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Zhao L, Zhou W, He J, Li DZ, Li HT. Positive selection and relaxed purifying selection contribute to rapid evolution of male-biased genes in a dioecious flowering plant. eLife 2024; 12:RP89941. [PMID: 38353667 PMCID: PMC10942601 DOI: 10.7554/elife.89941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2024] Open
Abstract
Sex-biased genes offer insights into the evolution of sexual dimorphism. Sex-biased genes, especially those with male bias, show elevated evolutionary rates of protein sequences driven by positive selection and relaxed purifying selection in animals. Although rapid sequence evolution of sex-biased genes and evolutionary forces have been investigated in animals and brown algae, less is known about evolutionary forces in dioecious angiosperms. In this study, we separately compared the expression of sex-biased genes between female and male floral buds and between female and male flowers at anthesis in dioecious Trichosanthes pilosa (Cucurbitaceae). In floral buds, sex-biased gene expression was pervasive, and had significantly different roles in sexual dimorphism such as physiology. We observed higher rates of sequence evolution for male-biased genes in floral buds compared to female-biased and unbiased genes. Male-biased genes under positive selection were mainly associated with functions to abiotic stress and immune responses, suggesting that high evolutionary rates are driven by adaptive evolution. Additionally, relaxed purifying selection may contribute to accelerated evolution in male-biased genes generated by gene duplication. Our findings, for the first time in angiosperms, suggest evident rapid evolution of male-biased genes, advance our understanding of the patterns and forces driving the evolution of sexual dimorphism in dioecious plants.
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Affiliation(s)
- Lei Zhao
- Germplasm Bank of Wild Species & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of SciencesKunming, YunnanChina
| | - Wei Zhou
- Germplasm Bank of Wild Species & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of SciencesKunming, YunnanChina
| | - Jun He
- Germplasm Bank of Wild Species & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of SciencesKunming, YunnanChina
| | - De-Zhu Li
- Germplasm Bank of Wild Species & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of SciencesKunming, YunnanChina
- Kunming College of Life Science, University of Chinese Academy of SciencesKunmingChina
| | - Hong-Tao Li
- Germplasm Bank of Wild Species & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of SciencesKunming, YunnanChina
- Kunming College of Life Science, University of Chinese Academy of SciencesKunmingChina
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2
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Kalita AI, Marois E, Kozielska M, Weissing FJ, Jaouen E, Möckel MM, Rühle F, Butter F, Basilicata MF, Keller Valsecchi CI. The sex-specific factor SOA controls dosage compensation in Anopheles mosquitoes. Nature 2023; 623:175-182. [PMID: 37769784 PMCID: PMC10620080 DOI: 10.1038/s41586-023-06641-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 09/13/2023] [Indexed: 10/03/2023]
Abstract
The Anopheles mosquito is one of thousands of species in which sex differences play a central part in their biology, as only females need a blood meal to produce eggs. Sex differentiation is regulated by sex chromosomes, but their presence creates a dosage imbalance between males (XY) and females (XX). Dosage compensation (DC) can re-equilibrate the expression of sex chromosomal genes. However, because DC mechanisms have only been fully characterized in a few model organisms, key questions about its evolutionary diversity and functional necessity remain unresolved1. Here we report the discovery of a previously uncharacterized gene (sex chromosome activation (SOA)) as a master regulator of DC in the malaria mosquito Anopheles gambiae. Sex-specific alternative splicing prevents functional SOA protein expression in females. The male isoform encodes a DNA-binding protein that binds the promoters of active X chromosomal genes. Expressing male SOA is sufficient to induce DC in female cells. Male mosquitoes lacking SOA or female mosquitoes ectopically expressing the male isoform exhibit X chromosome misregulation, which is compatible with viability but causes developmental delay. Thus, our molecular analyses of a DC master regulator in a non-model organism elucidates the evolutionary steps that lead to the establishment of a chromosome-specific fine-tuning mechanism.
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Affiliation(s)
| | - Eric Marois
- INSERM U1257, CNRS UPR9022, Université de Strasbourg, Strasbourg, France
| | - Magdalena Kozielska
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, Netherlands
| | - Franz J Weissing
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, Netherlands
| | - Etienne Jaouen
- INSERM U1257, CNRS UPR9022, Université de Strasbourg, Strasbourg, France
| | | | - Frank Rühle
- Institute of Molecular Biology (IMB), Mainz, Germany
| | - Falk Butter
- Institute of Molecular Biology (IMB), Mainz, Germany
- Institute of Molecular Virology and Cell Biology, Friedrich Loeffler Institute, Greifswald, Germany
| | - M Felicia Basilicata
- Institute of Molecular Biology (IMB), Mainz, Germany
- Institute of Human Genetics, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
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3
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Nicolini F, Ghiselli F, Luchetti A, Milani L. Bivalves as Emerging Model Systems to Study the Mechanisms and Evolution of Sex Determination: A Genomic Point of View. Genome Biol Evol 2023; 15:evad181. [PMID: 37850870 PMCID: PMC10588774 DOI: 10.1093/gbe/evad181] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 09/26/2023] [Accepted: 10/03/2023] [Indexed: 10/19/2023] Open
Abstract
Bivalves are a diverse group of molluscs that have recently attained a central role in plenty of biological research fields, thanks to their peculiar life history traits. Here, we propose that bivalves should be considered as emerging model systems also in sex-determination (SD) studies, since they would allow to investigate: 1) the transition between environmental and genetic SD, with respect to different reproductive backgrounds and sexual systems (from species with strict gonochorism to species with various forms of hermaphroditism); 2) the genomic evolution of sex chromosomes (SCs), considering that no heteromorphic SCs are currently known and that homomorphic SCs have been identified only in a few species of scallops; 3) the putative role of mitochondria at some level of the SD signaling pathway, in a mechanism that may resemble the cytoplasmatic male sterility of plants; 4) the evolutionary history of SD-related gene (SRG) families with respect to other animal groups. In particular, we think that this last topic may lay the foundations for expanding our understanding of bivalve SD, as our current knowledge is quite fragmented and limited to a few species. As a matter of fact, tracing the phylogenetic history and diversity of SRG families (such as the Dmrt, Sox, and Fox genes) would allow not only to perform more targeted functional experiments and genomic analyses, but also to foster the possibility of establishing a solid comparative framework.
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Affiliation(s)
- Filippo Nicolini
- Department of Biological, Geological and Environmental Science, University of Bologna, Bologna, Italy
- Fano Marine Center, Fano, Italy
| | - Fabrizio Ghiselli
- Department of Biological, Geological and Environmental Science, University of Bologna, Bologna, Italy
| | - Andrea Luchetti
- Department of Biological, Geological and Environmental Science, University of Bologna, Bologna, Italy
| | - Liliana Milani
- Department of Biological, Geological and Environmental Science, University of Bologna, Bologna, Italy
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4
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Kuang J, Michel K, Scoglio C. GeCoNet-Tool: a software package for gene co-expression network construction and analysis. BMC Bioinformatics 2023; 24:281. [PMID: 37434115 DOI: 10.1186/s12859-023-05382-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 06/09/2023] [Indexed: 07/13/2023] Open
Abstract
BACKGROUND Network analysis is a powerful tool for studying gene regulation and identifying biological processes associated with gene function. However, constructing gene co-expression networks can be a challenging task, particularly when dealing with a large number of missing values. RESULTS We introduce GeCoNet-Tool, an integrated gene co-expression network construction and analysis tool. The tool comprises two main parts: network construction and network analysis. In the network construction part, GeCoNet-Tool offers users various options for processing gene co-expression data derived from diverse technologies. The output of the tool is an edge list with the option of weights associated with each link. In network analysis part, the user can produce a table that includes several network properties such as communities, cores, and centrality measures. With GeCoNet-Tool, users can explore and gain insights into the complex interactions between genes.
