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Zhou C, Yang MJ, Hu Z, Shi P, Li YR, Guo YJ, Zhang T, Song H. Molecular evidence for the adaptive evolution in euryhaline bivalves. MARINE ENVIRONMENTAL RESEARCH 2023; 192:106240. [PMID: 37944349 DOI: 10.1016/j.marenvres.2023.106240] [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: 08/15/2023] [Revised: 09/26/2023] [Accepted: 10/23/2023] [Indexed: 11/12/2023]
Abstract
Marine bivalves inhabiting intertidal and estuarine areas are frequently exposed to salinity stress due to persistent rainfall and drought. Through prolonged adaptive evolution, numerous bivalves have developed eurysalinity, which are capable of tolerating a wide range of salinity fluctuations through the sophisticated regulation of physiological metabolism. Current research has predominantly focused on investigating the physiological responses of bivalves to salinity stress, leaving a significant gap in our understanding of the adaptive evolutionary characteristics in euryhaline bivalves. Here, comparative genomics analyses were performed in two groups of bivalve species, including 7 euryhaline species and 5 stenohaline species. We identified 24 significantly expanded gene families and 659 positively selected genes in euryhaline bivalves. A significant co-expansion of solute carrier family 23 (SLC23) facilitates the transmembrane transport of ascorbic acids in euryhaline bivalves. Positive selection of antioxidant genes, such as GST and TXNRD, augments the capacity of active oxygen species (ROS) scavenging under salinity stress. Additionally, we found that the positively selected genes were significantly enriched in KEGG pathways associated with carbohydrates, lipids and amino acids metabolism (ALDH, ADH, and GLS), as well as GO terms related to transmembrane transport and inorganic anion transport (SLC22, CLCND, and VDCC). Positive selection of MCT might contribute to prevent excessive accumulation of intracellular lactic acids during anaerobic metabolism. Positive selection of PLA2 potentially promote the removal of damaged membranes lipids under salinity stress. Our findings suggest that adaptive evolution has occurred in osmoregulation, ROS scavenging, energy metabolism, and membrane lipids adjustments in euryhaline bivalves. This study enhances our understanding of the molecular mechanisms underlying the remarkable salinity adaption of euryhaline bivalves.
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Affiliation(s)
- Cong Zhou
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China; CAS Engineering Laboratory for Marine Ranching, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; University of Chinese Academy of Sciences, Beijing, 100049, China; Shandong Province Key Laboratory of Experimental Marine Biology, Qingdao, 266071, China
| | - Mei-Jie Yang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China; CAS Engineering Laboratory for Marine Ranching, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Shandong Province Key Laboratory of Experimental Marine Biology, Qingdao, 266071, China
| | - Zhi Hu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China; CAS Engineering Laboratory for Marine Ranching, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Shandong Province Key Laboratory of Experimental Marine Biology, Qingdao, 266071, China
| | - Pu Shi
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China; CAS Engineering Laboratory for Marine Ranching, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; University of Chinese Academy of Sciences, Beijing, 100049, China; Shandong Province Key Laboratory of Experimental Marine Biology, Qingdao, 266071, China
| | - Yong-Ren Li
- Tianjin Key Laboratory of Aqua-ecology and Aquaculture, Fisheries College, Tianjin Agricultural University, Tianjin, 300384, China
| | - Yong-Jun Guo
- Tianjin Key Laboratory of Aqua-ecology and Aquaculture, Fisheries College, Tianjin Agricultural University, Tianjin, 300384, China
| | - Tao Zhang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China; CAS Engineering Laboratory for Marine Ranching, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Shandong Province Key Laboratory of Experimental Marine Biology, Qingdao, 266071, China.
| | - Hao Song
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China; CAS Engineering Laboratory for Marine Ranching, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Shandong Province Key Laboratory of Experimental Marine Biology, Qingdao, 266071, China.
