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Balbuena MS, Latorre-Estivalis JM, Farina WM. Identification of chemosensory genes in the stingless bee Tetragonisca fiebrigi. G3 (Bethesda) 2024; 14:jkae060. [PMID: 38498593 PMCID: PMC11075565 DOI: 10.1093/g3journal/jkae060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 01/15/2024] [Accepted: 03/02/2024] [Indexed: 03/20/2024]
Abstract
Reception of chemical information from the environment is crucial for insects' survival and reproduction. The chemosensory reception mainly occurs by the antennae and mouth parts of the insect, when the stimulus contacts the chemoreceptors located within the sensilla. Chemosensory receptor genes have been well-studied in some social hymenopterans such as ants, honeybees, and wasps. However, although stingless bees are the most representative group of eusocial bees, little is known about their odorant, gustatory, and ionotropic receptor genes. Here, we analyze the transcriptome of the proboscis and antennae of the stingless bee Tetragonisca fiebrigi. We identified and annotated 9 gustatory and 15 ionotropic receptors. Regarding the odorant receptors, we identified 204, and we were able to annotate 161 of them. In addition, we compared the chemosensory receptor genes of T. fiebrigi with those annotated for other species of Hymenoptera. We found that T. fiebrigi showed the largest number of odorant receptors compared with other bees. Genetic expansions were identified in the subfamilies 9-exon, which was also expanded in ants and paper wasps; in G02A, including receptors potentially mediating social behavior; and in GUnC, which has been related to pollen and nectar scent detection. Our study provides the first report of chemosensory receptor genes in T. fiebrigi and represents a resource for future molecular and physiological research in this and other stingless bee species.
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Affiliation(s)
- María Sol Balbuena
- Laboratorio de Insectos Sociales, Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), Universidad de Buenos Aires—CONICET, CABA C1428EGA, Argentina
- Laboratorio de Insectos Sociales, Departamento de Biodiversidad y Biología Experimental, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, CABA C1428EGA, Argentina
| | - Jose M Latorre-Estivalis
- Laboratorio de Insectos Sociales, Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), Universidad de Buenos Aires—CONICET, CABA C1428EGA, Argentina
- Laboratorio de Insectos Sociales, Departamento de Biodiversidad y Biología Experimental, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, CABA C1428EGA, Argentina
| | - Walter M Farina
- Laboratorio de Insectos Sociales, Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), Universidad de Buenos Aires—CONICET, CABA C1428EGA, Argentina
- Laboratorio de Insectos Sociales, Departamento de Biodiversidad y Biología Experimental, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, CABA C1428EGA, Argentina
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Tian CH, Liu XG, Xu CY, Huang JR, Fu JF, Wang GS, Zhang JY, Li GP, Yin XM, Feng HQ. Molecule characterization of chemosensory and metabolism-related genes in the proboscis of Athetis lepigone. Front Physiol 2023; 14:1287353. [PMID: 38187138 PMCID: PMC10766847 DOI: 10.3389/fphys.2023.1287353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 11/23/2023] [Indexed: 01/09/2024] Open
Abstract
Introduction: The moth species Athetis lepigone (Möschler) (Lepidoptera: Noctuidae), which has recently been identified as a pest of summer maize (Zea mays L.) in China, has demonstrated a rapid proliferation with in the Huang-Huai-Hai Plain region since its initial discovery in Hebei Province in 2005. It has become a prevalent pest of corn crops, and its ability to adapt quickly to its surroundings is currently being investigated. One of the key characteristics of its siphoning mouthparts is not only the feeding apparatus itself but also the chemosensory organs that enable the detection of chemical signals from the surrounding environment. However, there is a lack of comprehensive research on the genes responsible for chemosensory and metabolic mechanisms in the proboscises of male and female A. lepigone adults. Methods: In this study, we utilized transcriptome analysis to identify a total of fifty chemosensory genes from six distinct families, including 19 odorant-binding proteins (OBPs), 22 chemosensory proteins (CSPs), one co-receptor (Orco), six odorant receptors (ORs), four ionotropic receptors (IRs), and two sensory neuron membrane proteins (SNMPs) in the proboscis. Notably, seven OBPs, two CSPs, and one OR were discovered for the first time. Additionally, fourteen genes related to metabolism, including cytochrome P450 (CYPs) and carboxylesterases (CXEs), were also identified. Furthermore, a qualitative analysis was conducted on the relative transcript levels of eight related genes. The expression of 21 annotated chemosensory and metabolic genes was compared between A. lepigone adults and larvae using qRT-PCR, revealing tissue specificity. The majority of genes exhibited predominant expression in the antennae and proboscis during the adult stage, while showing slight expression in the combination of sixth-instar larval head oral appendages (maxilla, labium, and antenna) and pheromone gland-ovipositors of female adults. Results/discussion: Our study points to a new pest control strategies that these newly discovered genes have the potential to serve as targets for enhancing future pest control, including mating disruption and the use of food attractants. And it would be advantageous to ascertain the distribution of chemosensory gene expression and gain insights into the functionalities of these genes, thereby establishing a novel theoretical framework for the advancement of eco-friendly pesticides and efficient pest management strategies in the future.
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Affiliation(s)
- Cai-Hong Tian
- Henan Key Laboratory of Crop Pest Control, MOA Key Regional Crop Integrated Pest Management (IPM) Laboratory in Southern Part of Northern China, International Joint Research Laboratory for Crop Protection of Henan, Entomological Radar Station Zero of Henan Province for Field Scientific Observation and Research, Institute of Plant Protection, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Xiao-Guang Liu
- Henan International Laboratory for Green Pest Control, Henan Engineering Laboratory of Pest Biological Control, College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Cun-Yi Xu
- Henan Key Laboratory of Crop Pest Control, MOA Key Regional Crop Integrated Pest Management (IPM) Laboratory in Southern Part of Northern China, International Joint Research Laboratory for Crop Protection of Henan, Entomological Radar Station Zero of Henan Province for Field Scientific Observation and Research, Institute of Plant Protection, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Jian-Rong Huang
- Henan Key Laboratory of Crop Pest Control, MOA Key Regional Crop Integrated Pest Management (IPM) Laboratory in Southern Part of Northern China, International Joint Research Laboratory for Crop Protection of Henan, Entomological Radar Station Zero of Henan Province for Field Scientific Observation and Research, Institute of Plant Protection, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Jun-Feng Fu
- Yuzhou Plant Protection and Quarantine Station, Yuzhou, China
| | - Gen-Song Wang
- Henan Key Laboratory of Crop Pest Control, MOA Key Regional Crop Integrated Pest Management (IPM) Laboratory in Southern Part of Northern China, International Joint Research Laboratory for Crop Protection of Henan, Entomological Radar Station Zero of Henan Province for Field Scientific Observation and Research, Institute of Plant Protection, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Jun-Yi Zhang
- Henan Key Laboratory of Crop Pest Control, MOA Key Regional Crop Integrated Pest Management (IPM) Laboratory in Southern Part of Northern China, International Joint Research Laboratory for Crop Protection of Henan, Entomological Radar Station Zero of Henan Province for Field Scientific Observation and Research, Institute of Plant Protection, Henan Academy of Agricultural Sciences, Zhengzhou, China
- Henan International Laboratory for Green Pest Control, Henan Engineering Laboratory of Pest Biological Control, College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Guo-Ping Li
- Henan Key Laboratory of Crop Pest Control, MOA Key Regional Crop Integrated Pest Management (IPM) Laboratory in Southern Part of Northern China, International Joint Research Laboratory for Crop Protection of Henan, Entomological Radar Station Zero of Henan Province for Field Scientific Observation and Research, Institute of Plant Protection, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Xin-Ming Yin
- Henan International Laboratory for Green Pest Control, Henan Engineering Laboratory of Pest Biological Control, College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Hong-Qiang Feng
- Henan Key Laboratory of Crop Pest Control, MOA Key Regional Crop Integrated Pest Management (IPM) Laboratory in Southern Part of Northern China, International Joint Research Laboratory for Crop Protection of Henan, Entomological Radar Station Zero of Henan Province for Field Scientific Observation and Research, Institute of Plant Protection, Henan Academy of Agricultural Sciences, Zhengzhou, China
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Du HT, Lu JQ, Ji K, Wang CC, Yao ZC, Liu F, Li Y. Comparative Transcriptomic Assessment of Chemosensory Genes in Adult and Larval Olfactory Organs of Cnaphalocrocis medinalis. Genes (Basel) 2023; 14:2165. [PMID: 38136987 PMCID: PMC10742765 DOI: 10.3390/genes14122165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 11/27/2023] [Accepted: 11/28/2023] [Indexed: 12/24/2023] Open
Abstract
The rice leaf folder, Cnaphalocrocis medinalis (Lepidoptera: Pyralidae), is a notorious pest of rice in Asia. The larvae and adults of C. medinalis utilize specialized chemosensory systems to adapt to different environmental odors and physiological behaviors. However, the differences in chemosensory genes between the olfactory organs of these two different developmental stages remain unclear. Here, we conducted a transcriptome analysis of larvae heads, male antennae, and female antennae in C. medinalis and identified 131 putative chemosensory genes, including 32 OBPs (8 novel OBPs), 23 CSPs (2 novel CSPs), 55 ORs (17 novel ORs), 19 IRs (5 novel IRs) and 2 SNMPs. Comparisons between larvae and adults of C. medinalis by transcriptome and RT-qPCR analysis revealed that the number and expression of chemosensory genes in larval heads were less than that of adult antennae. Only 17 chemosensory genes (7 OBPs and 10 CSPs) were specifically or preferentially expressed in the larval heads, while a total of 101 chemosensory genes (21 OBPs, 9 CSPs, 51 ORs, 18 IRs, and 2 SNMPs) were specifically or preferentially expressed in adult antennae. Our study found differences in chemosensory gene expression between larvae and adults, suggesting their specialized functions at different developmental stages of C. medinalis. These results provide a theoretical basis for screening chemosensory genes as potential molecular targets and developing novel management strategies to control C. medinalis.
