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Pei H, Xie G, Yao X, Wang S, Yan J, Dai L, Wang Y. Exploring the binding affinity and characteristics of DcitOBP9 in citrus psyllids. Gene 2024; 923:148551. [PMID: 38759737 DOI: 10.1016/j.gene.2024.148551] [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: 01/31/2024] [Revised: 04/17/2024] [Accepted: 05/08/2024] [Indexed: 05/19/2024]
Abstract
Odorant-binding proteins (OBPs) are crucial in insect olfaction. The most abundant expressed OBP of citrus psyllids, DcitOBP9 encodes 148 amino acids. DcitOBP9 lacks a transmembrane structure and possesses a 17-amino acid signal peptide at the N-terminus. Characterized by the six conserved cysteine sites, DcitOBP9 is classified as the Classical-OBP family. RT-qPCR experiments revealed ubiquitous expression of DcitOBP9 across all developmental stages of the citrus psyllid, with predominant expression in adults antennae. Fluorescence competitive binding assays demonstrated DcitOBP9's strong affinity for ocimene, linalool, dodecanoic acid, and citral, and moderate affinity for dimethyl trisulfide. Additionally, it binds to myrcia, (-)-trans-caryophyllene, (±)-Citronellal, nonanal, and (+)-α-pinene. Among them, ocimene, linalool, and dodecanoic acid were dynamically bound to DcitOBP9, while citral was statically bound to DcitOBP9. Molecular docking simulations with the top five ligands indicated that amino acid residues V92, S72, P128, L91, L75, and A76 are pivotal in the interaction between DcitOBP9 and these odorants. These findings suggest DcitOBP9's involvement in the citrus psyllid's host plant recognition and selection behaviors, thereby laying a foundation for elucidating the potential physiological and biological functions of DcitOBP9 and developing attractants.
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Affiliation(s)
- Haoran Pei
- College of Plant Protection, Hunan Agricultural University, Changsha, Hunan 410128, China
| | - Gang Xie
- College of Plant Protection, Hunan Agricultural University, Changsha, Hunan 410128, China
| | - Xiang Yao
- College of Plant Protection, Hunan Agricultural University, Changsha, Hunan 410128, China
| | - Shenghui Wang
- College of Plant Protection, Hunan Agricultural University, Changsha, Hunan 410128, China
| | - Jin Yan
- College of Food Science and Technology, Hunan Agricultural University, Changsha, Hunan 410128, China
| | - Liangying Dai
- College of Plant Protection, Hunan Agricultural University, Changsha, Hunan 410128, China.
| | - Yunsheng Wang
- College of Plant Protection, Hunan Agricultural University, Changsha, Hunan 410128, China.
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2
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Gouda MNR, Subramanian S. Variations in the expression of odorant binding and chemosensory proteins in the developmental stages of whitefly Bemisia tabaci Asia II-1. Sci Rep 2024; 14:15046. [PMID: 38951601 PMCID: PMC11217293 DOI: 10.1038/s41598-024-65785-9] [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: 01/10/2024] [Accepted: 06/24/2024] [Indexed: 07/03/2024] Open
Abstract
The cotton whitefly, Bemisia tabaci, is considered as a species complex with 46 cryptic species, with Asia II-1 being predominant in Asia. This study addresses a significant knowledge gap in the characterization of odorant-binding proteins (OBPs) and chemosensory proteins (CSPs) in Asia II-1. We explored the expression patterns of OBPs and CSPs throughout their developmental stages and compared the motif patterns of these proteins. Significant differences in expression patterns were observed for the 14 OBPs and 14 CSPs of B. tabaci Asia II-1, with OBP8 and CSP4 showing higher expression across the developmental stages. Phylogenetic analysis reveals that OBP8 and CSP4 form distinct clades, with OBP8 appearing to be an ancestral gene, giving rise to the evolution of other odorant-binding proteins in B. tabaci. The genomic distribution of OBPs and CSPs highlights gene clustering on the chromosomes, suggesting functional conservation and evolutionary events following the birth-and-death model. Molecular docking studies indicate strong binding affinities of OBP8 and CSP4 with various odour compounds like β-caryophyllene, α-pinene, β-pinene and limonene, reinforcing their roles in host recognition and reproductive functions. This study elaborates on our understanding of the putative roles of different OBPs and CSPs in B. tabaci Asia II-1, hitherto unexplored. The dynamics of the expression of OBPs and CSPs and their interactions with odour compounds offer scope for developing innovative methods for controlling this global invasive pest.
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Affiliation(s)
- M N Rudra Gouda
- Division of Entomology, Indian Agricultural Research Institute, New Delhi, 110012, India
| | - S Subramanian
- Division of Entomology, Indian Agricultural Research Institute, New Delhi, 110012, India.
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3
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Pisarenco VA, Vizueta J, Rozas J. GALEON: a comprehensive bioinformatic tool to analyse and visualize gene clusters in complete genomes. Bioinformatics 2024; 40:btae439. [PMID: 38976642 PMCID: PMC11236287 DOI: 10.1093/bioinformatics/btae439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Revised: 06/12/2024] [Accepted: 07/05/2024] [Indexed: 07/10/2024] Open
Abstract
MOTIVATION Gene clusters, defined as a set of genes encoding functionally related proteins, are abundant in eukaryotic genomes. Despite the increasing availability of chromosome-level genomes, the comprehensive analysis of gene family evolution remains largely unexplored, particularly for large and highly dynamic gene families or those including very recent family members. These challenges stem from limitations in genome assembly contiguity, particularly in repetitive regions such as large gene clusters. Recent advancements in sequencing technology, such as long reads and chromatin contact mapping, hold promise in addressing these challenges. RESULTS To facilitate the identification, analysis, and visualization of physically clustered gene family members within chromosome-level genomes, we introduce GALEON, a user-friendly bioinformatic tool. GALEON identifies gene clusters by studying the spatial distribution of pairwise physical distances among gene family members along with the genome-wide gene density. The pipeline also enables the simultaneous analysis and comparison of two gene families and allows the exploration of the relationship between physical and evolutionary distances. This tool offers a novel approach for studying the origin and evolution of gene families. AVAILABILITY AND IMPLEMENTATION GALEON is freely available from https://www.ub.edu/softevol/galeon and https://github.com/molevol-ub/galeon.
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Affiliation(s)
- Vadim A Pisarenco
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Barcelona 08028, Spain
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona 08028, Spain
| | - Joel Vizueta
- Villum Centre for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen 2100, Denmark
| | - Julio Rozas
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Barcelona 08028, Spain
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona 08028, Spain
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4
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Park K, Choi H, Han IJ, Asefa WR, Jeong C, Yu S, Jeong H, Choi M, Yoon SE, Kim YJ, Choi MS, Kwon JY. Molecular and cellular organization of odorant binding protein genes in Drosophila. Heliyon 2024; 10:e29358. [PMID: 38694054 PMCID: PMC11058302 DOI: 10.1016/j.heliyon.2024.e29358] [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: 02/22/2024] [Revised: 04/01/2024] [Accepted: 04/05/2024] [Indexed: 05/03/2024] Open
Abstract
Chemosensation is important for the survival and reproduction of animals. The odorant binding proteins (OBPs) are thought to be involved in chemosensation together with chemosensory receptors. While OBPs were initially considered to deliver hydrophobic odorants to olfactory receptors in the aqueous lymph solution, recent studies suggest more complex roles in various organs. Here, we use GAL4 transgenes to systematically analyze the expression patterns of all 52 members of the Obp gene family and 3 related chemosensory protein genes in adult Drosophila, focusing on chemosensory organs such as the antenna, maxillary palp, pharynx, and labellum, and other organs such as the brain, ventral nerve cord, leg, wing, and intestine. The OBPs were observed to express in diverse organs and in multiple cell types, suggesting that these proteins can indeed carry out diverse functional roles. Also, we constructed 10 labellar-expressing Obp mutants, and obtained behavioral evidence that these OBPs may be involved in bitter sensing. The resources we constructed should be useful for future Drosophila OBP gene family research.
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Affiliation(s)
- Keehyun Park
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Hyungjun Choi
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - I Joon Han
- Sungkyunkwan University School of Medicine, Seoul, 06351, Republic of Korea
| | - Wayessa Rahel Asefa
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Chaiyoung Jeong
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Seungyun Yu
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Hanhee Jeong
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Minkook Choi
- Department of Oral Biology, Yonsei University College of Dentistry, Seoul, 03722, Republic of Korea
| | - Sung-Eun Yoon
- Korea Drosophila Resource Center, Gwangju, 61005, Republic of Korea
| | - Young-Joon Kim
- Korea Drosophila Resource Center, Gwangju, 61005, Republic of Korea
- School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju, 61005, Republic of Korea
| | - Min Sung Choi
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Jae Young Kwon
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Republic of Korea
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5
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Wang L, Hou M, Liang C, Xu Q, Lu Y, Zhao Z. Role of odorant binding protein C12 in the response of Tribolium castaneum to chemical agents. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2024; 201:105861. [PMID: 38685215 DOI: 10.1016/j.pestbp.2024.105861] [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: 09/07/2023] [Revised: 03/08/2024] [Accepted: 03/09/2024] [Indexed: 05/02/2024]
Abstract
Tribolium castaneum is a worldwide pest of stored grain that mainly damages flour, and not only causes serious loss of flour quality but also leads to deterioration of flour quality. Chemical detection plays a key role in insect behavior, and the role of odorant-binding proteins (OBPs) in insect chemical detection has been widely studied. OBPs can interact with small molecule compounds and thereby modulate variation in insecticide susceptibility in insects. In this study, a total of 65 small molecule compounds are selected to investigate the bound effect with TcOBP C12. The molecular docking results showed that β-caryophyllene, (-)-catechin, butylated hydroxytoluene, diphenyl phthalate and quercetin were the top five compounds, with docking binding energies of -6.11, -5.25, -5.09, -5.05, and - 5.03 Kcal/mol, respectively. Molecular dynamics analysis indicated that odorant binding protein C12 (TcOBP C12) exhibited high binding affinity to all five tested chemical ligands, evidenced by fluorescence quenching assay in vitro. In addition, the contact toxicity assay results suggested that these chemical agents caused a dose-dependent increase in mortality rate for T. castaneum adults. The TcOBP C12 gene was upregulated >2 times after a 24-h exposure, indicating that OBP C12 may play an important role for T. castaneum in response to these chemical agents. In conclusion, our results provide a theoretical basis for future insecticide experiments and pest management.
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Affiliation(s)
- Lei Wang
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang 212100, PR China
| | - Mingrui Hou
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang 212100, PR China
| | - Chuanqi Liang
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang 212100, PR China
| | - Qingfen Xu
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang 212100, PR China
| | - Yujie Lu
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang 212100, PR China; Jiangsu Provincial Engineering Research Center of Grain Bioprocessing, Zhenjiang 212100, PR China.
| | - Zongpei Zhao
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang 212100, PR China; Jiangsu Provincial Engineering Research Center of Grain Bioprocessing, Zhenjiang 212100, PR China.
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Rondón JJ, Pisarenco VA, Ramón Pardos-Blas J, Sánchez-Gracia A, Zardoya R, Rozas J. Comparative genomic analysis of chemosensory-related gene families in gastropods. Mol Phylogenet Evol 2024; 192:107986. [PMID: 38142794 DOI: 10.1016/j.ympev.2023.107986] [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: 07/18/2023] [Revised: 11/24/2023] [Accepted: 12/07/2023] [Indexed: 12/26/2023]
Abstract
Chemoreception is critical for the survival and reproduction of animals. Except for a reduced group of insects and chelicerates, the molecular identity of chemosensory proteins is poorly understood in invertebrates. Gastropoda is the extant mollusk class with the greatest species richness, including marine, freshwater, and terrestrial lineages, and likely, highly diverse chemoreception systems. Here, we performed a comprehensive comparative genome analysis taking advantage of the chromosome-level information of two Gastropoda species, one of which belongs to a lineage that underwent a whole genome duplication event. We identified thousands of previously uncharacterized chemosensory-related genes, the majority of them encoding G protein-coupled receptors (GPCR), mostly organized into clusters distributed across all chromosomes. We also detected gene families encoding degenerin epithelial sodium channels (DEG-ENaC), ionotropic receptors (IR), sensory neuron membrane proteins (SNMP), Niemann-Pick type C2 (NPC2) proteins, and lipocalins, although with a lower number of members. Our phylogenetic analysis of the GPCR gene family across protostomes revealed: (i) remarkable gene family expansions in Gastropoda; (ii) clades including members from all protostomes; and (iii) species-specific clades with a substantial number of receptors. For the first time, we provide new and valuable knowledge into the evolution of the chemosensory gene families in invertebrates other than arthropods.
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Affiliation(s)
- Johnma José Rondón
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA-CONICET), Buenos Aires, Argentina; Instituto de Ecología, Genética y Evolución de Buenos Aires (IEGEBA-CONICET) Buenos Aires, Argentina
| | - Vadim A Pisarenco
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona (UB), Barcelona, Spain; Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona (UB), Barcelona, Spain
| | - José Ramón Pardos-Blas
- Departamento de Biodiversidad y Biologı́a Evolutiva, Museo Nacional de Ciencias Naturales (MNCN-CSIC), Madrid, Spain
| | - Alejandro Sánchez-Gracia
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona (UB), Barcelona, Spain; Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona (UB), Barcelona, Spain
| | - Rafael Zardoya
- Departamento de Biodiversidad y Biologı́a Evolutiva, Museo Nacional de Ciencias Naturales (MNCN-CSIC), Madrid, Spain.
| | - Julio Rozas
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona (UB), Barcelona, Spain; Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona (UB), Barcelona, Spain.
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7
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Wang JJ, Ma C, Yue Y, Yang J, Chen LX, Wang YT, Zhao CC, Gao X, Chen HS, Ma WH, Zhou Z. Identification of candidate chemosensory genes in Bactrocera cucurbitae based on antennal transcriptome analysis. Front Physiol 2024; 15:1354530. [PMID: 38440345 PMCID: PMC10910661 DOI: 10.3389/fphys.2024.1354530] [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: 12/13/2023] [Accepted: 01/24/2024] [Indexed: 03/06/2024] Open
Abstract
The melon fly, Bactrocera cucurbitae (Coquillett) (Tephritidae: Diptera), is an invasive pest that poses a significant threat to agriculture in Africa and other regions. Flies are known to use their olfactory systems to recognise environmental chemical cues. However, the molecular components of the chemosensory system of B. cucurbitae are poorly characterised. To address this knowledge gap, we have used next-generation sequencing to analyse the antenna transcriptomes of sexually immature B. cucurbitae adults. The results have identified 160 potential chemosensory genes, including 35 odourant-binding proteins (OBPs), one chemosensory protein (CSP), three sensory neuron membrane proteins (SNMPs), 70 odourant receptors (ORs), 30 ionotropic receptors (IRs), and 21 gustatory receptors (GRs). Quantitative real-time polymerase chain reaction quantitative polymerase chain reaction was used to validate the results by assessing the expression profiles of 25 ORs and 15 OBPs. Notably, high expression levels for BcucOBP5/9/10/18/21/23/26 were observed in both the female and male antennae. Furthermore, BcucOROrco/6/7/9/13/15/25/27/28/42/62 exhibited biased expression in the male antennae, whereas BcucOR55 showed biased expression in the female antennae. This comprehensive investigation provides valuable insights into insect olfaction at the molecular level and will, thus, help to facilitate the development of enhanced pest management strategies in the future.
