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Liu W, Zhao K, Zhou A, Wang X, Ge X, Qiao H, Sun X, Yan C, Wang Y. Genome-wide annotation and comparative analysis revealed conserved cuticular protein evolution among non-biting midges with varied environmental adaptability. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2024; 51:101248. [PMID: 38797005 DOI: 10.1016/j.cbd.2024.101248] [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: 02/20/2024] [Revised: 05/02/2024] [Accepted: 05/15/2024] [Indexed: 05/29/2024]
Abstract
Chironomidae, non-biting midges, a diverse and abundant insect group in global aquatic ecosystems, represent an exceptional model for investigating genetic adaptability mechanisms in aquatic insects due to their extensive species diversity and resilience to various environmental conditions. The cuticle in insects acts as the primary defense against ecological pressures. Cuticular Proteins (CPs) determine cuticle characteristics, facilitating adaptation to diverse challenges. However, systematic annotation of CP genes has only been conducted for one Chironomidae species, Propsilocerus akamusi, by our team. In this study, we expanded this annotation by identifying CP genes in eight additional Chironomidae species, covering all Chironomidae species with available genome data. We identified a total of 889 CP genes, neatly categorized into nine CP families: 215 CPR RR1 genes, 272 CPR RR2 genes, 23 CPR RR3 genes, 21 CPF genes, 16 CPLCA genes, 19 CPLCG genes, 28 CPLCP genes, 77 CPAP genes, and 37 Tweedle genes. Subsequently, we conducted a comprehensive phylogenetic analysis of CPs within the Chironomidae family. This expanded annotation of CP genes across diverse Chironomidae species significantly contributes to our understanding of their remarkable adaptability.
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Affiliation(s)
- Wenbin Liu
- Tianjin Key Laboratory of Conservation and Utilization of Animal Diversity, College of Life Sciences, Tianjin Normal University, 300387 Tianjin, China
| | - Kangzhu Zhao
- Tianjin Key Laboratory of Conservation and Utilization of Animal Diversity, College of Life Sciences, Tianjin Normal University, 300387 Tianjin, China
| | - Anmo Zhou
- Tianjin Key Laboratory of Conservation and Utilization of Animal Diversity, College of Life Sciences, Tianjin Normal University, 300387 Tianjin, China
| | - Xinyu Wang
- Tianjin Key Laboratory of Conservation and Utilization of Animal Diversity, College of Life Sciences, Tianjin Normal University, 300387 Tianjin, China
| | - Xinyu Ge
- Tianjin Key Laboratory of Conservation and Utilization of Animal Diversity, College of Life Sciences, Tianjin Normal University, 300387 Tianjin, China
| | - Huanhuan Qiao
- Academy of Medical Engineering and Translational Medicine, Tianjin University, 300072 Tianjin, China
| | - Xiaoya Sun
- Tianjin Key Laboratory of Conservation and Utilization of Animal Diversity, College of Life Sciences, Tianjin Normal University, 300387 Tianjin, China
| | - Chuncai Yan
- Tianjin Key Laboratory of Conservation and Utilization of Animal Diversity, College of Life Sciences, Tianjin Normal University, 300387 Tianjin, China.
| | - Yiwen Wang
- Shanxi Key Laboratory of Nucleic Acid Biopesticides, Shanxi University, 237016 Shanxi, China; School of Pharmaceutical Science and Technology, Tianjin University, 300072 Tianjin, China.
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2
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Kozeretska I, Serga S, Kovalenko P, Gorobchyshyn V, Convey P. Belgica antarctica (Diptera: Chironomidae): A natural model organism for extreme environments. INSECT SCIENCE 2022; 29:2-20. [PMID: 33913258 DOI: 10.1111/1744-7917.12925] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 03/17/2021] [Accepted: 03/23/2021] [Indexed: 06/12/2023]
Abstract
Belgica antarctica (Diptera: Chironomidae), a brachypterous midge endemic to the maritime Antarctic, was first described in 1900. Over more than a century of study, a vast amount of information has been compiled on the species (3 750 000 Google search results as of January 10, 2021), encompassing its ecology and biology, life cycle and reproduction, polytene chromosomes, physiology, biochemistry and, increasingly, omics. In 2014, B. antarctica's genome was sequenced, further boosting research. Certain developmental stages can be cultured successfully in the laboratory. Taken together, this wealth of information allows the species to be viewed as a natural model organism for studies of adaptation and function in extreme environments.