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Affiliation(s)
- Hai-Tao Du
- College of Plant Protection, Yangzhou University, Yangzhou 225009, China; (H.-T.D.); (J.-Q.L.); (K.J.); (C.-C.W.); (Z.-C.Y.)
| | - Jia-Qi Lu
- College of Plant Protection, Yangzhou University, Yangzhou 225009, China; (H.-T.D.); (J.-Q.L.); (K.J.); (C.-C.W.); (Z.-C.Y.)
| | - Kun Ji
- College of Plant Protection, Yangzhou University, Yangzhou 225009, China; (H.-T.D.); (J.-Q.L.); (K.J.); (C.-C.W.); (Z.-C.Y.)
| | - Chu-Chu Wang
- College of Plant Protection, Yangzhou University, Yangzhou 225009, China; (H.-T.D.); (J.-Q.L.); (K.J.); (C.-C.W.); (Z.-C.Y.)
| | - Zhi-Chao Yao
- College of Plant Protection, Yangzhou University, Yangzhou 225009, China; (H.-T.D.); (J.-Q.L.); (K.J.); (C.-C.W.); (Z.-C.Y.)
| | - Fang Liu
- College of Plant Protection, Yangzhou University, Yangzhou 225009, China; (H.-T.D.); (J.-Q.L.); (K.J.); (C.-C.W.); (Z.-C.Y.)
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture & Agri-Product Safety, Yangzhou University, Yangzhou 225009, China
| | - Yao Li
- College of Plant Protection, Yangzhou University, Yangzhou 225009, China; (H.-T.D.); (J.-Q.L.); (K.J.); (C.-C.W.); (Z.-C.Y.)
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Kaleem Ullah RM, Jia B, Liang S, Sikandar A, Gao F, Wu H. Uncovering the Chemosensory System of a Subterranean Termite, Odontotermes formosanus (Shiraki) (Isoptera: Termitidae): Revealing the Chemosensory Genes and Gene Expression Patterns. Insects 2023; 14:883. [PMID: 37999082 PMCID: PMC10672159 DOI: 10.3390/insects14110883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Revised: 10/23/2023] [Accepted: 10/26/2023] [Indexed: 11/25/2023]
Abstract
Termites are eusocial insects. Chemical signals between colony members are crucial to the smooth running of colony operations, but little is known about their olfactory system and the roles played by various chemosensory genes in this process. Chemosensory genes are involved in basic olfactory perception in insects. Odontotermes formosanus (Shiraki) is one of the most damaging pests to agricultural crops, forests, and human-made structures. To better understand the olfactory system and the genes involved in olfactory processing in O. formosanus, we produced a transcriptome of worker termites. In this study, we identified 13 OforOBPs, 1 OforCSP, 15 OforORs, 9 OforGRs, and 4 OforSNMPs. Multiple sequence alignments were used in the phylogenetic study, which included data from other termite species and a wide variety of insect species. Moreover, we also investigated the mRNA expression levels using qRT-PCR. The significantly high expression levels of OforCSP1, OforOBP2, OforOR1, and OforSNMP1 suggest that these genes may play important roles in olfactory processing in termite social behavior, including caste differentiation, nestmate and non-nestmate discrimination, and the performance of colony operations among members. Our research establishes a foundation for future molecular-level functional studies of chemosensory genes in O. formosanus, which might lead to the identification of novel targets for termite integrated pest management.
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Affiliation(s)
- Rana Muhammad Kaleem Ullah
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory of Agric-Environment and Agric-Products Safety, College of Agriculture, Guangxi University, Nanning 530004, China; (R.M.K.U.); (A.S.); (F.G.)
| | - Bao Jia
- Nanning Institute of Termite Control, Nanning 530023, China; (B.J.); (S.L.)
| | - Sheng Liang
- Nanning Institute of Termite Control, Nanning 530023, China; (B.J.); (S.L.)
| | - Aatika Sikandar
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory of Agric-Environment and Agric-Products Safety, College of Agriculture, Guangxi University, Nanning 530004, China; (R.M.K.U.); (A.S.); (F.G.)
| | - Fukun Gao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory of Agric-Environment and Agric-Products Safety, College of Agriculture, Guangxi University, Nanning 530004, China; (R.M.K.U.); (A.S.); (F.G.)
| | - Haiyan Wu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory of Agric-Environment and Agric-Products Safety, College of Agriculture, Guangxi University, Nanning 530004, China; (R.M.K.U.); (A.S.); (F.G.)
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Negi A, Liao BY, Yeh SD. Long-read-based genome assembly of Drosophila gunungcola reveals fewer chemosensory genes in flower-breeding species. Genome Biol Evol 2023; 15:7079968. [PMID: 36930539 PMCID: PMC10063221 DOI: 10.1093/gbe/evad048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 02/21/2023] [Accepted: 02/24/2023] [Indexed: 03/18/2023] Open
Abstract
Drosophila gunungcola exhibits reproductive activities on the fresh flowers of several plant species and is an emerging model to study the co-option of morphological and behavioral traits in male courtship display. Here, we report a near-chromosome-level genome assembly that was constructed based on long-read Pac-Bio sequencing data (with ∼66x coverage) and annotated with the assistant from RNA-seq transcriptome data of whole organisms at various developmental stages. A nuclear genome of 189 Mb with 13,950 protein-coding genes and a mitogenome of 17.5 kb. Few inter-chromosomal rearrangements were found in the comparisons of synteny with D. elegans, its sister species, and D. melanogaster, suggesting that the gene compositions on each Muller element are evolutionarily conserved. Loss events of several OR and IR genes in D. gunungcola and D. elegans were revealed when orthologous genomic regions were compared across species in the D. melanogaster species group. This high-quality reference genome will facilitate further comparative studies on traits related to the evolution of sexual behavior and diet specialization.
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Affiliation(s)
- Ateesha Negi
- Department of Life Sciences, National Central University, Zhongli District, Taoyuan City 320, Taiwan, ROC
| | - Ben-Yang Liao
- Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Miaoli County, Taiwan, ROC
| | - Shu-Dan Yeh
- Department of Life Sciences, National Central University, Zhongli District, Taoyuan City 320, Taiwan, ROC
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Lu JH, Guan DL, Xu SQ, Huang H. De Novo Assembly and Characterization of the Transcriptome of an Omnivorous Camel Cricket (Tachycines meditationis). Int J Mol Sci 2023; 24. [PMID: 36835417 DOI: 10.3390/ijms24044005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Revised: 01/12/2023] [Accepted: 01/16/2023] [Indexed: 02/18/2023] Open
Abstract
Tachycines meditationis (Orthoptera: Rhaphidophoridae: Tachycines) is a widely distributed insect in eastern Asia. This species is common in urban environments, and its unique omnivorous diet may contribute to its success in various habitats. However, molecular studies on the species are scarce. Here, we obtained the first transcriptome sequence of T. meditationis and performed preliminary analyses to test whether the evolution of coding sequences fits the expectations based on the species' ecology. We retrieved 476,495 effective transcripts and annotated 46,593 coding sequences (CDS). We analysed the codon usage and found that directional mutation pressure was the leading cause of codon usage bias in this species. This genome-wide relaxed codon usage pattern in T. meditationis is surprising, given the potentially large population size of this species. Moreover, despite the omnivorous diet, the chemosensory genes of this species do not exhibit codon usage deviating significantly from the genome-level pattern. They also do not seem to experience more gene family expansion than other cave cricket species do. A thorough search for rapidly evolved genes using the dN/dS value showed that genes associated with substance synthesis and metabolic pathways, such as retinol metabolism, aminoacyl-tRNA biosynthesis, and fatty acid metabolism, underwent species-specific positive selection. While some results seem to contradict the species ecology, our transcriptome assembly provides a valuable molecular resource for future studies on camel cricket evolution and molecular genetics for feeding ecology in insects, in general.
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Zhu X, Yu Q, Gan X, Song L, Zhang K, Zuo T, Zhang J, Hu Y, Chen Q, Ren B. Transcriptome Analysis and Identification of Chemosensory Genes in Baryscapus dioryctriae (Hymenoptera: Eulophidae). Insects 2022; 13:1098. [PMID: 36555008 PMCID: PMC9780838 DOI: 10.3390/insects13121098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 11/19/2022] [Accepted: 11/26/2022] [Indexed: 06/17/2023]
Abstract
Baryscapus dioryctriae is a pupal endoparasitoid of many Pyralidae pests and has been used as a biocontrol agent against insect pests that heavily damage the cone and seed of the Korean pine. The olfactory system of wasps plays an essential role in sensing the chemical signals during their foraging, mating, host location, etc., and the chemosensory genes are involved in detecting and transducing these signals. Many chemosensory genes have been identified from the antennae of Hymenoptera; however, there are few reports on the chemosensory genes of Eulophidae wasps. In this study, the transcriptome databases based on ten different tissues of B. dioryctriae were first constructed, and 274 putative chemosensory genes, consisting of 27 OBPs, 9 CSPs, 3 NPC2s, 155 ORs, 49 GRs, 23 IRs and 8 SNMPs genes, were identified based on the transcriptomes and manual annotation. Phylogenetic trees of the chemosensory genes were constructed to investigate the orthologs between B. dioryctriae and other insect species. Additionally, twenty-eight chemosensory genes showed female antennae- and ovipositor-biased expression, which was validated by RT-qPCR. These findings not only built a molecular basis for further research on the processes of chemosensory perception in B. dioryctriae, but also enriched the identification of chemosensory genes from various tissues of Eulophidae wasps.
