopoides, as well as a novel virus infecting M. hyperodae, for which a complete genome was assembled. CONCLUSION AND SIGNIFICANCE These are the first published genomes for Microctonus wasps which have been deployed as biocontrol agents, in Aotearoa New Zealand. These assemblies will be valuable resources for continued investigation and monitoring of these biocontrol systems. Understanding the biology underpinning Microctonus biocontrol is crucial if we are to maintain its efficacy, or in the case of M. hyperodae to understand what may have influenced the significant decline of biocontrol efficacy. The potential for sexual reproduction in asexual Microctonus is significant given that empirical modelling suggests this asexual reproduction is likely to have contributed to biocontrol decline. Furthermore the identification of a novel virus in M. hyperodae highlights a previously unknown aspect of this biocontrol system, which may contribute to premature mortality of the host pest. These findings have potential to be exploited in future in attempt to increase the effectiveness of M. hyperodae biocontrol.
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Affiliation(s)
- Sarah N Inwood
- Bioprotection Aotearoa and Biochemistry Department, University of Otago, Dunedin, Aotearoa, New Zealand
| | - John Skelly
- Bioprotection Aotearoa and Biochemistry Department, University of Otago, Dunedin, Aotearoa, New Zealand
- Humble Bee Bio, Wellington, Aotearoa, New Zealand
| | - Joseph G Guhlin
- Genomics Aotearoa, University of Otago, Dunedin, Aotearoa, New Zealand
| | - Thomas W R Harrop
- Melbourne Bioinformatics, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Stephen L Goldson
- Biocontrol and Biosecurity Group, AgResearch Limited, Lincoln, Aotearoa, New Zealand
| | - Peter K Dearden
- Bioprotection Aotearoa and Biochemistry Department, University of Otago, Dunedin, Aotearoa, New Zealand.
- Genomics Aotearoa, University of Otago, Dunedin, Aotearoa, New Zealand.
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25
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Iino S, Oya S, Kakutani T, Kohno H, Kubo T. Identification of ecdysone receptor target genes in the worker honey bee brains during foraging behavior. Sci Rep 2023; 13:10491. [PMID: 37380789 DOI: 10.1038/s41598-023-37001-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Accepted: 06/14/2023] [Indexed: 06/30/2023] Open
Abstract
Ecdysone signaling plays central roles in morphogenesis and female ovarian development in holometabolous insects. In the European honey bee (Apis mellifera L.), however, ecdysone receptor (EcR) is expressed in the brains of adult workers, which have already undergone metamorphosis and are sterile with shrunken ovaries, during foraging behavior. Aiming at unveiling the significance of EcR signaling in the worker brain, we performed chromatin-immunoprecipitation sequencing of EcR to search for its target genes using the brains of nurse bees and foragers. The majority of the EcR targets were common between the nurse bee and forager brains and some of them were known ecdysone signaling-related genes. RNA-sequencing analysis revealed that some EcR target genes were upregulated in forager brains during foraging behavior and some were implicated in the repression of metabolic processes. Single-cell RNA-sequencing analysis revealed that EcR and its target genes were expressed mostly in neurons and partly in glial cells in the optic lobes of the forager brain. These findings suggest that in addition to its role during development, EcR transcriptionally represses metabolic processes during foraging behavior in the adult worker honey bee brain.
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Affiliation(s)
- Shiori Iino
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Satoyo Oya
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Tetsuji Kakutani
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Hiroki Kohno
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Takeo Kubo
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, 113-0033, Japan.
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26
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Bresnahan ST, Lee E, Clark L, Ma R, Rangel J, Grozinger CM, Li-Byarlay H. Examining parent-of-origin effects on transcription and RNA methylation in mediating aggressive behavior in honey bees (Apis mellifera). BMC Genomics 2023; 24:315. [PMID: 37308882 DOI: 10.1186/s12864-023-09411-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 05/27/2023] [Indexed: 06/14/2023] Open
Abstract
Conflict between genes inherited from the mother (matrigenes) and the father (patrigenes) is predicted to arise during social interactions among offspring if these genes are not evenly distributed among offspring genotypes. This intragenomic conflict drives parent-specific transcription patterns in offspring resulting from parent-specific epigenetic modifications. Previous tests of the kinship theory of intragenomic conflict in honey bees (Apis mellifera) provided evidence in support of theoretical predictions for variation in worker reproduction, which is associated with extreme variation in morphology and behavior. However, more subtle behaviors - such as aggression - have not been extensively studied. Additionally, the canonical epigenetic mark (DNA methylation) associated with parent-specific transcription in plant and mammalian model species does not appear to play the same role as in honey bees, and thus the molecular mechanisms underlying intragenomic conflict in this species is an open area of investigation. Here, we examined the role of intragenomic conflict in shaping aggression in honey bee workers through a reciprocal cross design and Oxford Nanopore direct RNA sequencing. We attempted to probe the underlying regulatory basis of this conflict through analyses of parent-specific RNA m6A and alternative splicing patterns. We report evidence that intragenomic conflict occurs in the context of honey bee aggression, with increased paternal and maternal allele-biased transcription in aggressive compared to non-aggressive bees, and higher paternal allele-biased transcription overall. However, we found no evidence to suggest that RNA m6A or alternative splicing mediate intragenomic conflict in this species.
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Affiliation(s)
- Sean T Bresnahan
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, USA.
| | - Ellen Lee
- Agricultural Research and Development Program, Central State University, Wilberforce, USA
- Department of Biological Sciences, Wright State University, Dayton, USA
| | - Lindsay Clark
- HPCBio, University of Illinois at Urbana-Champaign, Champaign, USA
- Research Scientific Computing Group, Seattle Children's Research Institute, Seattle, USA
| | - Rong Ma
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, USA
| | - Juliana Rangel
- Department of Entomology, Texas A&M University, College Station, USA
| | - Christina M Grozinger
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, USA
| | - Hongmei Li-Byarlay
- Agricultural Research and Development Program, Central State University, Wilberforce, USA.
- Department of Agricultural and Life Science, Central State University, Wilberforce, USA.
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27
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Lin Z, Zhu Z, Zhuang M, Wang Z, Zhang Y, Gao F, Niu Q, Ji T. Effects of local domestication warrant attention in honey bee population genetics. SCIENCE ADVANCES 2023; 9:eade7917. [PMID: 37134176 PMCID: PMC10156114 DOI: 10.1126/sciadv.ade7917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Honey bees, Apis mellifera, have for millennia been managed and exploited by humans and introduced into most suitable regions worldwide. However, given the lack of records for many introduction events, treating A. mellifera populations as native would predictably bias genetic studies regarding origin and evolution. Here, we used the Dongbei bee, a well-documented population, introduced beyond the natural distribution range approximately 100 years ago, to elucidate the effects of local domestication on animal population genetic analyses. Strong domestication pressure was detected in this population, and the genetic divergence between Dongbei bee and its ancestral subspecies was found to have occurred at the lineage level. Results of phylogenetic and time divergence analyses could consequently be misinterpreted. Proposing new subspecies or lineages and performing analyses of origin should thus strive to eliminate anthropogenic effects. We highlight the need for definitions of landrace and breed in honey bee sciences and make preliminary suggestions.