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Affiliation(s)
- Jing Jing Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
- National Nanfan Research Institute, Chinese Academy of Agricultural Sciences, Sanya, China
| | - Chao Ma
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
- National Nanfan Research Institute, Chinese Academy of Agricultural Sciences, Sanya, China
| | - Yang Yue
- National Nanfan Research Institute, Chinese Academy of Agricultural Sciences, Sanya, China
| | - Jingfang Yang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
- National Nanfan Research Institute, Chinese Academy of Agricultural Sciences, Sanya, China
| | - Li Xiang Chen
- National Nanfan Research Institute, Chinese Academy of Agricultural Sciences, Sanya, China
| | - Yi Ting Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
- National Nanfan Research Institute, Chinese Academy of Agricultural Sciences, Sanya, China
| | | | - Xuyuan Gao
- National Nanfan Research Institute, Chinese Academy of Agricultural Sciences, Sanya, China
- Guangxi Key Laboratory for Biology of Crop Diseases and Insect Pests, Institute of Plant Protection, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Hong Song Chen
- National Nanfan Research Institute, Chinese Academy of Agricultural Sciences, Sanya, China
- Guangxi Key Laboratory for Biology of Crop Diseases and Insect Pests, Institute of Plant Protection, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Wei Hua Ma
- Hubei Insect Resources Utilization and Sustainable Pest Management Key Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Zhongshi Zhou
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
- National Nanfan Research Institute, Chinese Academy of Agricultural Sciences, Sanya, China
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8
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Brown NC, Gordon B, McDonough-Goldstein CE, Misra S, Findlay GD, Clark AG, Wolfner MF. The seminal odorant binding protein Obp56g is required for mating plug formation and male fertility in Drosophila melanogaster. eLife 2023; 12:e86409. [PMID: 38126735 PMCID: PMC10834028 DOI: 10.7554/elife.86409] [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: 01/24/2023] [Accepted: 12/20/2023] [Indexed: 12/23/2023] Open
Abstract
In Drosophila melanogaster and other insects, the seminal fluid proteins (SFPs) and male sex pheromones that enter the female with sperm during mating are essential for fertility and induce profound post-mating effects on female physiology. The SFPs in D. melanogaster and other taxa include several members of the large gene family known as odorant binding proteins (Obps). Work in Drosophila has shown that some Obp genes are highly expressed in the antennae and can mediate behavioral responses to odorants, potentially by binding and carrying these molecules to odorant receptors. These observations have led to the hypothesis that the seminal Obps might act as molecular carriers for pheromones or other compounds important for male fertility, though functional evidence in any species is lacking. Here, we used functional genetics to test the role of the seven seminal Obps in D. melanogaster fertility and the post-mating response (PMR). We found that Obp56g is required for male fertility and the induction of the PMR, whereas the other six genes are dispensable. We found males lacking Obp56g fail to form a mating plug in the mated female's reproductive tract, leading to ejaculate loss and reduced sperm storage, likely due to its expression in the male ejaculatory bulb. We also examined the evolutionary history of these seminal Obp genes, as several studies have documented rapid evolution and turnover of SFP genes across taxa. We found extensive lability in gene copy number and evidence of positive selection acting on two genes, Obp22a and Obp51a. Comparative RNAseq data from the male reproductive tract of multiple Drosophila species revealed that Obp56g shows high male reproductive tract expression in a subset of taxa, though conserved head expression across the phylogeny. Together, these functional and expression data suggest that Obp56g may have been co-opted for a reproductive function over evolutionary time.
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Affiliation(s)
- Nora C Brown
- Department of Molecular Biology and Genetics, Cornell UniversityIthacaUnited States
| | - Benjamin Gordon
- Department of Molecular Biology and Genetics, Cornell UniversityIthacaUnited States
| | | | - Snigdha Misra
- Department of Molecular Biology and Genetics, Cornell UniversityIthacaUnited States
| | - Geoffrey D Findlay
- Department of Molecular Biology and Genetics, Cornell UniversityIthacaUnited States
- Department of Biology, College of the Holy CrossWorcesterUnited States
| | - Andrew G Clark
- Department of Molecular Biology and Genetics, Cornell UniversityIthacaUnited States
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9
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Dey M, Brown E, Charlu S, Keene A, Dahanukar A. Evolution of fatty acid taste in drosophilids. Cell Rep 2023; 42:113297. [PMID: 37864792 PMCID: PMC10697176 DOI: 10.1016/j.celrep.2023.113297] [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: 02/06/2023] [Revised: 09/01/2023] [Accepted: 10/02/2023] [Indexed: 10/23/2023] Open
Abstract
Comparative studies of related but ecologically distinct species can reveal how the nervous system evolves to drive behaviors that are particularly suited to certain environments. Drosophila melanogaster is a generalist that feeds and oviposits on most overripe fruits. A sibling species, D. sechellia, is an obligate specialist of Morinda citrifolia (noni) fruit, which is rich in fatty acids (FAs). To understand evolution of noni taste preference, we characterized behavioral and cellular responses to noni-associated FAs in three related drosophilids. We find that mixtures of sugar and noni FAs evoke strong aversion in the generalist species but not in D. sechellia. Surveys of taste sensory responses reveal noni FA- and species-specific differences in at least two mechanisms-bitter neuron activation and sweet neuron inhibition-that correlate with shifts in noni preference. Chemoreceptor mutant analysis in D. melanogaster predicts that multiple genetic changes account for evolution of gustatory preference in D. sechellia.
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Affiliation(s)
- Manali Dey
- Interdepartmental Neuroscience Program, University of California, Riverside, Riverside, CA 92521, USA
| | - Elizabeth Brown
- Department of Biology, Texas A&M University, College Station, TX 77843, USA
| | - Sandhya Charlu
- Biomedical Sciences Graduate Program, University of California, Riverside, Riverside, CA 92521, USA
| | - Alex Keene
- Department of Biology, Texas A&M University, College Station, TX 77843, USA
| | - Anupama Dahanukar
- Interdepartmental Neuroscience Program, University of California, Riverside, Riverside, CA 92521, USA; Biomedical Sciences Graduate Program, University of California, Riverside, Riverside, CA 92521, USA; Department of Molecular, Cell & Systems Biology, University of California, Riverside, Riverside, CA 92521, USA.
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10
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Enge S, Mérot C, Mozūraitis R, Apšegaitė V, Bernatchez L, Martens GA, Radžiutė S, Pavia H, Berdan EL. A supergene in seaweed flies modulates male traits and female perception. Proc Biol Sci 2023; 290:20231494. [PMID: 37817592 PMCID: PMC10565388 DOI: 10.1098/rspb.2023.1494] [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: 07/11/2023] [Accepted: 09/18/2023] [Indexed: 10/12/2023] Open
Abstract
Supergenes, tightly linked sets of alleles, offer some of the most spectacular examples of polymorphism persisting under long-term balancing selection. However, we still do not understand their evolution and persistence, especially in the face of accumulation of deleterious elements. Here, we show that an overdominant supergene in seaweed flies, Coelopa frigida, modulates male traits, potentially facilitating disassortative mating and promoting intraspecific polymorphism. Across two continents, the Cf-Inv(1) supergene strongly affected the composition of male cuticular hydrocarbons (CHCs) but only weakly affected CHC composition in females. Using gas chromatography-electroantennographic detection, we show that females can sense male CHCs and that there may be differential perception between genotypes. Combining our phenotypic results with RNA-seq data, we show that candidate genes for CHC biosynthesis primarily show differential expression for Cf-Inv(1) in males but not females. Conversely, candidate genes for odorant detection were differentially expressed in both sexes but showed high levels of divergence between supergene haplotypes. We suggest that the reduced recombination between supergene haplotypes may have led to rapid divergence in mate preferences as well as increasing linkage between male traits, and overdominant loci. Together this probably helped to maintain the polymorphism despite deleterious effects in homozygotes.
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Affiliation(s)
- Swantje Enge
- Department of Marine Sciences, University of Gothenburg, Tjärnö, Sweden
| | - Claire Mérot
- Département de biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Canada
- CNRS UMR 6553 Ecobio, Université de Rennes, OSUR, Rennes, France
| | - Raimondas Mozūraitis
- Department of Zoology, Stockholm University, Stockholm, Sweden
- Laboratory of Chemical and Behavioural Ecology, Institute of Ecology, Nature Research Centre, Vilnius, Lithuania
| | - Violeta Apšegaitė
- Laboratory of Chemical and Behavioural Ecology, Institute of Ecology, Nature Research Centre, Vilnius, Lithuania
| | - Louis Bernatchez
- Département de biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Canada
| | - Gerrit A. Martens
- Institute of Cell and Systems Biology of Animals, University of Hamburg, Hamburg, Germany
| | - Sandra Radžiutė
- Laboratory of Chemical and Behavioural Ecology, Institute of Ecology, Nature Research Centre, Vilnius, Lithuania
| | - Henrik Pavia
- Department of Marine Sciences, University of Gothenburg, Tjärnö, Sweden
| | - Emma L. Berdan
- Department of Marine Sciences, University of Gothenburg, Tjärnö, Sweden
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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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12
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Jia C, Mohamed A, Cattaneo AM, Huang X, Keyhani NO, Gu M, Zang L, Zhang W. Odorant-Binding Proteins and Chemosensory Proteins in Spodoptera frugiperda: From Genome-Wide Identification and Developmental Stage-Related Expression Analysis to the Perception of Host Plant Odors, Sex Pheromones, and Insecticides. Int J Mol Sci 2023; 24:ijms24065595. [PMID: 36982668 PMCID: PMC10056595 DOI: 10.3390/ijms24065595] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 02/22/2023] [Accepted: 02/24/2023] [Indexed: 03/17/2023] Open
Abstract
Spodoptera frugiperda is a worldwide generalist pest with remarkable adaptations to environments and stresses, including developmental stage-related behavioral and physiological adaptations, such as diverse feeding preferences, mate seeking, and pesticide resistance. Insects’ odorant-binding proteins (OBPs) and chemosensory proteins (CSPs) are essential for the chemical recognition during behavioral responses or other physiological processes. The genome-wide identification and the gene expression patterns of all these identified OBPs and CSPs across developmental stage-related S. frugiperda have not been reported. Here, we screened for genome-wide SfruOBPs and SfruCSPs, and analyzed the gene expression patterns of SfruOBPs and SfruCSPs repertoires across all developmental stages and sexes. We found 33 OBPs and 22 CSPs in the S. frugiperda genome. The majority of the SfruOBP genes were most highly expressed in the adult male or female stages, while more SfruCSP genes were highly expressed in the larval or egg stages, indicating their function complementation. The gene expression patterns of SfruOBPs and SfruCSPs revealed strong correlations with their respective phylogenic trees, indicating a correlation between function and evolution. In addition, we analyzed the chemical-competitive binding of a widely expressed protein, SfruOBP31, to host plant odorants, sex pheromones, and insecticides. Further ligands binding assay revealed a broad functional related binding spectrum of SfruOBP31 to host plant odorants, sex pheromones, and insecticides, suggesting its potential function in food, mate seeking, and pesticide resistance. These results provide guidance for future research on the development of behavioral regulators of S. frugiperda or other environmentally friendly pest-control strategies.
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Affiliation(s)
- Chen Jia
- National Key Laboratory of Green Pesticide, Guizhou University, Guiyang 550025, China
- Key Laboratory of Green Pesticide and Agricultural Bioengineering (Ministry of Education), Guizhou University, Guiyang 550025, China
| | - Amr Mohamed
- Department of Entomology, Faculty of Science, Cairo University, Giza 12613, Egypt
- Division of Invertebrate Zoology, American Museum of Natural History, 200 Central Park West, New York, NY 10024, USA
| | - Alberto Maria Cattaneo
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Box 190, Lomma—Campus Alnarp, 234 22 Lomma, Sweden
| | - Xiaohua Huang
- National Key Laboratory of Green Pesticide, Guizhou University, Guiyang 550025, China
- Key Laboratory of Green Pesticide and Agricultural Bioengineering (Ministry of Education), Guizhou University, Guiyang 550025, China
| | - Nemat O. Keyhani
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA
| | - Maiqun Gu
- National Key Laboratory of Green Pesticide, Guizhou University, Guiyang 550025, China
- Key Laboratory of Green Pesticide and Agricultural Bioengineering (Ministry of Education), Guizhou University, Guiyang 550025, China
| | - Liansheng Zang
- National Key Laboratory of Green Pesticide, Guizhou University, Guiyang 550025, China
- Key Laboratory of Green Pesticide and Agricultural Bioengineering (Ministry of Education), Guizhou University, Guiyang 550025, China
| | - Wei Zhang
- National Key Laboratory of Green Pesticide, Guizhou University, Guiyang 550025, China
- Key Laboratory of Green Pesticide and Agricultural Bioengineering (Ministry of Education), Guizhou University, Guiyang 550025, China
- Correspondence:
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13
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Mokashi SS, Shankar V, Johnstun JA, Mackay TFC, Anholt RRH. Pleiotropic fitness effects of a Drosophila odorant-binding protein. G3 (BETHESDA, MD.) 2023; 13:jkac307. [PMID: 36454098 PMCID: PMC9911060 DOI: 10.1093/g3journal/jkac307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 11/11/2022] [Accepted: 11/14/2022] [Indexed: 12/05/2022]
Abstract
Insect odorant-binding proteins (OBPs) are members of a rapidly evolving multigene family traditionally thought to facilitate chemosensation. However, studies on Drosophila have shown that members of this family have evolved functions beyond chemosensation, as evident from their expression in reproductive tissues and the brain. Previous studies implicated diverse functions of Obp56h, a member of the largest gene cluster of the D. melanogaster Obp repertoire. Here, we examined the effect of CRISPR/Cas9-mediated deletion of Obp56h on 2 fitness phenotypes, on resistance to starvation stress and heat stress, and on locomotion and sleep phenotypes. Obp56h-/- mutants show a strong sexually dimorphic effect on starvation stress survival, with females being more resistant to starvation stress than the control. In contrast, Obp56h-/- females, but not males, are highly sensitive to heat stress. Both sexes show changes in locomotion and sleep patterns. Transcriptional profiling of RNA from heads of Obp56h-/- flies and the wildtype control reveals differentially expressed genes, including gene products associated with antimicrobial immune responses and members of the Turandot family of stress-induced secreted peptides. In addition, differentially expressed genes of unknown function were identified in both sexes. Genes encoding components of the mitochondrial electron transport chain, cuticular proteins, gene products associated with regulation of feeding behavior (Lst and CCHa2), ribosomal proteins, lncRNAs, snoRNAs, tRNAs, and snRNAs show changes in transcript abundances in Obp56h-/- females. These differentially expressed genes are likely to contribute to Obp56h-mediated effects on the diverse phenotypes that arise upon deletion of this OBP.