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Affiliation(s)
- Xiaoyan Zhu
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, School of Life Sciences, Northeast Normal University, Changchun 130024, China
- Key Laboratory of Vegetation Ecology, MOE, Northeast Normal University, Changchun 130024, China
- Jilin Provincial Engineering Laboratory of Avian Ecology and Conservation Genetics, Northeast Normal University, Changchun 130118, China
| | - Qiling Yu
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, School of Life Sciences, Northeast Normal University, Changchun 130024, China
- Key Laboratory of Vegetation Ecology, MOE, Northeast Normal University, Changchun 130024, China
- Jilin Provincial Engineering Laboratory of Avian Ecology and Conservation Genetics, Northeast Normal University, Changchun 130118, China
| | - Xingyu Gan
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, School of Life Sciences, Northeast Normal University, Changchun 130024, China
- Key Laboratory of Vegetation Ecology, MOE, Northeast Normal University, Changchun 130024, China
- Jilin Provincial Engineering Laboratory of Avian Ecology and Conservation Genetics, Northeast Normal University, Changchun 130118, China
| | - Liwen Song
- Research Institute of Forest Protection, Jilin Provincial Academy of Forestry Sciences, Changchun 130033, China
| | - Kaipeng Zhang
- Research Institute of Forest Protection, Jilin Provincial Academy of Forestry Sciences, Changchun 130033, China
| | - Tongtong Zuo
- Research Institute of Forest Protection, Jilin Provincial Academy of Forestry Sciences, Changchun 130033, China
| | - Junjie Zhang
- Engineering Research Center of Natural Enemies, Institute of Biological Control, Jilin Agricultural University, Changchun 130118, China
| | - Ying Hu
- Engineering Research Center of Natural Enemies, Institute of Biological Control, Jilin Agricultural University, Changchun 130118, China
| | - Qi Chen
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, School of Life Sciences, Northeast Normal University, Changchun 130024, China
- Key Laboratory of Vegetation Ecology, MOE, Northeast Normal University, Changchun 130024, China
- Jilin Provincial Engineering Laboratory of Avian Ecology and Conservation Genetics, Northeast Normal University, Changchun 130118, China
| | - Bingzhong Ren
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, School of Life Sciences, Northeast Normal University, Changchun 130024, China
- Key Laboratory of Vegetation Ecology, MOE, Northeast Normal University, Changchun 130024, China
- Jilin Provincial Engineering Laboratory of Avian Ecology and Conservation Genetics, Northeast Normal University, Changchun 130118, China
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10
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Li X, Li JW, Sun WX, Li W, Gao HY, Liu TX, Qu MJ. Candidate Chemosensory Genes Identified in the Adult Antennae of Sympiezomias velatus and Binding Property of Odorant-Binding Protein 15. Front Physiol 2022; 13:907667. [PMID: 35711318 PMCID: PMC9193972 DOI: 10.3389/fphys.2022.907667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 04/28/2022] [Indexed: 11/13/2022] Open
Abstract
Chemosensory genes play important roles in insect behaviors and have thus become potential molecular targets for pest control based on the manipulation of chemoreception-driven behaviors. The great gray weevil Sympiezomias velatus (Chevrolat) (Coleoptera: Curculionidae) is an important agricultural pest that causes serious economic losses to many crops in China, but its chemosensory genes have not been reported. Here we assembled the antennal transcriptomes of female and male adult S. velatus and revealed the major chemosensory genes necessary for olfaction. A total of 138 candidate chemosensory genes in six families were identified, including 41 encoding odorant-binding proteins (OBPs), 11 encoding chemosensory proteins (CSPs), 62 encoding odorant receptors (ORs), 15 encoding gustatory receptors (GRs), six encoding ionotropic receptors (IRs), and three encoding sensory neuron membrane proteins (SNMPs). We analyzed their phylogenetic relationship based on the amino acid sequences of these chemosensory-related protein families in S. velatus and other insects, and the expression profiles based on their antennal transcriptomes. Chemosensory genes that show antenna-abundant/specific or sex-biased expression were observed, suggesting that these genes might have functions in olfaction. Furthermore, we chose an antenna-abundant OBP belonging to ABPX subfamily, SvelOBP15, to investigate its binding property. The results showed that among 33 tested compounds, SvelOBP15 displayed high binding affinities (Ki = 7.36-12.94 μmol/L) with farnesol, nerolidol, limonene and diisobutyl phthalate, indicating that SvelOBP15 plays olfactory roles by binding and transporting specific plant volatiles. These findings will help us better understand the olfactory systems of S. velatus, and provide a basis for functional elucidation of these chemosensory genes.
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Affiliation(s)
- Xiao Li
- Shandong Peanut Research Institute, Qingdao, China
| | - Jian-Wen Li
- College of Life Sciences, Yangtze University, Jingzhou, China.,Weinan Product Quality Supervision and Inspection Institute, Weinan, China
| | - Wen-Xiu Sun
- College of Life Sciences, Yangtze University, Jingzhou, China
| | - Wei Li
- College of Life Sciences, Yangtze University, Jingzhou, China
| | - Hua-Yuan Gao
- Peanut Research Institute, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Tong-Xian Liu
- College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, China
| | - Ming-Jing Qu
- Shandong Peanut Research Institute, Qingdao, China
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11
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Gao YQ, Chen ZZ, Liu MY, Song CY, Jia ZF, Liu FH, Qu C, Dewer Y, Zhao HP, Xu YY, Kang ZW. Characterization of Antennal Chemosensilla and Associated Chemosensory Genes in the Orange Spiny Whitefly, Aleurocanthus spiniferus (Quaintanca). Front Physiol 2022; 13:847895. [PMID: 35295577 PMCID: PMC8920487 DOI: 10.3389/fphys.2022.847895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 01/20/2022] [Indexed: 11/20/2022] Open
Abstract
The insect chemosensory system plays an important role in many aspects of insects' behaviors necessary for their survival. Despite the complexity of this system, an increasing number of studies have begun to understand its structure and function in different insect species. Nonetheless, the chemosensory system in the orange spiny whitefly Aleurocanthus spiniferus, as one of the most destructive insect pests of citrus in tropical Asia, has not been investigated yet. In this study, the sensillum types, morphologies and distributions of the male and female antennae of A. spiniferus were characterized using scanning electron microscopy. In both sexes, six different sensilla types were observed: trichodea sensilla, chaetica sensilla, microtrichia sensilla, coeloconic sensilla, basiconic sensilla, and finger-like sensilla. Moreover, we identified a total of 48 chemosensory genes, including 5 odorant-binding proteins (OBPs), 12 chemosensory proteins (CSPs), 3 sensory neuron membrane proteins (SNMPs), 6 odorant receptors (ORs), 8 gustatory receptors (GRs), and 14 ionotropic receptors (IRs) using transcriptome data analysis. Tissue-specific transcriptome analysis of these genes showed predominantly expression in the head (including antennae), whereas CSPs were broadly expressed in both head (including the antennae) and body tissue of adult A. spiniferus. In addition, the expression profiling of selected chemosensory genes at different developmental stages was examined by quantitative real time-PCR which was mapped to the transcriptome. We found that the majority of these genes were highly expressed in adults, while AspiORco, AspiGR1, AspiGR2, and AspiIR4 genes were only detected in the pupal stage. Together, this study provides a basis for future chemosensory and genomic studies in A. spiniferus and closely related species. Furthermore, this study not only provides insights for further research on the molecular mechanisms of A. spiniferus-plant interactions but also provides extensive potential targets for pest control.
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Affiliation(s)
- Yu-Qing Gao
- College of Plant Protection, Shandong Agricultural University, Tai’an, China
| | - Zhen-Zhen Chen
- College of Plant Protection, Shandong Agricultural University, Tai’an, China
| | - Meng-Yuan Liu
- College of Plant Protection, Shandong Agricultural University, Tai’an, China
| | - Chang-Yuan Song
- College of Plant Protection, Shandong Agricultural University, Tai’an, China
| | - Zhi-Fei Jia
- College of Plant Protection, Shandong Agricultural University, Tai’an, China
| | - Fang-Hua Liu
- College of Plant Protection, Shandong Agricultural University, Tai’an, China
| | - Cheng Qu
- Beijing Key Laboratory of Environment Friendly Management on Fruit Diseases and Pests in North China, Institute of Plant and Environment Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Youssef Dewer
- Phytotoxicity Research Department, Central Agricultural Pesticide Laboratory, Agricultural Research Center, Giza, Egypt
| | - Hai-Peng Zhao
- College of Plant Protection, Shandong Agricultural University, Tai’an, China
| | - Yong-Yu Xu
- College of Plant Protection, Shandong Agricultural University, Tai’an, China
| | - Zhi-Wei Kang
- College of Plant Protection, Shandong Agricultural University, Tai’an, China
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12
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Zhang S, Gao X, Wang L, Jiang W, Su H, Jing T, Cui J, Zhang L, Yang Y. Chromosome-level genome assemblies of two cotton-melon aphid Aphis gossypii biotypes unveil mechanisms of host adaption. Mol Ecol Resour 2021; 22:1120-1134. [PMID: 34601821 DOI: 10.1111/1755-0998.13521] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 09/22/2021] [Accepted: 09/24/2021] [Indexed: 11/30/2022]
Abstract
The cotton-melon aphid Aphis gossypii is a sap-sucking insect that is considered a serious global pest. The species is distributed over a large geographical range and uses a wide variety of hosts, with some populations being specialized to attack different plant species. Here, we provide de novo chromosome-level genome assemblies of a cotton specialist population (Hap1) and a cucurbit specialist population (Hap3). We achieved this by using a combination of third-generation sequencing platforms, namely Illumina and Hi-C sequencing technologies. We were able to anchor a total of 334.89 Mb (scaffold N50 of 89.13 Mb) and 359.95 Mb (scaffold N50 of 68.88 Mb) to four chromosomes for Hap1 and Hap3, respectively. Moreover, our results showed that the X-chromosome of Hap3 (113.01 Mb) was significantly longer than that of Hap1 (100.26 Mb), with a high level of sequence conservation between the aphid species. We also report variation in the number of protein-coding genes and repeat sequences between Hap1 and Hap3. In particular, olfactory and gustatory receptor genes underwent a high level of gene duplication and expansion events in A. gossypii, including between Hap1 and Hap3. Moreover, we identified two glutathione S-transferase genes which underwent single gene duplications in Hap3, and tandem duplication and inversion events affecting the cytochrome P450 monooxygenase between Hap1 and Hap3, all of which include the CYP3 family. Our results illustrate the variance in the genomic composition of two specialized A. gossypii populations and provide a helpful resource for the study of aphid population evolution, host adaption and insecticide resistance.