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Affiliation(s)
- Junyao Kuang
- Department of Electrical and Computer Engineering, Kansas State University, Manhattan, KS, 66506, USA.
| | - Kristin Michel
- Division of Biology, Kansas State University, Manhattan, KS, 66506, USA
| | - Caterina Scoglio
- Department of Electrical and Computer Engineering, Kansas State University, Manhattan, KS, 66506, USA
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5
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Darolti I, Mank JE. Sex-biased gene expression at single-cell resolution: cause and consequence of sexual dimorphism. Evol Lett 2023; 7:148-156. [PMID: 37251587 PMCID: PMC10210449 DOI: 10.1093/evlett/qrad013] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 03/08/2023] [Accepted: 04/06/2023] [Indexed: 05/31/2023] Open
Abstract
Gene expression differences between males and females are thought to be key for the evolution of sexual dimorphism, and sex-biased genes are often used to study the molecular footprint of sex-specific selection. However, gene expression is often measured from complex aggregations of diverse cell types, making it difficult to distinguish between sex differences in expression that are due to regulatory rewiring within similar cell types and those that are simply a consequence of developmental differences in cell-type abundance. To determine the role of regulatory versus developmental differences underlying sex-biased gene expression, we use single-cell transcriptomic data from multiple somatic and reproductive tissues of male and female guppies, a species that exhibits extensive phenotypic sexual dimorphism. Our analysis of gene expression at single-cell resolution demonstrates that nonisometric scaling between the cell populations within each tissue and heterogeneity in cell-type abundance between the sexes can influence inferred patterns of sex-biased gene expression by increasing both the false-positive and false-negative rates. Moreover, we show that, at the bulk level, the subset of sex-biased genes that are the product of sex differences in cell-type abundance can significantly confound patterns of coding-sequence evolution. Taken together, our results offer a unique insight into the effects of allometry and cellular heterogeneity on perceived patterns of sex-biased gene expression and highlight the power of single-cell RNA-sequencing in distinguishing between sex-biased genes that are the result of regulatory change and those that stem from sex differences in cell-type abundance, and hence are a consequence rather than a cause of sexual dimorphism.
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Affiliation(s)
- Iulia Darolti
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Judith E Mank
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
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6
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Hatchett WJ, Jueterbock AO, Kopp M, Coyer JA, Coelho SM, Hoarau G, Lipinska AP. Evolutionary dynamics of sex-biased gene expression in a young XY system: insights from the brown alga genus Fucus. New Phytol 2023; 238:422-437. [PMID: 36597732 DOI: 10.1111/nph.18710] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 12/16/2022] [Indexed: 06/17/2023]
Abstract
Sex-biased gene expression is considered to be an underlying cause of sexually dimorphic traits. Although the nature and degree of sex-biased expression have been well documented in several animal and plant systems, far less is known about the evolution of sex-biased genes in more distant eukaryotic groups. Here, we investigate sex-biased gene expression in two brown algal dioecious species, Fucus serratus and Fucus vesiculosus, where male heterogamety (XX/XY) has recently emerged. We find that in contrast to evolutionary distant plant and animal lineages, male-biased genes do not experience high turnover rates, but instead reveal remarkable conservation of bias and expression levels between the two species, suggesting their importance in sexual differentiation. Genes with consistent male bias were enriched in functions related to gamete production, along with sperm competition and include three flagellar proteins under positive selection. We present one of the first reports, outside of the animal kingdom, showing that male-biased genes display accelerated rates of coding sequence evolution compared with female-biased or unbiased genes. Our results imply that evolutionary forces affect male and female sex-biased genes differently on structural and regulatory levels, resulting in unique properties of differentially expressed transcripts during reproductive development in Fucus algae.
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Affiliation(s)
- William J Hatchett
- Faculty of Biosciences and Aquaculture, Nord University, 8026, Bodø, Norway
| | | | - Martina Kopp
- Faculty of Biosciences and Aquaculture, Nord University, 8026, Bodø, Norway
| | - James A Coyer
- Shoals Marine Laboratory, University of New Hampshire, Durham, NH, 03824, USA
| | - Susana M Coelho
- CNRS, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Sorbonne Université, Station Biologique de Roscoff, 29680, Roscoff, France
- Department of Algal Development and Evolution, Max Planck Institute for Biology, 72076, Tuebingen, Germany
| | - Galice Hoarau
- Faculty of Biosciences and Aquaculture, Nord University, 8026, Bodø, Norway
| | - Agnieszka P Lipinska
- CNRS, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Sorbonne Université, Station Biologique de Roscoff, 29680, Roscoff, France
- Department of Algal Development and Evolution, Max Planck Institute for Biology, 72076, Tuebingen, Germany
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7
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Venkataraman K, Shai N, Lakhiani P, Zylka S, Zhao J, Herre M, Zeng J, Neal LA, Molina H, Zhao L, Vosshall LB. Two novel, tightly linked, and rapidly evolving genes underlie Aedes aegypti mosquito reproductive resilience during drought. eLife 2023; 12:e80489. [PMID: 36744865 PMCID: PMC10076016 DOI: 10.7554/elife.80489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Accepted: 01/29/2023] [Indexed: 02/07/2023] Open
Abstract
Female Aedes aegypti mosquitoes impose a severe global public health burden as vectors of multiple viral pathogens. Under optimal environmental conditions, Aedes aegypti females have access to human hosts that provide blood proteins for egg development, conspecific males that provide sperm for fertilization, and freshwater that serves as an egg-laying substrate suitable for offspring survival. As global temperatures rise, Aedes aegypti females are faced with climate challenges like intense droughts and intermittent precipitation, which create unpredictable, suboptimal conditions for egg-laying. Here, we show that under drought-like conditions simulated in the laboratory, females retain mature eggs in their ovaries for extended periods, while maintaining the viability of these eggs until they can be laid in freshwater. Using transcriptomic and proteomic profiling of Aedes aegypti ovaries, we identify two previously uncharacterized genes named tweedledee and tweedledum, each encoding a small, secreted protein that both show ovary-enriched, temporally-restricted expression during egg retention. These genes are mosquito-specific, linked within a syntenic locus, and rapidly evolving under positive selection, raising the possibility that they serve an adaptive function. CRISPR-Cas9 deletion of both tweedledee and tweedledum demonstrates that they are specifically required for extended retention of viable eggs. These results highlight an elegant example of taxon-restricted genes at the heart of an important adaptation that equips Aedes aegypti females with 'insurance' to flexibly extend their reproductive schedule without losing reproductive capacity, thus allowing this species to exploit unpredictable habitats in a changing world.
