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Nunes WVB, Oliveira DS, Dias GDR, Carvalho AB, Caruso ÍP, Biselli JM, Guegen N, Akkouche A, Burlet N, Vieira C, Carareto CMA. A comprehensive evolutionary scenario for the origin and neofunctionalization of the Drosophila speciation gene Odysseus (OdsH). G3 (BETHESDA, MD.) 2024; 14:jkad299. [PMID: 38156703 PMCID: PMC10917504 DOI: 10.1093/g3journal/jkad299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 11/22/2023] [Accepted: 12/20/2023] [Indexed: 01/03/2024]
Abstract
Odysseus (OdsH) was the first speciation gene described in Drosophila related to hybrid sterility in offspring of mating between Drosophila mauritiana and Drosophila simulans. Its origin is attributed to the duplication of the gene unc-4 in the subgenus Sophophora. By using a much larger sample of Drosophilidae species, we showed that contrary to what has been previously proposed, OdsH origin occurred 62 MYA. Evolutionary rates, expression, and transcription factor-binding sites of OdsH evidence that it may have rapidly experienced neofunctionalization in male sexual functions. Furthermore, the analysis of the OdsH peptide allowed the identification of mutations of D. mauritiana that could result in incompatibility in hybrids. In order to find if OdsH could be related to hybrid sterility, beyond Sophophora, we explored the expression of OdsH in Drosophila arizonae and Drosophila mojavensis, a pair of sister species with incomplete reproductive isolation. Our data indicated that OdsH expression is not atypical in their male-sterile hybrids. In conclusion, we have proposed that the origin of OdsH occurred earlier than previously proposed, followed by neofunctionalization. Our results also suggested that its role as a speciation gene might be restricted to D. mauritiana and D. simulans.
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Affiliation(s)
- William Vilas Boas Nunes
- Institute of Biosciences, Humanities and Exact Sciences, São Paulo State University (Unesp), 2265 Cristóvão Colombo Street, 15054-000 São José do Rio Preto, Brazil
- Laboratoire de Biométrie et Biologie Evolutive UMR 5558, Université de Lyon, Université Lyon 1, CNRS, Bât. Grégor Mendel, 43 Boulevard 11 Novembre 1918, 69622 Villeurbanne, France
| | - Daniel Siqueira Oliveira
- Institute of Biosciences, Humanities and Exact Sciences, São Paulo State University (Unesp), 2265 Cristóvão Colombo Street, 15054-000 São José do Rio Preto, Brazil
- Laboratoire de Biométrie et Biologie Evolutive UMR 5558, Université de Lyon, Université Lyon 1, CNRS, Bât. Grégor Mendel, 43 Boulevard 11 Novembre 1918, 69622 Villeurbanne, France
| | - Guilherme de Rezende Dias
- Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, CCS sl A2-075, 373 Carlos Chagas Filho Avenue, 21941-971 Rio de Janeiro, Brazil
| | - Antonio Bernardo Carvalho
- Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, CCS sl A2-075, 373 Carlos Chagas Filho Avenue, 21941-971 Rio de Janeiro, Brazil
| | - Ícaro Putinhon Caruso
- Institute of Biosciences, Humanities and Exact Sciences, São Paulo State University (Unesp), 2265 Cristóvão Colombo Street, 15054-000 São José do Rio Preto, Brazil
| | - Joice Matos Biselli
- Institute of Biosciences, Humanities and Exact Sciences, São Paulo State University (Unesp), 2265 Cristóvão Colombo Street, 15054-000 São José do Rio Preto, Brazil
| | - Nathalie Guegen
- Faculté de Médecine, iGReD, Université Clermont Auvergne, CNRS, INSERM, 4 Bd Claude Bernard, 63000 Clermont-Ferrande, France
| | - Abdou Akkouche
- Faculté de Médecine, iGReD, Université Clermont Auvergne, CNRS, INSERM, 4 Bd Claude Bernard, 63000 Clermont-Ferrande, France
| | - Nelly Burlet
- Laboratoire de Biométrie et Biologie Evolutive UMR 5558, Université de Lyon, Université Lyon 1, CNRS, Bât. Grégor Mendel, 43 Boulevard 11 Novembre 1918, 69622 Villeurbanne, France
| | - Cristina Vieira
- Laboratoire de Biométrie et Biologie Evolutive UMR 5558, Université de Lyon, Université Lyon 1, CNRS, Bât. Grégor Mendel, 43 Boulevard 11 Novembre 1918, 69622 Villeurbanne, France
| | - Claudia M A Carareto
- Institute of Biosciences, Humanities and Exact Sciences, São Paulo State University (Unesp), 2265 Cristóvão Colombo Street, 15054-000 São José do Rio Preto, Brazil
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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] [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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Friedrich M. Close to complete conservation of the brachyceran opsin repertoire in the stalk-eyed fly Teleopsis dalmanni. JOURNAL OF EXPERIMENTAL ZOOLOGY. PART B, MOLECULAR AND DEVELOPMENTAL EVOLUTION 2023; 340:469-473. [PMID: 37814507 DOI: 10.1002/jez.b.23220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 07/02/2023] [Accepted: 08/22/2023] [Indexed: 10/11/2023]
Abstract
Due to the unique morphology of their adult visual system, stalk-eyed flies represent an important model of exaggerated trait evolution through sexual selection. Early physiological measurements indicated wavelength sensitivity peaks in the ultraviolet (360 nm), blue (450), blue-green (490 nm), and red (>550 nm) ranges in the compound eye retina of the stalk-eyed fly Teleopsis dalmanni, consistent with the trichromatic color and broad range motion detection vision system of brachyceran Diptera. A previous study of dipteran opsin gene diversification, however, detected only homologs of members of the long wavelength range sensitive opsin subfamilies Rh2 and Rh6 in T. dalmanni. Here, I report findings from analyzing the most recent T. dalmanni genome assembly, which revealed the conservation of most brachyceran opsin homologs except for the UV wavelength range-sensitive homolog Rh4. These results and other examples highlight the caution that needs to be applied to gene loss conclusions.
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Affiliation(s)
- Markus Friedrich
- Department of Biological Sciences, Wayne State University, Detroit, Michigan, USA
- Department of Ophthalmological, School of Medicine, Visual, and Anatomical Sciences, Wayne State University, Detroit, Michigan, USA
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Huang M, Meng JY, Zhou L, Yu C, Zhang CY. Expression and function of opsin genes associated with phototaxis in Zeugodacus cucurbitae Coquillett (Diptera: Tephritidae). PEST MANAGEMENT SCIENCE 2023; 79:4490-4500. [PMID: 37418556 DOI: 10.1002/ps.7651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 06/06/2023] [Accepted: 07/07/2023] [Indexed: 07/09/2023]
Abstract
BACKGROUND Zeugodacus cucuribitae is a major agricultural pest that causes significant damage to varieties of plants. Vision plays a critical role in phototactic behavior of herbivorous insects. However, the effect of opsin on the phototactic behavior in Z. cucuribitae remains unknown. The aim of this research is to explore the key opsin genes that associate with phototaxis behavior of Z. cucurbitae. RESULTS Five opsin genes were identified and their expression patterns were analyzed. The relative expression levels of ZcRh1, ZcRh4 and ZcRh6 were highest in 4-day-old larvae, ZcRh2 and ZcRh3 were highest in 3rd-instar larvae and 5-day-old pupae, respectively. Furthermore, five opsin genes had the highest expression levels in compound eyes, followed by the antennae and head, whereas the lower occurred in other tissues. The expression of the long-wavelength-sensitive (LW) opsins first decreased and then increased under green light exposure. In contrast, the expression of ultraviolet-sensitive (UV) opsins first increased and then decreased with the duration of UV exposure. Silencing of LW opsin (dsZcRh1, dsZcRh2, and dsZcRh6) and UV opsin (dsZcRh3 and dsZcRh4) reduced the phototactic efficiency of Z. cucurbitae to green light by 52.27%, 60.72%, and 67.89%, and to UV light by 68.59% and 61.73%, respectively. CONCLUSION The results indicate that RNAi inhibited the expression of opsin, thereby inhibiting the phototaxis of Z. cucurbitae. This result provides theoretical support for the physical control of Z. cucurbitae and lays the foundation for further exploration of the mechanism of insect phototaxis. © 2023 Society of Chemical Industry.
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Affiliation(s)
- Mei Huang
- Institute of Entomology, Guizhou Provincial Key Laboratory for Agricultural Pest Management of the Mountainous Region, College of Agriculture, Guizhou University, Guiyang, China
| | - Jian-Yu Meng
- Guizhou Tobacco Science Research Institute, Guiyang, China
| | - Lv Zhou
- Institute of Entomology, Guizhou Provincial Key Laboratory for Agricultural Pest Management of the Mountainous Region, College of Agriculture, Guizhou University, Guiyang, China
| | - Chun Yu
- Institute of Entomology, Guizhou Provincial Key Laboratory for Agricultural Pest Management of the Mountainous Region, College of Agriculture, Guizhou University, Guiyang, China
| | - Chang-Yu Zhang
- Institute of Entomology, Guizhou Provincial Key Laboratory for Agricultural Pest Management of the Mountainous Region, College of Agriculture, Guizhou University, Guiyang, China
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Niida T, Terashima Y, Aonuma H, Koshikawa S. Photoreceptor genes in a trechine beetle, Trechiama kuznetsovi, living in the upper hypogean zone. ZOOLOGICAL LETTERS 2023; 9:9. [PMID: 37173794 PMCID: PMC10176714 DOI: 10.1186/s40851-023-00208-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 04/21/2023] [Indexed: 05/15/2023]
Abstract
To address how organisms adapt to a new environment, subterranean organisms whose ancestors colonized subterranean habitats from surface habitats have been studied. Photoreception abilities have been shown to have degenerated in organisms living in caves and calcrete aquifers. Meanwhile, the organisms living in a shallow subterranean environment, which are inferred to reflect an intermediate stage in an evolutionary pathway to colonization of a deeper subterranean environment, have not been studied well. In the present study, we examined the photoreception ability in a trechine beetle, Trechiama kuznetsovi, which inhabits the upper hypogean zone and has a vestigial compound eye. By de novo assembly of genome and transcript sequences, we were able to identify photoreceptor genes and phototransduction genes. Specifically, we focused on opsin genes, where one long wavelength opsin gene and one ultraviolet opsin gene were identified. The encoded amino acid sequences had neither a premature stop codon nor a frameshift mutation, and appeared to be subject to purifying selection. Subsequently, we examined the internal structure of the compound eye and nerve tissue in the adult head, and found potential photoreceptor cells in the compound eye and nerve bundle connected to the brain. The present findings suggest that T. kuznetsovi has retained the ability of photoreception. This species represents a transitional stage of vision, in which the compound eye regresses, but it may retain the ability of photoreception using the vestigial eye.