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Affiliation(s)
- Shuai Zhang
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
| | - Xueke Gao
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Li Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Weili Jiang
- Basic Experimental Teaching Center of Life Sciences, Yangzhou University, Yangzhou, China
| | - Honghua Su
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
| | - Tianxing Jing
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
| | - Jinjie Cui
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Lijuan Zhang
- Department of Entomology, College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Yizhong Yang
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
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13
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Piron-Prunier F, Persyn E, Legeai F, McClure M, Meslin C, Robin S, Alves-Carvalho S, Mohammad A, Blugeon C, Jacquin-Joly E, Montagné N, Elias M, Gauthier J. Comparative transcriptome analysis at the onset of speciation in a mimetic butterfly-The Ithomiini Melinaea marsaeus. J Evol Biol 2021; 34:1704-1721. [PMID: 34570954 DOI: 10.1111/jeb.13940] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 08/16/2021] [Accepted: 09/03/2021] [Indexed: 11/28/2022]
Abstract
Ecological speciation entails divergent selection on specific traits and ultimately on the developmental pathways responsible for these traits. Selection can act on gene sequences but also on regulatory regions responsible for gene expression. Mimetic butterflies are a relevant system for speciation studies because wing colour pattern (WCP) often diverges between closely related taxa and is thought to drive speciation through assortative mating and increased predation on hybrids. Here, we generate the first transcriptomic resources for a mimetic butterfly of the tribe Ithomiini, Melinaea marsaeus, to examine patterns of differential expression between two subspecies and between tissues that express traits that likely drive reproductive isolation; WCP and chemosensory genes. We sequenced whole transcriptomes of three life stages to cover a large catalogue of transcripts, and we investigated differential expression between subspecies in pupal wing discs and antennae. Eighteen known WCP genes were expressed in wing discs and 115 chemosensory genes were expressed in antennae, with a remarkable diversity of chemosensory protein genes. Many transcripts were differentially expressed between subspecies, including two WCP genes and one odorant receptor. Our results suggest that in M. marsaeus the same genes as in other mimetic butterflies are involved in traits causing reproductive isolation, and point at possible candidates for the differences in those traits between subspecies. Differential expression analyses of other developmental stages and body organs and functional studies are needed to confirm and expand these results. Our work provides key resources for comparative genomics in mimetic butterflies, and more generally in Lepidoptera.
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Affiliation(s)
- Florence Piron-Prunier
- Institut de Systématique, Evolution, Biodiversité, MNHN, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France
| | - Emma Persyn
- Institute of Ecology and Environmental Sciences of Paris, Sorbonne Université, INRAE, CNRS, IRD, UPEC, Université de Paris, Paris, France
| | - Fabrice Legeai
- BIPAA, IGEPP, INRAE, Institut Agro, Univ Rennes, Rennes, France.,Univ Rennes, INRIA, CNRS, IRISA, Rennes, France
| | - Melanie McClure
- Institut de Systématique, Evolution, Biodiversité, MNHN, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France.,Laboratoire Écologie, Évolution,Interactions des Systèmes Amazoniens (LEEISA), Université de Guyane, CNRS, IFREMER, Cayenne, France
| | - Camille Meslin
- Institute of Ecology and Environmental Sciences of Paris, Sorbonne Université, INRAE, CNRS, IRD, UPEC, Université de Paris, Paris, France
| | - Stéphanie Robin
- BIPAA, IGEPP, INRAE, Institut Agro, Univ Rennes, Rennes, France.,Univ Rennes, INRIA, CNRS, IRISA, Rennes, France
| | | | - Ammara Mohammad
- Département de Biologie, Genomics Core Facility, Institut de Biologie de l'ENS (IBENS), École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Corinne Blugeon
- Département de Biologie, Genomics Core Facility, Institut de Biologie de l'ENS (IBENS), École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Emmanuelle Jacquin-Joly
- Institute of Ecology and Environmental Sciences of Paris, Sorbonne Université, INRAE, CNRS, IRD, UPEC, Université de Paris, Paris, France
| | - Nicolas Montagné
- Institute of Ecology and Environmental Sciences of Paris, Sorbonne Université, INRAE, CNRS, IRD, UPEC, Université de Paris, Paris, France
| | - Marianne Elias
- Institut de Systématique, Evolution, Biodiversité, MNHN, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France
| | - Jérémy Gauthier
- Univ Rennes, INRIA, CNRS, IRISA, Rennes, France.,Geneva Natural History Museum, Geneva, Switzerland
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14
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Wu L, Zhai X, Li L, Li Q, Liu F, Zhao H. Identification and Expression Profile of Chemosensory Genes in the Small Hive Beetle Aethina tumida. Insects 2021; 12:insects12080661. [PMID: 34442228 PMCID: PMC8396569 DOI: 10.3390/insects12080661] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 07/15/2021] [Accepted: 07/18/2021] [Indexed: 11/16/2022]
Abstract
Aethina tumida is a parasite and predator of honeybee causing severe loss to the bee industry. No effective and environmentally friendly methods are available to control this pest at present. Chemosensory genes play key roles in insect behavior which can potentially be used as targets for developing environmentally friendly pest control agents. In this study, the putative chemosensory genes in antennae and forelegs of A. tumida involved in olfaction or contact chemical communication of adults were investigated using RNA transcriptome sequencing and PCR methods. Based on transcriptomic data, unigenes encoding 38 odorant receptors (ORs), 24 ionotropic receptors (IRs), 14 gustatory receptors (GRs), 3 sensory neuron membrane proteins (SNMPs), 29 odorant binding proteins (OBPs), and 22 chemosensory proteins (CSPs) were identified. The analyses of tissue expression profiles revealed that genes encoding 38 ORs, 13 antennal IRs, 11 GRs, 1 SNMP, 24 OBPs, and 12 CSPs were predominately expressed in antennae. No significant differences in expression levels of these genes were found between males and females. Genes encoding 5 non-NMDA iGluRs, 3 GRs, 2 SNMPs, 5 OBPs, and 12 CSPs were predominately expressed in forelegs. RT-PCR assays for SNMPs, OBPs and CSPs further revealed that 3 OBPs (AtumOBP3, 26 and 28) and 3 CSPs (AtumCSP7, 8 and 21) were highly expressed in antennae. Our results enrich the gene inventory of A. tumida and facilitate the discovery of potential novel targets for developing new pest control measures.
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Affiliation(s)
- Lixian Wu
- 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 510260, China; (L.W.); (X.Z.); (L.L.); (Q.L.)
| | - Xin Zhai
- 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 510260, China; (L.W.); (X.Z.); (L.L.); (Q.L.)
| | - Liangbin Li
- 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 510260, China; (L.W.); (X.Z.); (L.L.); (Q.L.)
- College of Plant Protection, South China Agricultural University, Guangzhou 510642, China
| | - Qiang Li
- 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 510260, China; (L.W.); (X.Z.); (L.L.); (Q.L.)
- College of Animal Science, Shanxi Agricultural University, Taigu 030801, China
| | - Fang Liu
- 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 510260, China; (L.W.); (X.Z.); (L.L.); (Q.L.)
- Correspondence: (F.L.); (H.Z.)
| | - Hongxia Zhao
- 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 510260, China; (L.W.); (X.Z.); (L.L.); (Q.L.)
- Correspondence: (F.L.); (H.Z.)
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15
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Liu J, Liu H, Yi J, Mao Y, Li J, Sun D, An Y, Wu H. Transcriptome Characterization and Expression Analysis of Chemosensory Genes in Chilo sacchariphagus (Lepidoptera Crambidae), a Key Pest of Sugarcane. Front Physiol 2021; 12:636353. [PMID: 33762968 PMCID: PMC7982955 DOI: 10.3389/fphys.2021.636353] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 01/04/2021] [Indexed: 11/13/2022] Open
Abstract
Insect chemoreception involves many families of genes, including odourant/pheromone binding proteins (OBP/PBPs), chemosensory proteins (CSPs), odourant receptors (ORs), ionotropic receptors (IRs), and sensory neuron membrane proteins (SNMPs), which play irreplaceable roles in mediating insect behaviors such as host location, foraging, mating, oviposition, and avoidance of danger. However, little is known about the molecular mechanism of olfactory reception in Chilo sacchariphagus, which is a major pest of sugarcane. A set of 72 candidate chemosensory genes, including 31 OBPs/PBPs, 15 CSPs, 11 ORs, 13 IRs, and two SNMPs, were identified in four transcriptomes from different tissues and genders of C. sacchariphagus. Phylogenetic analysis was conducted on gene families and paralogs from other model insect species. Quantitative real-time PCR (qRT-PCR) showed that most of these chemosensory genes exhibited antennae-biased expression, but some had high expression in bodies. Most of the identified chemosensory genes were likely involved in chemoreception. This study provides a molecular foundation for the function of chemosensory proteins, and an opportunity for understanding how C. sacchariphagus behaviors are mediated via chemical cues. This research might facilitate the discovery of novel strategies for pest management in agricultural ecosystems.