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Affiliation(s)
- Iryna Kozeretska
- National Antarctic Scientific Center of Ukraine, 01601, Taras Shevchenko blv., 16, Kyiv, Ukraine
| | - Svitlana Serga
- National Antarctic Scientific Center of Ukraine, 01601, Taras Shevchenko blv., 16, Kyiv, Ukraine
- Taras Shevchenko National University of Kyiv, Department General and Medical Genetics, 01601, Volodymyrska str., 64/13, Kyiv, Ukraine
| | - Pavlo Kovalenko
- State Institution «Institute for Evolutionary Ecology of the National Academy of Sciences of Ukraine», Department of Population Dynamics, 03143, Lebedeva str., 37, Kyiv, Ukraine
| | - Volodymyr Gorobchyshyn
- State Institution «Institute for Evolutionary Ecology of the National Academy of Sciences of Ukraine», Department of Population Dynamics, 03143, Lebedeva str., 37, Kyiv, Ukraine
| | - Peter Convey
- British Antarctic Survey, NERC, High Cross, Madingley Road, Cambridge, CB3 0ET, United Kingdom
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3
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A High-Quality Genome Assembly from Short and Long Reads for the Non-biting Midge Chironomus riparius (Diptera). G3-GENES GENOMES GENETICS 2020; 10:1151-1157. [PMID: 32060047 PMCID: PMC7144091 DOI: 10.1534/g3.119.400710] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Chironomus riparius is of great importance as a study species in various fields like ecotoxicology, molecular genetics, developmental biology and ecology. However, only a fragmented draft genome exists to date, hindering the recent rush of population genomic studies in this species. Making use of 50 NGS datasets, we present a hybrid genome assembly from short and long sequence reads that make C. riparius’ genome one of the most contiguous Dipteran genomes published, the first complete mitochondrial genome of the species, and the respective recombination rate among the first insect recombination rates at all. The genome assembly and associated resources will be highly valuable to the broad community working with dipterans in general and chironomids in particular. The estimated recombination rate will help evolutionary biologists gaining a better understanding of commonalities and differences of genomic patterns in insects.
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4
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Zhang L, Yang J, Li H, You J, Chatterjee N, Zhang X. Development of the transcriptome for a sediment ecotoxicological model species, Chironomus dilutus. CHEMOSPHERE 2020; 244:125541. [PMID: 32050339 DOI: 10.1016/j.chemosphere.2019.125541] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 11/04/2019] [Accepted: 12/03/2019] [Indexed: 06/10/2023]
Abstract
Chironomus dilutus is a prominent model species in conventional sediment toxicity testing and sediment contamination diagnosis. However, lack of genomic data significantly limited its application in identifying toxicological mode of action (MOA) and molecular biomarkers of toxicants. Here the transcriptome of C. dilutus in full life span and both sexes (1st, 2nd, 3rd and 4th instar larvae, pupae, and adults) were developed and temporal gene expression across adjacent life stages were investigated to understand the regulation of development. Furthermore, transcriptional response of Midges (the 4th instar larvae) exposed to chemicals of different MOAs (CdCl2, nonylphenol and triclosan) were profiled based on the reference transcriptome. Consequently, a complete transcriptome of 31132 unigenes with N50 of 3117bp, covering 98.8% of the arthropod single-copy orthologs were assembled. While 364 genes were differentially expressed among adjacent larval stages, 7142 and 2127 of transcripts were significantly changed for the transition of larvae-pupae and pupae-adults, respectively. Finally, chemical-specific gene expression profile were identified in the midges, showed its potential in classifying distinct contaminants. Overall, the comprehensive transcriptome of C. dilutus developed here could not only facilitate the mechanistic understanding of environmental toxicants during critical life stage of aquatic insects, but also provide molecular diagnostic tools in sediment ecotoxicology.
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Affiliation(s)
- Lijuan Zhang
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu, 210023, China
| | - Jianghua Yang
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu, 210023, China
| | - Huizhen Li
- School of Environment and Guangdong Key Laboratory of Environmental Pollution and Health, Jinan University, Guangzhou, Guangdong, 510632, China.
| | - Jing You
- School of Environment and Guangdong Key Laboratory of Environmental Pollution and Health, Jinan University, Guangzhou, Guangdong, 510632, China
| | - Nivedita Chatterjee
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu, 210023, China
| | - Xiaowei Zhang
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu, 210023, China.
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5
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Shuryak I. Review of resistance to chronic ionizing radiation exposure under environmental conditions in multicellular organisms. JOURNAL OF ENVIRONMENTAL RADIOACTIVITY 2020; 212:106128. [PMID: 31818732 DOI: 10.1016/j.jenvrad.2019.106128] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 12/02/2019] [Accepted: 12/03/2019] [Indexed: 06/10/2023]
Abstract
Ionizing radiation resistance occurs among many phylogenetic groups and its mechanisms remain incompletely understood. Tolerances to acute and chronic irradiation do not always correlate because different mechanisms may be involved. The radioresistance phenomenon becomes even more complex in the field than in the laboratory because the effects of radioactive contamination on natural populations are intertwined with those of other factors, such as bioaccumulation of radionuclides, interspecific competition, seasonal variations in environmental conditions, and land use changes due to evacuation of humans from contaminated areas. Previous reviews of studies performed in radioactive sites like the Kyshtym, Chernobyl, and Fukushima accident regions, and of protracted irradiation experiments, often focused on detecting radiation effects at low doses in radiosensitive organisms. Here we review the literature with a different purpose: to identify organisms with high tolerance to chronic irradiation under environmental conditions, which maintained abundant populations and/or outcompeted more radiosensitive species at high dose rates. Taxa for which consistent evidence for radioresistance came from multiple studies conducted in different locations and at different times were found among plants (e.g. willow and birch trees, sedges), invertebrate and vertebrate animals (e.g. rotifers, some insects, crustaceans and freshwater fish). These organisms are not specialized "extremophiles", but tend to tolerate broad ranges of environmental conditions and stresses, have small genomes, reproduce quickly and/or disperse effectively over long distances. Based on these findings, resistance to radioactive contamination can be examined in a more broad context of chronic stress responses.