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Affiliation(s)
- Takuma Niida
- Graduate School of Environmental Science, Hokkaido University, Sapporo, Japan.
| | - Yuto Terashima
- Graduate School of Environmental Science, Hokkaido University, Sapporo, Japan
| | - Hitoshi Aonuma
- Department of Biology, Graduate School of Science, Kobe University, Kobe, Japan
| | - Shigeyuki Koshikawa
- Graduate School of Environmental Science, Hokkaido University, Sapporo, Japan.
- Faculty of Environmental Earth Science, Hokkaido University, Sapporo, Japan.
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Wang Y, Fang G, Xu P, Gao B, Liu X, Qi X, Zhang G, Cao S, Li Z, Ren X, Wang H, Cao Y, Pereira R, Huang Y, Niu C, Zhan S. Behavioral and genomic divergence between a generalist and a specialist fly. Cell Rep 2022; 41:111654. [DOI: 10.1016/j.celrep.2022.111654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 07/03/2022] [Accepted: 10/21/2022] [Indexed: 11/18/2022] Open
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Wang Y, Fang G, Chen X, Cao Y, Wu N, Cui Q, Zhu C, Qian L, Huang Y, Zhan S. The genome of the black cutworm Agrotis ipsilon. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2021; 139:103665. [PMID: 34624466 DOI: 10.1016/j.ibmb.2021.103665] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 09/29/2021] [Accepted: 09/29/2021] [Indexed: 06/13/2023]
Abstract
The black cutworm (BCW), Agrotis ipsilon, is a worldwide polyphagous and underground pest that causes a high level of economic loss to a wide range of crops through the damage of roots. This species performs non-directed migration throughout East and Southeast Asia seasonally. Lack of a genome information has limited further studies on its unique biology and the development of novel management approaches. In this study, we present a 476 Mb de novo assembly of BCW, along with a consensus gene set of 14,801 protein-coding gene models. Quality controls show that both genome assembly and annotations are high-quality and mostly complete. We focus manual annotation and comparative genomics on gene families that related to the unique attributes of this species, such as nocturnality, long-distance migration, and host adaptation. We find that the BCW genome encodes a similar gene repertoire in various migration-related gene families to the diural migratory butterfly Danaus plexiipus, with additional copies of long wavelength opsin and two eye development-related genes. On the other hand, we find that the genomes of BCW and many other polyphagous lepidopterans encode many more gustatory receptor genes, particularly the lineage-specific expanded bitter receptor genes, than the mono- or oligo-phagous species, suggesting a common role of gustatory receptors (GRs) expansion in host range expansion. The availability of a BCW genome provides valuable resources to study the molecular mechanisms of non-directed migration in lepidopteran pests and to develop novel strategies to control migratory nocturnal pests.
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Affiliation(s)
- Yaohui Wang
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Gangqi Fang
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China; CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China
| | - Xi'en Chen
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yanghui Cao
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Ningning Wu
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Qian Cui
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China; CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China
| | - Chenxu Zhu
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Lansa Qian
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yongping Huang
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China; CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China.
| | - Shuai Zhan
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China; CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China.
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Mishra AK, Fritsch C, Voutev R, Mann RS, Sprecher SG. Homothorax controls a binary Rhodopsin switch in Drosophila ocelli. PLoS Genet 2021; 17:e1009460. [PMID: 34314427 PMCID: PMC8345863 DOI: 10.1371/journal.pgen.1009460] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 08/06/2021] [Accepted: 07/02/2021] [Indexed: 11/26/2022] Open
Abstract
Visual perception of the environment is mediated by specialized photoreceptor (PR) neurons of the eye. Each PR expresses photosensitive opsins, which are activated by a particular wavelength of light. In most insects, the visual system comprises a pair of compound eyes that are mainly associated with motion, color or polarized light detection, and a triplet of ocelli that are thought to be critical during flight to detect horizon and movements. It is widely believed that the evolutionary diversification of compound eye and ocelli in insects occurred from an ancestral visual organ around 500 million years ago. Concurrently, opsin genes were also duplicated to provide distinct spectral sensitivities to different PRs of compound eye and ocelli. In the fruit fly Drosophila melanogaster, Rhodopsin1 (Rh1) and Rh2 are closely related opsins that originated from the duplication of a single ancestral gene. However, in the visual organs, Rh2 is uniquely expressed in ocelli whereas Rh1 is uniquely expressed in outer PRs of the compound eye. It is currently unknown how this differential expression of Rh1 and Rh2 in the two visual organs is controlled to provide unique spectral sensitivities to ocelli and compound eyes. Here, we show that Homothorax (Hth) is expressed in ocelli and confers proper rhodopsin expression. We find that Hth controls a binary Rhodopsin switch in ocelli to promote Rh2 expression and repress Rh1 expression. Genetic and molecular analysis of rh1 and rh2 supports that Hth acts through their promoters to regulate Rhodopsin expression in the ocelli. Finally, we also show that when ectopically expressed in the retina, hth is sufficient to induce Rh2 expression only at the outer PRs in a cell autonomous manner. We therefore propose that the diversification of rhodpsins in the ocelli and retinal outer PRs occurred by duplication of an ancestral gene, which is under the control of Homothorax. Sensory perception of light is mediated by specialized photoreceptor neurons of the eye. Each photoreceptor expresses unique photopigments called opsins and they are sensitive to particular wavelengths of light. In insects, ocelli and compound eyes are the main photosensory organs and they express different opsins. It is believed that opsins were duplicated during evolution to provide specificity to ocelli and the compound eye and this is corelated with their distinct functions. We show that Homothorax acts to control a binary Rhodopsin switch in the fruit fly Drosophila melanogaster to promote Rhodopsin 2 expression and represses Rhodopsin 1 expression in the ocelli. Genetic and molecular analysis showed that Homothorax acts through the promoters of rhosopsin 1 and rhosopsin 2 and controls their expression in the ocelli. We also show that Hth binding sites in the promoter region of rhodopsin 1 and rhodopsin 2 are conserved between different Drosophila species. We therefore proposed that Hth may have acted as a critical determinant during evolution which was required to provide specificity to the ocelli and compound eye by regulating a binary Rhodopsin switch in the ocelli.
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Affiliation(s)
- Abhishek Kumar Mishra
- Institute of Cell and Developmental Biology, Department of Biology, University of Fribourg, Fribourg, Switzerland
- * E-mail: (AKM); (SGS)
| | - Cornelia Fritsch
- Institute of Cell and Developmental Biology, Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Roumen Voutev
- Department of Biochemistry and Molecular Biophysics and Neuroscience, Mortimer B. Zukerman Mind Brain Behavior Institute, Columbia University, New York, United States of America
| | - Richard S. Mann
- Department of Biochemistry and Molecular Biophysics and Neuroscience, Mortimer B. Zukerman Mind Brain Behavior Institute, Columbia University, New York, United States of America
| | - Simon G. Sprecher
- Institute of Cell and Developmental Biology, Department of Biology, University of Fribourg, Fribourg, Switzerland
- * E-mail: (AKM); (SGS)
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9
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Feuda R, Goulty M, Zadra N, Gasparetti T, Rosato E, Pisani D, Rizzoli A, Segata N, Ometto L, Stabelli OR. Phylogenomics of Opsin Genes in Diptera Reveals Lineage-Specific Events and Contrasting Evolutionary Dynamics in Anopheles and Drosophila. Genome Biol Evol 2021; 13:6322995. [PMID: 34270718 PMCID: PMC8369074 DOI: 10.1093/gbe/evab170] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/14/2021] [Indexed: 12/12/2022] Open
Abstract
Diptera is one of the biggest insect orders and displays a large diversity of visual adaptations. Similarly to other animals, the dipteran visual process is mediated by opsin genes. Although the diversity and function of these genes are well studied in key model species, a comprehensive comparative genomic study across the dipteran phylogeny is missing. Here we mined the genomes of 61 dipteran species, reconstructed the evolutionary affinities of 528 opsin genes, and determined the selective pressure acting in different species. We found that opsins underwent several lineage-specific events, including an independent expansion of Long Wave Sensitive opsins in flies and mosquitoes, and numerous family-specific duplications and losses. Both the Drosophila and the Anopheles complement are derived in comparison with the ancestral dipteran state. Molecular evolutionary studies suggest that gene turnover rate, overall mutation rate, and site-specific selective pressure are higher in Anopheles than in Drosophila. Overall, our findings indicate an extremely variable pattern of opsin evolution in dipterans, showcasing how two similarly aged radiations, Anopheles and Drosophila, are characterized by contrasting dynamics in the evolution of this gene family. These results provide a foundation for future studies on the dipteran visual system.