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Affiliation(s)
- Jianbai Liu
- Guangdong Engineering Research Center for Pesticide and Fertilizer, Institute of Bioengineering, Guangdong Academy of Sciences, Guangzhou, China
| | - Huan Liu
- Guangdong Engineering Research Center for Pesticide and Fertilizer, Institute of Bioengineering, Guangdong Academy of Sciences, Guangzhou, China
- College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang, China
| | - Jiequn Yi
- Guangdong Engineering Research Center for Pesticide and Fertilizer, Institute of Bioengineering, Guangdong Academy of Sciences, Guangzhou, China
| | - Yongkai Mao
- Guangdong Engineering Research Center for Pesticide and Fertilizer, Institute of Bioengineering, Guangdong Academy of Sciences, Guangzhou, China
| | - Jihu Li
- Guangdong Engineering Research Center for Pesticide and Fertilizer, Institute of Bioengineering, Guangdong Academy of Sciences, Guangzhou, China
| | - Donglei Sun
- Guangdong Engineering Research Center for Pesticide and Fertilizer, Institute of Bioengineering, Guangdong Academy of Sciences, Guangzhou, China
| | - Yuxing An
- Guangdong Engineering Research Center for Pesticide and Fertilizer, Institute of Bioengineering, Guangdong Academy of Sciences, Guangzhou, China
| | - Han Wu
- Guangdong Engineering Research Center for Pesticide and Fertilizer, Institute of Bioengineering, Guangdong Academy of Sciences, Guangzhou, China
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16
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Shen S, Fan Z, Zhang X, Kong X, Liu F, Zhang Z, Zhang X, Hu X, Zhang S. The Characteristics of Chemosensory and Opsin Genes in Newly Emerged and Sexually Mature Agrilus planipennis, an Important Quarantine Forest Beetle. Front Genet 2021; 11:604757. [PMID: 33519910 PMCID: PMC7844324 DOI: 10.3389/fgene.2020.604757] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 12/18/2020] [Indexed: 12/13/2022] Open
Abstract
The emerald ash borer (EAB), Agrilus planipennis, is a highly destructive quarantine pest. The olfactory and visual systems of A. planipennis play different but critical roles at newly emerged and sexually mature stages; however, the molecular basis underlying these differences remain unclear. Consequently, based on deep transcriptome sequencing, we evaluated the expression levels of chemosensory-related proteins and opsins at the two developmental stages of A. planipennis. We found 15 new chemosensory-related genes in our transcriptome assembly compared with the previous genome assembly, including 6 that code for odorant-binding proteins (OBPs) and 9 for chemosensory proteins (CSPs). The expression of several chemosensory-related genes (OBP7, OBP10, CSP1, and CSP12) differed markedly between newly emerged and sexually mature A. planipennis. We also found that the expression of UV opsin 2 and LW opsin 1 was higher in sexually mature male A. planipennis, which may be associated with their strong visual mate detection ability. This study forms the basis for further investigation of the chemosensory and visual system of A. planipennis, and these differentially expressed genes between newly emerged and sexually mature stages may serve as targets for the management of this destructive forest pest after sexual maturity.
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Affiliation(s)
- Sifan Shen
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration, Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing, China.,College of Grassland Science and Technology, China Agricultural University, Beijing, China
| | - Zhizhi Fan
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration, Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing, China
| | - Xun Zhang
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration, Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing, China
| | - Xiangbo Kong
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration, Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing, China
| | - Fu Liu
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration, Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing, China
| | - Zhen Zhang
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration, Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing, China
| | - Xinhua Zhang
- Forest Control Station of Dawu County, Xiaogan, China
| | - Xiumei Hu
- Forest Control Station of Dawu County, Xiaogan, China
| | - Sufang Zhang
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration, Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing, China
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17
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Li R, Jiang GF, Shu XH, Wang YQ, Li MJ. Identification and Expression Profile Analysis of Chemosensory Genes From the Antennal Transcriptome of Bamboo Locust ( Ceracris kiangsu). Front Physiol 2020; 11:889. [PMID: 33013431 PMCID: PMC7509195 DOI: 10.3389/fphys.2020.00889] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Accepted: 06/30/2020] [Indexed: 11/29/2022] Open
Abstract
Studies of chemosensory genes are key to a better understanding of intra- and interspecific communications between insects and their environment and provide opportunities for developing environmentally friendly pesticides to target pest species. The bamboo locust Ceracris kiangsu Tsai (Orthoptera: Acrididae) is one of the most important bamboo leaf-eating insects in southern China. However, the genes underlying olfactory sensation are lacking in the bamboo locust. In this study, the transcriptomes of male and female C. kiangsu antennae were sequenced and analyzed. A total of 125 chemosensory genes, including 91 odorant receptors (ORs), 13 ionotropic receptors (IRs), 13 odorant-binding proteins (OBPs), six chemosensory proteins (CSPs), and two sensory neuron membrane proteins, were identified based on sequence alignment and phylogenetic analyses. The expression patterns of all candidate genes on the antennae of males and females, maxillary palps, tarsi, wings, and thoraxes-abdomens were confirmed by real-time quantitative PCR. The analyses demonstrated that most genes are highly expressed in the antennae, and 35 ORs, 7 IRs, 10 OBPs, and 1 CSP exhibit significantly male-biased expression patterns, indicating their potential functions in mating behavior and the recognition of female sex pheromones. In addition to the antennal-predominant genes, some were abundant in the maxillary palps and some in the non-olfactory tissues, suggesting their different functions in the olfactory system of C. kiangsu. Our research offers an extensive resource for investigating the chemoreception mechanism of C. kiangsu. Further studies of olfactory function will provide comprehensive methods and original strategies for integrated pest management.
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Affiliation(s)
- Ran Li
- College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Guo-Fang Jiang
- College of Oceanology and Food Science, Quanzhou Normal University, Quanzhou, China
| | - Xiao-Han Shu
- College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Yu-Qi Wang
- College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Ming-Jie Li
- College of Oceanology and Food Science, Quanzhou Normal University, Quanzhou, China
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18
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Sun D, Huang Y, Qin Z, Zhan H, Zhang J, Liu Y, Yang S. Identification of Candidate Olfactory Genes in the Antennal Transcriptome of the Stink Bug Halyomorpha halys. Front Physiol 2020; 11:876. [PMID: 32792985 PMCID: PMC7394822 DOI: 10.3389/fphys.2020.00876] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Accepted: 06/29/2020] [Indexed: 12/03/2022] Open
Abstract
The brown marmorated stink bug, Halyomorpha halys (Hemiptera: Pentatomidae), is a serious agricultural and urban pest that has become an invasive species in many parts of the world. Olfaction plays an indispensable role in regulating insect behaviors, such as host plant location, partners searching, and avoidance of predators. In this study, we sequenced and analyzed the antennal transcriptomes of both male and female adults of H. halys to better understand the olfactory mechanisms in this species. A total of 241 candidate chemosensory genes were identified, including 138 odorant receptors (ORs), 24 ionotropic receptors (IRs), 15 gustatory receptors (GRs), 44 odorant-binding proteins (OBPs), 17 chemosensory proteins (CSPs), and three sensory neuron membrane proteins (SNMPs). The results of semi-quantitative reverse transcription PCR (RT-PCR) assays showed that some HhalOBP and HhalCSP genes have tissue-specific and sex-biased expression patterns. Our results provide an insight into the molecular mechanisms of the olfactory system in H. halys and identify potential novel targets for pest control strategies.
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Affiliation(s)
- Dongdong Sun
- College of Life Sciences, Anhui Normal University, Wuhu, China
| | - Yuan Huang
- College of Life Sciences, Anhui Normal University, Wuhu, China
| | - Zhenjie Qin
- College of Life Sciences, Anhui Normal University, Wuhu, China.,State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Haixia Zhan
- College of Life Sciences, Anhui Normal University, Wuhu, China
| | - Jinping Zhang
- MoA-CABI Joint Laboratory for Bio-safety, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yang Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shiyong Yang
- College of Life Sciences, Anhui Normal University, Wuhu, China.,Anhui Provincial Key Laboratory for the Conservation and Exploitation of Biology Resources, College of Life Sciences, Anhui Normal University, Wuhu, China
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19
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Li Z, Zhang Y, An X, Wang Q, Khashaveh A, Gu S, Liu S, Zhang Y. Identification of Leg Chemosensory Genes and Sensilla in the Apolygus lucorum. Front Physiol 2020; 11:276. [PMID: 32351398 PMCID: PMC7174674 DOI: 10.3389/fphys.2020.00276] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 03/11/2020] [Indexed: 01/17/2023] Open
Abstract
Apolygus lucorum (Hemiptera: Miridae), one of the main insect pests, causes severe damage in cotton and many other economic crops. As is well-known, legs play important roles in the chemoreception of insects. In this study, the putative chemosensory proteins in legs of A. lucorum involved in close or contact chemical communication of adult bugs were investigated using RNA transcriptome sequencing and qPCR methods. Transcriptome data of forelegs, middle legs and hind legs of adult bugs demonstrated that 20 odorant binding protein (OBP) genes, eight chemosensory protein (CSP) genes, one odorant receptor (OR) gene, one ionotropic receptor (IR) gene and one sensory neuron membrane protein (SNMP) gene were identified in legs of A. lucorum. Compared to the previous antennae transcriptome data, five CSPs, IR21a and SNMP2a were newly identified in legs. Results of qPCR analysis indicated that all these putative chemosensory genes were ubiquitously expressed in forelegs, middle legs and hind legs of bugs. Furthermore, four types of sensilla on legs of A. lucorum including sensilla trichodea (subtypes: long straight sensilla trichodea, Str1; long curved sensilla trichodea, Str2), sensilla chaetica (subtypes: sensilla chaetica 1, Sch1; sensilla chaetica 2, Sch2; and sensilla chaetica 3, Sch3), sensilla basiconca (subtypes: medium-long sensilla basiconca, Sba1; short sensilla basiconca, Sba2) and Böhm bristles (BB) were found using scanning electron microscopy. Additionally, the largest number of sensilla was observed on hind legs, while the forelegs had the smallest number of sensilla. Our data provide valuable insights into understanding the chemoreception of legs in A. lucorum.