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Teng Z, Huo M, Zhou Y, Zhou Y, Liu Y, Lin Y, Zhang Q, Zhang Z, Wan F, Zhou H. Circadian Activity and Clock Genes in Pachycrepoideus vindemmiae: Implications for Field Applications and Circadian Clock Mechanisms of Parasitoid Wasps. INSECTS 2023; 14:insects14050486. [PMID: 37233114 DOI: 10.3390/insects14050486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Revised: 05/10/2023] [Accepted: 05/11/2023] [Indexed: 05/27/2023]
Abstract
Despite the importance of circadian rhythms in insect behavior, our understanding of circadian activity and the molecular oscillatory mechanism in parasitoid wasp circadian clocks is limited. In this study, behavioral activities expected to be under the control of the endogenous circadian system were characterized in an ectoparasitoid wasp, Pachycrepoideus vindemmiae. Most adults exhibited emergence between late night and early morning, while mating only occurred during the daytime, with a peak at midday. Oviposition had three peaks in the early morning, late day, or early night and late night. Additionally, we identified eight putative clock genes from P. vindemmiae. The quantitative PCR (qPCR) results indicate that most clock genes showed significant rhythmic expressions. Our comparative analysis of clock genes in P. vindemmiae and 43 other parasitoid wasps revealed that none of the wasps possessed the timeless and cry1 genes commonly found in some other insect species, suggesting that the circadian clock system in parasitoid wasps is distinct from that in other non-Hymenoptera insects such as Drosophila. Thus, this study attempted to build the first hypothetical circadian clock model for a parasitoid wasp, thus generating hypotheses and providing a platform for the future functional characterization of P. vindemmiae clock genes as well as those of other parasitoid wasps. Finally, these findings on P. vindemmiae circadian activity will aid the development of effective field release programs for biological control, which can be tested under field conditions.
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Affiliation(s)
- Ziwen Teng
- Shandong Engineering Research Center for Environment-Friendly Agricultural Pest Management, Shandong Province Laboratory for Biological Invasions and Ecological Security, China-Australia Cooperative Research Center for Crop Health and Biological Invasions, College of Plant Health & Medicine, Qingdao Agricultural University, Qingdao 266109, China
| | - Mengran Huo
- Shandong Engineering Research Center for Environment-Friendly Agricultural Pest Management, Shandong Province Laboratory for Biological Invasions and Ecological Security, China-Australia Cooperative Research Center for Crop Health and Biological Invasions, College of Plant Health & Medicine, Qingdao Agricultural University, Qingdao 266109, China
| | - Yanan Zhou
- Shandong Engineering Research Center for Environment-Friendly Agricultural Pest Management, Shandong Province Laboratory for Biological Invasions and Ecological Security, China-Australia Cooperative Research Center for Crop Health and Biological Invasions, College of Plant Health & Medicine, Qingdao Agricultural University, Qingdao 266109, China
| | - Yuqi Zhou
- Shandong Engineering Research Center for Environment-Friendly Agricultural Pest Management, Shandong Province Laboratory for Biological Invasions and Ecological Security, China-Australia Cooperative Research Center for Crop Health and Biological Invasions, College of Plant Health & Medicine, Qingdao Agricultural University, Qingdao 266109, China
| | - Yunjie Liu
- Shandong Engineering Research Center for Environment-Friendly Agricultural Pest Management, Shandong Province Laboratory for Biological Invasions and Ecological Security, China-Australia Cooperative Research Center for Crop Health and Biological Invasions, College of Plant Health & Medicine, Qingdao Agricultural University, Qingdao 266109, China
| | - Yan Lin
- Shandong Engineering Research Center for Environment-Friendly Agricultural Pest Management, Shandong Province Laboratory for Biological Invasions and Ecological Security, China-Australia Cooperative Research Center for Crop Health and Biological Invasions, College of Plant Health & Medicine, Qingdao Agricultural University, Qingdao 266109, China
| | - Qi Zhang
- Shandong Engineering Research Center for Environment-Friendly Agricultural Pest Management, Shandong Province Laboratory for Biological Invasions and Ecological Security, China-Australia Cooperative Research Center for Crop Health and Biological Invasions, College of Plant Health & Medicine, Qingdao Agricultural University, Qingdao 266109, China
| | - Zhiqi Zhang
- Shandong Engineering Research Center for Environment-Friendly Agricultural Pest Management, Shandong Province Laboratory for Biological Invasions and Ecological Security, China-Australia Cooperative Research Center for Crop Health and Biological Invasions, College of Plant Health & Medicine, Qingdao Agricultural University, Qingdao 266109, China
| | - Fanghao Wan
- Shandong Engineering Research Center for Environment-Friendly Agricultural Pest Management, Shandong Province Laboratory for Biological Invasions and Ecological Security, China-Australia Cooperative Research Center for Crop Health and Biological Invasions, College of Plant Health & Medicine, Qingdao Agricultural University, Qingdao 266109, China
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Hongxu Zhou