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Affiliation(s)
- Zheguang Lin
- Apicultural Research Institute, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Zhongxu Zhu
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong SAR, China
| | - Mingliang Zhuang
- Apiculture Science Institute of Jilin Province, Jilin 132108, China
| | - Zhi Wang
- Apiculture Science Institute of Jilin Province, Jilin 132108, China
| | - Yi Zhang
- Apicultural Research Institute, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Fuchao Gao
- Mudanjiang Branch of Heilongjiang Academy of Agricultural Sciences, Mudanjiang 157043, China
| | - Qingsheng Niu
- Apiculture Science Institute of Jilin Province, Jilin 132108, China
| | - Ting Ji
- Apicultural Research Institute, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
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28
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Zhu B, Jin P, Zhang Y, Shen Y, Wang W, Li S. Genomic and transcriptomic analyses support a silk gland origin of spider venom glands. BMC Biol 2023; 21:82. [PMID: 37055766 PMCID: PMC10099834 DOI: 10.1186/s12915-023-01581-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 03/29/2023] [Indexed: 04/15/2023] Open
Abstract
BACKGROUND Spiders comprise a hyperdiverse lineage of predators with venom systems, yet the origin of functionally novel spider venom glands remains unclear. Previous studies have hypothesized that spider venom glands originated from salivary glands or evolved from silk-producing glands present in early chelicerates. However, there is insufficient molecular evidence to indicate similarity among them. Here, we provide comparative analyses of genome and transcriptome data from various lineages of spiders and other arthropods to advance our understanding of spider venom gland evolution. RESULTS We generated a chromosome-level genome assembly of a model spider species, the common house spider (Parasteatoda tepidariorum). Module preservation, GO semantic similarity, and differentially upregulated gene similarity analyses demonstrated a lower similarity in gene expressions between the venom glands and salivary glands compared to the silk glands, which questions the validity of the salivary gland origin hypothesis but unexpectedly prefers to support the ancestral silk gland origin hypothesis. The conserved core network in the venom and silk glands was mainly correlated with transcription regulation, protein modification, transport, and signal transduction pathways. At the genetic level, we found that many genes in the venom gland-specific transcription modules show positive selection and upregulated expressions, suggesting that genetic variation plays an important role in the evolution of venom glands. CONCLUSIONS This research implies the unique origin and evolutionary path of spider venom glands and provides a basis for understanding the diverse molecular characteristics of venom systems.
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Affiliation(s)
- Bingyue Zhu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 101408, China
| | - Pengyu Jin
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yiming Zhang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 101408, China
| | - Yunxiao Shen
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 101408, China
| | - Wei Wang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- Key Laboratory of Ecology and Environmental Protection of Rare and Endangered Animals and Plants, Ministry of Education, Guangxi Normal University, Guilin, 541004, China
| | - Shuqiang Li
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
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Parejo M, Talenti A, Richardson M, Vignal A, Barnett M, Wragg D. AmelHap: Leveraging drone whole-genome sequence data to create a honey bee HapMap. Sci Data 2023; 10:198. [PMID: 37037860 PMCID: PMC10086014 DOI: 10.1038/s41597-023-02097-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 03/22/2023] [Indexed: 04/12/2023] Open
Abstract
Honey bee, Apis mellifera, drones are typically haploid, developing from an unfertilized egg, inheriting only their queen's alleles and none from the many drones she mated with. Thus the ordered combination or 'phase' of alleles is known, making drones a valuable haplotype resource. We collated whole-genome sequence data for 1,407 drones, including 45 newly sequenced Scottish drones, collectively representing 19 countries, 8 subspecies and various hybrids. Following alignment to Amel_HAv3.1, variant calling and quality filtering, we retained 17.4 M high quality variants across 1,328 samples with a genotyping rate of 98.7%. We demonstrate the utility of this haplotype resource, AmelHap, for genotype imputation, returning >95% concordance when up to 61% of data is missing in haploids and up to 12% of data is missing in diploids. AmelHap will serve as a useful resource for the community for imputation from low-depth sequencing or SNP chip data, accurate phasing of diploids for association studies, and as a comprehensive reference panel for population genetic and evolutionary analyses.
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Affiliation(s)
- M Parejo
- Applied Genomics and Bioinformatics, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - A Talenti
- The Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian, UK
| | - M Richardson
- University of Edinburgh, King's Buildings Campus, Edinburgh, UK
- Beebytes Analytics CIC, Roslin Innovation Centre, Easter Bush Campus, Midlothian, UK
| | - A Vignal
- GenPhySE, Université de Toulouse, INRAE, INPT, INP-ENVT, 31326, Castanet Tolosan, France
| | - M Barnett
- Beebytes Analytics CIC, Roslin Innovation Centre, Easter Bush Campus, Midlothian, UK
| | - D Wragg
- The Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian, UK.
- Beebytes Analytics CIC, Roslin Innovation Centre, Easter Bush Campus, Midlothian, UK.
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Zheng SY, Pan LX, Cheng FP, Jin MJ, Wang ZL. A Global Survey of the Full-Length Transcriptome of Apis mellifera by Single-Molecule Long-Read Sequencing. Int J Mol Sci 2023; 24:ijms24065827. [PMID: 36982901 PMCID: PMC10059051 DOI: 10.3390/ijms24065827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 03/08/2023] [Accepted: 03/12/2023] [Indexed: 03/30/2023] Open
Abstract
As important pollinators, honey bees play a crucial role in both maintaining the ecological balance and providing products for humans. Although several versions of the western honey bee genome have already been published, its transcriptome information still needs to be refined. In this study, PacBio single-molecule sequencing technology was used to sequence the full-length transcriptome of mixed samples from many developmental time points and tissues of A. mellifera queens, workers and drones. A total of 116,535 transcripts corresponding to 30,045 genes were obtained. Of these, 92,477 transcripts were annotated. Compared to the annotated genes and transcripts on the reference genome, 18,915 gene loci and 96,176 transcripts were newly identified. From these transcripts, 136,554 alternative splicing (AS) events, 23,376 alternative polyadenylation (APA) sites and 21,813 lncRNAs were detected. In addition, based on the full-length transcripts, we identified many differentially expressed transcripts (DETs) between queen, worker and drone. Our results provide a complete set of reference transcripts for A. mellifera that dramatically expand our understanding of the complexity and diversity of the honey bee transcriptome.