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Affiliation(s)
- Igor Shuryak
- Center for Radiological Research, Columbia University Irving Medical Center, 630 West 168th Street, VC-11-234/5, New York, NY, USA.
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6
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Poynton HC, Hasenbein S, Benoit JB, Sepulveda MS, Poelchau MF, Hughes DST, Murali SC, Chen S, Glastad KM, Goodisman MAD, Werren JH, Vineis JH, Bowen JL, Friedrich M, Jones J, Robertson HM, Feyereisen R, Mechler-Hickson A, Mathers N, Lee CE, Colbourne JK, Biales A, Johnston JS, Wellborn GA, Rosendale AJ, Cridge AG, Munoz-Torres MC, Bain PA, Manny AR, Major KM, Lambert FN, Vulpe CD, Tuck P, Blalock BJ, Lin YY, Smith ME, Ochoa-Acuña H, Chen MJM, Childers CP, Qu J, Dugan S, Lee SL, Chao H, Dinh H, Han Y, Doddapaneni H, Worley KC, Muzny DM, Gibbs RA, Richards S. The Toxicogenome of Hyalella azteca: A Model for Sediment Ecotoxicology and Evolutionary Toxicology. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:6009-6022. [PMID: 29634279 DOI: 10.15482/usda.adc/1415994] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Hyalella azteca is a cryptic species complex of epibenthic amphipods of interest to ecotoxicology and evolutionary biology. It is the primary crustacean used in North America for sediment toxicity testing and an emerging model for molecular ecotoxicology. To provide molecular resources for sediment quality assessments and evolutionary studies, we sequenced, assembled, and annotated the genome of the H. azteca U.S. Lab Strain. The genome quality and completeness is comparable with other ecotoxicological model species. Through targeted investigation and use of gene expression data sets of H. azteca exposed to pesticides, metals, and other emerging contaminants, we annotated and characterized the major gene families involved in sequestration, detoxification, oxidative stress, and toxicant response. Our results revealed gene loss related to light sensing, but a large expansion in chemoreceptors, likely underlying sensory shifts necessary in their low light habitats. Gene family expansions were also noted for cytochrome P450 genes, cuticle proteins, ion transporters, and include recent gene duplications in the metal sequestration protein, metallothionein. Mapping of differentially expressed transcripts to the genome significantly increased the ability to functionally annotate toxicant responsive genes. The H. azteca genome will greatly facilitate development of genomic tools for environmental assessments and promote an understanding of how evolution shapes toxicological pathways with implications for environmental and human health.
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Affiliation(s)
- Helen C Poynton
- School for the Environment , University of Massachusetts Boston , Boston , Massachusetts 02125 United States
| | - Simone Hasenbein
- Aquatic Systems Biology Unit , Technical University of Munich , D-85354 Freising , Germany
| | - Joshua B Benoit
- Department of Biological Sciences , University of Cincinnati , Cincinnati , Ohio 45221 United States
| | - Maria S Sepulveda
- Forestry and Natural Resources , Purdue University , West Lafayette , Indiana 47907 United States
| | - Monica F Poelchau
- Agricultural Research Service, National Agricultural Library , U.S. Department of Agriculture , Beltsville , Maryland 20705 United States
| | - Daniel S T Hughes
- Human Genome Sequencing Center , Baylor College of Medicine , Houston , Texas 77030 United States
| | - Shwetha C Murali
- Human Genome Sequencing Center , Baylor College of Medicine , Houston , Texas 77030 United States
| | - Shuai Chen
- Forestry and Natural Resources , Purdue University , West Lafayette , Indiana 47907 United States
- OmicSoft Corporation, Cary , North Carolina 27513 United States
| | - Karl M Glastad
- Perelman School of Medicine , University of Pennsylvania , Philadelphia , Pennsylvania 19104 United States
| | - Michael A D Goodisman
- School of Biological Sciences , Georgia Institute of Technology , Atlanta , Georgia 30332 United States
| | - John H Werren
- Biology Department , University of Rochester , Rochester , New York 14627 United States
| | - Joseph H Vineis
- Department of Marine and Environmental Sciences, Marine Science Center , Northeastern University , Nahant , Massachusetts 01908 United States
| | - Jennifer L Bowen
- Department of Marine and Environmental Sciences, Marine Science Center , Northeastern University , Nahant , Massachusetts 01908 United States
| | - Markus Friedrich
- Department of Biological Sciences , Wayne State University , Detroit Michigan 48202 United States
| | - Jeffery Jones
- Department of Biological Sciences , Wayne State University , Detroit Michigan 48202 United States
| | - Hugh M Robertson
- Department of Entomology , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 United States
| | - René Feyereisen
- Department of Plant and Environmental Sciences , University of Copenhagen , DK-1871 Frederiksberg , Denmark
| | - Alexandra Mechler-Hickson
- Center of Rapid Evolution (CORE) and Department of Integrative Biology , University of Wisconsin , Madison , Wisconsin 53706 United States
| | - Nicholas Mathers
- Center of Rapid Evolution (CORE) and Department of Integrative Biology , University of Wisconsin , Madison , Wisconsin 53706 United States
| | - Carol Eunmi Lee
- Center of Rapid Evolution (CORE) and Department of Integrative Biology , University of Wisconsin , Madison , Wisconsin 53706 United States
| | - John K Colbourne
- School of Biosciences , University of Birmingham , Birmingham B15 2TT U.K
| | - Adam Biales
- National Exposure Research Laboratory , United States Environmental Protection Agency , Cincinnati , Ohio 45268 United States
| | - J Spencer Johnston
- Department of Entomology , Texas A&M University , College Station , Texas 77843 United States
| | - Gary A Wellborn