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Affiliation(s)
- Roberto Feuda
- Department of Genetics and Genome Biology, University of Leicester, UK.,Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Matthew Goulty
- Department of Genetics and Genome Biology, University of Leicester, UK
| | - Nicola Zadra
- Research and Innovation Centre, Fondazione Edmund Mach (FEM), San Michele all'Adige, Italy.,Department CIBIO, University of Trento, Italy
| | | | - Ezio Rosato
- Department of Genetics and Genome Biology, University of Leicester, UK
| | | | - Annapaola Rizzoli
- Research and Innovation Centre, Fondazione Edmund Mach (FEM), San Michele all'Adige, Italy
| | | | - Lino Ometto
- Department of Biology and Biotechnology, University of Pavia, Italy
| | - Omar Rota Stabelli
- Research and Innovation Centre, Fondazione Edmund Mach (FEM), San Michele all'Adige, Italy.,Center Agriculture Food Environment (C3A), University of Trento, Italy
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10
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Oeyen JP, Baa-Puyoulet P, Benoit JB, Beukeboom LW, Bornberg-Bauer E, Buttstedt A, Calevro F, Cash EI, Chao H, Charles H, Chen MJM, Childers C, Cridge AG, Dearden P, Dinh H, Doddapaneni HV, Dolan A, Donath A, Dowling D, Dugan S, Duncan E, Elpidina EN, Friedrich M, Geuverink E, Gibson JD, Grath S, Grimmelikhuijzen CJP, Große-Wilde E, Gudobba C, Han Y, Hansson BS, Hauser F, Hughes DST, Ioannidis P, Jacquin-Joly E, Jennings EC, Jones JW, Klasberg S, Lee SL, Lesný P, Lovegrove M, Martin S, Martynov AG, Mayer C, Montagné N, Moris VC, Munoz-Torres M, Murali SC, Muzny DM, Oppert B, Parisot N, Pauli T, Peters RS, Petersen M, Pick C, Persyn E, Podsiadlowski L, Poelchau MF, Provataris P, Qu J, Reijnders MJMF, von Reumont BM, Rosendale AJ, Simao FA, Skelly J, Sotiropoulos AG, Stahl AL, Sumitani M, Szuter EM, Tidswell O, Tsitlakidis E, Vedder L, Waterhouse RM, Werren JH, Wilbrandt J, Worley KC, Yamamoto DS, van de Zande L, Zdobnov EM, Ziesmann T, Gibbs RA, Richards S, Hatakeyama M, Misof B, Niehuis O. Sawfly Genomes Reveal Evolutionary Acquisitions That Fostered the Mega-Radiation of Parasitoid and Eusocial Hymenoptera. Genome Biol Evol 2021; 12:1099-1188. [PMID: 32442304 PMCID: PMC7455281 DOI: 10.1093/gbe/evaa106] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/19/2020] [Indexed: 12/12/2022] Open
Abstract
The tremendous diversity of Hymenoptera is commonly attributed to the evolution of parasitoidism in the last common ancestor of parasitoid sawflies (Orussidae) and wasp-waisted Hymenoptera (Apocrita). However, Apocrita and Orussidae differ dramatically in their species richness, indicating that the diversification of Apocrita was promoted by additional traits. These traits have remained elusive due to a paucity of sawfly genome sequences, in particular those of parasitoid sawflies. Here, we present comparative analyses of draft genomes of the primarily phytophagous sawfly Athalia rosae and the parasitoid sawfly Orussus abietinus. Our analyses revealed that the ancestral hymenopteran genome exhibited traits that were previously considered unique to eusocial Apocrita (e.g., low transposable element content and activity) and a wider gene repertoire than previously thought (e.g., genes for CO2 detection). Moreover, we discovered that Apocrita evolved a significantly larger array of odorant receptors than sawflies, which could be relevant to the remarkable diversification of Apocrita by enabling efficient detection and reliable identification of hosts.
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Affiliation(s)
- Jan Philip Oeyen
- Center for Molecular Biodiversity Research, Zoologisches Forschungsmuseum Alexander Koenig, Bonn, Germany.,Lead Contact
| | | | | | - Leo W Beukeboom
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, The Netherlands
| | | | - Anja Buttstedt
- B CUBE-Center for Molecular Bioengineering, Technische Universität Dresden, Germany
| | - Federica Calevro
- INSA-Lyon, INRAE, BF2I, UMR0203, Université de Lyon, Villeurbanne, France
| | - Elizabeth I Cash
- School of Life Sciences, College of Liberal Arts and Sciences, Arizona State University.,Department of Environmental Science, Policy, and Management, College of Natural Resources, University of California, Berkeley
| | - Hsu Chao
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, Texas
| | - Hubert Charles
- INSA-Lyon, INRAE, BF2I, UMR0203, Université de Lyon, Villeurbanne, France
| | - Mei-Ju May Chen
- Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei, Taiwan
| | | | - Andrew G Cridge
- Genomics Aotearoa and Biochemistry Department, University of Otago, Dunedin, New Zealand
| | - Peter Dearden
- Genomics Aotearoa and Biochemistry Department, University of Otago, Dunedin, New Zealand
| | - Huyen Dinh
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, Texas
| | - Harsha Vardhan Doddapaneni
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, Texas
| | | | - Alexander Donath
- Center for Molecular Biodiversity Research, Zoologisches Forschungsmuseum Alexander Koenig, Bonn, Germany
| | - Daniel Dowling
- Institute for Evolution and Biodiversity, University of Münster, Germany
| | - Shannon Dugan
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, Texas
| | - Elizabeth Duncan
- School of Biology, Faculty of Biological Sciences, University of Leeds, United Kingdom
| | - Elena N Elpidina
- A.N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Russia
| | - Markus Friedrich
- Department of Biological Sciences, Wayne State University, Detroit
| | - Elzemiek Geuverink
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, The Netherlands
| | - Joshua D Gibson
- Department of Biology, Georgia Southern University, Statesboro.,Department of Entomology, Purdue University, West Lafayette
| | - Sonja Grath
- Division of Evolutionary Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | | | - Ewald Große-Wilde
- Department of Evolutionary Neuroethology, Max-Planck-Institute for Chemical Ecology, Jena, Germany.,Faculty of Forestry and Wood Sciences, Czech University of Life Sciences Prague (CULS), Praha 6-Suchdol, Czech Republic
| | - Cameron Gudobba
- Department of Psychiatry and Behavioral Neuroscience, University of Chicago
| | - Yi Han
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, Texas
| | - Bill S Hansson
- Department of Evolutionary Neuroethology, Max-Planck-Institute for Chemical Ecology, Jena, Germany
| | - Frank Hauser
- Department of Biology, University of Copenhagen, Denmark
| | - Daniel S T Hughes
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, Texas
| | - Panagiotis Ioannidis
- Department of Genetic Medicine and Development, University of Geneva Medical School, Switzerland.,Swiss Institute of Bioinformatics, Geneva, Switzerland.,Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Crete, Greece
| | - Emmanuelle Jacquin-Joly
- INRAE, CNRS, IRD, UPEC, Univ. P7, Institute of Ecology and Environmental Sciences of Paris, Sorbonne Université, Versailles, France
| | | | - Jeffery W Jones
- Department of Biological Sciences, Oakland University, Rochester
| | - Steffen Klasberg
- Institute for Evolution and Biodiversity, University of Münster, Germany
| | - Sandra L Lee
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, Texas
| | - Peter Lesný
- Institute of Evolutionary Biology and Ecology, Zoology and Evolutionary Biology, University of Bonn, Germany
| | - Mackenzie Lovegrove
- Genomics Aotearoa and Biochemistry Department, University of Otago, Dunedin, New Zealand
| | - Sebastian Martin
- Institute of Evolutionary Biology and Ecology, Zoology and Evolutionary Biology, University of Bonn, Germany
| | | | - Christoph Mayer
- Center for Molecular Biodiversity Research, Zoologisches Forschungsmuseum Alexander Koenig, Bonn, Germany
| | - Nicolas Montagné
- INRAE, CNRS, IRD, UPEC, Univ. P7, Institute of Ecology and Environmental Sciences of Paris, Sorbonne Université, Paris, France
| | - Victoria C Moris
- Department of Evolutionary Biology and Ecology, Institute of Biology I (Zoology), Albert Ludwig University Freiburg, Germany
| | - Monica Munoz-Torres
- Berkeley Bioinformatics Open-source Projects (BBOP), Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California
| | - Shwetha Canchi Murali
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, Texas
| | - Donna M Muzny
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, Texas
| | - Brenda Oppert
- USDA Agricultural Research Service, Center for Grain and Animal Health Research, Manhattan, Kansas
| | - Nicolas Parisot
- INSA-Lyon, INRAE, BF2I, UMR0203, Université de Lyon, Villeurbanne, France
| | - Thomas Pauli
- Department of Evolutionary Biology and Ecology, Institute of Biology I (Zoology), Albert Ludwig University Freiburg, Germany
| | - Ralph S Peters
- Arthropoda Department, Center for Taxonomy and Evolutionary Research, Zoologisches Forschungsmuseum Alexander Koenig, Bonn, Germany
| | - Malte Petersen
- Center for Molecular Biodiversity Research, Zoologisches Forschungsmuseum Alexander Koenig, Bonn, Germany.,Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | | | - Emma Persyn
- INRAE, CNRS, IRD, UPEC, Univ. P7, Institute of Ecology and Environmental Sciences of Paris, Sorbonne Université, Paris, France
| | - Lars Podsiadlowski
- Center for Molecular Biodiversity Research, Zoologisches Forschungsmuseum Alexander Koenig, Bonn, Germany
| | | | - Panagiotis Provataris
- Center for Molecular Biodiversity Research, Zoologisches Forschungsmuseum Alexander Koenig, Bonn, Germany