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Affiliation(s)
- Krithika Venkataraman
- Laboratory of Neurogenetics and Behavior, Rockefeller UniversityNew YorkUnited States
| | - Nadav Shai
- Laboratory of Neurogenetics and Behavior, Rockefeller UniversityNew YorkUnited States
- Howard Hughes Medical InstituteNew YorkUnited States
| | - Priyanka Lakhiani
- Laboratory of Neurogenetics and Behavior, Rockefeller UniversityNew YorkUnited States
- Laboratory of Evolutionary Genetics and Genomics, Rockefeller UniversityNew YorkUnited States
| | - Sarah Zylka
- Laboratory of Neurogenetics and Behavior, Rockefeller UniversityNew YorkUnited States
| | - Jieqing Zhao
- Laboratory of Neurogenetics and Behavior, Rockefeller UniversityNew YorkUnited States
| | - Margaret Herre
- Laboratory of Neurogenetics and Behavior, Rockefeller UniversityNew YorkUnited States
- Kavli Neural Systems InstituteNew YorkUnited States
| | - Joshua Zeng
- Laboratory of Neurogenetics and Behavior, Rockefeller UniversityNew YorkUnited States
| | - Lauren A Neal
- Laboratory of Neurogenetics and Behavior, Rockefeller UniversityNew YorkUnited States
| | - Henrik Molina
- Proteomics Resource Center, Rockefeller UniversityNew YorkUnited States
| | - Li Zhao
- Laboratory of Evolutionary Genetics and Genomics, Rockefeller UniversityNew YorkUnited States
| | - Leslie B Vosshall
- Laboratory of Neurogenetics and Behavior, Rockefeller UniversityNew YorkUnited States
- Howard Hughes Medical InstituteNew YorkUnited States
- Kavli Neural Systems InstituteNew YorkUnited States
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8
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Deng D, Xing S, Liu X, Ji Q, Zhai Z, Peng W. Transcriptome analysis of sex-biased gene expression in the spotted-wing Drosophila, Drosophila suzukii (Matsumura). G3 Genes|Genomes|Genetics 2022; 12:6588685. [PMID: 35587603 PMCID: PMC9339319 DOI: 10.1093/g3journal/jkac127] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 05/11/2022] [Indexed: 11/16/2022]
Abstract
Sexual dimorphism occurs widely throughout insects and has profound influences on evolutionary path. Sex-biased genes are considered to account for most of phenotypic differences between sexes. In order to explore the sex-biased genes potentially associated with sexual dimorphism and sexual development in Drosophila suzukii, a major devastating and invasive crop pest, we conducted whole-organism transcriptome profiling and sex-biased gene expression analysis on adults of both sexes. We identified transcripts of genes involved in several sex-specific physiological and functional processes, including transcripts involved in sex determination, reproduction, olfaction, and innate immune signals. A total of 11,360 differentially expressed genes were identified in the comparison, and 1,957 differentially expressed genes were female-biased and 4,231 differentially expressed genes were male-biased. The pathway predominantly enriched for differentially expressed genes was related to spliceosome, which might reflect the differences in the alternative splicing mechanism between males and females. Twenty-two sex determination and 16 sex-related reproduction genes were identified, and expression pattern analysis revealed that the majority of genes were differentially expressed between sexes. Additionally, the differences in sex-specific olfactory and immune processes were analyzed and the sex-biased expression of these genes may play important roles in pheromone and odor detection, and immune response. As a valuable dataset, our sex-specific transcriptomic data can significantly contribute to the fundamental elucidation of the molecular mechanisms of sexual dimorphism in fruit flies, and may provide candidate genes potentially useful for the development of genetic sexing strains, an important tool for sterile insect technique applications against this economically important species.
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Affiliation(s)
- Dan Deng
- Hunan Provincial Key Laboratory of Animal Intestinal Function and Regulation, State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan International Joint Laboratory of Animal Intestinal Ecology and Health, Hunan Normal University , Changsha 410081, China
| | - Shisi Xing
- Hunan Provincial Key Laboratory of Animal Intestinal Function and Regulation, State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan International Joint Laboratory of Animal Intestinal Ecology and Health, Hunan Normal University , Changsha 410081, China
| | - Xuxiang Liu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Key Lab of Biopesticide and Chemical Biology, Ministry of Education, Institute of Biological Control, Fujian Agriculture and Forestry University , Fuzhou 350002, China
| | - Qinge Ji
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Key Lab of Biopesticide and Chemical Biology, Ministry of Education, Institute of Biological Control, Fujian Agriculture and Forestry University , Fuzhou 350002, China
| | - Zongzhao Zhai
- Hunan Provincial Key Laboratory of Animal Intestinal Function and Regulation, State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan International Joint Laboratory of Animal Intestinal Ecology and Health, Hunan Normal University , Changsha 410081, China
| | - Wei Peng
- Hunan Provincial Key Laboratory of Animal Intestinal Function and Regulation, State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan International Joint Laboratory of Animal Intestinal Ecology and Health, Hunan Normal University , Changsha 410081, China
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9
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Miller D, Chen J, Liang J, Betrán E, Long M, Sharakhov IV. Retrogene Duplication and Expression Patterns Shaped by the Evolution of Sex Chromosomes in Malaria Mosquitoes. Genes (Basel) 2022; 13:genes13060968. [PMID: 35741730 PMCID: PMC9222922 DOI: 10.3390/genes13060968] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 05/23/2022] [Accepted: 05/25/2022] [Indexed: 12/19/2022] Open
Abstract
Genes that originate during evolution are an important source of novel biological functions. Retrogenes are functional copies of genes produced by retroduplication and as such are located in different genomic positions. To investigate retroposition patterns and retrogene expression, we computationally identified interchromosomal retroduplication events in nine portions of the phylogenetic history of malaria mosquitoes, making use of species that do or do not have classical sex chromosomes to test the roles of sex-linkage. We found 40 interchromosomal events and a significant excess of retroduplications from the X chromosome to autosomes among a set of young retrogenes. These young retroposition events occurred within the last 100 million years in lineages where all species possessed differentiated sex chromosomes. An analysis of available microarray and RNA-seq expression data for Anopheles gambiae showed that many of the young retrogenes evolved male-biased expression in the reproductive organs. Young autosomal retrogenes with increased meiotic or postmeiotic expression in the testes tend to be male biased. In contrast, older retrogenes, i.e., in lineages with undifferentiated sex chromosomes, do not show this particular chromosomal bias and are enriched for female-biased expression in reproductive organs. Our reverse-transcription PCR data indicates that most of the youngest retrogenes, which originated within the last 47.6 million years in the subgenus Cellia, evolved non-uniform expression patterns across body parts in the males and females of An. coluzzii. Finally, gene annotation revealed that mitochondrial function is a prominent feature of the young autosomal retrogenes. We conclude that mRNA-mediated gene duplication has produced a set of genes that contribute to mosquito reproductive functions and that different biases are revealed after the sex chromosomes evolve. Overall, these results suggest potential roles for the evolution of meiotic sex chromosome inactivation in males and of sexually antagonistic conflict related to mitochondrial energy function as the main selective pressures for X-to-autosome gene reduplication and testis-biased expression in these mosquito lineages.