- Shandong Engineering Research Center for Environment-Friendly Agricultural Pest Management, Shandong Province Laboratory for Biological Invasions and Ecological Security, China-Australia Cooperative Research Center for Crop Health and Biological Invasions, College of Plant Health & Medicine, Qingdao Agricultural University, Qingdao 266109, China
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Reynolds M, de Oliveira L, Vosburg C, Paris T, Massimino C, Norus J, Ortiz Y, Espino M, Davis N, Masse R, Neiman A, Holcomb R, Gervais K, Kemp M, Hoang M, Shippy TD, Hosmani PS, Flores-Gonzalez M, Pelz-Stelinski K, Qureshi JA, Mueller LA, Hunter WB, Benoit JB, Brown SJ, D’Elia T, Saha S. Annotation of putative circadian rhythm-associated genes in Diaphorina citri (Hemiptera: Liviidae). GIGABYTE 2022; 2022:gigabyte48. [PMID: 36824532 PMCID: PMC9662589 DOI: 10.46471/gigabyte.48] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Accepted: 03/28/2022] [Indexed: 11/09/2022] Open
Abstract
The circadian rhythm involves multiple genes that generate an internal molecular clock, allowing organisms to anticipate environmental conditions produced by the Earth's rotation on its axis. Here, we present the results of the manual curation of 27 genes that are associated with circadian rhythm in the genome of Diaphorina citri, the Asian citrus psyllid. This insect is the vector for the bacterial pathogen Candidatus Liberibacter asiaticus (CLas), the causal agent of citrus greening disease (Huanglongbing). This disease severely affects citrus industries and has drastically decreased crop yields worldwide. Based on cry1 and cry2 identified in the psyllid genome, D. citri likely possesses a circadian model similar to the lepidopteran butterfly, Danaus plexippus. Manual annotation will improve the quality of circadian rhythm gene models, allowing the future development of molecular therapeutics, such as RNA interference or antisense technologies, to target these genes to disrupt the psyllid biology.
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Affiliation(s)
- Max Reynolds
- Indian River State College, Fort Pierce, FL 34981, USA
| | | | - Chad Vosburg
- Indian River State College, Fort Pierce, FL 34981, USA,Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, University Park, PA 16802, USA
| | - Thomson Paris
- Entomology and Nematology Department, University of Florida, North Florida Research and Education Center, Research Road, Quincy 32351, Florida, USA
| | | | - Jordan Norus
- Indian River State College, Fort Pierce, FL 34981, USA
| | - Yasmin Ortiz
- Indian River State College, Fort Pierce, FL 34981, USA
| | | | - Nina Davis
- Indian River State College, Fort Pierce, FL 34981, USA
| | - Ron Masse
- Indian River State College, Fort Pierce, FL 34981, USA
| | - Alan Neiman
- Indian River State College, Fort Pierce, FL 34981, USA
| | | | - Kylie Gervais
- Indian River State College, Fort Pierce, FL 34981, USA
| | - Melissa Kemp
- Indian River State College, Fort Pierce, FL 34981, USA
| | - Maria Hoang
- Indian River State College, Fort Pierce, FL 34981, USA
| | - Teresa D. Shippy
- Division of Biology, Kansas State University, Manhattan, KS 66506, USA
| | | | | | - Kirsten Pelz-Stelinski
- Department of Entomology and Nematology, University of Florida, Lake Alfred, FL 33850, USA
| | - Jawwad A. Qureshi
- Indian River Research and Education Center, University of Florida, IFAS, 2199 South Rock Road, Fort Pierce, FL 34945-3138, USA,Southwest Florida Research and Education Center, University of Florida, IFAS, 2685 State Road 29 North, Immokalee, FL 34142, USA
| | | | - Wayne B. Hunter
- USDA-ARS, US Horticultural Research Laboratory, Fort Pierce, FL 34945, USA
| | - Joshua B. Benoit
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45221, USA
| | - Susan J. Brown
- Division of Biology, Kansas State University, Manhattan, KS 66506, USA
| | - Tom D’Elia
- Indian River State College, Fort Pierce, FL 34981, USA
| | - Surya Saha
- Boyce Thompson Institute, Ithaca, NY 14853, USA,Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, AZ 85721, USA, Corresponding author. E-mail:
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4
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Kohli S, Gulati P, Narang A, Maini J, Shamsudheen KV, Pandey R, Scaria V, Sivasubbu S, Brahmachari V. Genome and transcriptome analysis of the mealybug Maconellicoccus hirsutus: Correlation with its unique phenotypes. Genomics 2021; 113:2483-2494. [PMID: 34022346 DOI: 10.1016/j.ygeno.2021.05.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Revised: 04/02/2021] [Accepted: 05/17/2021] [Indexed: 11/27/2022]
Abstract
Mealybugs are aggressive pests with world-wide distribution and are suitable for the study of different phenomena like genomic imprinting and epigenetics. Genomic approaches facilitate these studies in absence of robust genetics in this system. We sequenced, de novo assembled, annotated Maconellicoccus hirsutus genome. We carried out comparative genomics it with four mealybug and eight other insect species, to identify expanded, specific and contracted gene classes that relate to pesticide and desiccation resistance. We identified horizontally transferred genes adding to the mutualism between the mealybug and its endosymbionts. Male and female transcriptome analysis indicates differential expression of metabolic pathway genes correlating with their physiology and the genes for sexual dimorphism. The significantly lower expression of endosymbiont genes in males relates to the depletion of endosymbionts in males during development.