- Department of Biology , University of Oklahoma , Norman , Oklahoma 73019 United States
| | - Andrew J Rosendale
- Department of Biological Sciences , University of Cincinnati , Cincinnati , Ohio 45221 United States
| | - Andrew G Cridge
- Laboratory for Evolution and Development, Department of Biochemistry , University of Otago , Dunedin , 9054 New Zealand
| | - Monica C Munoz-Torres
- Environmental Genomics and Systems Biology Division , Lawrence Berkeley National Laboratory , Berkeley , California 94720 United States
| | - Peter A Bain
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Urrbrae SA 5064 Australia
| | - Austin R Manny
- Department of Microbiology & Cell Science , University of Florida , Gainesville , Florida 32611 United States
| | - Kaley M Major
- School for the Environment , University of Massachusetts Boston , Boston , Massachusetts 02125 United States
| | - Faith N Lambert
- Center for Environmental and Human Toxicology, Department of Physiological Sciences , University of Florida , Gainesville , Florida 32611 United States
| | - Chris D Vulpe
- Center for Environmental and Human Toxicology, Department of Physiological Sciences , University of Florida , Gainesville , Florida 32611 United States
| | - Padrig Tuck
- School for the Environment , University of Massachusetts Boston , Boston , Massachusetts 02125 United States
| | - Bonnie J Blalock
- School for the Environment , University of Massachusetts Boston , Boston , Massachusetts 02125 United States
| | - Yu-Yu Lin
- Graduate Institute of Biomedical Electronics and Bioinformatics , National Taiwan University , Taipei , 10617 Taiwan
| | - Mark E Smith
- McConnell Group, Cincinnati , Ohio 45268 , United States
| | - Hugo Ochoa-Acuña
- Forestry and Natural Resources , Purdue University , West Lafayette , Indiana 47907 United States
| | - Mei-Ju May Chen
- Graduate Institute of Biomedical Electronics and Bioinformatics , National Taiwan University , Taipei , 10617 Taiwan
| | - Christopher P Childers
- Agricultural Research Service, National Agricultural Library , U.S. Department of Agriculture , Beltsville , Maryland 20705 United States
| | - Jiaxin Qu
- Human Genome Sequencing Center , Baylor College of Medicine , Houston , Texas 77030 United States
| | - Shannon Dugan
- Human Genome Sequencing Center , Baylor College of Medicine , Houston , Texas 77030 United States
| | - Sandra L Lee
- Human Genome Sequencing Center , Baylor College of Medicine , Houston , Texas 77030 United States
| | - Hsu Chao
- Human Genome Sequencing Center , Baylor College of Medicine , Houston , Texas 77030 United States
| | - Huyen Dinh
- Human Genome Sequencing Center , Baylor College of Medicine , Houston , Texas 77030 United States
| | - Yi Han
- Human Genome Sequencing Center , Baylor College of Medicine , Houston , Texas 77030 United States
| | | | - Kim C Worley
- Human Genome Sequencing Center , Baylor College of Medicine , Houston , Texas 77030 United States
- Department of Molecular and Human Genetics , Baylor College of Medicine , Houston , Texas 77030 United States
| | - Donna M Muzny
- Human Genome Sequencing Center , Baylor College of Medicine , Houston , Texas 77030 United States
| | - Richard A Gibbs
- Human Genome Sequencing Center , Baylor College of Medicine , Houston , Texas 77030 United States
| | - Stephen Richards
- Human Genome Sequencing Center , Baylor College of Medicine , Houston , Texas 77030 United States
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7
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Poynton HC, Hasenbein S, Benoit JB, Sepulveda MS, Poelchau MF, Hughes DST, Murali SC, Chen S, Glastad KM, Goodisman MAD, Werren JH, Vineis JH, Bowen JL, Friedrich M, Jones J, Robertson HM, Feyereisen R, Mechler-Hickson A, Mathers N, Lee CE, Colbourne JK, Biales A, Johnston JS, Wellborn GA, Rosendale AJ, Cridge AG, Munoz-Torres MC, Bain PA, Manny AR, Major KM, Lambert FN, Vulpe CD, Tuck P, Blalock BJ, Lin YY, Smith ME, Ochoa-Acuña H, Chen MJM, Childers CP, Qu J, Dugan S, Lee SL, Chao H, Dinh H, Han Y, Doddapaneni H, Worley KC, Muzny DM, Gibbs RA, Richards S. The Toxicogenome of Hyalella azteca: A Model for Sediment Ecotoxicology and Evolutionary Toxicology. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:6009-6022. [PMID: 29634279 PMCID: PMC6091588 DOI: 10.1021/acs.est.8b00837] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Hyalella azteca is a cryptic species complex of epibenthic amphipods of interest to ecotoxicology and evolutionary biology. It is the primary crustacean used in North America for sediment toxicity testing and an emerging model for molecular ecotoxicology. To provide molecular resources for sediment quality assessments and evolutionary studies, we sequenced, assembled, and annotated the genome of the H. azteca U.S. Lab Strain. The genome quality and completeness is comparable with other ecotoxicological model species. Through targeted investigation and use of gene expression data sets of H. azteca exposed to pesticides, metals, and other emerging contaminants, we annotated and characterized the major gene families involved in sequestration, detoxification, oxidative stress, and toxicant response. Our results revealed gene loss related to light sensing, but a large expansion in chemoreceptors, likely underlying sensory shifts necessary in their low light habitats. Gene family expansions were also noted for cytochrome P450 genes, cuticle proteins, ion transporters, and include recent gene duplications in the metal sequestration protein, metallothionein. Mapping of differentially expressed transcripts to the genome significantly increased the ability to functionally annotate toxicant responsive genes. The H. azteca genome will greatly facilitate development of genomic tools for environmental assessments and promote an understanding of how evolution shapes toxicological pathways with implications for environmental and human health.