| | - Jiaxin Qu
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, Texas
| | - Maarten J M F Reijnders
- Department of Ecology and Evolution, University of Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Björn Marcus von Reumont
- Institute for Insect Biotechnology, University of Gießen, Germany.,Center for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt, Germany
| | | | - Felipe A Simao
- Department of Genetic Medicine and Development, University of Geneva Medical School, Switzerland.,Swiss Institute of Bioinformatics, Geneva, Switzerland
| | - John Skelly
- Genomics Aotearoa and Biochemistry Department, University of Otago, Dunedin, New Zealand
| | | | - Aaron L Stahl
- Department of Biological Sciences, University of Cincinnati.,Department of Neuroscience, The Scripps Research Institute, Jupiter, Florida
| | - Megumi Sumitani
- Transgenic Silkworm Research Unit, Division of Biotechnology, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Owashi, Tsukuba, Japan
| | - Elise M Szuter
- School of Life Sciences, College of Liberal Arts and Sciences, Arizona State University
| | - Olivia Tidswell
- Biochemistry Department, University of Otago, Dunedin, New Zealand.,Zoology Department, University of Cambridge, United Kingdom
| | | | - Lucia Vedder
- Center for Bioinformatics Tübingen (ZBIT), University of Tübingen, Germany
| | - Robert M Waterhouse
- Department of Ecology and Evolution, University of Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | | | - Jeanne Wilbrandt
- Center for Molecular Biodiversity Research, Zoologisches Forschungsmuseum Alexander Koenig, Bonn, Germany.,Computational Biology Group, Leibniz Institute on Aging-Fritz Lipmann Institute, Jena, Germany
| | - Kim C Worley
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, Texas
| | - Daisuke S Yamamoto
- Division of Medical Zoology, Department of Infection and Immunity, Jichi Medical University, Yakushiji, Shimotsuke, Japan
| | - Louis van de Zande
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, The Netherlands
| | - Evgeny M Zdobnov
- Department of Genetic Medicine and Development, University of Geneva Medical School, Switzerland.,Swiss Institute of Bioinformatics, Geneva, Switzerland
| | - Tanja Ziesmann
- Center for Molecular Biodiversity Research, Zoologisches Forschungsmuseum Alexander Koenig, Bonn, Germany
| | - Richard A Gibbs
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, Texas
| | - Stephen Richards
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, Texas
| | - Masatsugu Hatakeyama
- Insect Genome Research and Engineering Unit, Division of Applied Genetics, Institute of Agrobiological Sciences, NARO, Owashi, Tsukuba, Japan
| | - Bernhard Misof
- Center for Molecular Biodiversity Research, Zoologisches Forschungsmuseum Alexander Koenig, Bonn, Germany
| | - Oliver Niehuis
- Department of Evolutionary Biology and Ecology, Institute of Biology I (Zoology), Albert Ludwig University Freiburg, Germany
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11
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Martin GJ, Lower SE, Suvorov A, Bybee SM. Molecular Evolution of Phototransduction Pathway Genes in Nocturnal and Diurnal Fireflies (Coleoptera: Lampyridae). INSECTS 2021; 12:insects12060561. [PMID: 34207188 PMCID: PMC8235688 DOI: 10.3390/insects12060561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 06/04/2021] [Accepted: 06/06/2021] [Indexed: 11/16/2022]
Abstract
Most organisms are dependent on sensory cues from their environment for survival and reproduction. Fireflies (Coleoptera: Lampyridae) represent an ideal system for studying sensory niche adaptation due to many species relying on bioluminescent communication; as well as a diversity of ecologies. Here; using transcriptomics; we examine the phototransduction pathway in this non-model organism; and provide some of the first evidence for positive selection in the phototransduction pathway beyond opsins in beetles. Evidence for gene duplications within Lampyridae are found in inactivation no afterpotential C and inactivation no afterpotential D. We also find strong support for positive selection in arrestin-2; inactivation no afterpotential D; and transient receptor potential-like; with weak support for positive selection in guanine nucleotide-binding protein G(q) subunit alpha and neither inactivation nor afterpotential C. Taken with other recent work in flies; butterflies; and moths; this represents an exciting new avenue of study as we seek to further understand diversification and constraint on the phototransduction pathway in light of organism ecology.
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Affiliation(s)
- Gavin J. Martin
- Department of Biology, Brigham Young University, Provo, UT 84602, USA; (A.S.); (S.M.B.)
- Monte L. Bean Museum, Brigham Young University, Provo, UT 84602, USA
- Correspondence:
| | - Sarah E. Lower
- Department of Biology, Bucknell University, Lewisburg, PA 17837, USA;
| | - Anton Suvorov
- Department of Biology, Brigham Young University, Provo, UT 84602, USA; (A.S.); (S.M.B.)
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Seth M. Bybee
- Department of Biology, Brigham Young University, Provo, UT 84602, USA; (A.S.); (S.M.B.)
- Monte L. Bean Museum, Brigham Young University, Provo, UT 84602, USA
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12
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Bao R, Friedrich M. Genomic signatures of globally enhanced gene duplicate accumulation in the megadiverse higher Diptera fueling intralocus sexual conflict resolution. PeerJ 2020; 8:e10012. [PMID: 33083121 PMCID: PMC7560327 DOI: 10.7717/peerj.10012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 08/31/2020] [Indexed: 12/03/2022] Open
Abstract
Gene duplication is an important source of evolutionary innovation. To explore the relative impact of gene duplication during the diversification of major insect model system lineages, we performed a comparative analysis of lineage-specific gene duplications in the fruit fly Drosophila melanogaster (Diptera: Brachycera), the mosquito Anopheles gambiae (Diptera: Culicomorpha), the red flour beetle Tribolium castaneum (Coleoptera), and the honeybee Apis mellifera (Hymenoptera). Focusing on close to 6,000 insect core gene families containing maximally six paralogs, we detected a conspicuously higher number of lineage-specific duplications in Drosophila (689) compared to Anopheles (315), Tribolium (386), and Apis (223). Based on analyses of sequence divergence, phylogenetic distribution, and gene ontology information, we present evidence that an increased background rate of gene duplicate accumulation played an exceptional role during the diversification of the higher Diptera (Brachycera), in part by providing enriched opportunities for intralocus sexual conflict resolution, which may have boosted speciation rates during the early radiation of the megadiverse brachyceran subclade Schizophora.
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Affiliation(s)
- Riyue Bao
- Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA.,Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Markus Friedrich
- Department of Biological Sciences, Wayne State University, Detroit, MI, USA.,School of Medicine, Department of Anatomy and Cell Biology, Wayne State University, Detroit, MI, USA
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13
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Macias-Muñoz A, Rangel Olguin AG, Briscoe AD. Evolution of Phototransduction Genes in Lepidoptera. Genome Biol Evol 2019; 11:2107-2124. [PMID: 31298692 PMCID: PMC6698658 DOI: 10.1093/gbe/evz150] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/10/2019] [Indexed: 12/17/2022] Open
Abstract
Vision is underpinned by phototransduction, a signaling cascade that converts light energy into an electrical signal. Among insects, phototransduction is best understood in Drosophila melanogaster. Comparison of D. melanogaster against three insect species found several phototransduction gene gains and losses, however, lepidopterans were not examined. Diurnal butterflies and nocturnal moths occupy different light environments and have distinct eye morphologies, which might impact the expression of their phototransduction genes. Here we investigated: 1) how phototransduction genes vary in gene gain or loss between D. melanogaster and Lepidoptera, and 2) variations in phototransduction genes between moths and butterflies. To test our prediction of phototransduction differences due to distinct visual ecologies, we used insect reference genomes, phylogenetics, and moth and butterfly head RNA-Seq and transcriptome data. As expected, most phototransduction genes were conserved between D. melanogaster and Lepidoptera, with some exceptions. Notably, we found two lepidopteran opsins lacking a D. melanogaster ortholog. Using antibodies we found that one of these opsins, a candidate retinochrome, which we refer to as unclassified opsin (UnRh), is expressed in the crystalline cone cells and the pigment cells of the butterfly, Heliconius melpomene. Our results also show that butterflies express similar amounts of trp and trpl channel mRNAs, whereas moths express ∼50× less trp, a potential adaptation to darkness. Our findings suggest that while many single-copy D. melanogaster phototransduction genes are conserved in lepidopterans, phototransduction gene expression differences exist between moths and butterflies that may be linked to their visual light environment.