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Affiliation(s)
- Surbhi Kohli
- Dr.B.R.Ambedkar Center for Biomedical Research, University of Delhi, Delhi, India
| | - Parul Gulati
- Dr.B.R.Ambedkar Center for Biomedical Research, University of Delhi, Delhi, India
| | - Ankita Narang
- Dr.B.R.Ambedkar Center for Biomedical Research, University of Delhi, Delhi, India.
| | - Jayant Maini
- Dr.B.R.Ambedkar Center for Biomedical Research, University of Delhi, Delhi, India
| | - K V Shamsudheen
- CSIR-Institute of Genomics and Integrative Biology, Delhi, India
| | - Rajesh Pandey
- CSIR-Institute of Genomics and Integrative Biology, Delhi, India
| | - Vinod Scaria
- CSIR-Institute of Genomics and Integrative Biology, Delhi, India
| | | | - Vani Brahmachari
- Dr.B.R.Ambedkar Center for Biomedical Research, University of Delhi, Delhi, India.
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5
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de Paula Freitas FC, Lourenço AP, Nunes FMF, Paschoal AR, Abreu FCP, Barbin FO, Bataglia L, Cardoso-Júnior CAM, Cervoni MS, Silva SR, Dalarmi F, Del Lama MA, Depintor TS, Ferreira KM, Gória PS, Jaskot MC, Lago DC, Luna-Lucena D, Moda LM, Nascimento L, Pedrino M, Oliveira FR, Sanches FC, Santos DE, Santos CG, Vieira J, Barchuk AR, Hartfelder K, Simões ZLP, Bitondi MMG, Pinheiro DG. The nuclear and mitochondrial genomes of Frieseomelitta varia - a highly eusocial stingless bee (Meliponini) with a permanently sterile worker caste. BMC Genomics 2020; 21:386. [PMID: 32493270 PMCID: PMC7268684 DOI: 10.1186/s12864-020-06784-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 05/14/2020] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Most of our understanding on the social behavior and genomics of bees and other social insects is centered on the Western honey bee, Apis mellifera. The genus Apis, however, is a highly derived branch comprising less than a dozen species, four of which genomically characterized. In contrast, for the equally highly eusocial, yet taxonomically and biologically more diverse Meliponini, a full genome sequence was so far available for a single Melipona species only. We present here the genome sequence of Frieseomelitta varia, a stingless bee that has, as a peculiarity, a completely sterile worker caste. RESULTS The assembly of 243,974,526 high quality Illumina reads resulted in a predicted assembled genome size of 275 Mb composed of 2173 scaffolds. A BUSCO analysis for the 10,526 predicted genes showed that these represent 96.6% of the expected hymenopteran orthologs. We also predicted 169,371 repetitive genomic components, 2083 putative transposable elements, and 1946 genes for non-coding RNAs, largely long non-coding RNAs. The mitochondrial genome comprises 15,144 bp, encoding 13 proteins, 22 tRNAs and 2 rRNAs. We observed considerable rearrangement in the mitochondrial gene order compared to other bees. For an in-depth analysis of genes related to social biology, we manually checked the annotations for 533 automatically predicted gene models, including 127 genes related to reproductive processes, 104 to development, and 174 immunity-related genes. We also performed specific searches for genes containing transcription factor domains and genes related to neurogenesis and chemosensory communication. CONCLUSIONS The total genome size for F. varia is similar to the sequenced genomes of other bees. Using specific prediction methods, we identified a large number of repetitive genome components and long non-coding RNAs, which could provide the molecular basis for gene regulatory plasticity, including worker reproduction. The remarkable reshuffling in gene order in the mitochondrial genome suggests that stingless bees may be a hotspot for mtDNA evolution. Hence, while being just the second stingless bee genome sequenced, we expect that subsequent targeting of a selected set of species from this diverse clade of highly eusocial bees will reveal relevant evolutionary signals and trends related to eusociality in these important pollinators.