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Affiliation(s)
- Sneha S Mokashi
- Department of Genetics and Biochemistry and Center for Human Genetics, Clemson University, 114 Gregor Mendel Circle, Greenwood, SC 29646, USA
| | - Vijay Shankar
- Department of Genetics and Biochemistry and Center for Human Genetics, Clemson University, 114 Gregor Mendel Circle, Greenwood, SC 29646, USA
| | - Joel A Johnstun
- Department of Biological Sciences, Program in Genetics, North Carolina State University, Raleigh, NC 27695, USA
| | - Trudy F C Mackay
- Department of Genetics and Biochemistry and Center for Human Genetics, Clemson University, 114 Gregor Mendel Circle, Greenwood, SC 29646, USA
| | - Robert R H Anholt
- Department of Genetics and Biochemistry and Center for Human Genetics, Clemson University, 114 Gregor Mendel Circle, Greenwood, SC 29646, USA
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14
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Brown NC, Gordon B, McDonough-Goldstein CE, Misra S, Findlay GD, Clark AG, Wolfner MF. The seminal odorant binding protein Obp56g is required for mating plug formation and male fertility in Drosophila melanogaster. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.03.526941. [PMID: 36798169 PMCID: PMC9934574 DOI: 10.1101/2023.02.03.526941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
In Drosophila melanogaster and other insects, the seminal fluid proteins (SFPs) and male sex pheromones that enter the female with sperm during mating are essential for fertility and induce profound post-mating effects on female physiology and behavior. The SFPs in D. melanogaster and other taxa include several members of the large gene family known as odorant binding proteins (Obps). Previous work in Drosophila has shown that some Obp genes are highly expressed in the antennae and can mediate behavioral responses to odorants, potentially by binding and carrying these molecules to odorant receptors. These observations have led to the hypothesis that the seminal Obps might act as molecular carriers for pheromones or other compounds important for male fertility in the ejaculate, though functional evidence in any species is lacking. Here, we used RNAi and CRISPR/Cas9 generated mutants to test the role of the seven seminal Obps in D. melanogaster fertility and the post-mating response (PMR). We found that Obp56g is required for male fertility and the induction of the PMR, whereas the other six genes had no effect on fertility when mutated individually. Obp56g is expressed in the male's ejaculatory bulb, an important tissue in the reproductive tract that synthesizes components of the mating plug. We found males lacking Obp56g fail to form a mating plug in the mated female's reproductive tract, leading to ejaculate loss and reduced sperm storage. We also examined the evolutionary history of these seminal Obp genes, as several studies have documented rapid evolution and turnover of SFP genes across taxa. We found extensive lability in gene copy number and evidence of positive selection acting on two genes, Obp22a and Obp51a. Comparative RNAseq data from the male reproductive tract of multiple Drosophila species revealed that Obp56g shows high male reproductive tract expression only in species of the melanogaster and obscura groups, though conserved head expression in all species tested. Together, these functional and expression data suggest that Obp56g may have been co-opted for a reproductive function over evolutionary time.
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Affiliation(s)
- Nora C. Brown
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, United States
| | - Benjamin Gordon
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, United States
- Present address: Department of Physiology and Biophysics, University of Illinois College of Medicine, Chicago, IL, United States
| | | | - Snigdha Misra
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, United States
- Present address: University of Petroleum and Energy Studies, Dehradun, UK, India
| | - Geoffrey D. Findlay
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, United States
- Department of Biology, College of the Holy Cross, Worcester, MA, United States
| | - Andrew G. Clark
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, United States
| | - Mariana F. Wolfner
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, United States
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15
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Coates BS, Walden KKO, Lata D, Vellichirammal NN, Mitchell RF, Andersson MN, McKay R, Lorenzen MD, Grubbs N, Wang YH, Han J, Xuan JL, Willadsen P, Wang H, French BW, Bansal R, Sedky S, Souza D, Bunn D, Meinke LJ, Miller NJ, Siegfried BD, Sappington TW, Robertson HM. A draft Diabrotica virgifera virgifera genome: insights into control and host plant adaption by a major maize pest insect. BMC Genomics 2023; 24:19. [PMID: 36639634 PMCID: PMC9840275 DOI: 10.1186/s12864-022-08990-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 11/04/2022] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND Adaptations by arthropod pests to host plant defenses of crops determine their impacts on agricultural production. The larval host range of western corn rootworm, Diabrotica virgifera virgifera (Coleoptera: Chrysomelidae), is restricted to maize and a few grasses. Resistance of D. v. virgifera to crop rotation practices and multiple insecticides contributes to its status as the most damaging pest of cultivated maize in North America and Europe. The extent to which adaptations by this pest contributes to host plant specialization remains unknown. RESULTS A 2.42 Gb draft D. v. virgifera genome, Dvir_v2.0, was assembled from short shotgun reads and scaffolded using long-insert mate-pair, transcriptome and linked read data. K-mer analysis predicted a repeat content of ≥ 61.5%. Ortholog assignments for Dvir_2.0 RefSeq models predict a greater number of species-specific gene duplications, including expansions in ATP binding cassette transporter and chemosensory gene families, than in other Coleoptera. A majority of annotated D. v. virgifera cytochrome P450s belong to CYP4, 6, and 9 clades. A total of 5,404 transcripts were differentially-expressed between D. v. virgifera larvae fed maize roots compared to alternative host (Miscanthus), a marginal host (Panicum virgatum), a poor host (Sorghum bicolor) and starvation treatments; Among differentially-expressed transcripts, 1,908 were shared across treatments and the least number were between Miscanthus compared to maize. Differentially-expressed transcripts were enriched for putative spliceosome, proteosome, and intracellular transport functions. General stress pathway functions were unique and enriched among up-regulated transcripts in marginal host, poor host, and starvation responses compared to responses on primary (maize) and alternate hosts. CONCLUSIONS Manual annotation of D. v. virgifera Dvir_2.0 RefSeq models predicted expansion of paralogs with gene families putatively involved in insecticide resistance and chemosensory perception. Our study also suggests that adaptations of D. v. virgifera larvae to feeding on an alternate host plant invoke fewer transcriptional changes compared to marginal or poor hosts. The shared up-regulation of stress response pathways between marginal host and poor host, and starvation treatments may reflect nutrient deprivation. This study provides insight into transcriptomic responses of larval feeding on different host plants and resources for genomic research on this economically significant pest of maize.
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Affiliation(s)
- Brad S. Coates
- grid.508983.fCorn Insects & Crop Genetics Research Unit, USDA-ARS, 2310 Pammel Dr, 532 Science II, Iowa State University, Ames, IA 50011 USA
| | - Kimberly K. O. Walden
- grid.35403.310000 0004 1936 9991Roy J. Carver Biotechnology Center, University of Illinois at Champaign-Urbana, Urbana, IL USA
| | - Dimpal Lata
- grid.62813.3e0000 0004 1936 7806Department of Biology, Illinois Institute of Technology, Chicago, IL USA
| | | | - Robert F. Mitchell
- grid.267474.40000 0001 0674 4543University of Wisconsin Oshkosh, Oshkosh, WI USA
| | - Martin N. Andersson
- grid.4514.40000 0001 0930 2361Department of Biology, Lund University, Lund, Sweden
| | - Rachel McKay
- grid.267474.40000 0001 0674 4543University of Wisconsin Oshkosh, Oshkosh, WI USA
| | - Marcé D. Lorenzen
- grid.40803.3f0000 0001 2173 6074Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC USA
| | - Nathaniel Grubbs
- grid.40803.3f0000 0001 2173 6074Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC USA
| | - Yu-Hui Wang
- grid.40803.3f0000 0001 2173 6074Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC USA
| | - Jinlong Han
- grid.40803.3f0000 0001 2173 6074Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC USA
| | - Jing Li Xuan
- grid.40803.3f0000 0001 2173 6074Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC USA
| | - Peter Willadsen
- grid.40803.3f0000 0001 2173 6074Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC USA
| | - Huichun Wang
- grid.24434.350000 0004 1937 0060Department of Entomology, University of Nebraska, Lincoln, NE USA
| | - B. Wade French
- grid.508981.dIntegrated Crop Systems Research Unit, USDA-ARS, Brookings, SD USA
| | - Raman Bansal
- grid.512850.bUSDA-ARS, San Joaquin Valley Agricultural Sciences Center, Parlier, CA USA
| | - Sammy Sedky
- grid.512850.bUSDA-ARS, San Joaquin Valley Agricultural Sciences Center, Parlier, CA USA
| | - Dariane Souza
- grid.15276.370000 0004 1936 8091Department of Entomology, University of Florida, Gainesville, FL USA
| | - Dakota Bunn
- grid.62813.3e0000 0004 1936 7806Department of Biology, Illinois Institute of Technology, Chicago, IL USA
| | - Lance J. Meinke
- grid.24434.350000 0004 1937 0060Department of Entomology, University of Nebraska, Lincoln, NE USA
| | - Nicholas J. Miller
- grid.62813.3e0000 0004 1936 7806Department of Biology, Illinois Institute of Technology, Chicago, IL USA
| | - Blair D. Siegfried
- grid.15276.370000 0004 1936 8091Department of Entomology, University of Florida, Gainesville, FL USA
| | - Thomas W. Sappington
- grid.508983.fCorn Insects & Crop Genetics Research Unit, USDA-ARS, 2310 Pammel Dr, 532 Science II, Iowa State University, Ames, IA 50011 USA
| | - Hugh M. Robertson
- grid.35403.310000 0004 1936 9991Department of Entomology, University of Illinois at Champaign-Urbana, Urbana, IL USA
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16
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Wang Y, Fang G, Xu P, Gao B, Liu X, Qi X, Zhang G, Cao S, Li Z, Ren X, Wang H, Cao Y, Pereira R, Huang Y, Niu C, Zhan S. Behavioral and genomic divergence between a generalist and a specialist fly. Cell Rep 2022; 41:111654. [DOI: 10.1016/j.celrep.2022.111654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 07/03/2022] [Accepted: 10/21/2022] [Indexed: 11/18/2022] Open
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17
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Identification of Candidate Chemosensory Gene Families by Head Transcriptomes Analysis in the Mexican Fruit Fly, Anastrepha ludens Loew (Diptera: Tephritidae). Int J Mol Sci 2022; 23:ijms231810531. [PMID: 36142444 PMCID: PMC9500802 DOI: 10.3390/ijms231810531] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Revised: 08/31/2022] [Accepted: 09/06/2022] [Indexed: 11/16/2022] Open
Abstract
Insect chemosensory systems, such as smell and taste, are mediated by chemosensory receptor and non-receptor protein families. In the last decade, many studies have focused on discovering these families in Tephritidae species of agricultural importance. However, to date, there is no information on the Mexican fruit fly Anastrepha ludens Loew, a priority pest of quarantine importance in Mexico and other countries. This work represents the first effort to identify, classify and characterize the six chemosensory gene families by analyzing two head transcriptomes of sexually immature and mature adults of A. ludens from laboratory-reared and wild populations, respectively. We identified 120 chemosensory genes encoding 31 Odorant-Binding Proteins (OBPs), 5 Chemosensory Proteins (CSPs), 2 Sensory Neuron Membrane Proteins (SNMPs), 42 Odorant Receptors (ORs), 17 Ionotropic Receptors (IRs), and 23 Gustatory Receptors (GRs). The 120 described chemosensory proteins of the Mexican fruit fly significantly contribute to the genetic databases of insects, particularly dipterans. Except for some OBPs, this work reports for the first time the repertoire of olfactory proteins for one species of the genus Anastrepha, which provides a further basis for studying the olfactory system in the family Tephritidae, one of the most important for its economic and social impact worldwide.
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18
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Rondón JJ, Moreyra NN, Pisarenco VA, Rozas J, Hurtado J, Hasson E. Evolution of the odorant-binding protein gene family in Drosophila. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.957247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Odorant-binding proteins (OBPs) are encoded by a gene family involved in the perception of olfactory signals in insects. This chemosensory gene family has been advocated as a candidate to mediate host preference and host shifts in insects, although it also participates in other physiological processes. Remarkable differences in the OBP gene repertoire have been described across insect groups, suggesting an accelerated gene turnover rate. The genus Drosophila, is a valuable resource for ecological genomics studies since it comprises groups of ecologically diverse species and there are genome data for many of them. Here, we investigate the molecular evolution of this chemosensory gene family across 19 Drosophila genomes, including the melanogaster and repleta species groups, which are mostly associated with rotting fruit and cacti, respectively. We also compared the OBP repertoire among the closely related species of the repleta group, associated with different subfamilies of Cactaceae that represent disparate chemical challenges for the flies. We found that the gene family size varies widely between species, ranging from 39 to 54 candidate OBPs. Indeed, more than 54% of these genes are organized in clusters and located on chromosomes X, 2, and 5, with a distribution conserved throughout the genus. The family sizes in the repleta group and D. virilis (virilis-repleta radiation) were smaller than in the melanogaster group. We tested alternative evolutionary models for OBP family size and turnover rates based on different ecological scenarios. We found heterogeneous gene turnover rates (GR) in comparisons involving columnar cactus specialists, prickly pear specialists, and fruit dwellers lineages, and signals of rapid molecular evolution compatible with positive selection in specific OBP genes. Taking ours and previous results together, we propose that this chemosensory gene family is involved in host adaptation and hypothesize that the adoption of the cactophilic lifestyle in the repleta group accelerated the evolution of members of the family.
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19
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Nieberding CM, Beldade P, Baumlé V, San Martin G, Arun A, Lognay G, Montagné N, Bastin-Héline L, Jacquin-Joly E, Noirot C, Klopp C, Visser B. Mosaic Evolution of Molecular Pathways for Sex Pheromone Communication in a Butterfly. Genes (Basel) 2022; 13:1372. [PMID: 36011283 PMCID: PMC9407440 DOI: 10.3390/genes13081372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 07/11/2022] [Accepted: 07/18/2022] [Indexed: 11/30/2022] Open
Abstract
Unraveling the origin of molecular pathways underlying the evolution of adaptive traits is essential for understanding how new lineages emerge, including the relative contribution of conserved ancestral traits and newly evolved derived traits. Here, we investigated the evolutionary divergence of sex pheromone communication from moths (mostly nocturnal) to butterflies (mostly diurnal) that occurred ~119 million years ago. In moths, it is the females that typically emit pheromones to attract male mates, but in butterflies males emit pheromones that are used by females for mate choice. The molecular bases of sex pheromone communication are well understood in moths, but they have remained relatively unexplored in butterflies. We used a combination of transcriptomics, real time qPCR, and phylogenetics to identify genes involved in the different steps (i.e., production, regulation, and reception) of sex pheromone communication of the butterfly Bicyclus anynana. Our results show that the biosynthesis and reception of sex pheromones relies both on moth-specific gene families (reductases) and on more ancestral insect gene families (desaturases, olfactory receptors, odorant binding proteins). Interestingly, B. anynana appears to use what was believed to be the moth-specific neuropeptide Pheromone Biosynthesis Activating Neuropeptide (PBAN) for regulating sex pheromone production. Altogether, our results suggest that a mosaic pattern best explains how sex pheromone communication evolved in butterflies, with some molecular components derived from moths, and others conserved from more ancient insect ancestors. This is the first large-scale investigation of the genetic pathways underlying sex pheromone communication in a butterfly.