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Affiliation(s)
- Aide Macias-Muñoz
- Department of Ecology and Evolutionary Biology, University of California, Irvine
| | | | - Adriana D Briscoe
- Department of Ecology and Evolutionary Biology, University of California, Irvine
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14
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Bao R, Dia SE, Issa HA, Alhusein D, Friedrich M. Comparative Evidence of an Exceptional Impact of Gene Duplication on the Developmental Evolution of Drosophila and the Higher Diptera. Front Ecol Evol 2018. [DOI: 10.3389/fevo.2018.00063] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
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15
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Tierney SM, Langille B, Humphreys WF, Austin AD, Cooper SJB. Massive Parallel Regression: A Précis of Genetic Mechanisms for Vision Loss in Diving Beetles. Integr Comp Biol 2018; 58:465-479. [DOI: 10.1093/icb/icy035] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Affiliation(s)
- Simon M Tierney
- Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith, NSW 2751, Australia
- Australian Centre for Evolutionary Biology and Biodiversity, School of Biological Sciences, The University of Adelaide, North Terrace, Adelaide, SA 5005, Australia
- School of Biosciences, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Barbara Langille
- Australian Centre for Evolutionary Biology and Biodiversity, School of Biological Sciences, The University of Adelaide, North Terrace, Adelaide, SA 5005, Australia
| | - William F Humphreys
- Australian Centre for Evolutionary Biology and Biodiversity, School of Biological Sciences, The University of Adelaide, North Terrace, Adelaide, SA 5005, Australia
- Department of Terrestrial Zoology, Western Australian Museum, Locked Bag 49, Welshpool DC, WA 6986, Australia
- School of Animal Biology, The University of Western Australia, Nedlands, WA 6907, Australia
| | - Andrew D Austin
- Australian Centre for Evolutionary Biology and Biodiversity, School of Biological Sciences, The University of Adelaide, North Terrace, Adelaide, SA 5005, Australia
| | - Steven J B Cooper
- Australian Centre for Evolutionary Biology and Biodiversity, School of Biological Sciences, The University of Adelaide, North Terrace, Adelaide, SA 5005, Australia
- Evolutionary Biology Unit, South Australian Museum, North Terrace, Adelaide, SA 5000, Australia
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16
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Kanost MR, Arrese EL, Cao X, Chen YR, Chellapilla S, Goldsmith MR, Grosse-Wilde E, Heckel DG, Herndon N, Jiang H, Papanicolaou A, Qu J, Soulages JL, Vogel H, Walters J, Waterhouse RM, Ahn SJ, Almeida FC, An C, Aqrawi P, Bretschneider A, Bryant WB, Bucks S, Chao H, Chevignon G, Christen JM, Clarke DF, Dittmer NT, Ferguson LCF, Garavelou S, Gordon KHJ, Gunaratna RT, Han Y, Hauser F, He Y, Heidel-Fischer H, Hirsh A, Hu Y, Jiang H, Kalra D, Klinner C, König C, Kovar C, Kroll AR, Kuwar SS, Lee SL, Lehman R, Li K, Li Z, Liang H, Lovelace S, Lu Z, Mansfield JH, McCulloch KJ, Mathew T, Morton B, Muzny DM, Neunemann D, Ongeri F, Pauchet Y, Pu LL, Pyrousis I, Rao XJ, Redding A, Roesel C, Sanchez-Gracia A, Schaack S, Shukla A, Tetreau G, Wang Y, Xiong GH, Traut W, Walsh TK, Worley KC, Wu D, Wu W, Wu YQ, Zhang X, Zou Z, Zucker H, Briscoe AD, Burmester T, Clem RJ, Feyereisen R, Grimmelikhuijzen CJP, Hamodrakas SJ, Hansson BS, Huguet E, Jermiin LS, Lan Q, Lehman HK, Lorenzen M, Merzendorfer H, Michalopoulos I, Morton DB, Muthukrishnan S, Oakeshott JG, Palmer W, Park Y, Passarelli AL, Rozas J, Schwartz LM, Smith W, Southgate A, Vilcinskas A, Vogt R, Wang P, Werren J, Yu XQ, Zhou JJ, Brown SJ, Scherer SE, Richards S, Blissard GW. Multifaceted biological insights from a draft genome sequence of the tobacco hornworm moth, Manduca sexta. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2016; 76:118-147. [PMID: 27522922 PMCID: PMC5010457 DOI: 10.1016/j.ibmb.2016.07.005] [Citation(s) in RCA: 120] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Revised: 06/27/2016] [Accepted: 07/14/2016] [Indexed: 05/19/2023]
Abstract
Manduca sexta, known as the tobacco hornworm or Carolina sphinx moth, is a lepidopteran insect that is used extensively as a model system for research in insect biochemistry, physiology, neurobiology, development, and immunity. One important benefit of this species as an experimental model is its extremely large size, reaching more than 10 g in the larval stage. M. sexta larvae feed on solanaceous plants and thus must tolerate a substantial challenge from plant allelochemicals, including nicotine. We report the sequence and annotation of the M. sexta genome, and a survey of gene expression in various tissues and developmental stages. The Msex_1.0 genome assembly resulted in a total genome size of 419.4 Mbp. Repetitive sequences accounted for 25.8% of the assembled genome. The official gene set is comprised of 15,451 protein-coding genes, of which 2498 were manually curated. Extensive RNA-seq data from many tissues and developmental stages were used to improve gene models and for insights into gene expression patterns. Genome wide synteny analysis indicated a high level of macrosynteny in the Lepidoptera. Annotation and analyses were carried out for gene families involved in a wide spectrum of biological processes, including apoptosis, vacuole sorting, growth and development, structures of exoskeleton, egg shells, and muscle, vision, chemosensation, ion channels, signal transduction, neuropeptide signaling, neurotransmitter synthesis and transport, nicotine tolerance, lipid metabolism, and immunity. This genome sequence, annotation, and analysis provide an important new resource from a well-studied model insect species and will facilitate further biochemical and mechanistic experimental studies of many biological systems in insects.
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Affiliation(s)
- Michael R Kanost
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS, 66506, USA.
| | - Estela L Arrese
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK, 74078, USA
| | - Xiaolong Cao
- Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, OK, 74078, USA
| | - Yun-Ru Chen
- Boyce Thompson Institute at Cornell University, Tower Road, Ithaca, NY, 14853, USA
| | - Sanjay Chellapilla
- KSU Bioinformatics Center, Division of Biology, Kansas State University, Manhattan, KS, 66506, USA
| | - Marian R Goldsmith
- Biological Sciences Department, University of Rhode Island, Kingston, RI, 02881, USA
| | - Ewald Grosse-Wilde
- Max Planck Institute for Chemical Ecology, Department of Evolutionary Neuroethology, Hans-Knoell-Strasse, 8, D-07745, Jena, Germany
| | - David G Heckel
- Department of Entomology, Max Planck Institute for Chemical Ecology, Hans-Knoell-Strasse 8, 07745, Jena, Germany
| | - Nicolae Herndon
- KSU Bioinformatics Center, Division of Biology, Kansas State University, Manhattan, KS, 66506, USA
| | - Haobo Jiang
- Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, OK, 74078, USA
| | - Alexie Papanicolaou
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, 2753, Australia
| | - Jiaxin Qu
- Human Genome Sequencing Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA
| | - Jose L Soulages
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK, 74078, USA
| | - Heiko Vogel
- Department of Entomology, Max Planck Institute for Chemical Ecology, Hans-Knoell-Strasse 8, 07745, Jena, Germany
| | - James Walters
- Department of Ecology and Evolutionary Biology, Univ. Kansas, Lawrence, KS, 66045, USA
| | - Robert M Waterhouse
- Department of Genetic Medicine and Development, University of Geneva Medical School, rue Michel-Servet 1, 1211, Geneva, Switzerland; Swiss Institute of Bioinformatics, rue Michel-Servet 1, 1211, Geneva, Switzerland; Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, 32 Vassar Street, Cambridge, MA, 02139, USA; The Broad Institute of MIT and Harvard, Cambridge, 415 Main Street, MA, 02142, USA
| | - Seung-Joon Ahn
- Department of Entomology, Max Planck Institute for Chemical Ecology, Hans-Knoell-Strasse 8, 07745, Jena, Germany
| | - Francisca C Almeida
- Departament de Genètica and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Chunju An
- Department of Entomology, China Agricultural University, Beijing, China
| | - Peshtewani Aqrawi
- Human Genome Sequencing Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA
| | - Anne Bretschneider
- Department of Entomology, Max Planck Institute for Chemical Ecology, Hans-Knoell-Strasse 8, 07745, Jena, Germany
| | - William B Bryant
- Division of Biology, Kansas State University, Manhattan, KS, 66506, USA
| | - Sascha Bucks
- Max Planck Institute for Chemical Ecology, Department of Evolutionary Neuroethology, Hans-Knoell-Strasse, 8, D-07745, Jena, Germany
| | - Hsu Chao
- Human Genome Sequencing Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA
| | - Germain Chevignon
- Institut de Recherche sur la Biologie de l'Insecte, UMR CNRS 7261, UFR Sciences et Techniques, Université François-Rabelais, Tours, France
| | - Jayne M Christen
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS, 66506, USA
| | - David F Clarke
- CSIRO Land and Water, Clunies Ross St, Acton, ACT, 2601, Australia
| | - Neal T Dittmer
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS, 66506, USA
| | | | - Spyridoula Garavelou
- Centre of Systems Biology, Biomedical Research Foundation, Academy of Athens, Athens, Greece
| | - Karl H J Gordon
- CSIRO Health and Biosecurity, Clunies Ross St, Acton, ACT, 2601, Australia
| | - Ramesh T Gunaratna
- Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, OK, 74078, USA
| | - Yi Han
- Human Genome Sequencing Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA
| | - Frank Hauser
- Center for Functional and Comparative Insect Genomics, Department of Biology, University of Copenhagen, Universitetsparken 15, DK-21oo, Copenhagen, Denmark
| | - Yan He
- Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, OK, 74078, USA
| | - Hanna Heidel-Fischer
- Department of Entomology, Max Planck Institute for Chemical Ecology, Hans-Knoell-Strasse 8, 07745, Jena, Germany
| | - Ariana Hirsh
- Department of Biology, Barnard College, Columbia University, 3009 Broadway, New York, NY, 10027, USA
| | - Yingxia Hu
- Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, OK, 74078, USA
| | - Hongbo Jiang
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, 400715, China
| | - Divya Kalra
- Human Genome Sequencing Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA