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Affiliation(s)
- Shuang-Yan Zheng
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang 330045, China
- Sino-German Joint Research Institute, Nanchang University, Nanchang 330047, China
| | - Lu-Xia Pan
- Honeybee Research Institute, Jiangxi Agricultural University, Nanchang 330045, China
- Jiangxi Province Key Laboratory of Honeybee Biology and Beekeeping, Jiangxi Agricultural University, Nanchang 330045, China
| | - Fu-Ping Cheng
- Honeybee Research Institute, Jiangxi Agricultural University, Nanchang 330045, China
- Jiangxi Province Key Laboratory of Honeybee Biology and Beekeeping, Jiangxi Agricultural University, Nanchang 330045, China
| | - Meng-Jie Jin
- Honeybee Research Institute, Jiangxi Agricultural University, Nanchang 330045, China
- Jiangxi Province Key Laboratory of Honeybee Biology and Beekeeping, Jiangxi Agricultural University, Nanchang 330045, China
| | - Zi-Long Wang
- Honeybee Research Institute, Jiangxi Agricultural University, Nanchang 330045, China
- Jiangxi Province Key Laboratory of Honeybee Biology and Beekeeping, Jiangxi Agricultural University, Nanchang 330045, China
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Morfin N, Harpur BA, De la Mora A, Guzman-Novoa E. Breeding honey bees ( Apis mellifera L.) for low and high Varroa destructor population growth: Gene expression of bees performing grooming behavior. FRONTIERS IN INSECT SCIENCE 2023; 3:951447. [PMID: 38469529 PMCID: PMC10926520 DOI: 10.3389/finsc.2023.951447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 02/03/2023] [Indexed: 03/13/2024]
Abstract
Introduction Social organisms, including honey bees (Apis mellifera L.), have defense mechanisms to control the multiplication and transmission of parasites and pathogens within their colonies. Self-grooming, a mechanism of behavioral immunity, seems to contribute to restrain the population growth of the ectoparasitic mite Varroa destructor in honey bee colonies. Because V. destructor is the most damaging parasite of honey bees, breeding them for resistance against the mite is a high priority of the beekeeping industry. Methods A bidirectional breeding program to select honey bee colonies with low and high V. destructor population growth (LVG and HVG, respectively) was conducted. Having high and low lines of bees allowed the study of genetic mechanisms underlying self-grooming behavior between the extreme genotypes. Worker bees were classified into two categories: 'light groomers' and 'intense groomers'. The brains of bees from the different categories (LVG-intense, LVG-light, HVG-intense, and HVG-light) were used for gene expression and viral quantification analyses. Differentially expressed genes (DEGs) associated with the LVG and HVG lines were identified. Results Four odorant-binding proteins and a gustatory receptor were identified as differentially expressed genes. A functional enrichment analysis showed 19 enriched pathways from a list of 219 down-regulated DEGs in HVG bees, including the Kyoto Encyclopedia of Genes and Genomes (KEGG) term of oxidative phosphorylation. Additionally, bees from the LVG line showed lower levels of Apis rhabdovirus 1 and 2, Varroa destructor virus -1 (VDV-1/DWV-B), and Deformed wing virus-A (DWV-A) compared to bees of the HVG line. The difference in expression of odorant-binding protein genes and a gustatory receptor between bee lines suggests a possible link between them and the perception of irritants to trigger rapid self-grooming instances that require the activation of energy metabolic pathways. Discussion These results provide new insights on the molecular mechanisms involved in honey bee grooming behavior. Differences in viral levels in the brains of LVG and HVG bees showed the importance of investigating the pathogenicity and potential impacts of neurotropic viruses on behavioral immunity. The results of this study advance the understanding of a trait used for selective breeding, self-grooming, and the potential of using genomic assisted selection to improve breeding programs.
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Affiliation(s)
- Nuria Morfin
- British Columbia Technology Transfer Program, British Columbia Honey Producers Association, Victoria, BC, Canada
- Department of Biochemistry & Molecular Biology, The University of British Columbia, Vancouver, BC, Canada
| | - Brock A. Harpur
- Department of Entomology, Purdue University, West Lafayette, IN, United States
| | - Alvaro De la Mora
- School of Environmental Sciences, University of Guelph, Guelph, ON, Canada
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Effect of Ascosphaera apis Infestation on the Activities of Four Antioxidant Enzymes in Asian Honey Bee Larval Guts. Antioxidants (Basel) 2023; 12:antiox12010206. [PMID: 36671067 PMCID: PMC9854781 DOI: 10.3390/antiox12010206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 01/05/2023] [Accepted: 01/12/2023] [Indexed: 01/18/2023] Open
Abstract
Ascosphaera apis infects exclusively bee larvae and causes chalkbrood, a lethal fungal disease that results in a sharp reduction in adult bees and colony productivity. However, little is known about the effect of A. apis infestation on the activities of antioxidant enzymes in bee larvae. Here, A. apis spores were purified and used to inoculate Asian honey bee (Apis cerana) larvae, followed by the detection of the host survival rate and an evaluation of the activities of four major antioxidant enzymes. At 6 days after inoculation (dpi) with A. apis spores, obvious symptoms of chalkbrood disease similar to what occurs in Apis mellifera larvae were observed. PCR identification verified the A. apis infection of A. cerana larvae. Additionally, the survival rate of larvae inoculated with A. apis was high at 1−2 dpi, which sharply decreased to 4.16% at 4 dpi and which reached 0% at 5 dpi, whereas that of uninoculated larvae was always high at 1~8 dpi, with an average survival rate of 95.37%, indicating the negative impact of A. apis infection on larval survival. As compared with those in the corresponding uninoculated groups, the superoxide dismutase (SOD) and catalase (CAT) activities in the 5- and 6-day-old larval guts in the A. apis−inoculated groups were significantly decreased (p < 0.05) and the glutathione S-transferase (GST) activity in the 4- and 5-day-old larval guts was significantly increased (p < 0.05), which suggests that the inhibition of SOD and CAT activities and the activation of GST activity in the larval guts was caused by A. apis infestation. In comparison with that in the corresponding uninoculated groups, the polyphenol oxidase (PPO) activity was significantly increased (p < 0.05) in the 5-day-old larval gut but significantly reduced (p < 0.01) in the 6-day-old larval gut, indicating that the PPO activity in the larval guts was first enhanced and then suppressed. Our findings not only unravel the response of A. cerana larvae to A. apis infestation from a biochemical perspective but also offer a valuable insight into the interaction between Asian honey bee larvae and A. apis.
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Analysis of the Toll and Spaetzle Genes Involved in Toll Pathway-Dependent Antimicrobial Gene Induction in the Red Flour Beetle, Tribolium castaneum (Coleoptera; Tenebrionidae). Int J Mol Sci 2023; 24:ijms24021523. [PMID: 36675034 PMCID: PMC9861120 DOI: 10.3390/ijms24021523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 01/10/2023] [Accepted: 01/11/2023] [Indexed: 01/14/2023] Open
Abstract
Insects rely only on their innate immune system to protect themselves from pathogens. Antimicrobial peptide (AMP) production is the main immune reaction in insects. In Drosophila melanogaster, the reaction is regulated mainly by the Toll and immune deficiency (IMD) pathways. Spaetzle proteins, activated by immune signals from upstream components, bind to Toll proteins, thus, activating the Toll pathway, which in turn, induces AMP genes. Previous studies have shown the difference in immune systems related to Toll and IMD pathways between D. melanogaster and Tribolium castaneum. In T. castaneum, nine Toll and seven spaetzle (spz) genes were identified. To extend our understanding of AMP production by T. castaneum, we conducted functional assays of Toll and spaetzle genes related to Toll-pathway-dependent AMP gene expression in T. castaneum under challenge with bacteria or budding yeast. The results revealed that Toll3 and Toll4 double-knockdown and spz7 knockdown strongly and moderately reduced the Toll-pathway-dependent expression of AMP genes, respectively. Moreover, Toll3 and Toll4 double-knockdown pupae more rapidly succumbed to entomopathogenic bacteria than the control pupae, but spz7 knockdown pupae did not. The results suggest that Toll3 and Toll4 play a large role in Toll-pathway-dependent immune reactions, whereas spz7 plays a small part.