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Affiliation(s)
- Duncan Miller
- Department of Entomology, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA; (D.M.); (J.L.)
| | - Jianhai Chen
- Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637, USA;
| | - Jiangtao Liang
- Department of Entomology, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA; (D.M.); (J.L.)
| | - Esther Betrán
- Department of Biology, University of Texas at Arlington, Arlington, TX 76019, USA;
| | - Manyuan Long
- Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637, USA;
- Correspondence: (M.L.); (I.V.S.)
| | - Igor V. Sharakhov
- Department of Entomology, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA; (D.M.); (J.L.)
- Department of Genetics and Cell Biology, Tomsk State University, 634050 Tomsk, Russia
- Correspondence: (M.L.); (I.V.S.)
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10
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Kuang J, Buchon N, Michel K, Scoglio C. A global [Formula: see text] gene co-expression network constructed from hundreds of experimental conditions with missing values. BMC Bioinformatics 2022; 23:170. [PMID: 35534830 PMCID: PMC9082846 DOI: 10.1186/s12859-022-04697-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 04/25/2022] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND Gene co-expression networks (GCNs) can be used to determine gene regulation and attribute gene function to biological processes. Different high throughput technologies, including one and two-channel microarrays and RNA-sequencing, allow evaluating thousands of gene expression data simultaneously, but these methodologies provide results that cannot be directly compared. Thus, it is complex to analyze co-expression relations between genes, especially when there are missing values arising for experimental reasons. Networks are a helpful tool for studying gene co-expression, where nodes represent genes and edges represent co-expression of pairs of genes. RESULTS In this paper, we establish a method for constructing a gene co-expression network for the Anopheles gambiae transcriptome from 257 unique studies obtained with different methodologies and experimental designs. We introduce the sliding threshold approach to select node pairs with high Pearson correlation coefficients. The resulting network, which we name AgGCN1.0, is robust to random removal of conditions and has similar characteristics to small-world and scale-free networks. Analysis of network sub-graphs revealed that the core is largely comprised of genes that encode components of the mitochondrial respiratory chain and the ribosome, while different communities are enriched for genes involved in distinct biological processes. CONCLUSION Analysis of the network reveals that both the architecture of the core sub-network and the network communities are based on gene function, supporting the power of the proposed method for GCN construction. Application of network science methodology reveals that the overall network structure is driven to maximize the integration of essential cellular functions, possibly allowing the flexibility to add novel functions.
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Affiliation(s)
- Junyao Kuang
- Department of Electrical and Computer Engineering, Kansas State University, Manhattan, KS 66506 USA
| | - Nicolas Buchon
- Department of Entomology, Cornell Institute of Host-Microbe Interactions and Disease, Cornell University, Ithaca, NY 14853 USA
| | - Kristin Michel
- Division of Biology, Kansas State University, Manhattan, KS 66506 USA
| | - Caterina Scoglio
- Department of Electrical and Computer Engineering, Kansas State University, Manhattan, KS 66506 USA
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11
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Esposito Verza A, Miggiano R, Lombardo F, Fiorillo C, Arcà B, Purghé B, Del Grosso E, Galli U, Rizzi M, Rossi F. Biochemical and structural analysis of a cytosolic sulfotransferase of the malaria vector Anopheles gambiae overexpressed in the reproductive tissues. Curr Res Struct Biol 2022; 4:246-255. [PMID: 35941867 PMCID: PMC9356239 DOI: 10.1016/j.crstbi.2022.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 05/30/2022] [Accepted: 07/11/2022] [Indexed: 12/01/2022] Open
Abstract
The temporary or permanent chemical modification of biomolecules is a crucial aspect in the physiology of all living species. However, while some modules are well characterised also in insects, others did not receive the same attention. This holds true for sulfo-conjugation that is catalysed by cytosolic sulfotransferases (SULT), a central component of the metabolism of endogenous low molecular weight molecules and xenobiotics. In particular, limited information is available about the functional roles of the mosquito predicted enzymes annotated as SULTs in genomic databases. The herein described research is the first example of a biochemical and structural study of a SULT of a mosquito species, in general, and of the malaria vector Anopheles gambiae in particular. We confirmed that the AGAP001425 transcript displays a peculiar expression pattern that is suggestive of a possible involvement in modulating the mosquito reproductive tissues physiology, a fact that could raise attention on the enzyme as a potential target for insect-containment strategies. The crystal structures of the enzyme in alternative ligand-bound states revealed elements distinguishing AgSULT-001425 from other characterized SULTs, including a peculiar conformational plasticity of a discrete region that shields the catalytic cleft and that could play a main role in the dynamics of the reaction and in the substrate selectivity of the enzyme. Along with further in vitro biochemical studies, our structural investigations could provide a framework for the discovery of small-molecule inhibitors to assess the effect of interfering with AgSULT-001425-mediated catalysis at the organismal level. Mosquito cytosolic sulfotransferases (SULT) are poorly characterized. A SULT-encoding gene is highly transcribed in Anopheles male reproductive system. The corresponding enzyme is a genuine SULT acting on small phenolic molecules. We solved the AgSULT crystal structure in its substrate-free and ligand-bound states. The peculiar features of AgSULT could drive the design of isozyme-specific inhibitors.
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Affiliation(s)
- Arianna Esposito Verza
- University of Piemonte Orientale, DSF Department of Pharmaceutical Sciences, Largo Donegani, 2, Novara, Italy
| | - Riccardo Miggiano
- University of Piemonte Orientale, DSF Department of Pharmaceutical Sciences, Largo Donegani, 2, Novara, Italy
| | - Fabrizio Lombardo
- Sapienza University of Rome, Department of Public Health and Infectious Diseases – Division of Parasitology, Piazzale Aldo Moro, 5, Rome, Italy
| | - Carmine Fiorillo
- Sapienza University of Rome, Department of Public Health and Infectious Diseases – Division of Parasitology, Piazzale Aldo Moro, 5, Rome, Italy
| | - Bruno Arcà
- Sapienza University of Rome, Department of Public Health and Infectious Diseases – Division of Parasitology, Piazzale Aldo Moro, 5, Rome, Italy
| | - Beatrice Purghé
- University of Piemonte Orientale, DSF Department of Pharmaceutical Sciences, Largo Donegani, 2, Novara, Italy
| | - Erika Del Grosso
- University of Piemonte Orientale, DSF Department of Pharmaceutical Sciences, Largo Donegani, 2, Novara, Italy
| | - Ubaldina Galli
- University of Piemonte Orientale, DSF Department of Pharmaceutical Sciences, Largo Donegani, 2, Novara, Italy
| | - Menico Rizzi
- University of Piemonte Orientale, DSF Department of Pharmaceutical Sciences, Largo Donegani, 2, Novara, Italy
| | - Franca Rossi
- University of Piemonte Orientale, DSF Department of Pharmaceutical Sciences, Largo Donegani, 2, Novara, Italy
- Corresponding author. University of Piemonte Orientale DSF - Department of Pharmaceutical Sciences, Largo Donegani, 2 - 28100, Novara, Italy.