| | - Christian Klinner
- Max Planck Institute for Chemical Ecology, Department of Evolutionary Neuroethology, Hans-Knoell-Strasse, 8, D-07745, Jena, Germany
| | - Christopher König
- Max Planck Institute for Chemical Ecology, Department of Evolutionary Neuroethology, Hans-Knoell-Strasse, 8, D-07745, Jena, Germany
| | - Christie Kovar
- Human Genome Sequencing Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA
| | - Ashley R Kroll
- Department of Biology, Reed College, Portland, OR, 97202, USA
| | - Suyog S Kuwar
- Department of Entomology, Max Planck Institute for Chemical Ecology, Hans-Knoell-Strasse 8, 07745, Jena, Germany
| | - Sandy L Lee
- Human Genome Sequencing Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA
| | - Rüdiger Lehman
- Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Bioresources Project Group, Winchesterstrasse 2, 35394, Gießen, Germany
| | - Kai Li
- College of Chemistry, Chemical Engineering, and Biotechnology, Donghua University, Shanghai, 201620, China
| | - Zhaofei Li
- College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Hanquan Liang
- McDermott Center for Human Growth and Development, UT Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX, 75390, USA
| | - Shanna Lovelace
- Department of Biological Sciences, University of Southern Maine, Portland, ME, 04104, USA
| | - Zhiqiang Lu
- College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Jennifer H Mansfield
- Department of Biology, Barnard College, Columbia University, 3009 Broadway, New York, NY, 10027, USA
| | - Kyle J McCulloch
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, 92697, USA
| | - Tittu Mathew
- Human Genome Sequencing Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA
| | - Brian Morton
- Department of Biology, Barnard College, Columbia University, 3009 Broadway, New York, NY, 10027, USA
| | - Donna M Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA
| | - David Neunemann
- Department of Entomology, Max Planck Institute for Chemical Ecology, Hans-Knoell-Strasse 8, 07745, Jena, Germany
| | - Fiona Ongeri
- Human Genome Sequencing Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA
| | - Yannick Pauchet
- Department of Entomology, Max Planck Institute for Chemical Ecology, Hans-Knoell-Strasse 8, 07745, Jena, Germany
| | - Ling-Ling Pu
- Human Genome Sequencing Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA
| | - Ioannis Pyrousis
- Centre of Systems Biology, Biomedical Research Foundation, Academy of Athens, Athens, Greece
| | - Xiang-Jun Rao
- School of Plant Protection, Anhui Agricultural University, Hefei, Anhui, China
| | - Amanda Redding
- Department of Biology, University of Rochester, Rochester, NY, 14627, USA
| | - Charles Roesel
- Department of Marine and Environmental Sciences, Northeastern University, Boston, MA, 02115, USA
| | - Alejandro Sanchez-Gracia
- Departament de Genètica and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Sarah Schaack
- Department of Biology, Reed College, Portland, OR, 97202, USA
| | - Aditi Shukla
- Department of Biology, Barnard College, Columbia University, 3009 Broadway, New York, NY, 10027, USA
| | - Guillaume Tetreau
- Department of Entomology, Cornell University, New York State Agricultural Experiment Station, Geneva, NY, 14456, USA
| | - Yang Wang
- Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, OK, 74078, USA
| | - Guang-Hua Xiong
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Walther Traut
- Institut fuer Biologie, Universitaet Luebeck, D-23538, Luebeck, Germany
| | - Tom K Walsh
- CSIRO Land and Water, Clunies Ross St, Acton, ACT, 2601, Australia
| | - Kim C Worley
- Human Genome Sequencing Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA
| | - Di Wu
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS, 66506, USA
| | - Wenbi Wu
- Division of Biology, Kansas State University, Manhattan, KS, 66506, USA
| | - Yuan-Qing Wu
- Human Genome Sequencing Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA
| | - Xiufeng Zhang
- Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, OK, 74078, USA
| | - Zhen Zou
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Hannah Zucker
- Neuroscience Program, Hamilton College, Clinton, NY, 13323, USA
| | - Adriana D Briscoe
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, 92697, USA
| | | | - Rollie J Clem
- Division of Biology, Kansas State University, Manhattan, KS, 66506, USA
| | - René Feyereisen
- Department of Crop Protection, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Cornelis J P Grimmelikhuijzen
- Center for Functional and Comparative Insect Genomics, Department of Biology, University of Copenhagen, Universitetsparken 15, DK-21oo, Copenhagen, Denmark
| | - Stavros J Hamodrakas
- Department of Cell Biology and Biophysics, Faculty of Biology, University of Athens, Athens, Greece
| | - Bill S Hansson
- Max Planck Institute for Chemical Ecology, Department of Evolutionary Neuroethology, Hans-Knoell-Strasse, 8, D-07745, Jena, Germany
| | - Elisabeth Huguet
- Institut de Recherche sur la Biologie de l'Insecte, UMR CNRS 7261, UFR Sciences et Techniques, Université François-Rabelais, Tours, France
| | - Lars S Jermiin
- CSIRO Land and Water, Clunies Ross St, Acton, ACT, 2601, Australia
| | - Que Lan
- Department of Entomology, University of Wisconsin, Madison, USA
| | - Herman K Lehman
- Biology Department and Neuroscience Program, Hamilton College, Clinton, NY, 13323, USA
| | - Marce Lorenzen
- Dept. Entomology, North Carolina State Univ., Raleigh, NC, 27695, USA
| | - Hans Merzendorfer
- University of Siegen, School of Natural Sciences and Engineering, Institute of Biology - Molecular Biology, Adolf-Reichwein-Strasse. 2, AR-C3010, 57076 Siegen, Germany
| | - Ioannis Michalopoulos
- Centre of Systems Biology, Biomedical Research Foundation, Academy of Athens, Athens, Greece
| | - David B Morton
- Department of Integrative Biosciences, School of Dentistry, BRB421, L595, Oregon Health & Science University, 3181 SW Sam Jackson Park Rd., Portland, OR, 97239, USA
| | - Subbaratnam Muthukrishnan
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS, 66506, USA
| | - John G Oakeshott
- CSIRO Land and Water, Clunies Ross St, Acton, ACT, 2601, Australia
| | - Will Palmer
- Department of Genetics, University of Cambridge, Downing St, Cambridge, CB2 3EH, UK
| | - Yoonseong Park
- Department of Entomology, Kansas State University, Manhattan, KS, 66506, USA
| | | | - Julio Rozas
- Departament de Genètica and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | | | - Wendy Smith
- Department of Biology, Northeastern University, Boston, MA, 02115, USA
| | - Agnes Southgate
- Department of Biology, College of Charleston, Charleston, SC, 29424, USA
| | - Andreas Vilcinskas
- Institute for Insect Biotechnology, Justus-Liebig-University, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany
| | - Richard Vogt
- Department of Biological Sciences, University of South Carolina, Columbia, SC, 29205, USA
| | - Ping Wang
- Department of Entomology, Cornell University, New York State Agricultural Experiment Station, Geneva, NY, 14456, USA
| | - John Werren
- Department of Biology, University of Rochester, Rochester, NY, 14627, USA
| | - Xiao-Qiang Yu
- University of Missouri-Kansas City, 5007 Rockhill Road, Kansas City, MO, 64110, USA
| | - Jing-Jiang Zhou
- Department of Biological Chemistry and Crop Protection, Rothamsted Research, Harpenden, Herts, AL5 2JQ, UK
| | - Susan J Brown
- KSU Bioinformatics Center, Division of Biology, Kansas State University, Manhattan, KS, 66506, USA
| | - Steven E Scherer
- Human Genome Sequencing Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA
| | - Stephen Richards
- Human Genome Sequencing Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA
| | - Gary W Blissard
- Boyce Thompson Institute at Cornell University, Tower Road, Ithaca, NY, 14853, USA
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17
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Friedrich M. Evo-Devo gene toolkit update: at least seven Pax transcription factor subfamilies in the last common ancestor of bilaterian animals. Evol Dev 2016; 17:255-7. [PMID: 26372059 DOI: 10.1111/ede.12137] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Markus Friedrich
- Department of Biological Sciences, Wayne State University, 5047 Gullen Mall, Detroit, MI 48202, USA.,Department of Anatomy and Cell Biology, Wayne State University, School of Medicine, 540 East Canfield Avenue, Detroit, MI 48201, USA
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18
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Meyer-Rochow VB. Compound eyes of insects and crustaceans: Some examples that show there is still a lot of work left to be done. INSECT SCIENCE 2015; 22:461-481. [PMID: 24574199 DOI: 10.1111/1744-7917.12117] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 01/10/2014] [Indexed: 06/03/2023]
Abstract
Similarities and differences between the 2 main kinds of compound eye (apposition and superposition) are briefly explained before several promising topics for research on compound eyes are being introduced. Research on the embryology and molecular control of the development of the insect clear-zone eye with superposition optics is one of the suggestions, because almost all of the developmental work on insect eyes in the past has focused on eyes with apposition optics. Age- and habitat-related ultrastructural studies of the retinal organization are another suggestion and the deer cad Lipoptena cervi, which has an aerial phase during which it is winged followed by a several months long parasitic phase during which it is wingless, is mentioned as a candidate species. Sexual dimorphism expressing itself in many species as a difference in eye structure and function provides another promising field for compound eye researchers and so is a focus on compound eye miniaturization in very small insects, especially those that are aquatic and belong to species, in which clear-zone eyes are diagnostic or are tiny insects that are not aquatic, but belong to taxa like the Diptera for instance, in which open rather than closed rhabdoms are the rule. Structures like interommatidial hairs and glands as well as corneal microridges are yet another field that could yield interesting results and in the past has received insufficient consideration. Finally, the dearth of information on distance vision and depth perception is mentioned and a plea is made to examine the photic environment inside the foam shelters of spittle bugs, chrysales of pupae and other structures shielding insects and crustaceans.