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Affiliation(s)
- Helen C Poynton
- School for the Environment , University of Massachusetts Boston , Boston , Massachusetts 02125 United States
| | - Simone Hasenbein
- Aquatic Systems Biology Unit , Technical University of Munich , D-85354 Freising , Germany
| | - Joshua B Benoit
- Department of Biological Sciences , University of Cincinnati , Cincinnati , Ohio 45221 United States
| | - Maria S Sepulveda
- Forestry and Natural Resources , Purdue University , West Lafayette , Indiana 47907 United States
| | - Monica F Poelchau
- Agricultural Research Service, National Agricultural Library , U.S. Department of Agriculture , Beltsville , Maryland 20705 United States
| | - Daniel S T Hughes
- Human Genome Sequencing Center , Baylor College of Medicine , Houston , Texas 77030 United States
| | - Shwetha C Murali
- Human Genome Sequencing Center , Baylor College of Medicine , Houston , Texas 77030 United States
| | - Shuai Chen
- Forestry and Natural Resources , Purdue University , West Lafayette , Indiana 47907 United States
- OmicSoft Corporation, Cary , North Carolina 27513 United States
| | - Karl M Glastad
- Perelman School of Medicine , University of Pennsylvania , Philadelphia , Pennsylvania 19104 United States
| | - Michael A D Goodisman
- School of Biological Sciences , Georgia Institute of Technology , Atlanta , Georgia 30332 United States
| | - John H Werren
- Biology Department , University of Rochester , Rochester , New York 14627 United States
| | - Joseph H Vineis
- Department of Marine and Environmental Sciences, Marine Science Center , Northeastern University , Nahant , Massachusetts 01908 United States
| | - Jennifer L Bowen
- Department of Marine and Environmental Sciences, Marine Science Center , Northeastern University , Nahant , Massachusetts 01908 United States
| | - Markus Friedrich
- Department of Biological Sciences , Wayne State University , Detroit Michigan 48202 United States
| | - Jeffery Jones
- Department of Biological Sciences , Wayne State University , Detroit Michigan 48202 United States
| | - Hugh M Robertson
- Department of Entomology , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 United States
| | - René Feyereisen
- Department of Plant and Environmental Sciences , University of Copenhagen , DK-1871 Frederiksberg , Denmark
| | - Alexandra Mechler-Hickson
- Center of Rapid Evolution (CORE) and Department of Integrative Biology , University of Wisconsin , Madison , Wisconsin 53706 United States
| | - Nicholas Mathers
- Center of Rapid Evolution (CORE) and Department of Integrative Biology , University of Wisconsin , Madison , Wisconsin 53706 United States
| | - Carol Eunmi Lee
- Center of Rapid Evolution (CORE) and Department of Integrative Biology , University of Wisconsin , Madison , Wisconsin 53706 United States
| | - John K Colbourne
- School of Biosciences , University of Birmingham , Birmingham B15 2TT U.K
| | - Adam Biales
- National Exposure Research Laboratory , United States Environmental Protection Agency , Cincinnati , Ohio 45268 United States
| | - J Spencer Johnston
- Department of Entomology , Texas A&M University , College Station , Texas 77843 United States
| | - Gary A Wellborn
- Department of Biology , University of Oklahoma , Norman , Oklahoma 73019 United States
| | - Andrew J Rosendale
- Department of Biological Sciences , University of Cincinnati , Cincinnati , Ohio 45221 United States
| | - Andrew G Cridge
- Laboratory for Evolution and Development, Department of Biochemistry , University of Otago , Dunedin , 9054 New Zealand
| | - Monica C Munoz-Torres
- Environmental Genomics and Systems Biology Division , Lawrence Berkeley National Laboratory , Berkeley , California 94720 United States
| | - Peter A Bain
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Urrbrae SA 5064 Australia
| | - Austin R Manny
- Department of Microbiology & Cell Science , University of Florida , Gainesville , Florida 32611 United States
| | - Kaley M Major
- School for the Environment , University of Massachusetts Boston , Boston , Massachusetts 02125 United States
| | - Faith N Lambert
- Center for Environmental and Human Toxicology, Department of Physiological Sciences , University of Florida , Gainesville , Florida 32611 United States
| | - Chris D Vulpe
- Center for Environmental and Human Toxicology, Department of Physiological Sciences , University of Florida , Gainesville , Florida 32611 United States
| | - Padrig Tuck
- School for the Environment , University of Massachusetts Boston , Boston , Massachusetts 02125 United States
| | - Bonnie J Blalock
- School for the Environment , University of Massachusetts Boston , Boston , Massachusetts 02125 United States
| | - Yu-Yu Lin
- Graduate Institute of Biomedical Electronics and Bioinformatics , National Taiwan University , Taipei , 10617 Taiwan
| | - Mark E Smith
- McConnell Group, Cincinnati , Ohio 45268 , United States
| | - Hugo Ochoa-Acuña
- Forestry and Natural Resources , Purdue University , West Lafayette , Indiana 47907 United States
| | - Mei-Ju May Chen
- Graduate Institute of Biomedical Electronics and Bioinformatics , National Taiwan University , Taipei , 10617 Taiwan
| | - Christopher P Childers