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Affiliation(s)
- Zibo Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yaoyao Zhang
- College of Plant Protection, Agricultural University of Hebei, Baoding, China
| | - Xingkui An
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Qi Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Adel Khashaveh
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shaohua Gu
- College of Plant Protection, China Agricultural University, Beijing, China
| | - Shun Liu
- College of Plant Protection, Agricultural University of Hebei, Baoding, China
| | - Yongjun Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
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20
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Tvedte ES, Walden KKO, McElroy KE, Werren JH, Forbes AA, Hood GR, Logsdon JM, Feder JL, Robertson HM. Genome of the Parasitoid Wasp Diachasma alloeum, an Emerging Model for Ecological Speciation and Transitions to Asexual Reproduction. Genome Biol Evol 2020; 11:2767-2773. [PMID: 31553440 PMCID: PMC6781843 DOI: 10.1093/gbe/evz205] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/20/2019] [Indexed: 12/24/2022] Open
Abstract
Parasitoid wasps are among the most speciose animals, yet have relatively few available genomic resources. We report a draft genome assembly of the wasp Diachasma alloeum (Hymenoptera: Braconidae), a host-specific parasitoid of the apple maggot fly Rhagoletis pomonella (Diptera: Tephritidae), and a developing model for understanding how ecological speciation can “cascade” across trophic levels. Identification of gene content confirmed the overall quality of the draft genome, and we manually annotated ∼400 genes as part of this study, including those involved in oxidative phosphorylation, chemosensation, and reproduction. Through comparisons to model hymenopterans such as the European honeybee Apis mellifera and parasitoid wasp Nasonia vitripennis, as well as a more closely related braconid parasitoid Microplitis demolitor, we identified a proliferation of transposable elements in the genome, an expansion of chemosensory genes in parasitoid wasps, and the maintenance of several key genes with known roles in sexual reproduction and sex determination. The D. alloeum genome will provide a valuable resource for comparative genomics studies in Hymenoptera as well as specific investigations into the genomic changes associated with ecological speciation and transitions to asexuality.
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Affiliation(s)
- Eric S Tvedte
- Department of Biology, University of Iowa, IA.,Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD
| | | | | | | | | | - Glen R Hood
- Department of Biological Sciences, Wayne State University, Detroit, MI
| | | | - Jeffrey L Feder
- Department of Biological Sciences, University of Notre Dame, IN
| | - Hugh M Robertson
- Department of Entomology, University of Illinois at Urbana-Champaign, IL
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21
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Manni M, Simao FA, Robertson HM, Gabaglio MA, Waterhouse RM, Misof B, Niehuis O, Szucsich NU, Zdobnov EM. The Genome of the Blind Soil-Dwelling and Ancestrally Wingless Dipluran Campodea augens: A Key Reference Hexapod for Studying the Emergence of Insect Innovations. Genome Biol Evol 2020; 12:3534-3549. [PMID: 31778187 PMCID: PMC6938034 DOI: 10.1093/gbe/evz260] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/26/2019] [Indexed: 12/13/2022] Open
Abstract
The dipluran two-pronged bristletail Campodea augens is a blind ancestrally wingless hexapod with the remarkable capacity to regenerate lost body appendages such as its long antennae. As sister group to Insecta (sensu stricto), Diplura are key to understanding the early evolution of hexapods and the origin and evolution of insects. Here we report the 1.2-Gb draft genome of C. augens and results from comparative genomic analyses with other arthropods. In C. augens, we uncovered the largest chemosensory gene repertoire of ionotropic receptors in the animal kingdom, a massive expansion that might compensate for the loss of vision. We found a paucity of photoreceptor genes mirroring at the genomic level the secondary loss of an ancestral external photoreceptor organ. Expansions of detoxification and carbohydrate metabolism gene families might reflect adaptations for foraging behavior, and duplicated apoptotic genes might underlie its high regenerative potential. The C. augens genome represents one of the key references for studying the emergence of genomic innovations in insects, the most diverse animal group, and opens up novel opportunities to study the under-explored biology of diplurans.
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Affiliation(s)
- Mosè Manni
- Department of Genetic Medicine and Development, Swiss Institute of Bioinformatics, University of Geneva Medical School, Switzerland
| | - Felipe A Simao
- Department of Genetic Medicine and Development, Swiss Institute of Bioinformatics, University of Geneva Medical School, Switzerland
| | - Hugh M Robertson
- Department of Entomology, University of Illinois at Urbana-Champaign
| | - Marco A Gabaglio
- Department of Genetic Medicine and Development, Swiss Institute of Bioinformatics, University of Geneva Medical School, Switzerland
| | - Robert M Waterhouse
- Department of Ecology and Evolution, Swiss Institute of Bioinformatics, University of Lausanne, Switzerland
| | - Bernhard Misof
- Center for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, Bonn, Germany
| | - Oliver Niehuis
- Department of Evolutionary Biology and Ecology, Albert Ludwig University, Institute of Biology I (Zoology), Freiburg, Germany
| | | | - Evgeny M Zdobnov
- Department of Genetic Medicine and Development, Swiss Institute of Bioinformatics, University of Geneva Medical School, Switzerland
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22
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Xu JW, Zhu XY, Chao QJ, Zhang YJ, Yang YX, Wang RR, Zhang Y, Xie MZ, Ge YT, Wu XL, Zhang F, Zhang YN, Ji L, Xu L. Chemosensory Gene Families in the Oligophagous Pear Pest Cacopsylla chinensis (Hemiptera: Psyllidae). Insects 2019; 10:insects10060175. [PMID: 31212973 PMCID: PMC6628306 DOI: 10.3390/insects10060175] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 06/07/2019] [Accepted: 06/12/2019] [Indexed: 01/28/2023]
Abstract
Chemosensory systems play an important role in insect behavior, and some key associated genes have potential as novel targets for pest control. Cacopsylla chinensis is an oligophagous pest and has become one of the main pests of pear trees, but little is known about the molecular-level means by which it locates its hosts. In this study, we assembled the head transcriptome of C. chinensis using Illumina sequencing, and 63,052 Unigenes were identified. A total of 36 candidate chemosensory genes were identified, including five different families: 12 odorant binding proteins (OBPs), 11 chemosensory proteins (CSPs), 7 odorant receptors (ORs), 4 ionotropic receptors (IRs), and 2 gustatory receptors (GRs). The number of chemosensory gene families is consistent with that found in other Hemipteran species, indicating that our approach successfully obtained the chemosensory genes of C. chinensis. The tissue expression of all genes using quantitative real-time PCR (qRT-PCR) found that some genes displayed male head, female head, or nymph-biased specific/expression. Our results enrich the gene inventory of C. chinensis and provide valuable resources for the analysis of the functions of some key genes. This will help in developing molecular targets for disrupting feeding behavior in C. chinensis.
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Affiliation(s)
- Ji-Wei Xu
- College of Life Sciences, Huaibei Normal University, Huaibei 235000, China.
| | - Xiu-Yun Zhu
- College of Life Sciences, Huaibei Normal University, Huaibei 235000, China.
| | - Qiu-Jie Chao
- College of Life Sciences, Huaibei Normal University, Huaibei 235000, China.
| | - Yong-Jie Zhang
- College of Life Sciences, Huaibei Normal University, Huaibei 235000, China.
| | - Yu-Xia Yang
- College of Life Sciences, Huaibei Normal University, Huaibei 235000, China.
| | - Ran-Ran Wang
- College of Life Sciences, Huaibei Normal University, Huaibei 235000, China.
| | - Yu Zhang
- College of Life Sciences, Huaibei Normal University, Huaibei 235000, China.
| | - Meng-Zhen Xie
- College of Life Sciences, Huaibei Normal University, Huaibei 235000, China.
| | - Ya-Ting Ge
- College of Life Sciences, Huaibei Normal University, Huaibei 235000, China.
| | - Xin-Lai Wu
- College of Life Sciences, Huaibei Normal University, Huaibei 235000, China.
| | - Fan Zhang
- Key Laboratory of Animal Resistance Research, College of Life Science, Shandong Normal University, Jinan 250000, China.
| | - Ya-Nan Zhang
- College of Life Sciences, Huaibei Normal University, Huaibei 235000, China.
| | - Lei Ji
- College of Life Sciences, Huaibei Normal University, Huaibei 235000, China.
| | - Lu Xu
- Key Lab of Food Quality and Safety of Jiangsu Province-State Key Laboratory Breeding Base, Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China.
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23
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Wen X, Wang Q, Gao P, Wen J. Identification and Comparison of Chemosensory Genes in the Antennal Transcriptomes of Eucryptorrhynchus scrobiculatus and E. brandti Fed on Ailanthus altissima. Front Physiol 2018; 9:1652. [PMID: 30515106 PMCID: PMC6256065 DOI: 10.3389/fphys.2018.01652] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 11/02/2018] [Indexed: 11/17/2022] Open
Abstract
The key to the coexistence of two or more species on the same host is ecological niche separation. Adult Eucryptorrhynchus scrobiculatus and E. brandti both feed on the tree of heaven, Ailanthus altissima, but on different sections of the plant. Olfaction plays a vital role in foraging for food resources. Chemosensory genes on the antennae, the main organ for insect olfaction, might explain their feeding differentiation. In the present study, we identified 130 and 129 putative chemosensory genes in E. scrobiculatus and E. brandti, respectively, by antennal transcriptome sequencing, including 31 odorant-binding proteins (OBPs), 11 chemosensory proteins (CSPs), 49 odorant receptors (ORs), 17 ionotropic receptors (IRs), 19 gustatory receptors (GRs), and three sensory neuron membrane proteins (SNMPs) in E. scrobiculatus and 28 OBPs, 11 CSPs, 45 ORs, 25 IRs, 17 GRs, and three SNMPs in E. brandti. We inferred that EscrOBP8 (EscrPBP1), EscrOBP24 (EscrPBP2) and EbraOBP8 (EbraPBP1), EbraOBP24 (EbraPBP2) were putative PBPs by the phylogenetic analysis. We identified species-specific OR transcripts (10 EscrORs and 8 EbraORs) with potential roles in the recognition of specific volatiles of A. altissima. In addition to conserved “antennal IRs,” we also found several “divergent IRs” orthologues in E. scrobiculatus and E. brandti, such as EscrIR16, EbraIR19, and EbraIR20. Compared with other chemosensory genes, GRs between E. scrobiculatus and E. brandti shared lower amino acid identities, which could explain the different feeding habits of the species. We examined OBP expression patterns in various tissues and sexes. Although amino acid sequence similarities were high between EscrOBPs and EbraOBPs, the homologous OBPs showed different tissue expression pattern between two weevils. Our systematic comparison of chemosensory genes in E. scrobiculatus and E. brandti provides a foundation for studies of olfaction and olfactory differentiation in the two weevils as well as a theoretical basis for studying species differentiation.