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Affiliation(s)
- Flávia C. de Paula Freitas
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP Brazil
- Departamento de Biologia Celular e do Desenvolvimento, Instituto de Ciências Biomédicas, Universidade Federal de Alfenas, Alfenas, MG Brazil
| | - Anete P. Lourenço
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP Brazil
- Departamento de Ciências Biológicas, Faculdade de Ciências Biológicas e da Saúde, Universidade Federal dos Vales do Jequitinhonha e Mucuri, Diamantina, MG Brazil
| | - Francis M. F. Nunes
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP Brazil
- Departamento de Genética e Evolução, Centro de Ciências Biológicas e da Saúde, Universidade Federal de São Carlos, São Carlos, SP Brazil
| | | | - Fabiano C. P. Abreu
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP Brazil
| | - Fábio O. Barbin
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP Brazil
| | - Luana Bataglia
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP Brazil
| | - Carlos A. M. Cardoso-Júnior
- Departamento de Biologia Celular e Molecular e Bioagentes Patogênicos, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Av. Bandeirantes 3900, Ribeirão Preto, SP 14049-900 Brazil
| | - Mário S. Cervoni
- Departamento de Biologia Celular e Molecular e Bioagentes Patogênicos, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Av. Bandeirantes 3900, Ribeirão Preto, SP 14049-900 Brazil
| | - Saura R. Silva
- Departamento de Tecnologia, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista “Júlio de Mesquita Filho”, Jaboticabal, SP Brazil
| | - Fernanda Dalarmi
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP Brazil
| | - Marco A. Del Lama
- Departamento de Genética e Evolução, Centro de Ciências Biológicas e da Saúde, Universidade Federal de São Carlos, São Carlos, SP Brazil
| | - Thiago S. Depintor
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP Brazil
| | - Kátia M. Ferreira
- Departamento de Genética e Evolução, Centro de Ciências Biológicas e da Saúde, Universidade Federal de São Carlos, São Carlos, SP Brazil
| | - Paula S. Gória
- Departamento de Genética e Evolução, Centro de Ciências Biológicas e da Saúde, Universidade Federal de São Carlos, São Carlos, SP Brazil
| | - Michael C. Jaskot
- Departamento de Genética e Evolução, Centro de Ciências Biológicas e da Saúde, Universidade Federal de São Carlos, São Carlos, SP Brazil
| | - Denyse C. Lago
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP Brazil
| | - Danielle Luna-Lucena
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP Brazil
| | - Livia M. Moda
- Departamento de Biologia Celular e do Desenvolvimento, Instituto de Ciências Biomédicas, Universidade Federal de Alfenas, Alfenas, MG Brazil
| | - Leonardo Nascimento
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP Brazil
| | - Matheus Pedrino
- Departamento de Genética e Evolução, Centro de Ciências Biológicas e da Saúde, Universidade Federal de São Carlos, São Carlos, SP Brazil
| | - Franciene Rabiço Oliveira
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP Brazil
| | - Fernanda C. Sanches
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP Brazil
- Departamento de Genética e Evolução, Centro de Ciências Biológicas e da Saúde, Universidade Federal de São Carlos, São Carlos, SP Brazil
| | - Douglas E. Santos
- Departamento de Biologia Celular e Molecular e Bioagentes Patogênicos, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Av. Bandeirantes 3900, Ribeirão Preto, SP 14049-900 Brazil
| | - Carolina G. Santos
- Departamento de Biologia Celular e Molecular e Bioagentes Patogênicos, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Av. Bandeirantes 3900, Ribeirão Preto, SP 14049-900 Brazil
| | - Joseana Vieira
- Departamento de Biologia Celular e do Desenvolvimento, Instituto de Ciências Biomédicas, Universidade Federal de Alfenas, Alfenas, MG Brazil
| | - Angel R. Barchuk
- Departamento de Biologia Celular e do Desenvolvimento, Instituto de Ciências Biomédicas, Universidade Federal de Alfenas, Alfenas, MG Brazil
| | - Klaus Hartfelder