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Affiliation(s)
- Caroline M. Nieberding
- Evolutionary Ecology and Genetics Group, Earth and Life Institute, UC Louvain, 1348 Louvain-la-Neuve, Belgium; (V.B.); (G.S.M.); (A.A.); (G.L.)
| | - Patrícia Beldade
- Center for Ecology, Evolution and Environmental Changes (cE3c) & Global Change and Sustainability Institute (CHANGE), Faculty of Sciences, University of Lisbon (FCUL), 1749-016 Lisboa, Portugal;
| | - Véronique Baumlé
- Evolutionary Ecology and Genetics Group, Earth and Life Institute, UC Louvain, 1348 Louvain-la-Neuve, Belgium; (V.B.); (G.S.M.); (A.A.); (G.L.)
| | - Gilles San Martin
- Evolutionary Ecology and Genetics Group, Earth and Life Institute, UC Louvain, 1348 Louvain-la-Neuve, Belgium; (V.B.); (G.S.M.); (A.A.); (G.L.)
| | - Alok Arun
- Evolutionary Ecology and Genetics Group, Earth and Life Institute, UC Louvain, 1348 Louvain-la-Neuve, Belgium; (V.B.); (G.S.M.); (A.A.); (G.L.)
| | - Georges Lognay
- Evolutionary Ecology and Genetics Group, Earth and Life Institute, UC Louvain, 1348 Louvain-la-Neuve, Belgium; (V.B.); (G.S.M.); (A.A.); (G.L.)
| | - Nicolas Montagné
- INRAE, CNRS, IRD, UPEC, Sorbonne Université, Institute of Ecology and Environmental Sciences of Paris, Université de Paris, 78000 Versailles, France; (N.M.); (L.B.-H.); (E.J.-J.)
| | - Lucie Bastin-Héline
- INRAE, CNRS, IRD, UPEC, Sorbonne Université, Institute of Ecology and Environmental Sciences of Paris, Université de Paris, 78000 Versailles, France; (N.M.); (L.B.-H.); (E.J.-J.)
| | - Emmanuelle Jacquin-Joly
- INRAE, CNRS, IRD, UPEC, Sorbonne Université, Institute of Ecology and Environmental Sciences of Paris, Université de Paris, 78000 Versailles, France; (N.M.); (L.B.-H.); (E.J.-J.)
| | - Céline Noirot
- Plateforme Bio-Informatique GenoToul, MIAT, INRAE, UR875 Mathématiques et Informatique Appliquées Toulouse, 31326 Castanet-Tolosan, France; (C.N.); (C.K.)
| | - Christophe Klopp
- Plateforme Bio-Informatique GenoToul, MIAT, INRAE, UR875 Mathématiques et Informatique Appliquées Toulouse, 31326 Castanet-Tolosan, France; (C.N.); (C.K.)
| | - Bertanne Visser
- Evolution and Ecophysiology Group, Department of Functional and Evolutionary Entomology, Gembloux Agro-Bio Tech, University of Liège, 5030 Gembloux, Belgium;
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Comparisons of chemosensory gene repertoires in human and non-human feeding Anopheles mosquitoes link olfactory genes to anthropophily. iScience 2022; 25:104521. [PMID: 35754720 PMCID: PMC9213756 DOI: 10.1016/j.isci.2022.104521] [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: 12/09/2021] [Revised: 05/08/2022] [Accepted: 05/30/2022] [Indexed: 11/06/2022] Open
Abstract
We investigate the genetic basis of anthropophily (human host use) in a non-model mosquito species group, the Anopheles farauti complex from the southwest Pacific. This complex has experienced multiple transitions from anthropophily to zoophily, contrasting with well-studied systems (the global species Aedes aegypti and the African Anopheles gambiae complex) that have evolved to be specialist anthropophiles. By performing tests of selection and assessing evolutionary patterns for >200 olfactory genes from nine genomes, we identify several candidate genes associated with differences in anthropophily in this complex. Based on evolutionary patterns (phylogenetic relationships, fixed amino acid differences, and structural differences) as well as results from selection analyses, we identify numerous genes that are likely to play an important role in mosquitoes’ ability to detect humans as hosts. Our findings contribute to the understanding of the evolution of insect olfactory gene families and mosquito host preference as well as having potential applied outcomes. Genomes of Anopheles mosquitoes with differing host preferences were sequenced Evolutionary comparisons were performed on >200 insect chemosensory genes These comparisons revealed candidate genes involved in human feeding Two of the main candidates identified were co-receptor Ir8a and Or75
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21
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Vyas M, Pagadala Damodaram KJ, Krishnarao G. Antennal Transcriptome of the Fruit-Sucking Moth Eudocima materna: Identification of Olfactory Genes and Preliminary Evidence for RNA-Editing Events in Odorant Receptors. Genes (Basel) 2022; 13:genes13071207. [PMID: 35885990 PMCID: PMC9323814 DOI: 10.3390/genes13071207] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 06/30/2022] [Accepted: 07/03/2022] [Indexed: 02/05/2023] Open
Abstract
Unappealing shriveled fruits are a characteristic of one of the most elusive fruit pests. The perpetrator, Eudocima materna, attacks the fruit at a fully formed stage and, therefore, the antennal transcriptome for this insect was deduced to identify the molecular elicitors involved in the attraction to its host plants. A total of 260 olfactory genes, including 16 odorant-binding proteins (OBPs), four pheromone-binding proteins (PBPs), 40 antennal-binding proteins (ABPs), 178 odorant receptors (ORs), 17 chemosensory proteins (CSPs) and five sensory neuron membrane proteins (SNMPs) were identified. Phylogenetic analysis shows the divergence of E. materna proteins from closely related lepidopterans and provides insights on genes that have exclusively evolved in this insect. STRING network analysis revealed interactions of olfactory proteins among themselves and the proteins of other groups. Interestingly, online tools predicted RNA-editing events in the odorant receptor sequences, suggesting the possibility of multiple protein forms. Transcripts matching transposable element sequences were also detected in the dataset. Thus, the work reported here provides a valuable resource to design molecular methods for pest control.
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22
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Yang R, Li D, Yi S, Wang M. Evolutionarily conserved odorant-binding proteins participate in establishing tritrophic interactions. iScience 2022; 25:104664. [PMID: 35811847 PMCID: PMC9263996 DOI: 10.1016/j.isci.2022.104664] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 05/06/2022] [Accepted: 06/20/2022] [Indexed: 11/15/2022] Open
Abstract
Attracting herbivores and their natural enemies is a standard method where plant volatiles mediate tritrophic interactions. However, it remains unknown whether the shared attraction has a shared chemosensory basis. Here we focus on the odorant-binding proteins (OBPs), a gene family integral to peripheral detection of odoriferous chemicals. Previous evidence suggests that the herbivorous beetle Monochamus alternatus and its parasitoid beetle Dastarcus helophoroides are attracted to stressed pines. In this study, (+)-fenchone, emitted by stressed pines, is found to be attracted to M. alternatus and D. helophoroides in behavioral assays. Meanwhile, two orthologous OBPs with a slower evolutionary rate, respectively, from the two insects are shown to bind with (+)-fenchone, and the attraction is abolished after RNAi. These results show the ability of evolutionarily conserved OBPs from herbivores and their enemies to detect the same plant volatiles, providing an olfactory mechanism of chemical signals–mediated tritrophic relationships. Monochamus alternatus and Dastarcus helophoroides are attracted to (+)-fenchone from host pines They harbor evolutionarily conserved odorant-binding proteins (OBPs) One pair of the conserved OBPs can bind with (+)-fenchone The behavioral preference is lost upon RNAi knockdown of the OBPs
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Affiliation(s)
- Ruinan Yang
- Hubei Insect Resources Utilization and Sustainable Pest Management Key Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Dongzhen Li
- Hubei Insect Resources Utilization and Sustainable Pest Management Key Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing 100091, China
| | - Shancheng Yi
- Hubei Insect Resources Utilization and Sustainable Pest Management Key Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Manqun Wang
- Hubei Insect Resources Utilization and Sustainable Pest Management Key Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- Corresponding author
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Wang Z, Yang F, Sun A, Song J, Shan S, Zhang Y, Wang S. Expressional and functional comparisons of five clustered odorant binding proteins in the brown marmorated stink bug Halyomorpha halys. Int J Biol Macromol 2022; 206:759-767. [DOI: 10.1016/j.ijbiomac.2022.03.084] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 03/09/2022] [Accepted: 03/14/2022] [Indexed: 12/26/2022]
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24
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Hurtado J, Almeida FC, Belliard SA, Revale S, Hasson E. Research gaps and new insights in the evolution of Drosophila seminal fluid proteins. INSECT MOLECULAR BIOLOGY 2022; 31:139-158. [PMID: 34747062 DOI: 10.1111/imb.12746] [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: 05/28/2021] [Revised: 09/20/2021] [Accepted: 10/25/2021] [Indexed: 06/13/2023]
Abstract
While the striking effects of seminal fluid proteins (SFPs) on females are fairly conserved among Diptera, most SFPs lack detectable homologues among the SFP repertoires of phylogenetically distant species. How such a rapidly changing proteome conserves functions across taxa is a fascinating question. However, this and other pivotal aspects of SFPs' evolution remain elusive because discoveries on these proteins have been mainly restricted to the model Drosophila melanogaster. Here, we provide an overview of the current knowledge on the inter-specific divergence of the SFP repertoire in Drosophila and compile the increasing amount of relevant genomic information from multiple species. Capitalizing on the accumulated knowledge in D. melanogaster, we present novel sets of high-confidence SFP candidates and transcription factors presumptively involved in regulating the expression of SFPs. We also address open questions by performing comparative genomic analyses that failed to support the existence of many conserved SFPs shared by most dipterans and indicated that gene co-option is the most frequent mechanism accounting for the origin of Drosophila SFP-coding genes. We hope our update establishes a starting point to integrate further data and thus widen the understanding of the intricate evolution of these proteins.
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Affiliation(s)
- Juan Hurtado
- Departamento de Ecología, Genética y Evolución, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires (UBA), CABA, Argentina
- Instituto de Ecología, Genética y Evolución de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), CABA, Argentina
| | - Francisca Cunha Almeida
- Departamento de Ecología, Genética y Evolución, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires (UBA), CABA, Argentina
- Instituto de Ecología, Genética y Evolución de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), CABA, Argentina
| | - Silvina Anahí Belliard
- Laboratorio de Insectos de Importancia Agronómica, IGEAF (INTA), GV-IABIMO (CONICET), Buenos Aires, Argentina
| | - Santiago Revale
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Esteban Hasson
- Departamento de Ecología, Genética y Evolución, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires (UBA), CABA, Argentina
- Instituto de Ecología, Genética y Evolución de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), CABA, Argentina
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25
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Plant Secondary Metabolites as Defense Tools against Herbivores for Sustainable Crop Protection. Int J Mol Sci 2022; 23:ijms23052690. [PMID: 35269836 PMCID: PMC8910576 DOI: 10.3390/ijms23052690] [Citation(s) in RCA: 78] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 02/15/2022] [Accepted: 02/22/2022] [Indexed: 02/04/2023] Open
Abstract
Plants have evolved several adaptive strategies through physiological changes in response to herbivore attacks. Plant secondary metabolites (PSMs) are synthesized to provide defensive functions and regulate defense signaling pathways to safeguard plants against herbivores. Herbivore injury initiates complex reactions which ultimately lead to synthesis and accumulation of PSMs. The biosynthesis of these metabolites is regulated by the interplay of signaling molecules comprising phytohormones. Plant volatile metabolites are released upon herbivore attack and are capable of directly inducing or priming hormonal defense signaling pathways. Secondary metabolites enable plants to quickly detect herbivore attacks and respond in a timely way in a rapidly changing scenario of pest and environment. Several studies have suggested that the potential for adaptation and/or resistance by insect herbivores to secondary metabolites is limited. These metabolites cause direct toxicity to insect pests, stimulate antixenosis mechanisms in plants to insect herbivores, and, by recruiting herbivore natural enemies, indirectly protect the plants. Herbivores adapt to secondary metabolites by the up/down regulation of sensory genes, and sequestration or detoxification of toxic metabolites. PSMs modulate multi-trophic interactions involving host plants, herbivores, natural enemies and pollinators. Although the role of secondary metabolites in plant-pollinator interplay has been little explored, several reports suggest that both plants and pollinators are mutually benefited. Molecular insights into the regulatory proteins and genes involved in the biosynthesis of secondary metabolites will pave the way for the metabolic engineering of biosynthetic pathway intermediates for improving plant tolerance to herbivores. This review throws light on the role of PSMs in modulating multi-trophic interactions, contributing to the knowledge of plant-herbivore interactions to enable their management in an eco-friendly and sustainable manner.
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26
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Divekar PA, Narayana S, Divekar BA, Kumar R, Gadratagi BG, Ray A, Singh AK, Rani V, Singh V, Singh AK, Kumar A, Singh RP, Meena RS, Behera TK. Plant Secondary Metabolites as Defense Tools against Herbivores for Sustainable Crop Protection. Int J Mol Sci 2022; 23:ijms23052690. [PMID: 35269836 DOI: 10.3390/ijms23052690/s1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 02/15/2022] [Accepted: 02/22/2022] [Indexed: 05/21/2023] Open
Abstract
Plants have evolved several adaptive strategies through physiological changes in response to herbivore attacks. Plant secondary metabolites (PSMs) are synthesized to provide defensive functions and regulate defense signaling pathways to safeguard plants against herbivores. Herbivore injury initiates complex reactions which ultimately lead to synthesis and accumulation of PSMs. The biosynthesis of these metabolites is regulated by the interplay of signaling molecules comprising phytohormones. Plant volatile metabolites are released upon herbivore attack and are capable of directly inducing or priming hormonal defense signaling pathways. Secondary metabolites enable plants to quickly detect herbivore attacks and respond in a timely way in a rapidly changing scenario of pest and environment. Several studies have suggested that the potential for adaptation and/or resistance by insect herbivores to secondary metabolites is limited. These metabolites cause direct toxicity to insect pests, stimulate antixenosis mechanisms in plants to insect herbivores, and, by recruiting herbivore natural enemies, indirectly protect the plants. Herbivores adapt to secondary metabolites by the up/down regulation of sensory genes, and sequestration or detoxification of toxic metabolites. PSMs modulate multi-trophic interactions involving host plants, herbivores, natural enemies and pollinators. Although the role of secondary metabolites in plant-pollinator interplay has been little explored, several reports suggest that both plants and pollinators are mutually benefited. Molecular insights into the regulatory proteins and genes involved in the biosynthesis of secondary metabolites will pave the way for the metabolic engineering of biosynthetic pathway intermediates for improving plant tolerance to herbivores. This review throws light on the role of PSMs in modulating multi-trophic interactions, contributing to the knowledge of plant-herbivore interactions to enable their management in an eco-friendly and sustainable manner.
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Affiliation(s)
- Pratap Adinath Divekar
- Indian Council of Agricultural Research-Indian Institute of Vegetable Research (IIVR), Varanasi 221305, India
| | - Srinivasa Narayana
- Institute of Agricultural Sciences, Banaras Hindu University, Varanasi 221305, India
| | | | - Rajeev Kumar
- Indian Council of Agricultural Research-Indian Institute of Vegetable Research (IIVR), Varanasi 221305, India
| | - Basana Gowda Gadratagi
- Indian Council of Agricultural Research-National Rice Research Institute, Cuttack 753006, India
| | - Aishwarya Ray
- Indira Gandhi Krishi Vishwavidyalaya, Raipur 492012, India
| | - Achuit Kumar Singh
- Indian Council of Agricultural Research-Indian Institute of Vegetable Research (IIVR), Varanasi 221305, India
| | - Vijaya Rani
- Indian Council of Agricultural Research-Indian Institute of Vegetable Research (IIVR), Varanasi 221305, India
| | - Vikas Singh
- Indian Council of Agricultural Research-Indian Institute of Vegetable Research, Regional Research Station, Sargatia, Kushinagar 274406, India
| | - Akhilesh Kumar Singh
- College of Horticulture, Banda University of Agriculture and Technology, Banda 210001, India
| | - Amit Kumar
- Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya, Sheopur 476339, India
| | - Rudra Pratap Singh
- Acharya Narendra Deva University of Agriculture and Technology, Ayodhya, Krishi Vigyan Kendra, Kotwa, Azamgarh 276207, India
| | - Radhe Shyam Meena
- Institute of Agricultural Sciences, Banaras Hindu University, Varanasi 221305, India
| | - Tusar Kanti Behera
- Indian Council of Agricultural Research-Indian Institute of Vegetable Research (IIVR), Varanasi 221305, India
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27
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Librado P, Rozas J. Reconstructing Gene Gains and Losses with BadiRate. Methods Mol Biol 2022; 2569:213-232. [PMID: 36083450 DOI: 10.1007/978-1-0716-2691-7_10] [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: 05/24/2023]
Abstract
Estimating gene gain and losses is paramount to understand the molecular mechanisms underlying adaptive evolution. Despite the advent of high-throughput sequencing, such analyses have been so far hampered by the poor contiguity of genome assemblies. The increasing affordability of long-read sequencing technologies will however revolutionize our capacity to identify gene gains and losses at an unprecedented resolution, even in non-model organisms. To thoroughly exploit all such multigene family variation, the software BadiRate implements a collection of birth-and-death stochastic models, aiming at estimating by maximum likelihood the gene turnover rates along the internal and external branches of a given phylogenetic species tree. Its statistical framework also provides versatility for inferring the gene family content at the internal phylogenetic nodes (and to estimate the minimum number of gene gains and losses in each branch), for statistically contrasting competing hypotheses (e.g., accelerations of the gene turnover rates at pre-defined clades), and for pinpointing gene family expansions or contractions likely driven by natural selection. In this chapter we review the theoretical models implemented in BadiRate and illustrate their applicability by analyzing a hypothetical data set of 14 microbial species.