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Gmel AI, Guichard M, Dainat B, Williams GR, Eynard S, Vignal A, Servin B, Neuditschko M. Identification of runs of homozygosity in Western honey bees ( Apis mellifera) using whole-genome sequencing data. Ecol Evol 2023; 13:e9723. [PMID: 36694553 PMCID: PMC9843643 DOI: 10.1002/ece3.9723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 12/15/2022] [Accepted: 12/19/2022] [Indexed: 01/19/2023] Open
Abstract
Runs of homozygosity (ROH) are continuous homozygous segments that arise through the transmission of haplotypes that are identical by descent. The length and distribution of ROH segments provide insights into the genetic diversity of populations and can be associated with selection signatures. Here, we analyzed reconstructed whole-genome queen genotypes, from a pool-seq data experiment including 265 Western honeybee colonies from Apis mellifera mellifera and Apis mellifera carnica. Integrating individual ROH patterns and admixture levels in a dynamic population network visualization allowed us to ascertain major differences between the two subspecies. Within A. m. mellifera, we identified well-defined substructures according to the genetic origin of the queens. Despite the current applied conservation efforts, we pinpointed 79 admixed queens. Genomic inbreeding (F ROH) strongly varied within and between the identified subpopulations. Conserved A. m. mellifera from Switzerland had the highest mean F ROH (3.39%), while queens originating from a conservation area in France, which were also highly admixed, showed significantly lower F ROH (0.45%). The majority of A. m. carnica queens were also highly admixed, except 12 purebred queens with a mean F ROH of 2.33%. Within the breed-specific ROH islands, we identified 14 coding genes for A. m. mellifera and five for A. m. carnica, respectively. Local adaption of A. m. mellifera could be suggested by the identification of genes involved in the response to ultraviolet light (Crh-BP, Uvop) and body size (Hex70a, Hex70b), while the A. m. carnica specific genes Cpr3 and Cpr4 are most likely associated with the lighter striping pattern, a morphological phenotype expected in this subspecies. We demonstrated that queen genotypes derived from pooled workers are useful tool to unravel the population dynamics in A. mellifera and provide fundamental information to conserve native honey bees.
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Affiliation(s)
- Annik Imogen Gmel
- Animal GenoPhenomics, Animal Production Systems and Animal HealthAgroscopePosieuxSwitzerland
| | - Matthieu Guichard
- Animal GenoPhenomics, Animal Production Systems and Animal HealthAgroscopePosieuxSwitzerland
- Swiss Bee Research CentreAgroscopeLiebefeldSwitzerland
| | | | | | - Sonia Eynard
- GenPhySEINRAE, INPT, INPENVTUniversité de ToulouseCastanet‐TolosanFrance
- UMT PrADEProtection des Abeilles Dans L'EnvironnementAvignonFrance
| | - Alain Vignal
- GenPhySEINRAE, INPT, INPENVTUniversité de ToulouseCastanet‐TolosanFrance
- UMT PrADEProtection des Abeilles Dans L'EnvironnementAvignonFrance
| | - Bertrand Servin
- GenPhySEINRAE, INPT, INPENVTUniversité de ToulouseCastanet‐TolosanFrance
- UMT PrADEProtection des Abeilles Dans L'EnvironnementAvignonFrance
| | | | - Markus Neuditschko
- Animal GenoPhenomics, Animal Production Systems and Animal HealthAgroscopePosieuxSwitzerland
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Yuan R, Zheng B, Li Z, Ma X, Shu X, Qu Q, Ye X, Li S, Tang P, Chen X. The chromosome-level genome of Chinese praying mantis Tenodera sinensis (Mantodea: Mantidae) reveals its biology as a predator. Gigascience 2022; 12:giad090. [PMID: 37882605 PMCID: PMC10600911 DOI: 10.1093/gigascience/giad090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 09/17/2023] [Accepted: 10/04/2023] [Indexed: 10/27/2023] Open
Abstract
BACKGROUND The Chinese praying mantis, Tenodera sinensis (Saussure), is a carnivorous insect that preys on a variety of arthropods and small vertebrates, including pest species. Several studies have been conducted to understand its behavior and physiology. However, there is limited knowledge about the genetic information underlying its genome evolution, digestive demands, and predatory behaviors. FINDINGS Here we have assembled the chromosome-level genome of T. sinensis, representing the first sequenced genome of the family Mantidae, with a genome size of 2.54 Gb and scaffold N50 of 174.78 Mb. Our analyses revealed that 98.6% of BUSCO genes are present, resulting in a well-annotated assembly compared to other insect genomes, containing 25,022 genes. The reconstructed phylogenetic analysis showed the expected topology placing the praying mantis in an appropriate position. Analysis of transposon elements suggested the Gypsy/Dirs family, which belongs to long terminal repeat (LTR) transposons, may be a key factor resulting in the larger genome size. The genome shows expansions in several digestion and detoxification associated gene families, including trypsin and glycosyl hydrolase (GH) genes, ATP-binding cassette (ABC) transporter, and carboxylesterase (CarE), reflecting the possible genomic basis of digestive demands. Furthermore, we have found 1 ultraviolet-sensitive opsin and 2 long-wavelength-sensitive (LWS) opsins, emphasizing the core role of LWS opsins in regulating predatory behaviors. CONCLUSIONS The high-quality genome assembly of the praying mantis provides a valuable repository for studying the evolutionary patterns of the mantis genomes and the gene expression profiles of insect predators.
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Affiliation(s)
- Ruizhong Yuan
- Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
- State Key Lab of Rice Biology, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, and Zhejiang Provincial Key Laboratory of Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou 310058, China
| | - Boying Zheng
- Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
- State Key Lab of Rice Biology, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, and Zhejiang Provincial Key Laboratory of Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou 310058, China
| | - Zekai Li
- Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
- State Key Lab of Rice Biology, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, and Zhejiang Provincial Key Laboratory of Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou 310058, China
| | - Xingzhou Ma
- Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
- State Key Lab of Rice Biology, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, and Zhejiang Provincial Key Laboratory of Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou 310058, China
| | - Xiaohan Shu
- Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
- State Key Lab of Rice Biology, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, and Zhejiang Provincial Key Laboratory of Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou 310058, China
- Hainan Institute, Zhejiang University, Sanya 572025, China
| | - Qiuyu Qu
- Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
- State Key Lab of Rice Biology, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, and Zhejiang Provincial Key Laboratory of Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou 310058, China
- Hainan Institute, Zhejiang University, Sanya 572025, China
| | - Xiqian Ye
- Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
- State Key Lab of Rice Biology, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, and Zhejiang Provincial Key Laboratory of Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou 310058, China
| | - Sheng Li
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China
- Guangmeiyuan R&D Center, Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, South China Normal University, Meizhou 514779, China
| | - Pu Tang
- Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
- State Key Lab of Rice Biology, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, and Zhejiang Provincial Key Laboratory of Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou 310058, China
| | - Xuexin Chen
- Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
- State Key Lab of Rice Biology, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, and Zhejiang Provincial Key Laboratory of Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou 310058, China
- Hainan Institute, Zhejiang University, Sanya 572025, China
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Matsumura Y, To TK, Kunieda T, Kohno H, Kakutani T, Kubo T. Mblk-1/E93, an ecdysone related-transcription factor, targets synaptic plasticity-related genes in the honey bee mushroom bodies. Sci Rep 2022; 12:21367. [PMID: 36494426 PMCID: PMC9734179 DOI: 10.1038/s41598-022-23329-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 10/29/2022] [Indexed: 12/13/2022] Open
Abstract
Among hymenopteran insects, aculeate species such as bees, ants, and wasps have enlarged and morphologically elaborate mushroom bodies (MBs), a higher-order brain center in the insect, implying their relationship with the advanced behavioral traits of aculeate species. The molecular bases leading to the acquisition of complicated MB functions, however, remains unclear. We previously reported the constitutive and MB-preferential expression of an ecdysone-signaling related transcription factor, Mblk-1/E93, in the honey bee brain. Here, we searched for target genes of Mblk-1 in the worker honey bee MBs using chromatin immunoprecipitation sequence analyses and found that Mblk-1 targets several genes involved in synaptic plasticity, learning, and memory abilities. We also demonstrated that Mblk-1 expression is self-regulated via Mblk-1-binding sites, which are located upstream of Mblk-1. Furthermore, we showed that the number of the Mblk-1-binding motif located upstream of Mblk-1 homologs increased associated with evolution of hymenopteran insects. Our findings suggest that Mblk-1, which has been focused on as a developmental gene transiently induced by ecdysone, has acquired a novel expression pattern to play a role in synaptic plasticity in honey bee MBs, raising a possibility that molecular evolution of Mblk-1 may have partly contributed to the elaboration of MB function in insects.