- Departamento de Biologia Celular e Molecular e Bioagentes Patogênicos, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Av. Bandeirantes 3900, Ribeirão Preto, SP 14049-900 Brazil
| | - Zilá L. P. Simões
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP Brazil
| | - Márcia M. G. Bitondi
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP Brazil
| | - Daniel G. Pinheiro
- Departamento de Tecnologia, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista “Júlio de Mesquita Filho”, Jaboticabal, SP Brazil
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6
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Li CJ, Yun XP, Yu XJ, Li B. Functional analysis of the circadian clock gene timeless in Tribolium castaneum. INSECT SCIENCE 2018; 25:418-428. [PMID: 28101904 DOI: 10.1111/1744-7917.12441] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Revised: 12/18/2016] [Accepted: 12/24/2016] [Indexed: 06/06/2023]
Abstract
Circadian rhythms are endogenous oscillations with a period of about 24 h driven by a circadian clock. So far, variable oscillators have been found in insects. To explore the circadian clock of Tribolium castaneum, we cloned the clock gene timeless (Tctimeless). Its open reading frame is 3240 bp in length and consists of 10 exons. Tctimeless is highly expressed in the late pupal stage. Tissue-specific expression analysis in late adult stages revealed high expression of Tctimeless in the head, epidermis, fat body and accessory glands. Silencing of Tctimeless by RNA interference (RNAi) at the late larval stages caused a failure to initiate eclosion. Tctimeless knockdown in late pupal stages led to a gender-independent decline in egg production and progeny survival. As a core clock gene, Tctimeless exhibited one expression peak in the middle of the circadian day. Knockdown of Tctimeless disrupted daily expression patterns of Tccycle, Tcclock, Tcperiod and itself, while Tctimeless and Tcperiod expression patterns over the circadian day were also perturbed when Tccycle or Tcclock is suppressed by RNAi. This study identified a complex transcriptional relationship among circadian clock genes in T. castaneum.
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Affiliation(s)
- Cheng-Jun Li
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
- Institute of Life Sciences, School of Food and Biological Engineering, Jiangsu University, Zhenjiang, Jiangsu Province, China
| | - Xiao-Pei Yun
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Xiao-Juan Yu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Bin Li
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
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Tvedte ES, Forbes AA, Logsdon JM. Retention of Core Meiotic Genes Across Diverse Hymenoptera. J Hered 2018; 108:791-806. [PMID: 28992199 DOI: 10.1093/jhered/esx062] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 07/13/2017] [Indexed: 12/20/2022] Open
Abstract
The cellular mechanisms of meiosis are critical for proper gamete formation in sexual organisms. Functional studies in model organisms have identified genes essential for meiosis, yet the extent to which this core meiotic machinery is conserved across non-model systems is not fully understood. Moreover, it is unclear whether deviation from canonical modes of sexual reproduction is accompanied by modifications in the genetic components involved in meiosis. We used a robust approach to identify and catalogue meiosis genes in Hymenoptera, an insect order typically characterized by haplodiploid reproduction. Using newly available genome data, we searched for 43 genes involved in meiosis in 18 diverse hymenopterans. Seven of eight genes with roles specific to meiosis were found across a majority of surveyed species, suggesting the preservation of core meiotic machinery in haplodiploid hymenopterans. Phylogenomic analyses of the inventory of meiosis genes and the identification of shared gene duplications and losses provided support for the grouping of species within Proctotrupomorpha, Ichneumonomorpha, and Aculeata clades, along with a paraphyletic Symphyta. The conservation of meiosis genes across Hymenoptera provides a framework for studying transitions between reproductive modes in this insect group.