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Affiliation(s)
- Pablo Librado
- Centre for Anthropobiology & Genomics of Toulouse, Université Paul Sabatier, Toulouse, France
| | - Julio Rozas
- Departament de Genètica, Microbiologia I Estadística, and Institut de Recerca de la Biodiversitat, Universitat de Barcelona, Barcelona, Spain.
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28
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Auer TO, Shahandeh MP, Benton R. Drosophila sechellia: A Genetic Model for Behavioral Evolution and Neuroecology. Annu Rev Genet 2021; 55:527-554. [PMID: 34530638 DOI: 10.1146/annurev-genet-071719-020719] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Defining the mechanisms by which animals adapt to their ecological niche is an important problem bridging evolution, genetics, and neurobiology. We review the establishment of a powerful genetic model for comparative behavioral analysis and neuroecology, Drosophila sechellia. This island-endemic fly species is closely related to several cosmopolitan generalists, including Drosophila melanogaster, but has evolved extreme specialism, feeding and reproducing exclusively on the noni fruit of the tropical shrub Morinda citrifolia. We first describe the development and use of genetic approaches to facilitate genotype/phenotype associations in these drosophilids. Next, we survey the behavioral, physiological, and morphological adaptations of D. sechellia throughout its life cycle and outline our current understanding of the genetic and cellular basis of these traits. Finally, we discuss the principles this knowledge begins to establish in the context of host specialization, speciation, and the neurobiology of behavioral evolution and consider open questions and challenges in the field.
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Affiliation(s)
- Thomas O Auer
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, CH-1015 Lausanne, Switzerland; , ,
| | - Michael P Shahandeh
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, CH-1015 Lausanne, Switzerland; , ,
| | - Richard Benton
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, CH-1015 Lausanne, Switzerland; , ,
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29
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Marchant A, Mougel F, Jacquin-Joly E, Almeida CE, Blanchet D, Bérenger JM, da Rosa JA, Harry M. Chemosensory Gene Expression for Two Closely Relative Species Rhodnius robustus and R. prolixus (Hemiptera, Reduviidade, Triatominae) Vectors of Chagas Disease. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.725504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Two closely related species, Rhodnius prolixus and Rhodnius robustus, are the vectors of Trypanosoma cruzi, which is the causative agent of Chagas disease, but clearly exhibit clear-cut differences in their ecological behavior. R. prolixus is considered as a domiciliated species, whereas R. robustus only sporadically visits human houses in Amazonia. We performed a chemosensory gene expression study via RNA-sequencing (RNA-seq) for the two species and also included a laboratory introgressed R. robustus strain. We built an assembled transcriptome for each sample and for both sexes and compiled all in a reference transcriptome for a differential gene expression study. Because the genes specifically expressed in one condition and not expressed in another may also reflect differences in the adaptation of organisms, a comparative study of the presence/absence of transcripts was also performed for the chemosensory transcripts, namely chemosensory proteins (CSPs), odorant-binding proteins (OBPs), odorant receptors (ORs), gustatory receptors (GRs), and ionotropic receptors (IRs), as well as takeout (TO) transcripts because TO proteins have been proposed to be associated with chemosensory perception in both olfactory and taste systems. In this study, 12 novel TO transcripts from the R. prolixus genome were annotated. Among the 199 transcripts, out of interest, annotated in this study, 93% were conserved between R. prolixus and the sylvatic R. robustus. Moreover, 10 transcripts out of interest were specifically expressed in one sex and absent in another. Three chemosensory transcripts were found to be expressed only in the reared R. prolixus (CSP19, OBP9, and OR89) and only one in sylvatic R. robustus (OR22). A large set of transcripts were found to be differentially expressed (DE) between males and females (1,630), with a majority of them (83%) overexpressed in males. Between environmental conditions, 8,596 transcripts were DE, with most (67%) overexpressed in the sylvatic R. robustus samples, including 17 chemosensory transcripts (4 CSPs, 1 OBP, 5 ORs, 1 GR, 4 IR, and 2 TO), but 4 genes (OBP19, OR13, OR40, and OR79) were overexpressed in the reared samples.
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30
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Davis JS, Pearcy MJ, Yew JY, Moyle LC. A shift to shorter cuticular hydrocarbons accompanies sexual isolation among Drosophila americana group populations. Evol Lett 2021; 5:521-540. [PMID: 34621538 PMCID: PMC8484720 DOI: 10.1002/evl3.246] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 04/08/2021] [Accepted: 06/13/2021] [Indexed: 12/15/2022] Open
Abstract
Because sensory signals often evolve rapidly, they could be instrumental in the emergence of reproductive isolation between species. However, pinpointing their specific contribution to isolating barriers, and the mechanisms underlying their divergence, remains challenging. Here, we demonstrate sexual isolation due to divergence in chemical signals between two populations of Drosophila americana (SC and NE) and one population of D. novamexicana, and dissect its underlying phenotypic and genetic mechanisms. Mating trials revealed strong sexual isolation between Drosophila novamexicana males and SC Drosophila americana females, as well as more moderate bi-directional isolation between D. americana populations. Mating behavior data indicate SC D. americana males have the highest courtship efficiency and, unlike males of the other populations, are accepted by females of all species. Quantification of cuticular hydrocarbon (CHC) profiles-chemosensory signals that are used for species recognition and mate finding in Drosophila-shows that the SC D. americana population differs from the other populations primarily on the basis of compound carbon chain-length. Moreover, manipulation of male CHC composition via heterospecific perfuming-specifically perfuming D. novamexicana males with SC D. americana males-abolishes their sexual isolation from these D. americana females. Of a set of candidates, a single gene-elongase CG17821-had patterns of gene expression consistent with a role in CHC differences between species. Sequence comparisons indicate D. novamexicana and our Nebraska (NE) D. americana population share a derived CG17821 truncation mutation that could also contribute to their shared "short" CHC phenotype. Together, these data suggest an evolutionary model for the origin and spread of this allele and its consequences for CHC divergence and sexual isolation in this group.
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Affiliation(s)
- Jeremy S. Davis
- Department of BiologyIndiana UniversityBloomingtonIndiana47405
- Department of BiologyUniversity of KentuckyLexingtonKentucky40508
| | | | - Joanne Y. Yew
- Pacific Biosciences Research CenterUniversity of Hawaii at MānoaHonoluluHawaii96822
| | - Leonie C. Moyle
- Department of BiologyIndiana UniversityBloomingtonIndiana47405
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31
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Latorre-Estivalis JM, Almeida FC, Pontes G, Dopazo H, Barrozo RB, Lorenzo MG. Evolution of the insect PPK gene family. Genome Biol Evol 2021; 13:6352500. [PMID: 34390578 PMCID: PMC8438182 DOI: 10.1093/gbe/evab185] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/05/2021] [Indexed: 11/12/2022] Open
Abstract
Insect pickpocket (PPK) receptors mediate diverse functions, among them the detection of mechano- and chemo-sensory stimuli. Notwithstanding their relevance, studies on their evolution only focused on Drosophila. We have analyzed the genomes of 26 species of 8 orders including holometabolous and hemimetabolous insects (Blattodea, Orthoptera, Hemiptera, Phthiraptera, Hymenoptera, Lepidoptera, Coleoptera, and Diptera), to characterize the evolution of this gene family. PPKs were detected in all genomes analyzed, with 578 genes distributed in 7 subfamilies. According to our phylogeny ppk17 is the most divergent member, composing the new subfamily VII. PPKs evolved under a gene birth-and-death model that generated lineage-specific expansions usually located in clusters, while purifying selection affected several orthogroups. Subfamily V was the largest, including a mosquito-specific expansion that can be considered a new target for pest control. PPKs present a high gene turnover generating considerable variation. On one hand, Musca domestica (59), Aedes albopictus (51), Culex quinquefasciatus (48), and Blattella germanica (41) presented the largest PPK repertoires. On the other hand, Pediculus humanus (only ppk17), bees and ants (6-9) had the smallest PPK sets. A subset of prevalent PPKs was identified, indicating very conserved functions for these receptors. Finally, at least twenty percent of the sequences presented calmodulin-binding motifs, suggesting that these PPKs may amplify sensory responses similarly as proposed for D. melanogaster ppk25. Overall, this work characterized the evolutionary history of these receptors revealing relevant unknown gene sequence features and clade-specific expansions.
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Affiliation(s)
- Jose Manuel Latorre-Estivalis
- Laboratorio de Insectos Sociales, Instituto de Fisiología, Biología Molecular y Neurociencias (IFIByNE), Universidad de Buenos Aires - CONICET, Buenos Aires, Argentina
| | - Francisca C Almeida
- Laboratorio de Genética Evolutiva, Departamento de Ecología, Genética y Evolución, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Gina Pontes
- Laboratorio de Eco-Fisiología de Insectos del Instituto de Biodiversidad y Biología Experimental y Aplicada (IBBEA-CONICET), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Hernán Dopazo
- Laboratorio de Genómica de Poblaciones y Evolución. Instituto de Ecología, Genética y Evolución de Buenos Aires (IEGEBA). CONICET. Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires. Argentina
| | - Romina B Barrozo
- Grupo de Neuroetología de Insectos Vectores, Laboratorio de Fisiología de Insectos, Instituto de Biodiversidad y Biología Experimental y Aplicada (IBBEA - UBA - CONICET), Departamento de Biología y Biodiversidad Experimental, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Marcelo Gustavo Lorenzo
- Vector Behaviour and Pathogen Interaction Group, Instituto René Rachou - FIOCRUZ, Belo Horizonte, Minas Gerais, Brazil
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32
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Leask M, Lovegrove M, Walker A, Duncan E, Dearden P. Evolution and genomic organization of the insect sHSP gene cluster and coordinate regulation in phenotypic plasticity. BMC Ecol Evol 2021; 21:154. [PMID: 34348652 PMCID: PMC8336396 DOI: 10.1186/s12862-021-01885-8] [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: 12/21/2020] [Accepted: 07/28/2021] [Indexed: 11/10/2022] Open
Abstract
Background Conserved syntenic gene complexes are rare in Arthropods and likely only retained due to functional constraint. Numerous sHSPs have been identified in the genomes of insects, some of which are located clustered in close proximity. Previous phylogenetic analyses of these clustered sHSP have been limited to a small number of holometabolous insect species and have not determined the pattern of evolution of the clustered sHSP genes (sHSP-C) in insect or Arthropod lineages. Results Using eight genomes from representative insect orders and three non-insect arthropod genomes we have identified that a syntenic cluster of sHSPs (sHSP-C) is a hallmark of most Arthropod genomes. Using 11 genomes from Hymenopteran species our phylogenetic analyses have refined the evolution of the sHSP-C in Hymenoptera and found that the sHSP-C is order-specific with evidence of birth-and-death evolution in the hymenopteran lineage. Finally we have shown that the honeybee sHSP-C is co-ordinately expressed and is marked by genomic features, including H3K27me3 histone marks consistent with coordinate regulation, during honeybee ovary activation. Conclusions The syntenic sHSP-C is present in most insect genomes, and its conserved coordinate expression and regulation implies that it is an integral genomic component of environmental response in arthropods. Supplementary Information The online version contains supplementary material available at 10.1186/s12862-021-01885-8.
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Affiliation(s)
- Megan Leask
- Department of Biochemistry, University of Otago, Dunedin, New Zealand.
| | - Mackenzie Lovegrove
- Department of Biochemistry, University of Otago, Dunedin, New Zealand.,Genomics Aotearoa and Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Abigail Walker
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Elizabeth Duncan
- School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Peter Dearden
- Department of Biochemistry, University of Otago, Dunedin, New Zealand.,Genomics Aotearoa and Department of Biochemistry, University of Otago, Dunedin, New Zealand
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Sierra I, Latorre-Estivalis JM, Traverso L, Gonzalez PV, Aptekmann A, Nadra AD, Masuh H, Ons S. Transcriptomic analysis and molecular docking reveal genes involved in the response of Aedes aegypti larvae to an essential oil extracted from Eucalyptus. PLoS Negl Trop Dis 2021; 15:e0009587. [PMID: 34270558 PMCID: PMC8318226 DOI: 10.1371/journal.pntd.0009587] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 07/28/2021] [Accepted: 06/22/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Aedes aegypti (L.) is an urban mosquito, vector of several arboviruses that cause severe diseases in hundreds of million people each year. The resistance to synthetic insecticides developed by Ae. aegypti populations worldwide has contributed to failures in vector control campaigns, increasing the impact of arbovirus diseases. In this context, plant-derived essential oils with larvicidal activity could be an attractive alternative for vector control. However, the mode of action and the detoxificant response of mosquitoes to plant derived compounds have not been established, impairing the optimization of their use. METHODS AND FINDINGS Here we compare gene expression in Ae. aegypti larvae after 14 hrs of exposure to Eucalyptus camaldulensis essential oil with a control group exposed to vehicle (acetone) for the same lapse, by using RNA-Seq. We found differentially expressed genes encoding for cuticle proteins, fatty-acid synthesis, membrane transporters and detoxificant related gene families (i.e. heat shock proteins, cytochromes P450, glutathione transferases, UDP-glycosyltransferases and ABC transporters). Finally, our RNA-Seq and molecular docking results provide evidence pointing to a central involvement of chemosensory proteins in the detoxificant response in mosquitoes. CONCLUSIONS AND SIGNIFICANCE Our work contributes to the understanding of the physiological response of Ae. aegypti larvae to an intoxication with a natural toxic distilled from Eucalyptus leafs. The results suggest an involvement of most of the gene families associated to detoxification of xenobiotics in insects. Noteworthy, this work provides important information regarding the implication of chemosensory proteins in the detoxification of a natural larvicide. Understanding the mode of detoxification of Eucalyptus distilled compounds could contribute to their implementation as a tool in mosquito control.