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Affiliation(s)
- Yasuhiro Matsumura
- grid.26999.3d0000 0001 2151 536XDepartment of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Taiko Kim To
- grid.26999.3d0000 0001 2151 536XDepartment of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Takekazu Kunieda
- grid.26999.3d0000 0001 2151 536XDepartment of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Hiroki Kohno
- grid.26999.3d0000 0001 2151 536XDepartment of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Tetsuji Kakutani
- grid.26999.3d0000 0001 2151 536XDepartment of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Takeo Kubo
- grid.26999.3d0000 0001 2151 536XDepartment of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
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Avalos A, Bilodeau L. Russian honey bee genotype identification through enhanced marker panel set. FRONTIERS IN INSECT SCIENCE 2022; 2:998310. [PMID: 38468798 PMCID: PMC10926385 DOI: 10.3389/finsc.2022.998310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 10/14/2022] [Indexed: 03/13/2024]
Abstract
Russian honey bees (RHB) are a breeding population developed by USDA-ARS as an effort to provide Varroa-resistant honey bees to beekeepers. The selection strategy for this breeding population was the first in honey bees to incorporate genetic stock identification (GSI). The original GSI approach has been in use for over a decade, and though effective, novel technologies and analytical approaches recently developed provide an opportunity for improvement. Here we outline a novel genotyping assay that capitalizes on the markers used in the GSI as well as new loci recently identified in a whole genome pooled study of commercial honey bee stocks. Our approach utilizes a microfluidic platform and machine learning analyses to arrive at an accurate, high throughput assay. This novel approach provides an improved tool that can be readily incorporated into breeding decisions towards healthier more productive bees.
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Affiliation(s)
- Arian Avalos
- Honey Bee Breeding, Genetics, and Physiology Research Laboratory, USDA-ARS, Baton Rouge, LA, United States
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Yokoi K, Wakamiya T, Bono H. Meta-Analysis of the Public RNA-Seq Data of the Western Honeybee Apis mellifera to Construct Reference Transcriptome Data. INSECTS 2022; 13:931. [PMID: 36292879 PMCID: PMC9604386 DOI: 10.3390/insects13100931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 10/05/2022] [Accepted: 10/13/2022] [Indexed: 06/16/2023]
Abstract
The Western honeybee (Apis mellifera) is valuable in biological research and agriculture. Its genome sequence was published before those for other insect species. RNA-Seq data for A. mellifera have been applied in several recently published studies. Nevertheless, these data have not been prepared for use in subsequent meta-analyses. To promote A. mellifera transcriptome analysis, we constructed reference transcriptome data using the reference genome sequence and RNA-Seq data curated from about 1,000 runs of public databases. The new reference transcriptome data construct comprised 149,685 transcripts, and 194,174 protein sequences were predicted. Approximately 50-60% of the predicted protein sequences were functionally annotated using the protein sequence data for several model and insect species. Novel candidate immune-related transcripts were searched by meta-analysis using immune-response-related RNA-Seq and reference transcriptome data. Three to twenty candidate transcripts including autophagy-related protein 3 were upregulated or downregulated in response to both viral and bacterial infections. The constructed reference transcriptome data may facilitate future transcriptome analyses of A. mellifera.
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Affiliation(s)
- Kakeru Yokoi
- Insect Design Technology Module, Division of Insect Advanced Technology, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), 1-2 Owashi, Tsukuba 305-8634, Ibaraki, Japan
| | - Takeshi Wakamiya
- Laboratory of Genome Informatics, Graduate School of Integrated Sciences for Life, Hiroshima University, 3-10-23 Kagamiyama, Higashi-Hiroshima City 739-0046, Hiroshima, Japan
| | - Hidemasa Bono
- Laboratory of Genome Informatics, Graduate School of Integrated Sciences for Life, Hiroshima University, 3-10-23 Kagamiyama, Higashi-Hiroshima City 739-0046, Hiroshima, Japan
- Laboratory of BioDX, Genome Editing Innovation Center, Hiroshima University, 3-10-23 Kagamiyama, Higashi-Hiroshima City 739-0046, Hiroshima, Japan
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Ma C, Ahmat B, Li J. Effect of queen cell numbers on royal jelly production and quality. Curr Res Food Sci 2022; 5:1818-1825. [PMID: 36254242 PMCID: PMC9568691 DOI: 10.1016/j.crfs.2022.10.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 09/15/2022] [Accepted: 10/10/2022] [Indexed: 10/31/2022] Open
Abstract
Royal jelly (RJ) is a popular functional food with a wealth of health-promoting effects. Over 90% of the global RJ is produced in China mainly by a high RJ-producing honeybee (RJB) strain that can accept and feed a great number of queen larvae for RJ production. To elucidate RJ changes due to queen cell numbers (QCNs), we compared the yield, larval acceptance rate, metabolic and proteomic profiles, and antioxidant activities of RJ from 1 to 5 strips of queen cells (64 per strip) in RJB colonies. As QCNs increased, the larval acceptance rate was not found to vary (p = 0.269) whereas the RJ weight per cell began to significantly decline in the 5-strip colonies (p < 0.05). Increased QCNs had a profound impact on RJ metabolic profiles and mainly reduced fatty acid levels. Remarkably, the 10-hydroxy-2-decenoic acid (10-HDA) content, a most important indicator of RJ quality, declined gradually from 2.01% in the 1-strip colonies to 1.52% in the 5-strip colonies (p < 0.001). RJ proteomic profiles were minimally altered and antioxidant activities were not significantly changed by QCNs. Collectively, the metabolomics and proteomics data and the antioxidant activity test represent a global evaluation of the quality of RJ produced with different QCNs. Our findings gain new insights into higher-quality RJ production using the high-yielding RJBs.
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Affiliation(s)
| | | | - Jianke Li
- Corresponding author. No. 2 Yuanmingyuan West Road, Haidian District, Beijing, China.
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Wei X, Evans JD, Chen Y, Huang Q. Spillover and genome selection of the gut parasite Nosema ceranae between honey bee species. Front Cell Infect Microbiol 2022; 12:1026154. [PMID: 36304932 PMCID: PMC9592821 DOI: 10.3389/fcimb.2022.1026154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 09/26/2022] [Indexed: 11/20/2022] Open
Abstract
Nosema ceranae is a honey bee gut parasite that has recently spilled to another honey bee host through trading. The impact of infection on the native host is minor, which is substantial in the novel host. In this study, artificial inoculation simulated the parasite transmission from the native to the novel host. We found that the parasite initiated proliferation earlier in the novel host than in the native host. Additionally, parasite gene expression was significantly higher when infecting the novel host compared with the native host, leading to a significantly higher number of spores. Allele frequencies were similar for spores of parasites infecting both native and novel hosts. This suggests that the high number of spores found in the novel host was not caused by a subset of more fit spores from native hosts. Native hosts also showed a higher number of up-regulated genes in response to infection when compared with novel hosts. Our data further showed that native hosts suppressed parasite gene expression and arguably sacrificed cells to limit the parasite. The results provide novel insights into host defenses and gene selection during a parasite spillover event.