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12
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Alcalay Y, Fuchs S, Galizi R, Bernardini F, Haghighat-Khah RE, Rusch DB, Adrion JR, Hahn MW, Tortosa P, Rotenberry R, Papathanos PA. The Potential for a Released Autosomal X-Shredder Becoming a Driving-Y Chromosome and Invasively Suppressing Wild Populations of Malaria Mosquitoes. Front Bioeng Biotechnol 2021; 9:752253. [PMID: 34957064 PMCID: PMC8698249 DOI: 10.3389/fbioe.2021.752253] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 10/15/2021] [Indexed: 11/16/2022] Open
Abstract
Sex-ratio distorters based on X-chromosome shredding are more efficient than sterile male releases for population suppression. X-shredding is a form of sex distortion that skews spermatogenesis of XY males towards the preferential transmission of Y-bearing gametes, resulting in a higher fraction of sons than daughters. Strains harboring X-shredders on autosomes were first developed in the malaria mosquito Anopheles gambiae, resulting in strong sex-ratio distortion. Since autosomal X-shredders are transmitted in a Mendelian fashion and can be selected against, their frequency in the population declines once releases are halted. However, unintended transfer of X-shredders to the Y-chromosome could produce an invasive meiotic drive element, that benefits from its biased transmission to the predominant male-biased offspring and its effective shielding from female negative selection. Indeed, linkage to the Y-chromosome of an active X-shredder instigated the development of the nuclease-based X-shredding system. Here, we analyze mechanisms whereby an autosomal X-shredder could become unintentionally Y-linked after release by evaluating the stability of an established X-shredder strain that is being considered for release, exploring its potential for remobilization in laboratory and wild-type genomes of An. gambiae and provide data regarding expression on the mosquito Y-chromosome. Our data suggest that an invasive X-shredder resulting from a post-release movement of such autosomal transgenes onto the Y-chromosome is unlikely.
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Affiliation(s)
- Yehonatan Alcalay
- Department of Entomology, Robert H. Smith Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, Rehovot, Israel
| | - Silke Fuchs
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Roberto Galizi
- Centre for Applied Entomology and Parasitology, School of Life Sciences, Keele University, Keele, United Kingdom
| | - Federica Bernardini
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | | | - Douglas B Rusch
- Center for Genomics and Bioinformatics, Indiana University, Bloomington, IN, United States
| | - Jeffrey R Adrion
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, United States
| | - Matthew W Hahn
- Department of Biology, Indiana University, Bloomington, IN, United States.,Department of Computer Science, Indiana University, Bloomington, IN, United States
| | - Pablo Tortosa
- Unité Mixte de Recherche Processus Infectieux en Milieu Insulaire Tropical (UMR PIMIT), Université de La Réunion, INSERM 1187, CNRS 9192, IRD 249, Plateforme de Recherche CYROI, Saint Denis, France
| | - Rachel Rotenberry
- Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Philippos Aris Papathanos
- Department of Entomology, Robert H. Smith Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, Rehovot, Israel
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13
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Terradas G, Hermann A, James AA, McGinnis W, Bier E. High-resolution in situ analysis of Cas9 germline transcript distributions in gene-drive Anopheles mosquitoes. G3 (Bethesda) 2021; 12:6428532. [PMID: 34791161 PMCID: PMC8728002 DOI: 10.1093/g3journal/jkab369] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 10/14/2021] [Indexed: 11/12/2022]
Abstract
Gene drives are programmable genetic elements that can spread beneficial traits into wild populations to aid in vector-borne pathogen control. Two different drives have been developed for population modification of mosquito vectors. The Reckh drive (vasa-Cas9) in Anopheles stephensi displays efficient allelic conversion through males but generates frequent drive-resistant mutant alleles when passed through females. In contrast, the AgNos-Cd1 drive (nos-Cas9) in An. gambiae achieves almost complete allelic conversion through both genders. Here, we examined the subcellular localization of RNA transcripts in the mosquito germline. In both transgenic lines, Cas9 is strictly co-expressed with endogenous genes in stem and pre-meiotic cells of the testes, where both drives display highly efficient conversion. However, we observed distinct co-localization patterns for the two drives in female reproductive tissues. These studies suggest potential determinants underlying efficient drive through the female germline. We also evaluated expression patterns of alternative germline genes for future gene-drive designs.
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Affiliation(s)
- Gerard Terradas
- Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, 92093, USA.,Tata Institute for Genetics and Society, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Anita Hermann
- Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, 92093, USA.,Tata Institute for Genetics and Society, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Anthony A James
- Department of Microbiology and Molecular Genetics, University of California, Irvine, CA, 92697, USA.,Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, 92697, USA
| | - William McGinnis
- Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Ethan Bier
- Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, 92093, USA.,Tata Institute for Genetics and Society, University of California, San Diego, La Jolla, CA, 92093, USA
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14
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Huylmans AK, Macon A, Hontoria F, Vicoso B. Transitions to asexuality and evolution of gene expression in Artemia brine shrimp. Proc Biol Sci 2021; 288:20211720. [PMID: 34547909 PMCID: PMC8456138 DOI: 10.1098/rspb.2021.1720] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 08/31/2021] [Indexed: 11/12/2022] Open
Abstract
While sexual reproduction is widespread among many taxa, asexual lineages have repeatedly evolved from sexual ancestors. Despite extensive research on the evolution of sex, it is still unclear whether this switch represents a major transition requiring major molecular reorganization, and how convergent the changes involved are. In this study, we investigated the phylogenetic relationship and patterns of gene expression of sexual and asexual lineages of Eurasian Artemia brine shrimp, to assess how gene expression patterns are affected by the transition to asexuality. We find only a few genes that are consistently associated with the evolution of asexuality, suggesting that this shift may not require an extensive overhauling of the meiotic machinery. While genes with sex-biased expression have high rates of expression divergence within Eurasian Artemia, neither female- nor male-biased genes appear to show unusual evolutionary patterns after sexuality is lost, contrary to theoretical expectations.