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Affiliation(s)
- Ivana Sierra
- Laboratorio de Neurobiología de Insectos. Centro Regional de Estudios Genómicos. Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina
| | - Jose Manuel Latorre-Estivalis
- Laboratorio de Neurobiología de Insectos. Centro Regional de Estudios Genómicos. Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina
| | - Lucila Traverso
- Laboratorio de Neurobiología de Insectos. Centro Regional de Estudios Genómicos. Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina
| | - Paula V. Gonzalez
- Centro de Investigaciones de Plagas e Insecticidas (CIPEIN-UNIDEF/CITEDEF/CONICET), Buenos Aires, Argentina
| | - Ariel Aptekmann
- Department of Marine and Coastal Sciences, Rutgers University, School of Environmental and Biological Sciences, New Brunswick, New Jersey, United States of America
| | - Alejandro Daniel Nadra
- Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Fisiología y Biología Molecular y Celular. Instituto de Biociencias, Biotecnología y Biología Traslacional (iB3). Buenos Aires, Argentina
| | - Héctor Masuh
- Centro de Investigaciones de Plagas e Insecticidas (CIPEIN-UNIDEF/CITEDEF/CONICET), Buenos Aires, Argentina
| | - Sheila Ons
- Laboratorio de Neurobiología de Insectos. Centro Regional de Estudios Genómicos. Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina
- * E-mail:
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Escuer P, Pisarenco VA, Fernández-Ruiz AA, Vizueta J, Sánchez-Herrero JF, Arnedo MA, Sánchez-Gracia A, Rozas J. The chromosome-scale assembly of the Canary Islands endemic spider Dysdera silvatica (Arachnida, Araneae) sheds light on the origin and genome structure of chemoreceptor gene families in chelicerates. Mol Ecol Resour 2021; 22:375-390. [PMID: 34268885 DOI: 10.1111/1755-0998.13471] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 06/21/2021] [Accepted: 07/12/2021] [Indexed: 11/28/2022]
Abstract
Here, we present the chromosome-level genome assembly of Dysdera silvatica Schmidt, 1981, a nocturnal ground-dwelling spider endemic from the Canary Islands. The genus Dysdera has undergone a remarkable diversification in this archipelago mostly associated with shifts in the level of trophic specialization, becoming an excellent model to study the genomic drivers of adaptive radiations. The new assembly (1.37 Gb; scaffold N50 of 174.2 Mb), was performed using the chromosome conformation capture scaffolding technique, represents a continuity improvement of more than 4500 times with respect to the previous version. The seven largest scaffolds or pseudochromosomes, which cover 87% of the total assembly size, probably correspond with the seven chromosomes of the karyotype of this species, including a characteristic large X chromosome. To illustrate the value of this new resource we performed a comprehensive analysis of the two major arthropod chemoreceptor gene families (i.e., gustatory and ionotropic receptors). We identified 545 chemoreceptor sequences distributed across all pseudochromosomes, with a notable underrepresentation in the X chromosome. At least 54% of them localize in 83 genomic clusters with a significantly lower evolutionary distances between them than the average of the family, suggesting a recent origin of many of them. This chromosome-level assembly is the first high-quality genome representative of the Synspermiata clade, and just the third among spiders, representing a new valuable resource to gain insights into the structure and organization of chelicerate genomes, including the role that structural variants, repetitive elements and large gene families played in the extraordinary biology of spiders.
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Affiliation(s)
- Paula Escuer
- Departament de Genètica, Microbiologia i Estadística & Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Vadim A Pisarenco
- Departament de Genètica, Microbiologia i Estadística & Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Angel A Fernández-Ruiz
- Departament de Genètica, Microbiologia i Estadística & Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Joel Vizueta
- Departament de Genètica, Microbiologia i Estadística & Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain.,Section for Ecology and Evolution, Department of Biology, Villum Centre for Biodiversity Genomics, University of Copenhagen, Copenhagen, Denmark
| | - Jose F Sánchez-Herrero
- High Content Genomics and Bioinformatics Unit, Institut d'Investigació en Ciències de la Salut Germans Trias i Pujol, Badalona, Spain
| | - Miquel A Arnedo
- Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals & Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Alejandro Sánchez-Gracia
- Departament de Genètica, Microbiologia i Estadística & Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Julio Rozas
- Departament de Genètica, Microbiologia i Estadística & Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
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Huang C, Zhang X, He D, Wu Q, Tang R, Xing L, Liu W, Wang W, Liu B, Xi Y, Yang N, Wan F, Qian W. Comparative Genomics Provide Insights Into Function and Evolution of Odorant Binding Proteins in Cydia pomonella. Front Physiol 2021; 12:690185. [PMID: 34305643 PMCID: PMC8294088 DOI: 10.3389/fphys.2021.690185] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 06/15/2021] [Indexed: 11/13/2022] Open
Abstract
Insect olfaction is vital for foraging, mating, host-seeking, and avoidance of predators/pathogens. In insects, odorant binding proteins (OBPs) are involved in transporting hydrophobic odor molecules from the external environment to receptor neurons. The codling moth, Cydia pomonella, one of the most destructive insect fruit pests, causes enormous economic losses. However, little is known about the number, variety, gains and losses, and evolution of OBP genes in C. pomonella. Here we report the identification of 40 OBPs in C. pomonella, most (75%) of which are classic OBPs, using genomic and transcriptomic analyses. Two OBP genes were lost in C. pomonella relative to possible distant ancestor in Lepidoptera lineage based on an analysis of gene gains and losses. The phylogenetic tree and chromosome location showed that the expansion of OBP genes mainly resulted from tandem duplications, as the CpomGOBP2 gene was duplicated twice along with loss of CpomPBPB. Two positive selection sites of the CpomGOBP1 gene were identified while other OBP genes evolved under purifying selection. Our results provide fundamental knowledge of OBP genes allowing further study of their function in C. pomonella.
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Affiliation(s)
- Cong Huang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Xue Zhang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, China
| | - Dongfeng He
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Hubei Engineering Research Center for Pest Forewarning and Management, Yangtze University, Jingzhou, China
| | - Qiang Wu
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Rui Tang
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, China
| | - Longsheng Xing
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Wanxue Liu
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Wenkai Wang
- Hubei Engineering Research Center for Pest Forewarning and Management, Yangtze University, Jingzhou, China
| | - Bo Liu
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Yu Xi
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Nianwan Yang
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Fanghao Wan
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, China
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Wanqiang Qian
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
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Kattupalli D, Barbadikar KM, Balija V, Ballichatla S, R A, Padmakumari AP, Saxena S, Gaikwad K, Yerram S, Kokku P, Madhav MS. The Draft Genome of Yellow Stem Borer, an Agriculturally Important Pest, Provides Molecular Insights into Its Biology, Development and Specificity Towards Rice for Infestation. INSECTS 2021; 12:insects12060563. [PMID: 34205299 PMCID: PMC8234988 DOI: 10.3390/insects12060563] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Revised: 05/20/2021] [Accepted: 05/23/2021] [Indexed: 11/16/2022]
Abstract
Simple Summary Yellow stem borer (YSB), is the most destructive and widely occurring pest that attacks rice throughout the growing season. Rice (Oryza sativa L.) is a major staple cereal worldwide, providing essential caloric requirements for more than half of the world’s population. Annual losses to rice borers are approximately 5–10%, but losses in individual fields may reach up to 50–60%. The use of traditional pest management strategies in controlling YSB is somewhat challenging due to its unique internal feeding habit. Genome sequence information of economically important crop pests is important for designing or developing pest-resistant rice varieties. In an approach to achieve this, we present our first-ever study on the draft genome sequence of YSB. The information provided from our current study might be useful in developing genome-based approaches for the management of pest species. Abstract Yellow stem borer (YSB), Scirpophaga incertulas (Walker) (Lepidoptera: Crambidae), a major monophagous insect pest of rice, causes significant yield losses. The rice–YSB interaction is very dynamic, making it difficult for management. The development of resistant lines has been unsuccessful as there are no effective resistant sources in the germplasm. Genome information is necessary for a better understanding of interaction with rice in terms of its recognition, response, and infestation mechanism. The draft genome of YSB is predicted to have 46,057 genes with an estimated size of 308 Mb, being correlated with the flow cytometry analysis. The existence of complex metabolic mechanisms and genes related to specific behavior was identified, being conditioned by a higher level of regulation. We deciphered the possible visual, olfactory, and gustatory mechanisms responsible for its evolution as a monophagous pest. Comparative genomic analysis revealed that YSB is unique in the way it has evolved. The obvious presence of high-immunity-related genes, well-developed RNAi machinery, and diverse effectors provides a means for developing genomic tools for its management. The identified 21,696 SSR markers can be utilized for diversity analysis of populations across the rice-growing regions. We present the first draft genome of YSB. The information emanated paves a way for biologists to design novel pest management strategies as well as for the industry to design new classes of safer and specific insecticide molecules.
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Affiliation(s)
- Divya Kattupalli
- Biotechnology Section, Division of Crop Improvement, ICAR-Indian Institute of Rice Research, Hyderabad 500030, India; (D.K.); (K.M.B.); (V.B.); (S.B.)
| | - Kalyani M. Barbadikar
- Biotechnology Section, Division of Crop Improvement, ICAR-Indian Institute of Rice Research, Hyderabad 500030, India; (D.K.); (K.M.B.); (V.B.); (S.B.)
| | - Vishalakshi Balija
- Biotechnology Section, Division of Crop Improvement, ICAR-Indian Institute of Rice Research, Hyderabad 500030, India; (D.K.); (K.M.B.); (V.B.); (S.B.)
| | - Suneel Ballichatla
- Biotechnology Section, Division of Crop Improvement, ICAR-Indian Institute of Rice Research, Hyderabad 500030, India; (D.K.); (K.M.B.); (V.B.); (S.B.)
| | - Athulya R
- Entomology Section, Division of Crop Protection, ICAR-Indian Institute of Rice Research, Hyderabad 500030, India; (A.R.); (A.P.P.); (S.Y.)
| | - Ayyagari Phani Padmakumari
- Entomology Section, Division of Crop Protection, ICAR-Indian Institute of Rice Research, Hyderabad 500030, India; (A.R.); (A.P.P.); (S.Y.)
| | - Swati Saxena
- Genomics Lab, ICAR-National Institute of Plant Biotechnology, New Delhi 110012, India; (S.S.); (K.G.)
| | - Kishor Gaikwad
- Genomics Lab, ICAR-National Institute of Plant Biotechnology, New Delhi 110012, India; (S.S.); (K.G.)
| | - Sridhar Yerram
- Entomology Section, Division of Crop Protection, ICAR-Indian Institute of Rice Research, Hyderabad 500030, India; (A.R.); (A.P.P.); (S.Y.)
| | - Premalatha Kokku
- Department of Chemistry, Osmania University, Hyderabad 500007, India;
| | - Maganti Sheshu Madhav
- Biotechnology Section, Division of Crop Improvement, ICAR-Indian Institute of Rice Research, Hyderabad 500030, India; (D.K.); (K.M.B.); (V.B.); (S.B.)
- Correspondence:
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Abstract
When laying eggs, plataspid stinkbugs deposit small packets called “symbiont capsules.” Newborn stinkbugs suck the capsules to acquire a bacterial mutualist. Without the symbiont, the babies cannot grow and die. Due to the long-lasting symbiosis, the symbiont has experienced genome reduction and become uncultivable. Within the capsules, however, the symbiont can survive for over a week outside the host. Why and how? Here, we uncover a molecular secret implemented in the symbiont capsules. Mother stinkbugs massively produce a special intestinal secretion protein, PMDP, at the expense of their own survival. PMDP embeds the fragile symbiont cells and protects them within the capsules. The host-provisioned molecule for sustaining symbiosis may be utilized for cultivation and/or preservation of fastidious microorganisms. Microbial symbioses significantly contribute to diverse organisms, where long-lasting associations tend to result in symbiont genome erosion, uncultivability, extinction, and replacement. How such inherently deteriorating symbiosis can be harnessed to stable partnership is of general evolutionary interest. Here, we report the discovery of a host protein essential for sustaining symbiosis. Plataspid stinkbugs obligatorily host an uncultivable and genome-reduced gut symbiont, Ishikawaella. Upon oviposition, females deposit “capsules” for symbiont delivery to offspring. Within the capsules, the fragile symbiotic bacteria survive the harsh conditions outside the host until acquired by newborn nymphs to establish vertical transmission. We identified a single protein dominating the capsule content, which is massively secreted by female-specific intestinal organs, embedding the symbiont cells, and packaged into the capsules. Knockdown of the protein resulted in symbiont degeneration, arrested capsule production, symbiont transmission failure, and retarded nymphal growth, unveiling its essential function for ensuring symbiont survival and vertical transmission. The protein originated from a lineage of odorant-binding protein-like multigene family, shedding light on the origin of evolutionary novelty regarding symbiosis. Experimental suppression of capsule production extended the female’s lifespan, uncovering a substantial cost for maintaining symbiosis. In addition to the host’s guardian protein, the symbiont’s molecular chaperone, GroEL, was overproduced in the capsules, highlighting that the symbiont’s eroding functionality is compensated for by stabilizer molecules of host and symbiont origins. Our finding provides insight into how intimate host–symbiont associations can be maintained over evolutionary time despite the symbiont’s potential vulnerability to degeneration and malfunctioning.
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Balart-García P, Cieslak A, Escuer P, Rozas J, Ribera I, Fernández R. Smelling in the dark: Phylogenomic insights into the chemosensory system of a subterranean beetle. Mol Ecol 2021; 30:2573-2590. [PMID: 33856058 DOI: 10.1111/mec.15921] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 03/22/2021] [Accepted: 03/26/2021] [Indexed: 12/15/2022]
Abstract
The chemosensory system has experienced relevant changes in subterranean animals, facilitating the perception of specific chemical signals critical to survival in their particular environment. However, the genomic basis of chemoreception in cave-dwelling fauna has been largely unexplored. We generated de novo transcriptomes for antennae and body samples of the troglobitic beetle Speonomus longicornis (whose characters suggest an extreme adaptation to a deep subterranean environment) in order to investigate the evolutionary origin and diversification of the chemosensory gene repertoire across coleopterans through a phylogenomic approach. Our results suggested a diminished diversity of odourant and gustatory gene repertoires compared to polyphagous beetles that inhabit surface habitats. Moreover, S. longicornis showed a large diversity of odourant-binding proteins, suggesting an important role of these proteins in capturing airborne chemical cues. We identified a gene duplication of the ionotropic coreceptor IR25a, a highly conserved single-copy gene in protostomes involved in thermal and humidity sensing. In addition, no homologous genes to sugar receptors or the ionotropic receptor IR41a were detected. Our findings suggest that the chemosensory gene repertoire of this cave beetle may result from adaptation to the highly specific ecological niche it occupies, and that gene duplication and loss may have played an important role in the evolution of gene families involved in chemoreception. Altogether, our results shed light on the genomic basis of chemoreception in a cave-dwelling invertebrate and pave the road towards understanding the genomic underpinnings of adaptation to the subterranean lifestyle at a deeper level.
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Affiliation(s)
- Pau Balart-García
- Institute of Evolutionary Biology (CSIC - Universitat Pompeu Fabra), Barcelona, Spain
| | - Alexandra Cieslak
- Institute of Evolutionary Biology (CSIC - Universitat Pompeu Fabra), Barcelona, Spain
| | - Paula Escuer
- Department of Genetics, Microbiology and Statistics, Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Julio Rozas
- Department of Genetics, Microbiology and Statistics, Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Ignacio Ribera
- Institute of Evolutionary Biology (CSIC - Universitat Pompeu Fabra), Barcelona, Spain
| | - Rosa Fernández
- Institute of Evolutionary Biology (CSIC - Universitat Pompeu Fabra), Barcelona, Spain
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Olafson PU, Aksoy S, Attardo GM, Buckmeier G, Chen X, Coates CJ, Davis M, Dykema J, Emrich SJ, Friedrich M, Holmes CJ, Ioannidis P, Jansen EN, Jennings EC, Lawson D, Martinson EO, Maslen GL, Meisel RP, Murphy TD, Nayduch D, Nelson DR, Oyen KJ, Raszick TJ, Ribeiro JMC, Robertson HM, Rosendale AJ, Sackton TB, Saelao P, Swiger SL, Sze SH, Tarone AM, Taylor DB, Warren WC, Waterhouse RM, Weirauch MT, Werren JH, Wilson RK, Zdobnov EM, Benoit JB. The genome of the stable fly, Stomoxys calcitrans, reveals potential mechanisms underlying reproduction, host interactions, and novel targets for pest control. BMC Biol 2021; 19:41. [PMID: 33750380 PMCID: PMC7944917 DOI: 10.1186/s12915-021-00975-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 02/03/2021] [Indexed: 01/01/2023] Open
Abstract
Background The stable fly, Stomoxys calcitrans, is a major blood-feeding pest of livestock that has near worldwide distribution, causing an annual cost of over $2 billion for control and product loss in the USA alone. Control of these flies has been limited to increased sanitary management practices and insecticide application for suppressing larval stages. Few genetic and molecular resources are available to help in developing novel methods for controlling stable flies. Results This study examines stable fly biology by utilizing a combination of high-quality genome sequencing and RNA-Seq analyses targeting multiple developmental stages and tissues. In conjunction, 1600 genes were manually curated to characterize genetic features related to stable fly reproduction, vector host interactions, host-microbe dynamics, and putative targets for control. Most notable was characterization of genes associated with reproduction and identification of expanded gene families with functional associations to vision, chemosensation, immunity, and metabolic detoxification pathways. Conclusions The combined sequencing, assembly, and curation of the male stable fly genome followed by RNA-Seq and downstream analyses provide insights necessary to understand the biology of this important pest. These resources and new data will provide the groundwork for expanding the tools available to control stable fly infestations. The close relationship of Stomoxys to other blood-feeding (horn flies and Glossina) and non-blood-feeding flies (house flies, medflies, Drosophila) will facilitate understanding of the evolutionary processes associated with development of blood feeding among the Cyclorrhapha. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-021-00975-9.