- Agricultural Research Service, National Agricultural Library , U.S. Department of Agriculture , Beltsville , Maryland 20705 United States
| | - Jiaxin Qu
- Human Genome Sequencing Center , Baylor College of Medicine , Houston , Texas 77030 United States
| | - Shannon Dugan
- Human Genome Sequencing Center , Baylor College of Medicine , Houston , Texas 77030 United States
| | - Sandra L Lee
- Human Genome Sequencing Center , Baylor College of Medicine , Houston , Texas 77030 United States
| | - Hsu Chao
- Human Genome Sequencing Center , Baylor College of Medicine , Houston , Texas 77030 United States
| | - Huyen Dinh
- Human Genome Sequencing Center , Baylor College of Medicine , Houston , Texas 77030 United States
| | - Yi Han
- Human Genome Sequencing Center , Baylor College of Medicine , Houston , Texas 77030 United States
| | | | - Kim C Worley
- Human Genome Sequencing Center , Baylor College of Medicine , Houston , Texas 77030 United States
- Department of Molecular and Human Genetics , Baylor College of Medicine , Houston , Texas 77030 United States
| | - Donna M Muzny
- Human Genome Sequencing Center , Baylor College of Medicine , Houston , Texas 77030 United States
| | - Richard A Gibbs
- Human Genome Sequencing Center , Baylor College of Medicine , Houston , Texas 77030 United States
| | - Stephen Richards
- Human Genome Sequencing Center , Baylor College of Medicine , Houston , Texas 77030 United States
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8
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Wiegmann BM, Richards S. Genomes of Diptera. CURRENT OPINION IN INSECT SCIENCE 2018; 25:116-124. [PMID: 29602357 DOI: 10.1016/j.cois.2018.01.007] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 01/23/2018] [Indexed: 06/08/2023]
Abstract
Diptera (true flies) are among the most diverse holometabolan insect orders and were the first eukaryotic order to have a representative genome fully sequenced. 110 fly species have publically available genome assemblies and many hundreds of population-level genomes have been generated in the model organisms Drosophila melanogaster and the malaria mosquito Anopheles gambiae. Comparative genomics carried out in a phylogenetic context is illuminating many aspects of fly biology, providing unprecedented insight into variability in genome structure, gene content, genetic mechanisms, and rates and patterns of evolution in genes, populations, and species. Despite the rich availability of genomic resources in flies, there remain many fly lineages to which new genome sequencing efforts should be directed. Such efforts would be most valuable in fly families or clades that exhibit multiple origins of key fly behaviors such as blood feeding, phytophagy, parasitism, pollination, and mycophagy.
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Affiliation(s)
- Brian M Wiegmann
- Department of Entomology & Plant Pathology, North Carolina State University, Raleigh, NC 27695, United States.
| | - Stephen Richards
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77006, United States
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9
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Tang G, Yao J, Li D, He Y, Zhu YC, Zhang X, Zhu KY. Cytochrome P450 genes from the aquatic midge Chironomus tentans: Atrazine-induced up-regulation of CtCYP6EX3 enhanced the toxicity of chlorpyrifos. CHEMOSPHERE 2017; 186:68-77. [PMID: 28768160 DOI: 10.1016/j.chemosphere.2017.07.137] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Revised: 07/25/2017] [Accepted: 07/26/2017] [Indexed: 06/07/2023]
Abstract
The open reading frames of 19 cytochrome P450 monooxygenase (CYP) genes were sequenced from Chironomus tentans, a commonly used freshwater invertebrate model. Phylogenetic analysis of the 19 CYPs along with a previously reported CYP (CtCYP4G33) revealed that they belong to three different clans, including 3 in CYP4, 15 in CYP3, and 2 in mitochondria clan. When third-instar larvae were exposed to atrazine at 5000 μg/L, the transcription of CtCYP6EX3, CtCYP6EV3, CtCYP9AT1 and CtCYPEX1 was significantly up-regulated. To examine whether CtCYP6EX3 played a role in oxidative activation of chlorpyrifos to chlorpyrifos-oxon, we evaluated larval susceptibility to chlorpyrifos after CtCYP6EX3 transcript was suppressed by RNAi. The larvae fed chitosan/dsCtCYP6EX3 nanoparticles showed a significantly decreased CtCYP6EX3 transcript (53.1%) as compared with the control larvae fed chitosan/dsGFP nanoparticles. When the CtCYP6EX3-silenced larvae were exposed to chlorpyrifos at 6 μg/L or its binary mixture with atrazine (chlorpyrifos at 3 μg/L and atrazine at 1000 μg/L), the larvae became less susceptible to the pesticides as their mortalities decreased by 24.1% and 20.5%, respectively. These results along with our previous findings suggested that the increased toxicity of chlorpyrifos was likely due to an enhanced oxidative process from chlorpyrifos to chlorpyrifos-oxon by CtCYP6EX3 as RNAi of CtCYP6EX3 led to decreased susceptibility of C. tentans larvae to chlorpyrifos alone and the binary mixture of atrazine and chlorpyrifos. However, further study would be necessary to validate our results by functional assays using heterologously expressed CtCYP6EX3 enzyme.