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19
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Mahato S, Morita S, Tucker AE, Liang X, Jackowska M, Friedrich M, Shiga Y, Zelhof AC. Common transcriptional mechanisms for visual photoreceptor cell differentiation among Pancrustaceans. PLoS Genet 2014; 10:e1004484. [PMID: 24991928 PMCID: PMC4084641 DOI: 10.1371/journal.pgen.1004484] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Accepted: 05/16/2014] [Indexed: 12/27/2022] Open
Abstract
A hallmark of visual rhabdomeric photoreceptors is the expression of a rhabdomeric opsin and uniquely associated phototransduction molecules, which are incorporated into a specialized expanded apical membrane, the rhabdomere. Given the extensive utilization of rhabdomeric photoreceptors in the eyes of protostomes, here we address whether a common transcriptional mechanism exists for the differentiation of rhabdomeric photoreceptors. In Drosophila, the transcription factors Pph13 and Orthodenticle (Otd) direct both aspects of differentiation: rhabdomeric opsin transcription and rhabdomere morphogenesis. We demonstrate that the orthologs of both proteins are expressed in the visual systems of the distantly related arthropod species Tribolium castaneum and Daphnia magna and that their functional roles are similar in these species. In particular, we establish that the Pph13 homologs have the ability to bind a subset of Rhodopsin core sequence I sites and that these sites are present in key phototransduction genes of both Tribolium and Daphnia. Furthermore, Pph13 and Otd orthologs are capable of executing deeply conserved functions of photoreceptor differentiation as evidenced by the ability to rescue their respective Drosophila mutant phenotypes. Pph13 homologs are equivalent in their ability to direct both rhabdomere morphogenesis and opsin expression within Drosophila, whereas Otd paralogs demonstrate differential abilities to regulate photoreceptor differentiation. Finally, loss-of-function analyses in Tribolium confirm the conserved requirement of Pph13 and Otd in regulating both rhabdomeric opsin transcription and rhabdomere morphogenesis. Taken together, our data identify components of a regulatory framework for rhabdomeric photoreceptor differentiation in Pancrustaceans, providing a foundation for defining ancestral regulatory modules of rhabdomeric photoreceptor differentiation. Visual systems are populated by one of two fundamental types of photoreceptors, ciliary and rhabdomeric. Each photoreceptor type is defined by the opsin molecule expressed and the final morphological form adapted to house the phototransduction machinery. Here we address whether a common transcriptional mechanisms exists for the differentiation of rhabdomeric photoreceptors. We demonstrate that orthologs of two Drosophila (fruit fly) transcription factors, Pph13 and Orthodenticle, are expressed in photoreceptors of Pancrustaceans, Tribolium (red flour beetle) and Daphnia (water flea), and are capable of executing conserved functions of rhabdomeric photoreceptor differentiation. In particular, Tribolium and Daphnia orthologs are capable of substituting and rescuing the photoreceptor differentiation defects observed in their corresponding Drosophila mutants. Furthermore, loss of function analysis in Tribolium of both Pph13 and orthodenticle genes demonstrate they regulate opsin transcription and morphogenesis of the photoreceptor apical membrane. Our data illuminate a framework for rhabdomeric photoreceptor differentiation and provide the foundation for defining the ancestral regulatory modules for rhabdomeric differentiation and potential modifications that underlie the functional diversity observed in rhabdomeric photoreceptors.
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Affiliation(s)
- Simpla Mahato
- Department of Biology, Indiana University, Bloomington, Indiana, United States of America
| | - Shinichi Morita
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo, Japan
| | - Abraham E. Tucker
- Department of Biology, Southern Arkansas University, Magnolia, Arkansas, United States of America
| | - Xulong Liang
- Department of Biology, Indiana University, Bloomington, Indiana, United States of America
| | - Magdalena Jackowska
- Department of Biological Sciences, Wayne State University, Detroit, Michigan, United States of America
| | - Markus Friedrich
- Department of Biological Sciences, Wayne State University, Detroit, Michigan, United States of America
- Department of Anatomy and Cell Biology, Wayne State University, School of Medicine, Detroit, Michigan, United States of America
| | - Yasuhiro Shiga
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo, Japan
| | - Andrew C. Zelhof
- Department of Biology, Indiana University, Bloomington, Indiana, United States of America
- * E-mail:
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20
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Speiser DI, Lampe RI, Lovdahl VR, Carrillo-Zazueta B, Rivera AS, Oakley TH. Evasion of Predators Contributes to the Maintenance of Male Eyes in Sexually Dimorphic Euphilomedes Ostracods (Crustacea). Integr Comp Biol 2013; 53:78-88. [DOI: 10.1093/icb/ict025] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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21
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Takagi A, Kurita K, Terasawa T, Nakamura T, Bando T, Moriyama Y, Mito T, Noji S, Ohuchi H. Functional analysis of the role of eyes absent and sine oculis in the developing eye of the cricket Gryllus bimaculatus. Dev Growth Differ 2012; 54:227-40. [PMID: 22348272 DOI: 10.1111/j.1440-169x.2011.01325.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
In the cricket Gryllus bimaculatus, a hemimetabolous insect, the compound eyes begin to form in the embryo and increase 5-6 fold in size during the postembryonic development of the nymphal stage. Retinal stem cells in the anteroventral proliferation zone (AVPZ) of the nymphal eye proliferate to increase retinal progenitors, which then differentiate to form new ommatidia in the anterior region of the eye. However, mechanisms underlying this type of eye formation have not been well elucidated yet. Here, we found that the homologues of the retinal determination transcription factor genes of eyes absent (eya) and sine oculis (so) are expressed during the cricket embryonic eye formation. eya is also expressed intensely in the AVPZ of the nymphal eye. To explore their functions, we performed knockdown by RNA interference (RNAi). Knockdown of Gb'eya resulted in loss of the embryonic eye. In the nymphal eye, RNAi against Gb'eya or Gb'so impaired retinal morphology by apparently transforming cornea structures into head cuticle. These results imply that Gb'eya and Gb'so are essential for the differentiation of the retinal progenitor cells and maintaining retinal structures during eye development.
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Affiliation(s)
- Akira Takagi
- Department of Life Systems, Institute of Technology and Science, University of Tokushima, 2-1 Minami-Jyosanjima-cho, Tokushima City 770-8506, Japan
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22
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Trautwein MD, Wiegmann BM, Beutel R, Kjer KM, Yeates DK. Advances in insect phylogeny at the dawn of the postgenomic era. ANNUAL REVIEW OF ENTOMOLOGY 2012; 57:449-468. [PMID: 22149269 DOI: 10.1146/annurev-ento-120710-100538] [Citation(s) in RCA: 142] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Most species on Earth are insects and thus, understanding their evolutionary relationships is key to understanding the evolution of life. Insect relationships are increasingly well supported, due largely to technological advances in molecular sequencing and phylogenetic computational analysis. In this postgenomic era, insect systematics will be furthered best by integrative methods aimed at hypothesis corroboration from molecular, morphological, and paleontological evidence. This review of the current consensus of insect relationships provides a foundation for comparative study and offers a framework to evaluate incoming genomic evidence. Notable recent phylogenetic successes include the resolution of Holometabola, including the identification of the enigmatic Strepsiptera as a beetle relative and the early divergence of Hymenoptera; the recognition of hexapods as a crustacean lineage within Pancrustacea; and the elucidation of Dictyoptera orders, with termites placed as social cockroaches. Regions of the tree that require further investigation include the earliest winged insects (Palaeoptera) and Polyneoptera (orthopteroid lineages).
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Affiliation(s)
- Michelle D Trautwein
- Department of Entomology, North Carolina State University, Raleigh, North Carolina 27695, USA.
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23
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Friedrich M, Chen R, Daines B, Bao R, Caravas J, Rai PK, Zagmajster M, Peck SB. Phototransduction and clock gene expression in the troglobiont beetle Ptomaphagus hirtus of Mammoth cave. J Exp Biol 2011; 214:3532-41. [DOI: 10.1242/jeb.060368] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
SUMMARY
Obligatory cave species exhibit dramatic trait modifications such as eye reduction, loss of pigmentation and an increase in touch receptors. As molecular studies of cave adaptation have largely concentrated on vertebrate models, it is not yet possible to probe for genetic universalities underlying cave adaptation. We have therefore begun to study the strongly cave-adapted small carrion beetle Ptomaphagus hirtus. For over 100 years, this flightless signature inhabitant of Mammoth Cave, the world's largest known cave system, has been considered blind despite the presence of residual lens structures. By deep sequencing of the adult head transcriptome, we discovered the transcripts of all core members of the phototransduction protein machinery. Combined with the absence of transcripts of select structural photoreceptor and eye pigmentation genes, these data suggest a reduced but functional visual system in P. hirtus. This conclusion was corroborated by a negative phototactic response of P. hirtus in light/dark choice tests. We further detected the expression of the complete circadian clock gene network in P. hirtus, raising the possibility of a role of light sensation in the regulation of oscillating processes. We speculate that P. hirtus is representative of a large number of animal species with highly reduced but persisting visual capacities in the twilight zone of the subterranean realm. These can now be studied on a broad comparative scale given the efficiency of transcript discovery by next-generation sequencing.
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Affiliation(s)
- Markus Friedrich
- Department of Biological Sciences, Wayne State University, 5047 Gullen Mall, Detroit, MI 48202, USA
- Department of Anatomy and Cell Biology, Wayne State University, School of Medicine, 540 East Canfield Avenue, Detroit, MI 48201, USA
| | - Rui Chen
- Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
- Program in Developmental Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
- Structural and Computational Biology and Molecular Biophysics Graduate Program, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Bryce Daines
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Riyue Bao
- Department of Biological Sciences, Wayne State University, 5047 Gullen Mall, Detroit, MI 48202, USA
| | - Jason Caravas
- Department of Biological Sciences, Wayne State University, 5047 Gullen Mall, Detroit, MI 48202, USA
| | - Puneet K. Rai
- Department of Biological Sciences, Wayne State University, 5047 Gullen Mall, Detroit, MI 48202, USA
| | - Maja Zagmajster
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Vecna pot 111, SI-1000 Ljubljana, Slovenia
| | - Stewart B. Peck
- Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, ON, Canada, K1S 5B6
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24
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Friedrich M, Caravas J. New insights from hemichordate genomes: prebilaterian origin and parallel modifications in the paired domain of the Pax gene eyegone. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2011; 316:387-92. [PMID: 21506261 DOI: 10.1002/jez.b.21412] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2011] [Revised: 02/26/2011] [Accepted: 03/02/2011] [Indexed: 11/08/2022]
Abstract
The evolutionary origin of the Drosophila Pax transcription factor gene eyegone (eyg) has long been enigmatic owing to the failure in detecting orthologs in other species and the unusual N-terminal truncation of the DNA-binding paired domain (PD). Based on the discovery of eyg orthologs in representatives of hemichordate phyla, we show that the origin of eyg predated metazoan diversification and that the PD experienced similar but independent N-terminal modifications in the lineages to sea urchins and insects. Sequence conservation patterns further raise the possibility of persisting functionality in the N-terminal PD of strongly modified eyg orthologs. Finally, we note that the evolutionary histories of eyg and the vertebrate Pax6 isoform 5a, which have been considered functional homologs, are not correlated. Taken together, these findings identify Drosophila eyg as the baptizing member of an ancient Pax gene subfamily and recommend abandoning its classification as Pax6(5a)-related gene.