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Affiliation(s)
- Pia U Olafson
- Livestock Arthropod Pests Research Unit, USDA-ARS, Kerrville, TX, USA.
| | - Serap Aksoy
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Geoffrey M Attardo
- Department of Entomology and Nematology, University of California - Davis, Davis, CA, USA
| | - Greta Buckmeier
- Livestock Arthropod Pests Research Unit, USDA-ARS, Kerrville, TX, USA
| | - Xiaoting Chen
- The Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Craig J Coates
- Department of Entomology, Texas A & M University, College Station, TX, USA
| | - Megan Davis
- Livestock Arthropod Pests Research Unit, USDA-ARS, Kerrville, TX, USA
| | - Justin Dykema
- Department of Biological Sciences, Wayne State University, Detroit, MI, USA
| | - Scott J Emrich
- Department of Electrical Engineering & Computer Science, University of Tennessee, Knoxville, TN, USA
| | - Markus Friedrich
- Department of Biological Sciences, Wayne State University, Detroit, MI, USA
| | - Christopher J Holmes
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, USA
| | - Panagiotis Ioannidis
- Department of Genetic Medicine and Development, University of Geneva Medical School and Swiss Institute of Bioinformatics, 1211, Geneva, Switzerland
| | - Evan N Jansen
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, USA
| | - Emily C Jennings
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, USA
| | - Daniel Lawson
- The European Molecular Biology Laboratory, The European Bioinformatics Institute, The Wellcome Genome Campus, Hinxton, CB10 1SD, UK
| | | | - Gareth L Maslen
- The European Molecular Biology Laboratory, The European Bioinformatics Institute, The Wellcome Genome Campus, Hinxton, CB10 1SD, UK
| | - Richard P Meisel
- Department of Biology and Biochemistry, University of Houston, Houston, TX, USA
| | - Terence D Murphy
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Dana Nayduch
- Arthropod-borne Animal Diseases Research Unit, USDA-ARS, Manhattan, KS, USA
| | - David R Nelson
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Kennan J Oyen
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, USA
| | - Tyler J Raszick
- Department of Entomology, Texas A & M University, College Station, TX, USA
| | - José M C Ribeiro
- Section of Vector Biology, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, Rockville, MD, USA
| | - Hugh M Robertson
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | | | - Timothy B Sackton
- Informatics Group, Faculty of Arts and Sciences, Harvard University, Cambridge, MA, USA
| | - Perot Saelao
- Livestock Arthropod Pests Research Unit, USDA-ARS, Kerrville, TX, USA
| | - Sonja L Swiger
- Department of Entomology, Texas A&M AgriLife Research and Extension Center, Stephenville, TX, USA
| | - Sing-Hoi Sze
- Department of Computer Science & Engineering, Department of Biochemistry & Biophysics, Texas A & M University, College Station, TX, USA
| | - Aaron M Tarone
- Department of Entomology, Texas A & M University, College Station, TX, USA
| | - David B Taylor
- Agroecosystem Management Research Unit, USDA-ARS, Lincoln, NE, USA
| | - Wesley C Warren
- University of Missouri, Bond Life Sciences Center, Columbia, MO, USA
| | - Robert M Waterhouse
- Department of Ecology and Evolution, University of Lausanne, and Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland
| | - Matthew T Weirauch
- Center for Autoimmune Genomics and Etiology, Divisions of Biomedical Informatics and Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - John H Werren
- Department of Biology, University of Rochester, Rochester, NY, USA
| | - Richard K Wilson
- Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA.,College of Medicine, Ohio State University, Columbus, OH, USA
| | - Evgeny M Zdobnov
- Department of Genetic Medicine and Development, University of Geneva Medical School and Swiss Institute of Bioinformatics, 1211, Geneva, Switzerland
| | - Joshua B Benoit
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, USA.
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Isolation, Identification, and Bioinformatic Analysis of Antibacterial Proteins and Peptides from Immunized Hemolymph of Red Palm Weevil Rhynchophorus ferrugineus. Biomolecules 2021; 11:biom11010083. [PMID: 33440876 PMCID: PMC7826645 DOI: 10.3390/biom11010083] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 01/01/2021] [Accepted: 01/05/2021] [Indexed: 01/09/2023] Open
Abstract
Red palm weevil (Rhynchophorus ferrugineus Olivier, 1791, Coleoptera: Curculionidae) is a destructive pest of palms, rapidly extending its native geographical range and causing large economic losses worldwide. The present work describes isolation, identification, and bioinformatic analysis of antibacterial proteins and peptides from the immunized hemolymph of this beetle. In total, 17 different bactericidal or bacteriostatic compounds were isolated via a series of high-pressure liquid chromatography steps, and their partial amino acid sequences were determined by N-terminal sequencing or by mass spectrometry. The bioinformatic analysis of the results facilitated identification and description of corresponding nucleotide coding sequences for each peptide and protein, based on the recently published R. ferrugineus transcriptome database. The identified compounds are represented by several well-known bactericidal factors: two peptides similar to defensins, one cecropin-A1-like peptide, and one attacin-B-like protein. Interestingly, we have also identified some unexpected compounds comprising five isoforms of pheromone-binding proteins as well as seven isoforms of odorant-binding proteins. The particular role of these factors in insect response to bacterial infection needs further investigation.
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Olaide OY, Tchouassi DP, Yusuf AA, Pirk CW, Masiga DK, Saini RK, Torto B. Effect of zebra skin-derived compounds on field catches of the human African trypanosomiasis vector Glossina fuscipes fuscipes. Acta Trop 2021; 213:105745. [PMID: 33160957 DOI: 10.1016/j.actatropica.2020.105745] [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: 06/26/2020] [Revised: 10/21/2020] [Accepted: 10/23/2020] [Indexed: 10/23/2022]
Abstract
The riverine tsetse fly Glossina fuscipes fuscipes is a major vector of trypanosome pathogens causing African trypanosomiasis. This fly species uses a combination of olfactory and visual cues to locate its hosts. Previously, traps and targets baited with visual cues have been used in vector control, but the development of olfactory-based tools has been challenging. Recently, repellents have shown promise as olfactory-based tools in tsetse vector control. Here, we evaluated a three-component blend comprising 6-methyl-5-hepten-2-one, acetophenone and geranyl acetone (blend K), previously identified as a repellent for savannah tsetse flies in zebra skin odor, on G. f. fuscipes populations. Using a series of 6 × 6 randomized Latin square-designed experiments, G. f. fuscipes catches in biconical traps were monitored on four islands of Lake Victoria in western Kenya between July and September 2019, after the long rainy season. Traps were baited with blend K and individual components of this blend. The known tsetse repellent blend WRC (waterbuck repellent compounds) and trap alone were included as controls. Daily catch data in thirty-six replicate trials were analyzed using generalized linear model with negative binomial error structure using the package "MASS" in R. Treatment, day and site were set as predictor variables. Our results showed that, blend K significantly reduced G. f. fuscipes catches by 25.6% (P < 0.01) compared to the control trap alone but was not significantly different from WRC which reduced catches by 20.7% (P < 0.05). Of the individual compounds, geranyl acetone solely significantly reduced catches by 29.1% (P < 0.01) which did not differ from blend K or WRC. We conclude that geranyl acetone accounts for the repellent effect of blend K on the riverine tsetse fly, G. f. fuscipes, demonstrating the ecological importance of animal skin odors in the host-seeking behavior of medically-important tsetse fly vectors.
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42
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Wang H, Ma YF, Wang MM, Chen GL, Dewer Y, He M, Zhang F, Yang YF, Liu JF, He P. Expression, Affinity, and Functional Characterization of the Specific Binding of Two Putative Pheromone-Binding Proteins in the Omnivorous German Cockroach Blattella germanica. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:13573-13583. [PMID: 32955873 DOI: 10.1021/acs.jafc.0c02456] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The German cockroach Blattella germanica (L.) is an important pest in medical, veterinary, and public health. Studies on the olfaction mechanism of hemimetabolous insects have rarely been reported, especially in cockroaches. Pheromone-binding proteins (PBPs) play a vital role in insect sex pheromone recognition, which solubilize and carry the hydrophobic pheromonal compounds through the antennal lymph to receptors. In this study, two potential PBPs (BgerOBP26 and BgerOBP40) were identified on the basis of their biased expression in male antennae using tissue transcriptome data and verified by the quantitative real-time polymerase chain reaction approach. We then expressed and purified the two identified odorant-binding proteins (OBPs) using the Escherichia coli expression system and affinity purification. In vitro binding studies showed that the two OBPs display stronger binding affinities to the female volatile sex pheromone blattellaquinone than to its analogues and contact sex pheromone components. Finally, three-dimensional modeling of the two OBPs and dock conformation with sex pheromone molecules showed BgerOBP26 has a larger odorant cavity and more conservative active amino acid residues than BgerOBP40. These results illuminated the binding characteristics of potential PBPs of B. germanica, which could lay the groundwork for improved understanding of many aspects of the chemical ecology of B. germanica. Moreover, this information complements the understanding of the olfactory molecular mechanism in cockroaches and provides potential gene targets for B. germanica control.
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Affiliation(s)
- Hong Wang
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Huaxi District, Guiyang 550025, People's Republic of China
| | - Yun-Feng Ma
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Huaxi District, Guiyang 550025, People's Republic of China
| | - Mei-Mei Wang
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Huaxi District, Guiyang 550025, People's Republic of China
| | - Guang-Lei Chen
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Huaxi District, Guiyang 550025, People's Republic of China
| | - Youssef Dewer
- Bioassay Research Department, Central Agricultural Pesticide Laboratory, Agricultural Research Center, 7 Nadi El-Seid Street, Dokki 12618, Giza, Egypt
| | - Ming He
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Huaxi District, Guiyang 550025, People's Republic of China
| | - Fan Zhang
- Key Laboratory of Animal Resistance Research, College of Life Science, Shandong Normal University, 88 East Wenhua Road, Jinan 250014, People's Republic of China
| | - Yu-Feng Yang
- Zunyi Medical University Zhuhai Campus, Zhuhai, Guangdong 519040, People's Republic of China
| | - Jian-Feng Liu
- Institute of Entomology, Provincial Key Laboratory for Agricultural Pest Management in Mountainous Region, Guizhou University, Huaxi District, Guiyang, Guizhou 550025, People's Republic of China
| | - Peng He
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Huaxi District, Guiyang 550025, People's Republic of China
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Zhang H, Chen JL, Lin JH, Lin JT, Wu ZZ. Odorant-binding proteins and chemosensory proteins potentially involved in host plant recognition in the Asian citrus psyllid, Diaphorina citri. PEST MANAGEMENT SCIENCE 2020; 76:2609-2618. [PMID: 32083388 DOI: 10.1002/ps.5799] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 02/18/2020] [Accepted: 02/21/2020] [Indexed: 06/10/2023]
Abstract
BACKGROUND Odorant-binding proteins (OBPs) and chemosensory proteins (CSPs) are two families of small water-soluble proteins involved in odor detection and subsequent signal transmission. Determination of their binding mechanisms and specificity towards different odorants is important for developing OBPs/CSPs as targets in pest control management. RESULTS We re-annotated genes encoding putative OBPs and CSPs in the Asian citrus psyllid (Diaphorina citri) draft genome using various bioinformatic tools. Genes encoding nine OBPs (seven Classic and two Plus-C) and 12 CSPs were identified, consistent with our previous transcriptomic results. Tissue-specific and developmental expression analyses suggested that genes encoding six OBPs and four CSPs were predominantly expressed in antennae, and displayed various expression patterns in different development stages, suggesting potential involvement in olfactory perception. Competitive fluorescence binding assays with 13 candidate ligands, including known host plant volatiles, sex pheromone components and repellents, showed that DcitOBP3 could bind to various odorants, whereas DcitOBP6, 8 and 9 bound specifically to host plant terpenoids. DcitCSP1 and 12 could also bind to certain terpenoids with high binding specificity. CONCLUSION OBP- and CSP-encoding genes were systematically identified by annotating the draft D. citri genome and those potentially involved in odorant detection and signal transmission were identified by analyzing their tissue-expression profiles and odorant-binding affinities, particularly to the peripheral molecular perception of host plant terpenoids. The identified genes may provide potential targets for efficient pest control. © 2020 Society of Chemical Industry.
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Affiliation(s)
- He Zhang
- Guangzhou City Key Laboratory of Subtropical Fruit Tree Outbreak Control, Zhongkai University of Agriculture and Engineering, Guangzhou, People's Republic of China
| | - Jun-Long Chen
- Guangzhou City Key Laboratory of Subtropical Fruit Tree Outbreak Control, Zhongkai University of Agriculture and Engineering, Guangzhou, People's Republic of China
| | - Jia-Hao Lin
- Guangzhou City Key Laboratory of Subtropical Fruit Tree Outbreak Control, Zhongkai University of Agriculture and Engineering, Guangzhou, People's Republic of China
| | - Jin-Tian Lin
- Guangzhou City Key Laboratory of Subtropical Fruit Tree Outbreak Control, Zhongkai University of Agriculture and Engineering, Guangzhou, People's Republic of China
| | - Zhong-Zhen Wu
- Guangzhou City Key Laboratory of Subtropical Fruit Tree Outbreak Control, Zhongkai University of Agriculture and Engineering, Guangzhou, People's Republic of China
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Vizueta J, Sánchez‐Gracia A, Rozas J. bitacora
: A comprehensive tool for the identification and annotation of gene families in genome assemblies. Mol Ecol Resour 2020; 20:1445-1452. [DOI: 10.1111/1755-0998.13202] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 05/17/2020] [Accepted: 05/27/2020] [Indexed: 02/06/2023]
Affiliation(s)
- Joel Vizueta
- Departament de Genètica, Microbiologia i Estadística and Institut de Recerca de la Biodiversitat (IRBio) Universitat de Barcelona Barcelona Spain
| | - Alejandro Sánchez‐Gracia
- Departament de Genètica, Microbiologia i Estadística and Institut de Recerca de la Biodiversitat (IRBio) Universitat de Barcelona Barcelona Spain
| | - Julio Rozas
- Departament de Genètica, Microbiologia i Estadística and Institut de Recerca de la Biodiversitat (IRBio) Universitat de Barcelona Barcelona Spain
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Mbaluto CM, Ayelo PM, Duffy AG, Erdei AL, Tallon AK, Xia S, Caballero-Vidal G, Spitaler U, Szelényi MO, Duarte GA, Walker WB, Becher PG. Insect chemical ecology: chemically mediated interactions and novel applications in agriculture. ARTHROPOD-PLANT INTERACTIONS 2020; 14:671-684. [PMID: 33193908 PMCID: PMC7650581 DOI: 10.1007/s11829-020-09791-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 10/16/2020] [Indexed: 05/19/2023]
Abstract
Insect chemical ecology (ICE) evolved as a discipline concerned with plant-insect interactions, and also with a strong focus on intraspecific pheromone-mediated communication. Progress in this field has rendered a more complete picture of how insects exploit chemical information in their surroundings in order to survive and navigate their world successfully. Simultaneously, this progress has prompted new research questions about the evolution of insect chemosensation and related ecological adaptations, molecular mechanisms that mediate commonly observed behaviors, and the consequences of chemically mediated interactions in different ecosystems. Themed meetings, workshops, and summer schools are ideal platforms for discussing scientific advancements as well as identifying gaps and challenges within the discipline. From the 11th to the 22nd of June 2018, the 11th annual PhD course in ICE was held at the Swedish University of Agricultural Sciences (SLU) Alnarp, Sweden. The course was made up of 35 student participants from 22 nationalities (Fig. 1a) as well as 32 lecturers. Lectures and laboratory demonstrations were supported by literature seminars, and four broad research areas were covered: (1) multitrophic interactions and plant defenses, (2) chemical communication focusing on odor sensing, processing, and behavior, (3) disease vectors, and (4) applied aspects of basic ICE research in agriculture. This particular article contains a summary and brief synthesis of these main emergent themes and discussions from the ICE 2018 course. In addition, we also provide suggestions on teaching the next generation of ICE scientists, especially during unprecedented global situations.