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Affiliation(s)
- Xiuxiu Wei
- Honeybee Research Institute, Jiangxi Agricultural University, Nanchang, China
| | - Jay D. Evans
- USDA-ARS Bee Research Laboratory, BARC-East Building 306, Beltsville, MD, United States
| | - Yanping Chen
- USDA-ARS Bee Research Laboratory, BARC-East Building 306, Beltsville, MD, United States
| | - Qiang Huang
- Honeybee Research Institute, Jiangxi Agricultural University, Nanchang, China
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, United States
- *Correspondence: Qiang Huang,
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41
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Lago DC, Hasselmann M, Hartfelder K. Sex- and caste-specific transcriptomes of larval honey bee (Apis mellifera L.) gonads: DMRT A2 and Hsp83 are differentially expressed and regulated by juvenile hormone. INSECT MOLECULAR BIOLOGY 2022; 31:593-608. [PMID: 35524973 DOI: 10.1111/imb.12782] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 04/21/2022] [Indexed: 06/14/2023]
Abstract
The gonads of honey bee, Apis mellifera, queens and drones are each composed of hundreds of serial units, the ovarioles and testioles, while the ovaries of the adult subfertile workers consist of only few ovarioles. We performed a comparative RNA-seq analysis on early fifth-instar (L5F1) larval gonads, which is a critical stage in gonad development of honey bee larvae. A total of 1834 genes were identified as differentially expressed (Padj < 0.01) among the three sex and caste phenotypes. The Gene Ontology analysis showed significant enrichment for metabolism, protein or ion binding, and oxidoreductase activity, and a KEGG analysis revealed metabolic pathways as enriched. In a principal component analysis for the total transcriptomes and hierarchical clustering of the DEGs, we found higher similarity between the queen and worker ovary transcriptomes compared to the drone testis, despite the onset of programmed cell death in the worker ovaries. Four DEGs were selected for RT-qPCR analyses, including their response to juvenile hormone (JH), which is a critical factor in the caste-specific development of the ovaries. Among these, DMRT A2 and Hsp83 were found upregulated by JH and, thus, emerged as potential molecular markers for sex- and caste-specific gonad development in honey bees.
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Affiliation(s)
- Denyse Cavalcante Lago
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Martin Hasselmann
- Department of Livestock Population Genomics, Institute of Animal Science, University of Hohenheim, Stuttgart, Germany
| | - Klaus Hartfelder
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
- Departamento de Biologia Celular, Molecular e Bioagentes Patogênicos, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
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Liberti J, Kay T, Quinn A, Kesner L, Frank ET, Cabirol A, Richardson TO, Engel P, Keller L. The gut microbiota affects the social network of honeybees. Nat Ecol Evol 2022; 6:1471-1479. [PMID: 35995848 PMCID: PMC7613669 DOI: 10.1038/s41559-022-01840-w] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 06/27/2022] [Indexed: 01/14/2023]
Abstract
The gut microbiota influences animal neurodevelopment and behaviour but has not previously been documented to affect group-level properties of social organisms. Here, we use honeybees to probe the effect of the gut microbiota on host social behaviour. We found that the microbiota increased the rate and specialization of head-to-head interactions between bees. Microbiota colonization was associated with higher abundances of one-third of the metabolites detected in the brain, including amino acids with roles in synaptic transmission and brain energetic function. Some of these metabolites were significant predictors of the number of social interactions. Microbiota colonization also affected brain transcriptional processes related to amino acid metabolism and epigenetic modifications in a brain region involved in sensory perception. These results demonstrate that the gut microbiota modulates the emergent colony social network of honeybees and suggest changes in chromatin accessibility and amino acid biosynthesis as underlying processes.
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Affiliation(s)
- Joanito Liberti
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland.
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland.
| | - Tomas Kay
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Andrew Quinn
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Lucie Kesner
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Erik T Frank
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Department of Animal Ecology and Tropical Biology, University of Würzburg, Würzburg, Germany
| | - Amélie Cabirol
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Thomas O Richardson
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Philipp Engel
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland.
| | - Laurent Keller
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland.
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Yokoi K, Kimura K, Bono H. Revealing Landscapes of Transposable Elements in Apis Species by Meta-Analysis. INSECTS 2022; 13:insects13080698. [PMID: 36005323 PMCID: PMC9408917 DOI: 10.3390/insects13080698] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 07/29/2022] [Accepted: 08/01/2022] [Indexed: 12/04/2022]
Abstract
Transposable elements (TEs) are grouped into several families with diverse sequences. Owing to their diversity, studies involving the detection, classification, and annotation of TEs are difficult tasks. Moreover, simple comparisons of TEs among different species with different methods can lead to misinterpretations. The genome data of several honey bee (Apis) species are available in public databases. Therefore, we conducted a meta-analysis of TEs, using 11 sets of genome data for Apis species, in order to establish data of “landscape of TEs”. Consensus TE sequences were constructed and their distributions in the Apis genomes were determined. Our results showed that TEs belonged to four to seven TE families among 13 and 15 families of TEs detected in classes I and II respectively mainly consisted of Apis TEs and that more DNA/TcMar-Mariner consensus sequences and copies were present in all Apis genomes tested. In addition, more consensus sequences and copy numbers of DNA/TcMar-Mariner were detected in Apis mellifera than in other Apis species. These results suggest that TcMar-Mariner might exert A. mellifera-specific effects on the host A. mellifera species. In conclusion, our unified approach enabled comparison of Apis genome sequences to determine the TE landscape, which provide novel evolutionary insights into Apis species.
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Affiliation(s)
- Kakeru Yokoi
- Insect Design Technology Group, Division of Insect Advanced Technology, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), 1-2 Owashi, Tsukuba, Ibaraki 305-8634, Japan
- Correspondence: ; Tel.: +81-29-838-6129
| | - Kiyoshi Kimura
- Smart Livestock Facilities Group, Division of Advanced Feeding Technology Research, National Institute of Livestock and Grassland Science (NILGS), National Agriculture and Food Research Organization (NARO), Tsukuba, 2 Ikenodai, Tsukuba, Ibaraki 305-0901, Japan;
| | - Hidemasa Bono
- Laboratory of BioDX, Genome Editing Innovation Center, Hiroshima University, 3-10-23 Kagamiyama, Higashi-Hiroshima City, Hiroshima 739-0046, Japan;
- Laboratory of Genome Informatics, Graduate School of Integrated Sciences for Life, Hiroshima University, 3-10-23 Kagamiyama, Higashi-Hiroshima City, Hiroshima 739-0046, Japan
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44
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Zhang J, Zhu M, Li Q, Tang T, Wen L, Zhong J, Zhang R, Yu XQ, Lu Y. Genome-wide identification and characterization of basic helix-loop-helix transcription factors in Spodoptera litura upon pathogen infection. INSECT SCIENCE 2022; 29:977-992. [PMID: 34687267 DOI: 10.1111/1744-7917.12979] [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: 07/12/2021] [Revised: 09/03/2021] [Accepted: 10/05/2021] [Indexed: 06/13/2023]
Abstract
Basic helix-loop-helix (bHLH) transcription factors play an important role in a wide range of metabolic and developmental processes in eukaryotes, and bHLH proteins also participate in immune responses, especially in plants. However, their roles in insects upon entomopathogen infection are unknown. In this study, 54 bHLH genes in 41 families were identified in a polyphagous pest, Spodoptera litura, including a new bHLH gene in group B, which is specifically present in Lepidoptera and was thus named Lep. The conserved amino acids in the bHLH domain, structural architecture, and chromosomal distribution of bHLH genes in S. litura were analyzed. The bHLH genes in Plutella xylostella and Apis mellifera were also updated, and genome-wide comparison and phylogenetic analysis of bHLH members in 5 holometabolous insects were performed. The expression profiles of S. litura bHLH (SlbHLH) genes in 3 tissues at different developmental stages and their responses to S. litura nucleopolyhedrovirus (SpltNPV), Nomuraea rileyi (Nr), and Bacillus thuringiensis (Bt) infection were investigated. More SlbHLHs in group B were expressed and differentially expressed during pathogen infections, and SlbHLHs tended to be downregulated in the midgut of S. litura larvae after B. thuringiensis treatment. Our study provides an overview of bHLH family members in S. litura and their responses to different pathogens used for pest biocontrol. These findings on bHLH members may contribute to uncovering the mechanism of host-pathogen interaction.