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Affiliation(s)
- Eric S Tvedte
- Department of Biology, University of Iowa, Iowa City, IA 52242
| | - Andrew A Forbes
- Department of Biology, University of Iowa, Iowa City, IA 52242
| | - John M Logsdon
- Department of Biology, University of Iowa, Iowa City, IA 52242
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Nose M, Tokuoka A, Bando T, Tomioka K. timeless2 plays an important role in reproduction and circadian rhythms in the cricket Gryllus bimaculatus. JOURNAL OF INSECT PHYSIOLOGY 2018; 105:9-17. [PMID: 29287788 DOI: 10.1016/j.jinsphys.2017.12.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Revised: 11/30/2017] [Accepted: 12/23/2017] [Indexed: 06/07/2023]
Abstract
The timeless2 (tim2) gene is an insect orthologue of the mammalian clock gene Timeless (mTim). Although its functional role has been extensively studied in mammals, little is known regarding its role in insects. In the present study, we obtained tim2 cDNA (Gb'tim2) from the cricket Gryllus bimaculatus and characterized its functional role in embryonic development, egg production, and circadian rhythms. Gb'tim2 gave rise to a 1432 amino acid protein, and showed approximately 65% homology to that of Drosophila melanogaster. When treated with parental Gb'tim2RNAi, less than 2% of the treated eggs hatched. On the other hand, control eggs treated with DsRed2RNAi demonstrated a hatching rate of 70%. In most of the Gb'tim2RNAi treated embryos, development was arrested in early stages. Egg production in ovaries of adult virgin females treated with Gb'tim2RNAi was significantly reduced. In addition, while Gb'tim2RNAi crickets exhibited clear locomotor rhythm synchronized with light cycles, their light-on peak was weaker than that of control crickets. Under constant darkness, the activity rhythm of Gb'tim2RNAi crickets was often split into two components running with different periods. Molecular analysis revealed that Gb'tim2RNAi treatment downregulated mRNA levels of Gb'per and Gb'Clk, and enhanced Gb'cyc expression rhythm; no distinct effect was found on Gb'tim expression levels. The change in Gb'per, Gb'Clk and Gb'cyc levels may underlie the altered behavioral rhythms in Gb'tim2RNAi crickets. Both Gb'ClkRNAi and Gb'cycRNAi downregulated Gb'tim2 expression, which suggested that transcription of Gb'tim2 is mediated by Gb'CLK and Gb'CYC through E-box. These results suggested that Gb'tim2 may be involved in both reproduction and circadian rhythm regulation in crickets.
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Affiliation(s)
- Motoki Nose
- Graduate School of Natural Science and Technology, Okayama University, Okayama 700-8530, Japan
| | - Atsushi Tokuoka
- Graduate School of Natural Science and Technology, Okayama University, Okayama 700-8530, Japan
| | - Tetsuya Bando
- Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama 700-8558, Japan
| | - Kenji Tomioka
- Graduate School of Natural Science and Technology, Okayama University, Okayama 700-8530, Japan.
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The effect of Wolbachia on diapause, fecundity, and clock gene expression in Trichogramma brassicae (Hymenoptera: Trichogrammatidae). Dev Genes Evol 2017; 227:401-410. [PMID: 29188381 DOI: 10.1007/s00427-017-0597-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 11/23/2017] [Indexed: 02/07/2023]
Abstract
The short day lengths of late summer in moderate regions are used to induce diapause in various insects. Many studies have shown the maternal effect of photoperiod on diapause induction of Trichogramma wasps, but there is no study to show the relationship between photoperiodic regimes and clock genes in these useful biological control agents. Here, we investigated the role of photoperiods on diapause, fecundity, and clock gene expression (clk, cyc, cry2, per, and timeout) in asexual and sexual Trichogramma brassicae as a model insect to find any differences between two strains. Asexual strain was infected by Wolbachia, an endosymbiont bacterium. The diapause percentage was significantly higher under short days (8 h in sexual and 12 h in the asexual T. brassicae), although the diapause percentage of the sexual strain was significantly higher than the asexual one in all the photoperiods. The ANOVA revealed no significant changes between different photoperiods in the clock gene expression in the sexual strain but significant photoperiodic changes in clk, cyc, and timeout in the asexual strain. Our results showed that the mRNA levels of clock genes of asexual T. brassicae were significantly lower than those of sexual strain. The fecundity was significantly higher in the asexual strain. These results suggest that Wolbachia infection makes disturbance on the clock gene expression which consequently reduces the percentage of diapause but increases the fecundity in asexual T. brassicae.