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Affiliation(s)
- Ann Kathrin Huylmans
- Institute of Science and Technology Austria, Am Campus 1, Klosterneuburg 3400, Austria
| | - Ariana Macon
- Institute of Science and Technology Austria, Am Campus 1, Klosterneuburg 3400, Austria
| | - Francisco Hontoria
- Instituto de Acuicultura de Torre de la Sal (IATS-CSIC), 12595 Ribera de Cabanes, Castellón, Spain
| | - Beatriz Vicoso
- Institute of Science and Technology Austria, Am Campus 1, Klosterneuburg 3400, Austria
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15
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Jayaswal V, Ndo C, Ma HC, Clifton BD, Pombi M, Cabrera K, Couhet A, Mouline K, Diabaté A, Dabiré R, Ayala D, Ranz JM. Intraspecific Transcriptome Variation and Sex-Biased Expression in Anopheles arabiensis. Genome Biol Evol 2021; 13:6357708. [PMID: 34432020 PMCID: PMC8449828 DOI: 10.1093/gbe/evab199] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/22/2021] [Indexed: 01/17/2023] Open
Abstract
The magnitude and functional patterns of intraspecific transcriptional variation in the anophelines, including those of sex-biased genes underlying sex-specific traits relevant for malaria transmission, remain understudied. As a result, how changes in expression levels drive adaptation in these species is poorly understood. We sequenced the female, male, and larval transcriptomes of three populations of Anopheles arabiensis from Burkina Faso. One-third of the genes were differentially expressed between populations, often involving insecticide resistance-related genes in a sample type-specific manner, and with the females showing the largest number of differentially expressed genes. At the genomic level, the X chromosome appears depleted of differentially expressed genes compared with the autosomes, chromosomes harboring inversions do not exhibit evidence for enrichment of such genes, and genes that are top contributors to functional enrichment patterns of population differentiation tend to be clustered in the genome. Further, the magnitude of variation for the sex expression ratio across populations did not substantially differ between male- and female-biased genes, except for some populations in which male-limited expressed genes showed more variation than their female counterparts. In fact, female-biased genes exhibited a larger level of interpopulation variation than male-biased genes, both when assayed in males and females. Beyond uncovering the extensive adaptive potential of transcriptional variation in An. Arabiensis, our findings suggest that the evolutionary rate of changes in expression levels on the X chromosome exceeds that on the autosomes, while pointing to female-biased genes as the most variable component of the An. Arabiensis transcriptome.
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Affiliation(s)
- Vivek Jayaswal
- School of Mathematics and Statistics, The University of Sydney, Sydney, NSW, Australia
| | - Cyrille Ndo
- Institut de Recherche en Sciences de la Santé, Bobo-Dioulasso, Burkina Faso
| | - Hsiu-Ching Ma
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, California, USA
| | - Bryan D Clifton
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, California, USA
| | - Marco Pombi
- Dipartimento di Sanità Pubblica e Malattie Infettive, University of Rome "Sapienza", Rome, Italy
| | - Kevin Cabrera
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, California, USA
| | - Anna Couhet
- Unité Mixte de Recherche Maladies Infectieuses et Vecteurs: Ecologie, Génétique, Evolution et Contrôle, University of Montpellier, CNRS, Montpellier, IRD, France
| | - Karine Mouline
- Unité Mixte de Recherche Maladies Infectieuses et Vecteurs: Ecologie, Génétique, Evolution et Contrôle, University of Montpellier, CNRS, Montpellier, IRD, France
| | - Abdoulaye Diabaté
- Institut de Recherche en Sciences de la Santé, Bobo-Dioulasso, Burkina Faso
| | - Roch Dabiré
- Institut de Recherche en Sciences de la Santé, Bobo-Dioulasso, Burkina Faso
| | - Diego Ayala
- Unité Mixte de Recherche Maladies Infectieuses et Vecteurs: Ecologie, Génétique, Evolution et Contrôle, University of Montpellier, CNRS, Montpellier, IRD, France
| | - José M Ranz
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, California, USA
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16
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Keller Valsecchi CI, Marois E, Basilicata MF, Georgiev P, Akhtar A. Distinct mechanisms mediate X chromosome dosage compensation in Anopheles and Drosophila. Life Sci Alliance 2021; 4:4/9/e202000996. [PMID: 34266874 PMCID: PMC8321682 DOI: 10.26508/lsa.202000996] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 06/27/2021] [Accepted: 06/28/2021] [Indexed: 12/14/2022] Open
Abstract
CRISPR knockout of msl-2 and epigenome analyses in Anopheles reveal that X chromosome dosage compensation in mosquitos and Drosophila is achieved by two different molecular mechanisms. Sex chromosomes induce potentially deleterious gene expression imbalances that are frequently corrected by dosage compensation (DC). Three distinct molecular strategies to achieve DC have been previously described in nematodes, fruit flies, and mammals. Is this a consequence of distinct genomes, functional or ecological constraints, or random initial commitment to an evolutionary trajectory? Here, we study DC in the malaria mosquito Anopheles gambiae. The Anopheles and Drosophila X chromosomes evolved independently but share a high degree of homology. We find that Anopheles achieves DC by a mechanism distinct from the Drosophila MSL complex–histone H4 lysine 16 acetylation pathway. CRISPR knockout of Anopheles msl-2 leads to embryonic lethality in both sexes. Transcriptome analyses indicate that this phenotype is not a consequence of defective X chromosome DC. By immunofluorescence and ChIP, H4K16ac does not preferentially enrich on the male X. Instead, the mosquito MSL pathway regulates conserved developmental genes. We conclude that a novel mechanism confers X chromosome up-regulation in Anopheles. Our findings highlight the pluralism of gene-dosage buffering mechanisms even under similar genomic and functional constraints.
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Affiliation(s)
| | - Eric Marois
- Université de Strasbourg, Centre National de la Recherche Scientifique (CNRS) UPR9022, Inserm U1257, Strasbourg, France
| | - M Felicia Basilicata
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany.,Institute of Molecular Biology (IMB), Mainz, Germany
| | - Plamen Georgiev
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Asifa Akhtar
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
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17
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Whittle CA, Kulkarni A, Extavour CG. Evolutionary dynamics of sex-biased genes expressed in cricket brains and gonads. J Evol Biol 2021; 34:1188-1211. [PMID: 34114713 DOI: 10.1111/jeb.13889] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 05/31/2021] [Indexed: 12/14/2022]
Abstract
Sex-biased gene expression, particularly sex-biased expression in the gonad, has been linked to rates of protein sequence evolution (nonsynonymous to synonymous substitutions, dN/dS) in animals. However, in insects, sex-biased expression studies remain centred on a few holometabolous species. Moreover, other major tissue types such as the brain remain underexplored. Here, we studied sex-biased gene expression and protein evolution in a hemimetabolous insect, the cricket Gryllus bimaculatus. We generated novel male and female RNA-seq data for two sexual tissue types, the gonad and somatic reproductive system, and for two core components of the nervous system, the brain and ventral nerve cord. From a genome-wide analysis, we report several core findings. Firstly, testis-biased genes had accelerated evolution, as compared to ovary-biased and unbiased genes, which was associated with positive selection events. Secondly, although sex-biased brain genes were much less common than for the gonad, they exhibited a striking tendency for rapid protein sequence evolution, an effect that was stronger for the female than male brain. Further, some sex-biased brain genes were linked to sexual functions and mating behaviours, which we suggest may have accelerated their evolution via sexual selection. Thirdly, a tendency for narrow cross-tissue expression breadth, suggesting low pleiotropy, was observed for sex-biased brain genes, suggesting relaxed purifying selection, which we speculate may allow enhanced freedom to evolve adaptive protein functional changes. The findings of rapid evolution of testis-biased genes and male and female-biased brain genes are discussed with respect to pleiotropy, positive selection and the mating biology of this cricket.