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Affiliation(s)
- Xiaojian Wen
- Beijing Key Laboratory for Forest Pests Control, College of Forestry, Beijing Forestry University, Beijing, China
| | - Qian Wang
- Beijing Key Laboratory for Forest Pests Control, College of Forestry, Beijing Forestry University, Beijing, China
| | - Peng Gao
- Beijing Key Laboratory for Forest Pests Control, College of Forestry, Beijing Forestry University, Beijing, China
| | - Junbao Wen
- Beijing Key Laboratory for Forest Pests Control, College of Forestry, Beijing Forestry University, Beijing, China
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24
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Guo M, Chen Q, Liu Y, Wang G, Han Z. Chemoreception of Mouthparts: Sensilla Morphology and Discovery of Chemosensory Genes in Proboscis and Labial Palps of Adult Helicoverpa armigera (Lepidoptera: Noctuidae). Front Physiol 2018; 9:970. [PMID: 30131703 PMCID: PMC6091246 DOI: 10.3389/fphys.2018.00970] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 07/02/2018] [Indexed: 01/21/2023] Open
Abstract
Siphoning mouthparts, consisting of proboscis and labial palps, are the exclusive feeding organs and important chemosensory organs in most adult Lepidoptera. In this study, the general morphology of the mouthpart organs and precision architecture of the proboscis was described in adult Helicoverpa armigera. Three major sensilla types with nine subtypes including three novel subtypes were identified. The novel sensilla styloconica subtype 2 was the only one having a multiporous structure, which may play olfactory roles. For further understanding of the chemosensory functions of mouthpart organs, we conducted transcriptome analysis on labial palps and proboscises. A total of 84 chemosensory genes belonging to six different families including 4 odorant receptors (ORs), 6 ionotropic receptors (IRs), 7 gustatory receptors (GRs), 39 odorant binding proteins (OBPs), 26 chemosensory proteins (CSPs), and 2 sensory neuron membrane proteins (SNMPs) were identified. Furthermore, eight OBPs and six CSPs were identified as the novel genes. The expression level of candidate chemosensory genes in the proboscis and labial palps was evaluated by the differentially expressed gene (DEG) analysis, and the expression of candidate chemosensory receptor genes in different tissues was further investigated by quantitative real-time PCR (qRT-PCR). All the candidate receptors were detected by DEG analysis and qRT-PCR, but only a small part of the OR or IR genes was specifically or partially expressed in proboscis or labial palps, such as HarmOR58 and HarmIR75p.1, however, most of the GRs were abundantly expressed in proboscis or labial palps. The reported CO2 receptors such as HarmGR1, GR2, and GR3 were mainly expressed in labial palps. HarmGR5, GR6, and GR8, belonging to the "sugar receptor" clade, were mainly expressed in proboscis or antenna and were therefore suggested to perceive saccharide. The results suggest that the mouthparts are mutually cooperative but functionally concentrated system. These works contribute to the understanding of chemical signal recognition in mouthpart organs and provide the foundation for further functional studies.
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Affiliation(s)
- Mengbo Guo
- Education Ministry Key Laboratory of Integrated Management of Crop Diseases and Pests, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Qiuyan Chen
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yang Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Guirong Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhaojun Han
- Education Ministry Key Laboratory of Integrated Management of Crop Diseases and Pests, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
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25
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Wang D, Pentzold S, Kunert M, Groth M, Brandt W, Pasteels JM, Boland W, Burse A. A subset of chemosensory genes differs between two populations of a specialized leaf beetle after host plant shift. Ecol Evol 2018; 8:8055-8075. [PMID: 30250684 PMCID: PMC6145003 DOI: 10.1002/ece3.4246] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Revised: 04/13/2018] [Accepted: 04/17/2018] [Indexed: 01/26/2023] Open
Abstract
Due to its fundamental role in shaping host selection behavior, we have analyzed the chemosensory repertoire of Chrysomela lapponica. This specialized leaf beetle evolved distinct populations which shifted from the ancestral host plant, willow (Salix sp., Salicaceae), to birch (Betula rotundifolia, Betulaceae). We identified 114 chemosensory candidate genes in adult C. lapponica: 41 olfactory receptors (ORs), eight gustatory receptors, 17 ionotropic receptors, four sensory neuron membrane proteins, 32 odorant binding proteins (OBPs), and 12 chemosensory proteins (CSP) by RNA-seq. Differential expression analyses in the antennae revealed significant upregulation of one minus-C OBP (Clap OBP27) and one CSP (Clap CSP12) in the willow feeders. In contrast, one OR (Clap OR17), four minus-C OBPs (Clap OBP02, 07, 13, 20), and one plus-C OBP (Clap OBP32) were significantly upregulated in birch feeders. The differential expression pattern in the legs was more complex. To narrow down putative ligands acting as cues for host discrimination, the relative abundance and diversity of volatiles of the two host plant species were analyzed. In addition to salicylaldehyde (willow-specific), both plant species differed mainly in their emission rate of terpenoids such as (E,E)-α-farnesene (high in willow) or 4,8-dimethylnona-1,3,7-triene (high in birch). Qualitatively, the volatiles were similar between willow and birch leaves constituting an "olfactory bridge" for the beetles. Subsequent structural modeling of the three most differentially expressed OBPs and docking studies using 22 host volatiles indicated that ligands bind with varying affinity. We suggest that the evolution of particularly minus-C OBPs and ORs in C. lapponica facilitated its host plant shift via chemosensation of the phytochemicals from birch as novel host plant.
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Affiliation(s)
- Ding Wang
- Department of Bioorganic ChemistryMax Planck Institute for Chemical EcologyJenaGermany
| | - Stefan Pentzold
- Department of Bioorganic ChemistryMax Planck Institute for Chemical EcologyJenaGermany
| | - Maritta Kunert
- Department of Bioorganic ChemistryMax Planck Institute for Chemical EcologyJenaGermany
| | - Marco Groth
- Leibniz Institute on Aging – Fritz Lipmann InstituteJenaGermany
| | | | | | - Wilhelm Boland
- Department of Bioorganic ChemistryMax Planck Institute for Chemical EcologyJenaGermany
| | - Antje Burse
- Department of Bioorganic ChemistryMax Planck Institute for Chemical EcologyJenaGermany
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26
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Abstract
Insects rely on chemical information to locate food, choose mates, and detect potential predators. It has been hypothesized that adaptive changes in the olfactory system facilitated the diversification of numerous insect lineages. For instance, evolutionary changes of Odorant Receptor (OR) genes often occur in parallel with modifications in life history strategies. Corbiculate bees display a diverse array of behaviors that are controlled through olfaction, including varying degrees of social organization, and manifold associations with floral resources. Here we investigated the molecular mechanisms driving the evolution of the OR gene family in corbiculate bees in comparison to other chemosensory gene families. Our results indicate that the genomic organization of the OR gene family has remained highly conserved for ∼80 Myr, despite exhibiting major changes in repertoire size among bee lineages. Moreover, the evolution of OR genes appears to be driven mostly by lineage-specific gene duplications in few genomic regions that harbor large numbers of OR genes. A selection analysis revealed that OR genes evolve under positive selection, with the strongest signals detected in recently duplicated copies. Our results indicate that chromosomal translocations had a minimal impact on OR evolution, and instead local molecular mechanisms appear to be main drivers of OR repertoire size. Our results provide empirical support to the longstanding hypothesis that positive selection shaped the diversification of the OR gene family. Together, our results shed new light on the molecular mechanisms underlying the evolution of olfaction in insects.
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Affiliation(s)
- Philipp Brand
- Department for Evolution and Ecology, Center for Population Biology, University of California, Davis.,Population Biology Graduate Group, Center for Population Biology, University of California, Davis
| | - Santiago R Ramírez
- Department for Evolution and Ecology, Center for Population Biology, University of California, Davis
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27
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Eyres I, Duvaux L, Gharbi K, Tucker R, Hopkins D, Simon JC, Ferrari J, Smadja CM, Butlin RK. Targeted re-sequencing confirms the importance of chemosensory genes in aphid host race differentiation. Mol Ecol 2016; 26:43-58. [PMID: 27552184 PMCID: PMC6849616 DOI: 10.1111/mec.13818] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 08/18/2016] [Accepted: 08/22/2016] [Indexed: 01/01/2023]
Abstract
Host‐associated races of phytophagous insects provide a model for understanding how adaptation to a new environment can lead to reproductive isolation and speciation, ultimately enabling us to connect barriers to gene flow to adaptive causes of divergence. The pea aphid (Acyrthosiphon pisum) comprises host races specializing on legume species and provides a unique system for examining the early stages of diversification along a gradient of genetic and associated adaptive divergence. As host choice produces assortative mating, understanding the underlying mechanisms of choice will contribute directly to understanding of speciation. As host choice in the pea aphid is likely mediated by smell and taste, we use capture sequencing and SNP genotyping to test for the role of chemosensory genes in the divergence between eight host plant species across the continuum of differentiation and sampled at multiple locations across western Europe. We show high differentiation of chemosensory loci relative to control loci in a broad set of pea aphid races and localities, using a model‐free approach based on principal component analysis. Olfactory and gustatory receptors form the majority of highly differentiated genes and include loci that were already identified as outliers in a previous study focusing on the three most closely related host races. Consistent indications that chemosensory genes may be good candidates for local adaptation and barriers to gene flow in the pea aphid open the way to further investigations aiming to understand their impact on gene flow and to determine their precise functions in response to host plant metabolites.