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Affiliation(s)
- Jie Zhang
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Mengyao Zhu
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Qilin Li
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Ting Tang
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Liang Wen
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Jielai Zhong
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Ruonan Zhang
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Xiao-Qiang Yu
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, China
- Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Yuzhen Lu
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, China
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45
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Minio A, Cochetel N, Vondras AM, Massonnet M, Cantu D. Assembly of complete diploid-phased chromosomes from draft genome sequences. G3 GENES|GENOMES|GENETICS 2022; 12:6605224. [PMID: 35686922 PMCID: PMC9339290 DOI: 10.1093/g3journal/jkac143] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 05/30/2022] [Indexed: 01/27/2023]
Abstract
De novo genome assembly is essential for genomic research. High-quality genomes assembled into phased pseudomolecules are challenging to produce and often contain assembly errors because of repeats, heterozygosity, or the chosen assembly strategy. Although algorithms that produce partially phased assemblies exist, haploid draft assemblies that may lack biological information remain favored because they are easier to generate and use. We developed HaploSync, a suite of tools that produces fully phased, chromosome-scale diploid genome assemblies, and performs extensive quality control to limit assembly artifacts. HaploSync scaffolds sequences from a draft diploid assembly into phased pseudomolecules guided by a genetic map and/or the genome of a closely related species. HaploSync generates a report that visualizes the relationships between current and legacy sequences, for both haplotypes, and displays their gene and marker content. This quality control helps the user identify misassemblies and guides Haplosync’s correction of scaffolding errors. Finally, HaploSync fills assembly gaps with unplaced sequences and resolves collapsed homozygous regions. In a series of plant, fungal, and animal kingdom case studies, we demonstrate that HaploSync efficiently increases the assembly contiguity of phased chromosomes, improves completeness by filling gaps, corrects scaffolding, and correctly phases highly heterozygous, complex regions.
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Affiliation(s)
- Andrea Minio
- Department of Viticulture and Enology, University of California Davis , Davis, CA 95616, USA
| | - Noé Cochetel
- Department of Viticulture and Enology, University of California Davis , Davis, CA 95616, USA
| | - Amanda M Vondras
- Department of Viticulture and Enology, University of California Davis , Davis, CA 95616, USA
| | - Mélanie Massonnet
- Department of Viticulture and Enology, University of California Davis , Davis, CA 95616, USA
| | - Dario Cantu
- Department of Viticulture and Enology, University of California Davis , Davis, CA 95616, USA
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46
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Abstract
The question of the heritability of behavior has been of long fascination to scientists and the broader public. It is now widely accepted that most behavioral variation has a genetic component, although the degree of genetic influence differs widely across behaviors. Starting with Mendel's remarkable discovery of "inheritance factors," it has become increasingly clear that specific genetic variants that influence behavior can be identified. This goal is not without its challenges: Unlike pea morphology, most natural behavioral variation has a complex genetic architecture. However, we can now apply powerful genome-wide approaches to connect variation in DNA to variation in behavior as well as analyses of behaviorally related variation in brain gene expression, which together have provided insights into both the genetic mechanisms underlying behavior and the dynamic relationship between genes and behavior, respectively, in a wide range of species and for a diversity of behaviors. Here, we focus on two systems to illustrate both of these approaches: the genetic basis of burrowing in deer mice and transcriptomic analyses of division of labor in honey bees. Finally, we discuss the troubled relationship between the field of behavioral genetics and eugenics, which reminds us that we must be cautious about how we discuss and contextualize the connections between genes and behavior, especially in humans.
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Affiliation(s)
- Hopi E. Hoekstra
- Department of Organismic & Evolutionary Biology, Harvard University, Cambridge, MA 02138
- Department of Molecular & Cellular Biology, Harvard University, Cambridge, MA 02138
- Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138
- HHMI, Harvard University, Cambridge, MA 02138
| | - Gene E. Robinson
- Department of Entomology, University of Illinois at Urbana–Champaign, Urbana, IL 61801
- Neuroscience Program, University of Illinois at Urbana–Champaign, Urbana, IL 61801
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana–Champaign, Urbana, IL 61801
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47
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A high-quality genome of the dobsonfly Neoneuromus ignobilis reveals molecular convergences in aquatic insects. Genomics 2022; 114:110437. [PMID: 35902070 DOI: 10.1016/j.ygeno.2022.110437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Revised: 07/03/2022] [Accepted: 07/21/2022] [Indexed: 11/22/2022]
Abstract
Neoneuromus ignobilis is an archaic holometabolous aquatic predatory insect. However, a lack of genomic resources hinders the use of whole genome sequencing to explore their genetic basis and molecular mechanisms for adaptive evolution. Here, we provided a high-contiguity, chromosome-level genome assembly of N. ignobilis using high coverage Nanopore and PacBio reads with the Hi-C technique. The final assembly is 480.67 MB in size, containing 12 telomere-ended pseudochromosomes with only 17 gaps. We compared 42 hexapod species genomes including six independent lineages comprising 11 aquatic insects, and found convergent expansions of long wavelength-sensitive and blue-sensitive opsins, thermal stress response TRP channels, and sulfotransferases in aquatic insects, which may be related to their aquatic adaptation. We also detected strong nonrandom signals of convergent amino acid substitutions in aquatic insects. Collectively, our comparative genomic analysis revealed the evidence of molecular convergences in aquatic insects during both gene family evolution and convergent amino acid substitutions.
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48
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Leipart V, Ludvigsen J, Kent M, Sandve S, To TH, Árnyasi M, Kreibich CD, Dahle B, Amdam GV. Identification of 121 variants of honey bee Vitellogenin protein sequences with structural differences at functional sites. Protein Sci 2022; 31:e4369. [PMID: 35762708 PMCID: PMC9207902 DOI: 10.1002/pro.4369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 05/21/2022] [Indexed: 12/04/2022]
Abstract
Proteins are under selection to maintain central functions and to accommodate needs that arise in ever‐changing environments. The positive selection and neutral drift that preserve functions result in a diversity of protein variants. The amount of diversity differs between proteins: multifunctional or disease‐related proteins tend to have fewer variants than proteins involved in some aspects of immunity. Our work focuses on the extensively studied protein Vitellogenin (Vg), which in honey bees (Apis mellifera) is multifunctional and highly expressed and plays roles in immunity. Yet, almost nothing is known about the natural variation in the coding sequences of this protein or how amino acid‐altering variants might impact structure–function relationships. Here, we map out allelic variation in honey bee Vg using biological samples from 15 countries. The successful barcoded amplicon Nanopore sequencing of 543 bees revealed 121 protein variants, indicating a high level of diversity in Vg. We find that the distribution of non‐synonymous single nucleotide polymorphisms (nsSNPs) differs between protein regions with different functions; domains involved in DNA and protein–protein interactions contain fewer nsSNPs than the protein's lipid binding cavities. We outline how the central functions of the protein can be maintained in different variants and how the variation pattern may inform about selection from pathogens and nutrition.