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Affiliation(s)
- Crispus M. Mbaluto
- Molecular Interaction Ecology, German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Pusch straße 4, 04103 Leipzig, Germany
- Institute of Biodiversity, Friedrich-Schiller-Universität Jena, Dornburger Str. 159, 07743 Jena, Germany
| | - Pascal M. Ayelo
- International Centre of Insect Physiology and Ecology (Icipe), P.O. Box 30772-00100, Nairobi, Kenya
- Department of Zoology and Entomology, University of Pretoria, Hatfield, Private Bag X20, Pretoria, 0028 South Africa
| | - Alexandra G. Duffy
- Evolutionary Ecology Laboratories, Department of Biology, Brigham Young University, 4102 Life Science Building, Provo, UT 84602 USA
| | - Anna L. Erdei
- Zoology Department, Plant Protection Institute, Centre for Agricultural Research, Herman Ottó str. 15, Budapest, 1022 Hungary
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, P.O. Box 102, 23053 Alnarp, Sweden
| | - Anaїs K. Tallon
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, P.O. Box 102, 23053 Alnarp, Sweden
| | - Siyang Xia
- Department of Ecology and Evolutionary Biology, Yale University, 21 Sachem Street, New Haven, CT 06511 USA
| | - Gabriela Caballero-Vidal
- INRAE, Institute of Ecology and Environmental Sciences of Paris, CNRS, IRD, UPEC, Sorbonne Université, Université Paris Diderot, Route de Saint-Cyr, 78026 Versailles Cedex, France
| | - Urban Spitaler
- Institute of Plant Health, Laimburg Research Centre, Laimburg 6, 3904 Ora, South Tyrol Italy
- Department of Crop Sciences, Institute of Plant Protection, University of Natural Resources and Life Sciences (BOKU), Gregor-Mendel-Straße 33, 1180 Vienna, Austria
| | - Magdolna O. Szelényi
- Zoology Department, Plant Protection Institute, Centre for Agricultural Research, Herman Ottó str. 15, Budapest, 1022 Hungary
| | - Gonçalo A. Duarte
- LEAF-Linking Landscape, Environment, Agriculture and Food Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, 1349-017 Lisbon, Portugal
| | - William B. Walker
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, P.O. Box 102, 23053 Alnarp, Sweden
| | - Paul G. Becher
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, P.O. Box 102, 23053 Alnarp, Sweden
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Finet C, Slavik K, Pu J, Carroll SB, Chung H. Birth-and-Death Evolution of the Fatty Acyl-CoA Reductase (FAR) Gene Family and Diversification of Cuticular Hydrocarbon Synthesis in Drosophila. Genome Biol Evol 2019; 11:1541-1551. [PMID: 31076758 PMCID: PMC6546124 DOI: 10.1093/gbe/evz094] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/29/2019] [Indexed: 12/12/2022] Open
Abstract
The birth-and-death evolutionary model proposes that some members of a multigene family are phylogenetically stable and persist as a single copy over time, whereas other members are phylogenetically unstable and undergo frequent duplication and loss. Functional studies suggest that stable genes are likely to encode essential functions, whereas rapidly evolving genes reflect phenotypic differences in traits that diverge rapidly among species. One such class of rapidly diverging traits are insect cuticular hydrocarbons (CHCs), which play dual roles in chemical communications as short-range recognition pheromones as well as protecting the insect from desiccation. Insect CHCs diverge rapidly between related species leading to ecological adaptation and/or reproductive isolation. Because the CHC and essential fatty acid biosynthetic pathways share common genes, we hypothesized that genes involved in the synthesis of CHCs would be evolutionary unstable, whereas those involved in fatty acid-associated essential functions would be evolutionary stable. To test this hypothesis, we investigated the evolutionary history of the fatty acyl-CoA reductases (FARs) gene family that encodes enzymes in CHC synthesis. We compiled a unique data set of 200 FAR proteins across 12 Drosophila species. We uncovered a broad diversity in FAR content which is generated by gene duplications, subsequent gene losses, and alternative splicing. We also show that FARs expressed in oenocytes and presumably involved in CHC synthesis are more unstable than FARs from other tissues. Taken together, our study provides empirical evidence that a comparative approach investigating the birth-and-death evolution of gene families can identify candidate genes involved in rapidly diverging traits between species.
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Affiliation(s)
- Cédric Finet
- Université de Lyon, Institut de Génomique Fonctionnelle de Lyon, CNRS UMR 5242, École Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, France
| | - Kailey Slavik
- Howard Hughes Medical Institute and Laboratory of Molecular Biology, University of Wisconsin, Madison.,PhD Program in Virology, Division of Medical Sciences, Harvard University, Boston, MA, USA
| | - Jian Pu
- Department of Entomology, Michigan State University
| | - Sean B Carroll
- Howard Hughes Medical Institute and Laboratory of Molecular Biology, University of Wisconsin, Madison.,Department of Biology, University of Maryland, College Park, MD
| | - Henry Chung
- Department of Entomology, Michigan State University.,Ecology, Evolutionary Biology and Behavior, Michigan State University
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Peng W, Zheng WW, Tariq K, Yu SN, Zhang HY. MicroRNA Let-7 targets the ecdysone signaling pathway E75 gene to control larval-pupal development in Bactrocera dorsalis. INSECT SCIENCE 2019; 26:229-239. [PMID: 28945006 DOI: 10.1111/1744-7917.12542] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Revised: 09/14/2017] [Accepted: 09/17/2017] [Indexed: 06/07/2023]
Abstract
MicroRNAs (miRNAs) regulate various biological processes during insect development; however, their role in larval-pupal development in oriental fruit fly, Bactrocera dorsalis (Hendel) remains unknown. In the current study, we address the biological function of a conserved miRNA, Bdo-Let-7 in the regulation of BdE75 gene, which belongs to the ecdysone signaling pathway and participates in the larval-pupal development in B. dorsalis. Using dual luciferase reporter assay in HEK293T cells we show that Bdo-Let-7 miRNA interacts with the 3' untranslated region of BdE75 gene and suppresses its expression. The Bdo-Let-7 and BdE75 are also co-expressed in the larval-pupal stages and in different tissues of B. dorsalis. In in vivo experiments, the injection of Bdo-Let-7 agomir and antagomir in third instar larvae down- and up-regulated the expression of BdE75, respectively. The 20-hydroxyecdysone (20E) injection assay shows that 20E up-regulated the expression of Bdo-Let-7 on the 5th day of the larvae. Moreover, abnormal pupation and eclosion were observed after larval Bdo-Let-7 antagomir injection. Based on these results, we show that Bdo-Let-7 regulates the ecdysone signaling pathway through the exact dose of BdE75 gene, and is indispensable for normal larval-pupal development in B. dorsalis.
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Affiliation(s)
- Wei Peng
- Key laboratory of Horticultural Plant Biology (MOE) and Institute of Urban and Horticultural Entomology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Wei-Wei Zheng
- Key laboratory of Horticultural Plant Biology (MOE) and Institute of Urban and Horticultural Entomology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Kaleem Tariq
- Key laboratory of Horticultural Plant Biology (MOE) and Institute of Urban and Horticultural Entomology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- Department of Agriculture, Abdul Wali Khan University Mardan, Khyber Pakhtunkhwa, Pakistan
| | - Shu-Ning Yu
- Key laboratory of Horticultural Plant Biology (MOE) and Institute of Urban and Horticultural Entomology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Hong-Yu Zhang
- Key laboratory of Horticultural Plant Biology (MOE) and Institute of Urban and Horticultural Entomology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
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48
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Markow TA. Host use and host shifts in Drosophila. CURRENT OPINION IN INSECT SCIENCE 2019; 31:139-145. [PMID: 31109667 DOI: 10.1016/j.cois.2019.01.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2018] [Revised: 01/14/2019] [Accepted: 01/15/2019] [Indexed: 05/28/2023]
Abstract
Over a thousand Drosophila species have radiated onto a wide range of feeding and breeding sites. These radiations involve adaptations for locating, accepting, and growing in hosts with highly differing characteristics. In a number of species, owing to the availability of sequenced genomes, particular steps in host specialization and genes that control them, are being identified. Many cases of specialization involve the ability to detoxify some component of the host. Examples include Drosophila sechellia and the octanoic acid in Morinda citrifolia, alpha-amanitin in mycophagous drosophilids, and the alkaloids in cactophilic species. Owing to the known ecologies of many species for which genomes exist, the Drosophila model system provides an unprecedented opportunity to simultaneously examine the genes underlying HOST LOCATION, HOST ACCEPTANCE and HOST USE, the types of selection acting upon them and any coevolutionary interactions among the genes underlying these steps.
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Affiliation(s)
- Therese Ann Markow
- National Laboratory for the Genomics of Biodiversity, CINVESTAV, Irapuato, Mexico; Division of Biological Sciences, University of California at San Diego, La Jolla, CA, USA.
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Rane RV, Pearce SL, Li F, Coppin C, Schiffer M, Shirriffs J, Sgrò CM, Griffin PC, Zhang G, Lee SF, Hoffmann AA, Oakeshott JG. Genomic changes associated with adaptation to arid environments in cactophilic Drosophila species. BMC Genomics 2019; 20:52. [PMID: 30651071 PMCID: PMC6335815 DOI: 10.1186/s12864-018-5413-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 12/26/2018] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Insights into the genetic capacities of species to adapt to future climate change can be gained by using comparative genomic and transcriptomic data to reconstruct the genetic changes associated with such adaptations in the past. Here we investigate the genetic changes associated with adaptation to arid environments, specifically climatic extremes and new cactus hosts, through such an analysis of five repleta group Drosophila species. RESULTS We find disproportionately high rates of gene gains in internal branches in the species' phylogeny where cactus use and subsequently cactus specialisation and high heat and desiccation tolerance evolved. The terminal branch leading to the most heat and desiccation resistant species, Drosophila aldrichi, also shows disproportionately high rates of both gene gains and positive selection. Several Gene Ontology terms related to metabolism were enriched in gene gain events in lineages where cactus use was evolving, while some regulatory and developmental genes were strongly selected in the Drosophila aldrichi branch. Transcriptomic analysis of flies subjected to sublethal heat shocks showed many more downregulation responses to the stress in a heat sensitive versus heat resistant species, confirming the existence of widespread regulatory as well as structural changes in the species' differing adaptations. Gene Ontology terms related to metabolism were enriched in the differentially expressed genes in the resistant species while terms related to stress response were over-represented in the sensitive one. CONCLUSION Adaptations to new cactus hosts and hot desiccating environments were associated with periods of accelerated evolutionary change in diverse biochemistries. The hundreds of genes involved suggest adaptations of this sort would be difficult to achieve in the timeframes projected for anthropogenic climate change.
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Affiliation(s)
- Rahul V. Rane
- CSIRO, Clunies Ross St, GPO Box 1700, Acton, ACT 2601 Australia
- Bio21 Institute, School of BioSciences, University of Melbourne, 30 Flemington Road, Parkville, 3010 Australia
| | | | - Fang Li
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Chris Coppin
- CSIRO, Clunies Ross St, GPO Box 1700, Acton, ACT 2601 Australia
| | - Michele Schiffer
- Bio21 Institute, School of BioSciences, University of Melbourne, 30 Flemington Road, Parkville, 3010 Australia
| | - Jennifer Shirriffs
- Bio21 Institute, School of BioSciences, University of Melbourne, 30 Flemington Road, Parkville, 3010 Australia
| | - Carla M. Sgrò
- School of Biological Sciences, Monash University, Melbourne, 3800 Australia
| | - Philippa C. Griffin
- Bio21 Institute, School of BioSciences, University of Melbourne, 30 Flemington Road, Parkville, 3010 Australia
| | - Goujie Zhang
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
- Centre for Social Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, København, Denmark
| | - Siu F. Lee
- CSIRO, Clunies Ross St, GPO Box 1700, Acton, ACT 2601 Australia
- Bio21 Institute, School of BioSciences, University of Melbourne, 30 Flemington Road, Parkville, 3010 Australia
| | - Ary A. Hoffmann
- Bio21 Institute, School of BioSciences, University of Melbourne, 30 Flemington Road, Parkville, 3010 Australia
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Yang H, Jaime M, Polihronakis M, Kanegawa K, Markow T, Kaneshiro K, Oliver B. Re-annotation of eight Drosophila genomes. Life Sci Alliance 2018; 1:e201800156. [PMID: 30599046 PMCID: PMC6305970 DOI: 10.26508/lsa.201800156] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 12/15/2018] [Accepted: 12/16/2018] [Indexed: 12/11/2022] Open
Abstract
The sequenced genomes of the Drosophila phylogeny are a central resource for comparative work supporting the understanding of the Drosophila melanogaster non-mammalian model system. These have also facilitated evolutionary studies on the selected and random differences that distinguish the thousands of extant species of Drosophila. However, full utility has been hampered by uneven genome annotation. We have generated a large expression profile dataset for nine species of Drosophila and trained a transcriptome assembly approach on D. melanogaster that best matched the extensively curated annotation. We then applied this to the other species to add more than 10000 transcript models per species. We also developed new orthologs to facilitate cross-species comparisons. We validated the new annotation of the distantly related Drosophila grimshawi with an extensive collection of newly sequenced cDNAs. This re-annotation will facilitate understanding both the core commonalities and the species differences in this important group of model organisms, and suggests a strategy for annotating the many forthcoming genomes covering the tree of life.
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Affiliation(s)
- Haiwang Yang
- Section of Developmental Genomics, Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Maria Jaime
- Section of Developmental Genomics, Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Maxi Polihronakis
- Drosophila Species Stock Center, Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - Kelvin Kanegawa
- Hawaiian Drosophila Research Stock Center, Pacific Biosciences Research Center, University of Hawai'i at Manoa, Honolulu, HI, USA
| | - Therese Markow
- National Laboratory of Genomics for Biodiversity (LANGEBIO), Irapuato, Guanajuato, Mexico.,Drosophila Species Stock Center, Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - Kenneth Kaneshiro
- Hawaiian Drosophila Research Stock Center, Pacific Biosciences Research Center, University of Hawai'i at Manoa, Honolulu, HI, USA
| | - Brian Oliver
- Section of Developmental Genomics, Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
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