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Affiliation(s)
- Isobel Eyres
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Alfred Denny Building, Sheffield, S10 2TN, UK
| | - Ludovic Duvaux
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Alfred Denny Building, Sheffield, S10 2TN, UK
| | - Karim Gharbi
- Edinburgh Genomics, Ashworth Laboratories, University of Edinburgh, EH9 3JT, Edinburgh, UK
| | - Rachel Tucker
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Alfred Denny Building, Sheffield, S10 2TN, UK
| | - David Hopkins
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Alfred Denny Building, Sheffield, S10 2TN, UK
| | - Jean-Christophe Simon
- Institut de Génétique, Environnement et Protection des Plantes, UMR 1349 IGEPP, Domaine de la Motte, INRA, 35653, Le Rheu Cedex, France
| | - Julia Ferrari
- Department of Biology, University of York, York YO10 5DD, UK
| | - Carole M Smadja
- Institut des Sciences de l'Evolution (UMR 5554 CNRS-IRD-CIRAD-Université de Montpellier), Université de Montpellier, cc065, Place Bataillon, Campus Triolet, 34095, Montpellier Cedex 05, France
| | - Roger K Butlin
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Alfred Denny Building, Sheffield, S10 2TN, UK
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Shiao MS, Chang JM, Fan WL, Lu MYJ, Notredame C, Fang S, Kondo R, Li WH. Expression Divergence of Chemosensory Genes between Drosophila sechellia and Its Sibling Species and Its Implications for Host Shift. Genome Biol Evol 2015; 7:2843-58. [PMID: 26430061 PMCID: PMC4684695 DOI: 10.1093/gbe/evv183] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Drosophila sechellia relies exclusively on the fruits of Morinda citrifolia, which are toxic to most insects, including its sibling species Drosophila melanogaster and Drosophila simulans. Although several odorant binding protein (Obp) genes and olfactory receptor (Or) genes have been suggested to be associated with the D. sechellia host shift, a broad view of how chemosensory genes have contributed to this shift is still lacking. We therefore studied the transcriptomes of antennae, the main organ responsible for detecting food resource and oviposition, of D. sechellia and its two sibling species. We wanted to know whether gene expression, particularly chemosensory genes, has diverged between D. sechellia and its two sibling species. Using a very stringent definition of differential gene expression, we found a higher percentage of chemosensory genes differentially expressed in the D. sechellia lineage (7.8%) than in the D. simulans lineage (5.4%); for upregulated chemosensory genes, the percentages were 8.8% in D. sechellia and 5.2% in D. simulans. Interestingly, Obp50a exhibited the highest upregulation, an approximately 100-fold increase, and Or85c--previously reported to be a larva-specific gene--showed approximately 20-fold upregulation in D. sechellia. Furthermore, Ir84a (ionotropic receptor 84a), which has been proposed to be associated with male courtship behavior, was significantly upregulated in D. sechellia. We also found expression divergence in most of the chemosensory gene families between D. sechellia and the two sibling species. Our observations suggest that the host shift of D. sechellia was associated with the enrichment of differentially expressed, particularly upregulated, chemosensory genes.
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Affiliation(s)
- Meng-Shin Shiao
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan Research Center, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Jia-Ming Chang
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003, Barcelona, Spain Universitat Pompeu Fabra (UPF), Barcelona, Spain Institute of Human Genetics (IGH), UPR 1142, CNRS, Montpellier, France
| | - Wen-Lang Fan
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan Whole-Genome Research Core Laboratory of Human Diseases, Chang Gung Memorial Hospital, Keelung, Taiwan
| | - Mei-Yeh Jade Lu
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Cedric Notredame
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003, Barcelona, Spain Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Shu Fang
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Rumi Kondo
- Graduate School of Humanities and Sciences, Ochanomizu University, Tokyo, Japan
| | - Wen-Hsiung Li
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan Department of Ecology and Evolution, University of Chicago
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29
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Abstract
Copy number variation (CNV) makes a major contribution to overall genetic variation and is suspected to play an important role in adaptation. However, aside from a few model species, the extent of CNV in natural populations has seldom been investigated. Here, we report on CNV in the pea aphid Acyrthosiphon pisum, a powerful system for studying the genetic architecture of host-plant adaptation and speciation thanks to multiple host races forming a continuum of genetic divergence. Recent studies have highlighted the potential importance of chemosensory genes, including the gustatory and olfactory receptor gene families (Gr and Or, respectively), in the process of host race formation. We used targeted resequencing to achieve a very high depth of coverage, and thereby revealed the extent of CNV of 434 genes, including 150 chemosensory genes, in 104 individuals distributed across eight host races of the pea aphid. We found that CNV was widespread in our global sample, with a significantly higher occurrence in multigene families, especially in Ors. We also observed a decrease in the gene probability of being completely duplicated or deleted (CDD) with increase in coding sequence length. Genes with CDD variants were usually more polymorphic for copy number, especially in the P450 gene family where toxin resistance may be related to gene dosage. We found that Gr were overrepresented among genes discriminating host races, as were CDD genes and pseudogenes. Our observations shed new light on CNV dynamics and are consistent with CNV playing a role in both local adaptation and speciation.
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Affiliation(s)
- Ludovic Duvaux
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
| | - Quentin Geissmann
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
| | - Karim Gharbi
- Edinburgh Genomics, Ashworth Laboratories, University of Edinburgh, Edinburgh, United Kingdom
| | - Jing-Jiang Zhou
- Department of Biological Chemistry and Crop Protection, Rothamsted Research, Harpenden, United Kingdom
| | - Julia Ferrari
- Department of Biology, University of York, York, United Kingdom
| | - Carole M Smadja
- Institut des Sciences de l'Evolution (UMR 5554), CNRS, IRD, Université Montpellier 2, Montpellier, France
| | - Roger K Butlin
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom Sven Lovén Centre for Marine Sciences-Tjärnö, University of Gothenburg, Strömstad, Sweden
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Yoder AD, Chan LM, dos Reis M, Larsen PA, Campbell CR, Rasoloarison R, Barrett M, Roos C, Kappeler P, Bielawski J, Yang Z. Molecular evolutionary characterization of a V1R subfamily unique to strepsirrhine primates. Genome Biol Evol 2014; 6:213-27. [PMID: 24398377 PMCID: PMC3914689 DOI: 10.1093/gbe/evu006] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Vomeronasal receptor genes have frequently been invoked as integral to the establishment and maintenance of species boundaries among mammals due to the elaborate one-to-one correspondence between semiochemical signals and neuronal sensory inputs. Here, we report the most extensive sample of vomeronasal receptor class 1 (V1R) sequences ever generated for a diverse yet phylogenetically coherent group of mammals, the tooth-combed primates (suborder Strepsirrhini). Phylogenetic analysis confirms our intensive sampling from a single V1R subfamily, apparently unique to the strepsirrhine primates. We designate this subfamily as V1Rstrep. The subfamily retains extensive repertoires of gene copies that descend from an ancestral gene duplication that appears to have occurred prior to the diversification of all lemuriform primates excluding the basal genus Daubentonia (the aye-aye). We refer to the descendent clades as V1Rstrep-α and V1Rstrep-β. Comparison of the two clades reveals different amino acid compositions corresponding to the predicted ligand-binding site and thus potentially to altered functional profiles between the two. In agreement with previous studies of the mouse lemur (genus, Microcebus), the majority of V1Rstrep gene copies appear to be intact and under strong positive selection, particularly within transmembrane regions. Finally, despite the surprisingly high number of gene copies identified in this study, it is nonetheless probable that V1R diversity remains underestimated in these nonmodel primates and that complete characterization will be limited until high-coverage assembled genomes are available.
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31
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Almeida FC, Sánchez-Gracia A, Campos JL, Rozas J. Family size evolution in Drosophila chemosensory gene families: a comparative analysis with a critical appraisal of methods. Genome Biol Evol 2014; 6:1669-82. [PMID: 24951565 PMCID: PMC4122928 DOI: 10.1093/gbe/evu130] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Gene turnover rates and the evolution of gene family sizes are important aspects of genome evolution. Here, we use curated sequence data of the major chemosensory gene families from Drosophila—the gustatory receptor, odorant receptor, ionotropic receptor, and odorant-binding protein families—to conduct a comparative analysis among families, exploring different methods to estimate gene birth and death rates, including an ad hoc simulation study. Remarkably, we found that the state-of-the-art methods may produce very different rate estimates, which may lead to disparate conclusions regarding the evolution of chemosensory gene family sizes in Drosophila. Among biological factors, we found that a peculiarity of D. sechellia’s gene turnover rates was a major source of bias in global estimates, whereas gene conversion had negligible effects for the families analyzed herein. Turnover rates vary considerably among families, subfamilies, and ortholog groups although all analyzed families were quite dynamic in terms of gene turnover. Computer simulations showed that the methods that use ortholog group information appear to be the most accurate for the Drosophila chemosensory families. Most importantly, these results reveal the potential of rate heterogeneity among lineages to severely bias some turnover rate estimation methods and the need of further evaluating the performance of these methods in a more diverse sampling of gene families and phylogenetic contexts. Using branch-specific codon substitution models, we find further evidence of positive selection in recently duplicated genes, which attests to a nonneutral aspect of the gene birth-and-death process.
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Affiliation(s)
- Francisca C Almeida
- Departament de Genètica and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Spain Present address: CONICET, Departamento de Ecología, Genética y Evolución, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Instituto IEGEBA, Buenos Aires, Argentina
| | - Alejandro Sánchez-Gracia
- Departament de Genètica and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Spain
| | - Jose Luis Campos
- Departament de Genètica and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Spain Present address: Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Julio Rozas
- Departament de Genètica and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Spain
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