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Affiliation(s)
- Carrie A Whittle
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Arpita Kulkarni
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA.,Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Cassandra G Extavour
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA.,Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
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18
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Campos M, Rona LDP, Willis K, Christophides GK, MacCallum RM. Unravelling population structure heterogeneity within the genome of the malaria vector Anopheles gambiae. BMC Genomics 2021; 22:422. [PMID: 34103015 PMCID: PMC8185951 DOI: 10.1186/s12864-021-07722-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 05/18/2021] [Indexed: 12/26/2022] Open
Abstract
Background Whole genome re-sequencing provides powerful data for population genomic studies, allowing robust inferences of population structure, gene flow and evolutionary history. For the major malaria vector in Africa, Anopheles gambiae, other genetic aspects such as selection and adaptation are also important. In the present study, we explore population genetic variation from genome-wide sequencing of 765 An. gambiae and An. coluzzii specimens collected from across Africa. We used t-SNE, a recently popularized dimensionality reduction method, to create a 2D-map of An. gambiae and An. coluzzii genes that reflect their population structure similarities. Results The map allows intuitive navigation among genes distributed throughout the so-called “mainland” and numerous surrounding “island-like” gene clusters. These gene clusters of various sizes correspond predominantly to low recombination genomic regions such as inversions and centromeres, and also to recent selective sweeps. Because this mosquito species complex has been studied extensively, we were able to support our interpretations with previously published findings. Several novel observations and hypotheses are also made, including selective sweeps and a multi-locus selection event in Guinea-Bissau, a known intense hybridization zone between An. gambiae and An. coluzzii. Conclusions Our results present a rich dataset that could be utilized in functional investigations aiming to shed light onto An. gambiae s.l genome evolution and eventual speciation. In addition, the methodology presented here can be used to further characterize other species not so well studied as An. gambiae, shortening the time required to progress from field sampling to the identification of genes and genomic regions under unique evolutionary processes. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07722-y.
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Affiliation(s)
- Melina Campos
- Department of Life Sciences, Imperial College London, London, UK
| | - Luisa D P Rona
- Department of Life Sciences, Imperial College London, London, UK.,Department of Cell Biology, Embryology and Genetics, Federal University of Santa Catarina (UFSC), Florianópolis, Brazil.,National Institute of Science and Technology in Molecular Entomology, National Council for Scientific and Technological Development (INCT-EM, CNPq), Rio de Janeiro, Brazil
| | - Katie Willis
- Department of Life Sciences, Imperial College London, London, UK
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19
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Mysore K, Hapairai LK, Li P, Roethele JB, Sun L, Igiede J, Misenti JK, Duman-Scheel M. A functional requirement for sex-determination M/m locus region lncRNA genes in Aedes aegypti female larvae. Sci Rep 2021; 11:10657. [PMID: 34017069 DOI: 10.1038/s41598-021-90194-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Accepted: 04/30/2021] [Indexed: 01/25/2023] Open
Abstract
Although many putative long non-coding RNA (lncRNA) genes have been identified in insect genomes, few of these genes have been functionally validated. A screen for female-specific larvicides that facilitate Aedes aegypti male sex separation uncovered multiple interfering RNAs with target sites in lncRNA genes located in the M/m locus region, including loci within or tightly linked to the sex determination locus. Larval consumption of a Saccharomyces cerevisiae (yeast) strain engineered to express interfering RNA corresponding to lncRNA transcripts resulted in significant female death, yet had no impact on male survival or fitness. Incorporation of the yeast larvicides into mass culturing protocols facilitated scaled production and separation of fit adult males, indicating that yeast larvicides could benefit mosquito population control strategies that rely on mass releases of male mosquitoes. These studies functionally verified a female-specific developmental requirement for M/m locus region lncRNA genes, suggesting that sexually antagonistic lncRNA genes found within this highly repetitive pericentromeric DNA sequence may be contributing to the evolution of A. aegypti sex chromosomes.
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20
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Jiang H, Lin JQ, Sun L, Xu YC, Fang SG. Sex-Biased Gene Expression and Evolution in the Cerebrum and Syrinx of Chinese Hwamei ( Garrulax canorus). Genes (Basel) 2021; 12:genes12040569. [PMID: 33919806 PMCID: PMC8070764 DOI: 10.3390/genes12040569] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 04/01/2021] [Accepted: 04/12/2021] [Indexed: 11/16/2022] Open
Abstract
It is common that males and females display sexual dimorphisms, which usually result from sex-biased gene expression. Chinese hwamei (Garrulax canorus) is a good model for studying sex-biased gene expression because the song between the sexes is quite different. In this study, we analyze cerebrum and syrinx sex-biased gene expression and evolution using the de novo assembled Chinese hwamei transcriptome. In both the cerebrum and syrinx, our study revealed that most female-biased genes were actively expressed in females only, while most male-biased genes were actively expressed in both sexes. In addition, both male- and female-biased genes were enriched on the putative Z chromosome, suggesting the existence of sexually antagonistic genes and the insufficient dosage compensation of the Z-linked genes. We also identified a 9 Mb sex linkage region on the putative 4A chromosome which enriched more than 20% of female-biased genes. Resultantly, male-biased genes in both tissues had significantly higher Ka/Ks and effective number of codons (ENCs) than unbiased genes, and this suggested that male-biased genes which exhibit accelerated divergence may have resulted from positive selection. Taken together, our results initially revealed the reasons for the differences in singing behavior between males and females of Chinese hwamei.
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Affiliation(s)
- Hua Jiang
- MOE Key Laboratory of Biosystems Homeostasis & Protection, State Conservation Centre for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou 310058, China; (H.J.); (J.-Q.L.); (L.S.)
| | - Jian-Qing Lin
- MOE Key Laboratory of Biosystems Homeostasis & Protection, State Conservation Centre for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou 310058, China; (H.J.); (J.-Q.L.); (L.S.)
| | - Li Sun
- MOE Key Laboratory of Biosystems Homeostasis & Protection, State Conservation Centre for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou 310058, China; (H.J.); (J.-Q.L.); (L.S.)
| | - Yan-Chun Xu
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China;
- National Forestry and Grassland Administration Research Center of Engineering Technology for Wildlife Conservation, Harbin 150040, China
| | - Sheng-Guo Fang
- MOE Key Laboratory of Biosystems Homeostasis & Protection, State Conservation Centre for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou 310058, China; (H.J.); (J.-Q.L.); (L.S.)