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Affiliation(s)
- Guanghui Tang
- College of Forestry, Northwest A&F University, Yangling, Shaanxi 712100, China; Department of Entomology, Kansas State University, Manhattan, KS 66502, USA
| | - Jianxiu Yao
- Department of Entomology, Kansas State University, Manhattan, KS 66502, USA; USDA-ARS, Southern Insect Management Unit, Stoneville, MS 38776, USA
| | - Daqi Li
- Department of Entomology, Kansas State University, Manhattan, KS 66502, USA; Institute of Applied Biology, Shanxi University, Taiyuan, Shaanxi 030006, China
| | - Yanping He
- Department of Entomology, Kansas State University, Manhattan, KS 66502, USA; College of Food Science and Engineering, Wuhan Polytechnic University, Wuhan 430023, China
| | - Yu-Cheng Zhu
- USDA-ARS, Southern Insect Management Unit, Stoneville, MS 38776, USA
| | - Xin Zhang
- Department of Entomology, Kansas State University, Manhattan, KS 66502, USA
| | - Kun Yan Zhu
- Department of Entomology, Kansas State University, Manhattan, KS 66502, USA.
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10
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Oppold AM, Schmidt H, Rose M, Hellmann SL, Dolze F, Ripp F, Weich B, Schmidt-Ott U, Schmidt E, Kofler R, Hankeln T, Pfenninger M. Chironomus riparius
(Diptera) genome sequencing reveals the impact of minisatellite transposable elements on population divergence. Mol Ecol 2017; 26:3256-3275. [DOI: 10.1111/mec.14111] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Revised: 02/23/2017] [Accepted: 03/06/2017] [Indexed: 12/22/2022]
Affiliation(s)
- Ann-Marie Oppold
- Molecular Ecology Group; Institute for Ecology, Evolution & Diversity; Goethe-University Frankfurt am Main; Max-von-Laue-Str. 9, 60438 Frankfurt am Main Hessen Germany
- Senckenberg Biodiversity and Climate Research Centre; Georg-Voigt-Str. 14-16 60325 Frankfurt am Main Hessen Germany
| | - Hanno Schmidt
- Senckenberg Biodiversity and Climate Research Centre; Georg-Voigt-Str. 14-16 60325 Frankfurt am Main Hessen Germany
| | - Marcel Rose
- Molecular Ecology Group; Institute for Ecology, Evolution & Diversity; Goethe-University Frankfurt am Main; Max-von-Laue-Str. 9, 60438 Frankfurt am Main Hessen Germany
| | - Sören Lukas Hellmann
- Institute of Molecular Genetics; Johannes Gutenberg-University; Johann-Joachim-Becherweg 30a 55128 Mainz Rheinland-Pfalz Germany
| | - Florian Dolze
- Institute of Molecular Genetics; Johannes Gutenberg-University; Johann-Joachim-Becherweg 30a 55128 Mainz Rheinland-Pfalz Germany
| | - Fabian Ripp
- Institute of Molecular Genetics; Johannes Gutenberg-University; Johann-Joachim-Becherweg 30a 55128 Mainz Rheinland-Pfalz Germany
| | - Bettina Weich
- Institute of Molecular Genetics; Johannes Gutenberg-University; Johann-Joachim-Becherweg 30a 55128 Mainz Rheinland-Pfalz Germany
| | - Urs Schmidt-Ott
- Department of Organismal Biology and Anatomy; University of Chicago; 920 E. 58th Street, 1061C Chicago IL 60637 USA
| | - Erwin Schmidt
- Institute of Molecular Genetics; Johannes Gutenberg-University; Johann-Joachim-Becherweg 30a 55128 Mainz Rheinland-Pfalz Germany
| | - Robert Kofler
- Institut für Populationsgenetik; Vetmeduni Vienna 1210 Vienna Austria
| | - Thomas Hankeln
- Institute of Molecular Genetics; Johannes Gutenberg-University; Johann-Joachim-Becherweg 30a 55128 Mainz Rheinland-Pfalz Germany
| | - Markus Pfenninger
- Molecular Ecology Group; Institute for Ecology, Evolution & Diversity; Goethe-University Frankfurt am Main; Max-von-Laue-Str. 9, 60438 Frankfurt am Main Hessen Germany
- Senckenberg Biodiversity and Climate Research Centre; Georg-Voigt-Str. 14-16 60325 Frankfurt am Main Hessen Germany
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11
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Wang Y, White MM, Kvist S, Moncalvo JM. Genome-Wide Survey of Gut Fungi (Harpellales) Reveals the First Horizontally Transferred Ubiquitin Gene from a Mosquito Host. Mol Biol Evol 2016; 33:2544-54. [PMID: 27343289 PMCID: PMC5026252 DOI: 10.1093/molbev/msw126] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Harpellales, an early-diverging fungal lineage, is associated with the digestive tracts of aquatic arthropod hosts. Concurrent with the production and annotation of the first four Harpellales genomes, we discovered that Zancudomyces culisetae, one of the most widely distributed Harpellales species, encodes an insect-like polyubiquitin chain. Ubiquitin and ubiquitin-like proteins are universally involved in protein degradation and regulation of immune response in eukaryotic organisms. Phylogenetic analyses inferred that this polyubiquitin variant has a mosquito origin. In addition, its amino acid composition, animal-like secondary structure, as well as the fungal nature of flanking genes all further support this as a horizontal gene transfer event. The single-copy polyubiquitin gene from Z. culisetae has lower GC ratio compared with homologs of insect taxa, which implies homogenization of the gene since its putatively ancient transfer. The acquired polyubiquitin gene may have served to improve important functions within Z. culisetae, by perhaps exploiting the insect hosts' ubiquitin-proteasome systems in the gut environment. Preliminary comparisons among the four Harpellales genomes highlight the reduced genome size of Z. culisetae, which corroborates its distinguishable symbiotic lifestyle. This is the first record of a horizontally transferred ubiquitin gene from disease-bearing insects to the gut-dwelling fungal endobiont and should invite further exploration in an evolutionary context.