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Affiliation(s)
- Markus Friedrich
- Department of Biological Sciences, Wayne State University, Detroit, Michigan 48202, USA.
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25
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Datta RR, Cruickshank T, Kumar JP. Differential selection within the Drosophila retinal determination network and evidence for functional divergence between paralog pairs. Evol Dev 2011; 13:58-71. [PMID: 21210943 DOI: 10.1111/j.1525-142x.2010.00456.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The retinal determination (RD) network in Drosophila comprises 14 known nuclear proteins that include DNA-binding proteins, transcriptional coactivators, kinases, and phosphatases. The composition of the network varies considerably throughout the animal kingdom, with the network in several basal insects having fewer members and with vertebrates having potentially significantly higher numbers of RD genes. One important contributing factor for the variation in gene number within the network is gene duplication. For example, 10 members of the RD network in Drosophila are derived from duplication events. Here we present an analysis of the coding regions of the five pairs of duplicate genes from within the RD network of several different Drosophila species. We demonstrate that there is differential selection across the coding regions of all RD genes. Additionally, some of the most significant differences in ratios of non-silent-to-silent site substitutions (d(N)/d(S)) between paralog pairs are found within regions that have no ascribed function. Previous structure/function analyses of several duplicate genes have identified areas within one gene that contain novel activities when compared with its paralog. The evolutionary analysis presented here identifies these same areas in the paralogs as being under high levels of relaxed selection. We suggest that sequence divergence between paralogs and selection signatures can be used as a reasonable predictor of functional changes in rapidly evolving motifs.
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Affiliation(s)
- Rhea R Datta
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
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26
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ZarinKamar N, Yang X, Bao R, Friedrich F, Beutel R, Friedrich M. The Pax gene eyegone facilitates repression of eye development in Tribolium. EvoDevo 2011; 2:8. [PMID: 21463500 PMCID: PMC3082225 DOI: 10.1186/2041-9139-2-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2011] [Accepted: 04/04/2011] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND The Pax transcription factor gene eyegone (eyg) participates in many developmental processes in Drosophila, including the Notch signaling activated postembryonic growth of the eye primordium, global development of the adult head and the development of the antenna. In contrast to other Pax genes, the functional conservation of eyg in species other than Drosophila has not yet been explored. RESULTS We investigated the role of eyg during the postembryonic development of the red flour beetle Tribolium castaneum. Our results indicate conserved roles in antennal but not in eye development. Besides segmentation defects in the antenna, Tribolium eyg knockdown animals were characterized by eye enlargement due to the formation of surplus ommatidia at the central anterior edge of the compound eye. This effect resulted from the failure of the developing gena to locally repress retinal differentiation, which underlies the formation of the characteristic anterior notch in the Tribolium eye. Neither varying the induction time point of eyg knockdown nor knocking down components of the Janus kinase/Signal Transducer and Activators of Transcription signaling pathway in combination with eyg reduced eye size like in Drosophila. CONCLUSIONS Taken together, expression and knockdown data suggest that Tribolium eyg serves as a competence factor that facilitates the repression of retinal differentiation in response to an unknown signal produced in the developing gena. At the comparative level, our findings reveal diverged roles of eyg associated with the evolution of different modes of postembryonic head development in endopterygote insects as well as diversified head morphologies in darkling beetles.
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Affiliation(s)
- Nazanin ZarinKamar
- Department of Biological Sciences, Wayne State University, 5047 Gullen Mall, Detroit, MI 48202, USA
| | - Xiaoyun Yang
- Department of Biological Sciences, Wayne State University, 5047 Gullen Mall, Detroit, MI 48202, USA
| | - Riyue Bao
- Department of Biological Sciences, Wayne State University, 5047 Gullen Mall, Detroit, MI 48202, USA
| | - Frank Friedrich
- Institut fur Spezielle Zoologie und Evolutionsbiologie, Friedrich Schiller Universitat Jena, Erbertstrasse 1, 07743 Jena, Germany
| | - Rolf Beutel
- Institut fur Spezielle Zoologie und Evolutionsbiologie, Friedrich Schiller Universitat Jena, Erbertstrasse 1, 07743 Jena, Germany
| | - Markus Friedrich
- Department of Biological Sciences, Wayne State University, 5047 Gullen Mall, Detroit, MI 48202, USA.,Department of Anatomy and Cell Biology, Wayne State University, School of Medicine, 540 East Canfield Avenue, Detroit, MI 48201, USA
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Amore G, Casares F. Size matters: the contribution of cell proliferation to the progression of the specification Drosophila eye gene regulatory network. Dev Biol 2010; 344:569-77. [PMID: 20599903 DOI: 10.1016/j.ydbio.2010.06.015] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2010] [Revised: 06/03/2010] [Accepted: 06/08/2010] [Indexed: 01/02/2023]
Abstract
Organ development is a complex process in which the activity of scores of interacting transcription factors and signaling pathways need to be integrated with proliferative growth. Developmental gene regulatory networks (GRNs) allow capturing essential regulatory pathways at a systems-level and provide an effective way of approaching such complexity. However typical GRNs studies focus on very early embryonic stages (usually pre-gastrulation) or late stages, when there is little or no cell proliferation, and therefore do not consider how organ growth is integrated in the developmental process. This can be conveniently investigated in the Drosophila melanogaster eye primordium. Here we present a working model meant to illustrate how during a critical period, the second larval stage, changes in cells' proliferative pattern are coordinated with the initiation of the Retinal Determination (RD) gene program. Such changes are regulated in response to two different sources of signal (Wnt1/wg and BMP2/4/dpp) produced by the anterior and posterior ends of the primordium, respectively. The dpp signaling is necessary to trigger the RD program. However in order for it to be effective, cells receiving Dpp have to be out of the wg signaling range. This is obtained thanks to the proliferative growth that precedes the onset of RD expression. With this network model many of the gene regulatory steps previously known to participate in growth and patterning are linked. Analysis of the model highlights a few essential regulatory principles, as well as poses new questions. In addition, these principles might operate during the growth and patterning of other organs.
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Affiliation(s)
- Gabriele Amore
- Animal Physiology and Evolutionary Laboratory-Stazione Zoologica Anton Dohrn, Napoli, Italy.
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Rivera AS, Pankey MS, Plachetzki DC, Villacorta C, Syme AE, Serb JM, Omilian AR, Oakley TH. Gene duplication and the origins of morphological complexity in pancrustacean eyes, a genomic approach. BMC Evol Biol 2010; 10:123. [PMID: 20433736 PMCID: PMC2888819 DOI: 10.1186/1471-2148-10-123] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2009] [Accepted: 04/30/2010] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Duplication and divergence of genes and genetic networks is hypothesized to be a major driver of the evolution of complexity and novel features. Here, we examine the history of genes and genetic networks in the context of eye evolution by using new approaches to understand patterns of gene duplication during the evolution of metazoan genomes. We hypothesize that 1) genes involved in eye development and phototransduction have duplicated and are retained at higher rates in animal clades that possess more distinct types of optical design; and 2) genes with functional relationships were duplicated and lost together, thereby preserving genetic networks. To test these hypotheses, we examine the rates and patterns of gene duplication and loss evident in 19 metazoan genomes, including that of Daphnia pulex - the first completely sequenced crustacean genome. This is of particular interest because the pancrustaceans (hexapods+crustaceans) have more optical designs than any other major clade of animals, allowing us to test specifically whether the high amount of disparity in pancrustacean eyes is correlated with a higher rate of duplication and retention of vision genes. RESULTS Using protein predictions from 19 metazoan whole-genome projects, we found all members of 23 gene families known to be involved in eye development or phototransduction and deduced their phylogenetic relationships. This allowed us to estimate the number and timing of gene duplication and loss events in these gene families during animal evolution. When comparing duplication/retention rates of these genes, we found that the rate was significantly higher in pancrustaceans than in either vertebrates or non-pancrustacean protostomes. Comparing patterns of co-duplication across Metazoa showed that while these eye-genes co-duplicate at a significantly higher rate than those within a randomly shuffled matrix, many genes with known functional relationships in model organisms did not co-duplicate more often than expected by chance. CONCLUSIONS Overall, and when accounting for factors such as differential rates of whole-genome duplication in different groups, our results are broadly consistent with the hypothesis that genes involved in eye development and phototransduction duplicate at a higher rate in Pancrustacea, the group with the greatest variety of optical designs. The result that these genes have a significantly high number of co-duplications and co-losses could be influenced by shared functions or other unstudied factors such as synteny. Since we did not observe co-duplication/co-loss of genes for all known functional modules (e.g. specific regulatory networks), the interactions among suites of known co-functioning genes (modules) may be plastic at the temporal scale of analysis performed here. Other factors in addition to gene duplication - such as cis-regulation, heterotopy, and co-option - are also likely to be strong factors in the diversification of eye types.
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