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Affiliation(s)
- Vilde Leipart
- Faculty of Environmental Sciences and Natural Resource Management, Norwegian University of Life Sciences, Ås, Norway
| | - Jane Ludvigsen
- Faculty of Environmental Sciences and Natural Resource Management, Norwegian University of Life Sciences, Ås, Norway.,Fürst Medisinsk Laboratorium, Oslo, Norway
| | - Matthew Kent
- Department of Animal and Aquacultural Sciences, Centre for Integrative Genetics (CIGENE), Norwegian University of Life Sciences, Ås, Norway
| | - Simen Sandve
- Department of Animal and Aquacultural Sciences, Centre for Integrative Genetics (CIGENE), Norwegian University of Life Sciences, Ås, Norway
| | - Thu-Hien To
- Department of Animal and Aquacultural Sciences, Centre for Integrative Genetics (CIGENE), Norwegian University of Life Sciences, Ås, Norway
| | - Mariann Árnyasi
- Department of Animal and Aquacultural Sciences, Centre for Integrative Genetics (CIGENE), Norwegian University of Life Sciences, Ås, Norway
| | - Claus D Kreibich
- Faculty of Environmental Sciences and Natural Resource Management, Norwegian University of Life Sciences, Ås, Norway
| | - Bjørn Dahle
- Faculty of Environmental Sciences and Natural Resource Management, Norwegian University of Life Sciences, Ås, Norway.,Norwegian Beekeepers Association, Kløfta, Norway
| | - Gro V Amdam
- Faculty of Environmental Sciences and Natural Resource Management, Norwegian University of Life Sciences, Ås, Norway.,School of Life Sciences, Arizona State University, Tempe, Arizona, USA
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49
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Kamiyama T, Shimada-Niwa Y, Tanaka H, Katayama M, Kuwabara T, Mori H, Kunihisa A, Itoh T, Toyoda A, Niwa R. Whole-genome sequencing analysis and protocol for RNA interference of the endoparasitoid wasp Asobara japonica. DNA Res 2022; 29:6605221. [PMID: 35686927 PMCID: PMC9233498 DOI: 10.1093/dnares/dsac019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 06/06/2022] [Indexed: 11/13/2022] Open
Abstract
Asobara japonica is an endoparasitic wasp that parasitizes Drosophila flies. It synthesizes various toxic components in the venom gland and injects them into host larvae during oviposition. To identify and characterize these toxic components for enabling parasitism, we performed the whole-genome sequencing (WGS) and devised a protocol for RNA interference (RNAi) with A. japonica. Because it has a parthenogenetic lineage due to Wolbachia infection, we generated a clonal strain from a single wasp to obtain highly homogenous genomic DNA. The WGS analysis revealed that the estimated genome size was 322 Mb with a heterozygosity of 0.132%. We also performed RNA-seq analyses for gene annotation. Based on the qualified WGS platform, we cloned ebony-Aj, which encodes the enzyme N-β-alanyl dopamine synthetase, which is involved in melanin production. The microinjection of double-stranded RNA (dsRNA) targeting ebony-Aj led to body colour changes in adult wasps, phenocopying ebony-Dm mutants. Furthermore, we identified putative venom genes as a target of RNAi, confirming that dsRNA injection-based RNAi specifically suppressed the expression of the target gene in wasp adults. Taken together, our results provide a powerful genetic toolkit for studying the molecular mechanisms of parasitism.
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Affiliation(s)
- Takumi Kamiyama
- Graduate School of Life and Environmental Sciences, University of Tsukuba , Tsukuba 305-8577, Japan
- Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba , Tsukuba 305-8577, Japan
| | - Yuko Shimada-Niwa
- Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba , Tsukuba 305-8577, Japan
- Precursory Research for Embryonic Science and Technology (PREST), Japan Science and Technology Agency (JST) , Tokyo 102-0076, Japan
| | - Hiroyuki Tanaka
- Department of Biological Information, Tokyo Institute of Technology , Meguro, Tokyo 152-8550, Japan
| | - Minami Katayama
- Graduate School of Life and Environmental Sciences, University of Tsukuba , Tsukuba 305-8577, Japan
| | - Takayoshi Kuwabara
- College of Biological Sciences, University of Tsukuba , Tsukuba 305-8577, Japan
| | - Hitoha Mori
- College of Biological Sciences, University of Tsukuba , Tsukuba 305-8577, Japan
| | - Akari Kunihisa
- College of Biological Sciences, University of Tsukuba , Tsukuba 305-8577, Japan
| | - Takehiko Itoh
- Department of Biological Information, Tokyo Institute of Technology , Meguro, Tokyo 152-8550, Japan
| | - Atsushi Toyoda
- Comparative Genomics Laboratory, National Institute of Genetics , Mishima, Shizuoka 411-8540, Japan
| | - Ryusuke Niwa
- Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba , Tsukuba 305-8577, Japan
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Li Q, Li M, Zhu M, Zhong J, Wen L, Zhang J, Zhang R, Gao Q, Yu XQ, Lu Y. Genome-wide identification and comparative analysis of Cry toxin receptor families in 7 insect species with a focus on Spodoptera litura. INSECT SCIENCE 2022; 29:783-800. [PMID: 34405540 DOI: 10.1111/1744-7917.12961] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 07/30/2021] [Accepted: 08/12/2021] [Indexed: 06/13/2023]
Abstract
Cadherin, aminopeptidase N (APN) and alkaline phosphatase (ALP) have been characterized as Cry receptors. In this study, comparative genomic analysis of the 3 receptor families was performed in 7 insects. ALPs and APNs are divided into three and eight clades in phylogenetic trees, respectively. ALPs in clade 3 and APNs in clade 1 contain multiple paralogs within each species and most paralogs are located closely in chromosomes. Drosophila melanogaster has expanded APNs in clade 5 and were lowly expressed in midgut. Cadherins are divided into 16 clades; they may diverge before holometabolous insect speciation except for BtR and Cad89D-like clades. Eight insects from different orders containing BtR orthologs are sensitive to Cry1A or Cry3A, while five species without BtR are insensitive to both toxins. Most APNs in clade 1, several ALPs in clade 3, BtR and Cad89D-like genes were highly or moderately expressed in larval midgut of Spodoptera litura and the other six species, and several members in these clades have been identified as Cry receptors. Expressions of putative S. litura Cry receptors in the midgut after exposing to Bt toxins were also analyzed.
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Affiliation(s)
- Qilin Li
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Mengge Li
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Mengyao Zhu
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Jielai Zhong
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Liang Wen
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Jie Zhang
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Ruonan Zhang
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Qiang Gao
- College of Biology, Hunan University, Changsha, 410082, China
| | - Xiao-Qiang Yu
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Yuzhen Lu
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
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