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Zhu L, Liu W, Tan QQ, Lei CL, Wang XP. Differential expression of circadian clock genes in two strains of beetles reveals candidates related to photoperiodic induction of summer diapause. Gene 2017; 603:9-14. [DOI: 10.1016/j.gene.2016.12.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Revised: 11/22/2016] [Accepted: 12/08/2016] [Indexed: 11/16/2022]
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Li D, Su Y, Tu J, Wei R, Fan X, Yin H, Hu Y, Xu H, Yao Y, Yang D, Yang M. Evolutionary conservation of the circadian gene timeout in Metazoa. ANIM BIOL 2016. [DOI: 10.1163/15707563-00002482] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Timeless (Tim) is considered to function as an essential circadian clock gene in Drosophila. Putative homologues of the Drosophila timeless gene have been identified in both mice and humans. While Drosophila contains two paralogs, timeless and timeout, acting in clock/light entrainment and chromosome integrity/photoreception, respectively, mammals contain only one Tim homolog. In this paper, we study the phylogeny of the timeless/timeout family in 48 species [including 1 protozoan (Guillardia theta), 1 nematode (Caenorhabditis elegans), 8 arthropods and 38 chordates], for which whole genome data are available by using MEGA (Molecular Evolutionary Genetics Analysis). Phylogenetic Analysis by Maximum Likelihood (PAML) was used to analyze the selective pressure acting on metazoan timeless/timeout genes. Our phylogeny clearly separates insect timeless and timeout lineages and shows that non-insect animal Tim genes are homologs of insect timeout. In this study, we explored the relatively rapidly evolving timeless lineage that was apparently lost from most deuterostomes, including chordates, and from Caenorhabditis elegans. In contrast, we found that the timeout protein, often confusingly called “timeless” in the vertebrate literature, is present throughout the available animal genomes. Selection results showed that timeout is under weaker negative selection than timeless. Finally, our phylogeny of timeless/timeout showed an evolutionary conservation of the circadian clock gene timeout in Metazoa. This conservation is in line with its multifunctionality, being essential for embryonic development and maintenance of chromosome integrity, among others.
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Affiliation(s)
- Diyan Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, P. R. China
| | - Yuan Su
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, P. R. China
| | - Jianbo Tu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, P. R. China
| | - Ranlei Wei
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, P. R. China
| | - Xiaolan Fan
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, P. R. China
| | - Huadong Yin
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, P. R. China
| | - Yaodong Hu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, P. R. China
| | - Huailiang Xu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, P. R. China
| | - Yongfang Yao
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, P. R. China
| | - Deying Yang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, P. R. China
| | - Mingyao Yang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, P. R. China
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Tomioka K, Matsumoto A. Circadian molecular clockworks in non-model insects. CURRENT OPINION IN INSECT SCIENCE 2015; 7:58-64. [PMID: 32846680 DOI: 10.1016/j.cois.2014.12.006] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Revised: 12/11/2014] [Accepted: 12/12/2014] [Indexed: 06/11/2023]
Abstract
The recent development of molecular genetic technology is promoting studies on the clock mechanism of various non-model insect species, revealing diversity and commonality of their molecular clock machinery. Like in Drosophila, their clocks generally consist of clock genes including period, timeless, Clock, and cycle, except for hymenopteran species which lack timeless in their genome. Unlike in Drosophila, however, some insects show vertebrate-like traits: The clock machinery involves mammalian type cryptochrome, cycle is rhythmically expressed, and Clock is constitutively expressed. Although the oscillatory mechanisms of the clock are still to be investigated in most insects, RNAi and genome editing technology should accelerate the study, leading toward understanding the origin of variable overt behavioral rhythms such as nocturnal, diurnal, and crepuscular activity rhythms.
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Affiliation(s)
- Kenji Tomioka
- Graduate School of Natural Science and Technology, Okayama University, Okayama 700-8530, Japan.
| | - Akira Matsumoto
- Department of Biology, Juntendo University School of Medicine, 1-1 Hiraga Gakuendai, Inzai, Chiba 270-1695, Japan
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Potential conservation of circadian clock proteins in the phylum Nematoda as revealed by bioinformatic searches. PLoS One 2014; 9:e112871. [PMID: 25396739 PMCID: PMC4232591 DOI: 10.1371/journal.pone.0112871] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Accepted: 10/15/2014] [Indexed: 11/19/2022] Open
Abstract
Although several circadian rhythms have been described in C. elegans, its molecular clock remains elusive. In this work we employed a novel bioinformatic approach, applying probabilistic methodologies, to search for circadian clock proteins of several of the best studied circadian model organisms of different taxa (Mus musculus, Drosophila melanogaster, Neurospora crassa, Arabidopsis thaliana and Synechoccocus elongatus) in the proteomes of C. elegans and other members of the phylum Nematoda. With this approach we found that the Nematoda contain proteins most related to the core and accessory proteins of the insect and mammalian clocks, which provide new insights into the nematode clock and the evolution of the circadian system.
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