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Affiliation(s)
- Yan Wang
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada Department of Natural History, Royal Ontario Museum, Toronto, ON, Canada
| | - Merlin M White
- Department of Biological Sciences, Boise State University
| | - Sebastian Kvist
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada Department of Natural History, Royal Ontario Museum, Toronto, ON, Canada
| | - Jean-Marc Moncalvo
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada Department of Natural History, Royal Ontario Museum, Toronto, ON, Canada
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12
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Björk P, Persson JO, Wieslander L. Intranuclear binding in space and time of exon junction complex and NXF1 to premRNPs/mRNPs in vivo. J Cell Biol 2016; 211:63-75. [PMID: 26459599 PMCID: PMC4602041 DOI: 10.1083/jcb.201412017] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
The exon junction core complex associates with Balbiani ring (BR) premRNPs during transcription and in relation to splicing, whereas the export factor NXF1 is recruited in the interchromatin, and BR mRNPs become export competent only after passage through the interchromatin. Eukaryotic gene expression requires the ordered association of numerous factors with precursor messenger RNAs (premRNAs)/messenger RNAs (mRNAs) to achieve efficiency and regulation. Here, we use the Balbiani ring (BR) genes to demonstrate the temporal and spatial association of the exon junction complex (EJC) core with gene-specific endogenous premRNAs and mRNAs. The EJC core components bind cotranscriptionally to BR premRNAs during or very rapidly after splicing. The EJC core does not recruit the nonsense-mediated decay mediaters UPF2 and UPF3 until the BR messenger RNA protein complexes (mRNPs) enter the interchromatin. Even though several known adapters for the export factor NXF1 become part of BR mRNPs already at the gene, NXF1 binds to BR mRNPs only in the interchromatin. In steady state, a subset of the BR mRNPs in the interchromatin binds NXF1, UPF2, and UPF3. This binding appears to occur stochastically, and the efficiency approximately equals synthesis and export of the BR mRNPs. Our data provide unique in vivo information on how export competent eukaryotic mRNPs are formed.
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Affiliation(s)
- Petra Björk
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Jan-Olov Persson
- Department of Mathematics, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Lars Wieslander
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, SE-106 91 Stockholm, Sweden
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13
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Björk P, Wieslander L. The Balbiani Ring Story: Synthesis, Assembly, Processing, and Transport of Specific Messenger RNA-Protein Complexes. Annu Rev Biochem 2015; 84:65-92. [PMID: 26034888 DOI: 10.1146/annurev-biochem-060614-034150] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Eukaryotic gene expression is the result of the integrated action of multimolecular machineries. These machineries associate with gene transcripts, often already nascent precursor messenger RNAs (pre-mRNAs). They rebuild the transcript and convey properties allowing the processed transcript, the mRNA, to be exported to the cytoplasm, quality controlled, stored, translated, and degraded. To understand these integrated processes, one must understand the temporal and spatial aspects of the fate of the gene transcripts in relation to interacting molecular machineries. Improved methodology is necessary to study gene expression in vivo for endogenous genes. A complementary approach is to study biological systems that provide exceptional experimental possibilities. We describe such a system, the Balbiani ring (BR) genes in polytene cells in the dipteran Chironomus tentans. The BR genes, along with their pre-mRNA-protein complexes (pre-mRNPs) and mRNA-protein complexes (mRNPs), allow the visualization of intact cell nuclei and enable analyses of where and when different molecular machineries associate with and act on the BR pre-mRNAs and mRNAs.
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Affiliation(s)
- Petra Björk
- Department of Molecular Biosciences, Wenner-Gren Institute, Stockholm University, SE-106 91 Stockholm, Sweden;
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