- Correspondence: ; Tel.: +86-571-88206472
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21
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Chen XI, Mei Y, Chen M, Jing D, He Y, Liu F, He K, Li F. InSexBase: an annotated genomic resource of sex chromosomes and sex-biased genes in insects. Database (Oxford) 2021; 2021:6122465. [PMID: 33507270 PMCID: PMC7904046 DOI: 10.1093/database/baab001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 11/09/2020] [Accepted: 01/06/2021] [Indexed: 11/13/2022]
Abstract
Sex determination and the regulation of sexual dimorphism are among the most fascinating topics in modern biology. As the most species-rich group of sexually reproducing organisms on Earth, insects have multiple sex determination systems. Though sex chromosomes and sex-biased genes are well-studied in dozens of insects, their gene sequences are scattered in various databases. Moreover, a shortage of annotation hinders the deep mining of these data. Here, we collected the chromosome-level sex chromosome data of 49 insect species, including 34 X chromosomes, 15 Z chromosomes, 5 W chromosomes and 2 Y chromosomes. We also obtained Y-linked contigs of four insects species—Anopheles gambiae, Drosophila innubila, Drosophila yakuba and Tribolium castaneum. The unannotated chromosome-level sex chromosomes were annotated using a standard pipeline, yielding a total of 123 030 protein-coding genes, 2 159 427 repeat sequences, 894 miRNAs, 1574 rRNAs, 5105 tRNAs, 395 snoRNAs (small nucleolar RNA), 54 snRNAs (small nuclear RNA) and 5959 other ncRNAs (non-coding RNA). In addition, 36 781 sex-biased genes were identified by analyzing 62 RNA-seq (RNA sequencing) datasets. Together with 5707 sex-biased genes from the Drosophila genus collected from the Sex-Associated Gene Database, we obtained a total of 42 488 sex-biased genes from 13 insect species. All these data were deposited into InSexBase, a new user-friendly database of insect sex chromosomes and sex-biased genes. Database URL:http://www.insect-genome.com/Sexdb/.
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Affiliation(s)
- X I Chen
- Ministry of Agriculture and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects & Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, Yuhangtang Rd 866, Xihu District, Hanzghou, 310058, China
| | - Yang Mei
- Ministry of Agriculture and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects & Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, Yuhangtang Rd 866, Xihu District, Hanzghou, 310058, China
| | - Mengyao Chen
- Ministry of Agriculture and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects & Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, Yuhangtang Rd 866, Xihu District, Hanzghou, 310058, China
| | - Dong Jing
- Ministry of Agriculture and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects & Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, Yuhangtang Rd 866, Xihu District, Hanzghou, 310058, China
| | - Yumin He
- Ministry of Agriculture and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects & Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, Yuhangtang Rd 866, Xihu District, Hanzghou, 310058, China
| | - Feiling Liu
- Ministry of Agriculture and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects & Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, Yuhangtang Rd 866, Xihu District, Hanzghou, 310058, China
| | - Kang He
- Ministry of Agriculture and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects & Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, Yuhangtang Rd 866, Xihu District, Hanzghou, 310058, China
| | - Fei Li
- Ministry of Agriculture and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects & Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, Yuhangtang Rd 866, Xihu District, Hanzghou, 310058, China
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22
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Chuang YM, Agunbiade TA, Tang XD, Freudzon M, Almeras L, Fikrig E. The Effects of A Mosquito Salivary Protein on Sporozoite Traversal of Host Cells. J Infect Dis 2020; 224:544-553. [PMID: 33306099 DOI: 10.1093/infdis/jiaa759] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 12/09/2020] [Indexed: 01/03/2023] Open
Abstract
Malaria begins when Plasmodium-infected Anopheles mosquitoes take a blood meal on a vertebrate. During the initial probing process, mosquitoes inject saliva and sporozoites into the host skin. Components of mosquito saliva have the potential to influence sporozoite functionality. Sporozoite-associated mosquito saliva protein 1 (SAMSP1; AGAP013726) was among several proteins identified when sporozoites were isolated from saliva, suggesting it may have an effect on Plasmodium. Recombinant SAMSP1 enhanced sporozoite gliding and cell traversal activity in vitro. Moreover, SAMSP1 decreased neutrophil chemotaxis in vivo and in vitro, thereby also exerting an influence on the host environment in which the sporozoites reside. Active or passive immunization of mice with SAMSP1 or SAMSP1 antiserum diminished the initial Plasmodium burden after infection. Passive immunization of mice with SAMSP1 antiserum also added to the protective effect of a circumsporozoite protein monoclonal antibody. SAMSP1 is, therefore, a mosquito saliva protein that can influence sporozoite infectivity in the vertebrate host.
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Affiliation(s)
- Yu-Min Chuang
- Section of Infectious Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Tolulope A Agunbiade
- Department of Entomology and Nematology, University of Florida, Gainesville, Florida, USA
| | - Xu-Dong Tang
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, China
| | - Marianna Freudzon
- Department of Dermatology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Lionel Almeras
- Unité de Parasitologie et Entomologie, Département de Microbiologie et Maladies Infectieuses, Institut de Recherche Biomédicale des Armées, Marseille, France.,Aix Marseille Université, IRD, AP-HM, SSA, UMR Vecteurs-Infections Tropicales et Méditerranéennes, IHU-Méditerranée Infection, Marseille, France
| | - Erol Fikrig
- Section of Infectious Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
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23
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O’Leary S, Adelman ZN. CRISPR/Cas9 knockout of female-biased genes AeAct-4 or myo-fem in Ae. aegypti results in a flightless phenotype in female, but not male mosquitoes. PLoS Negl Trop Dis 2020; 14:e0008971. [PMID: 33338046 PMCID: PMC7781531 DOI: 10.1371/journal.pntd.0008971] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 01/04/2021] [Accepted: 11/11/2020] [Indexed: 02/04/2023] Open
Abstract
Aedes aegypti is a vector of dengue, chikungunya, and Zika viruses. Current vector control strategies such as community engagement, source reduction, and insecticides have not been sufficient to prevent viral outbreaks. Thus, interest in novel strategies involving genetic engineering is growing. Female mosquitoes rely on flight to mate with males and obtain a bloodmeal from a host. We hypothesized that knockout of genes specifically expressed in female mosquitoes associated with the indirect flight muscles would result in a flightless female mosquito. Using CRISPR-Cas9 we generated loss-of-function mutations in several genes hypothesized to control flight in mosquitoes, including actin (AeAct-4) and myosin (myo-fem) genes expressed specifically in the female flight muscle. Genetic knockout of these genes resulted in 100% flightless females, with homozygous males able to fly, mate, and produce offspring, albeit at a reduced rate when compared to wild type males. Interestingly, we found that while AeAct-4 was haplosufficient, with most heterozygous individuals capable of flight, this was not the case for myo-fem, where about half of individuals carrying only one intact copy could not fly. These findings lay the groundwork for developing novel mechanisms of controlling Ae. aegypti populations, and our results suggest that this mechanism could be applicable to other vector species of mosquito.
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Affiliation(s)
- Sarah O’Leary
- Department of Entomology, Texas A&M University, College Station, Texas, United States of America
- Interdisciplinary Program in Genetics, Texas A&M University, College Station, Texas, United States of America
| | - Zach N. Adelman
- Department of Entomology, Texas A&M University, College Station, Texas, United States of America
- Interdisciplinary Program in Genetics, Texas A&M University, College Station, Texas, United States of America
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24
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Finch G, Nandyal S, Perretta C, Davies B, Rosendale AJ, Holmes CJ, Gantz JD, Spacht DE, Bailey ST, Chen X, Oyen K, Didion EM, Chakraborty S, Lee RE, Denlinger DL, Matter SF, Attardo GM, Weirauch MT, Benoit JB. Multi-level analysis of reproduction in an Antarctic midge identifies female and male accessory gland products that are altered by larval stress and impact progeny viability. Sci Rep 2020; 10:19791. [PMID: 33188214 PMCID: PMC7666147 DOI: 10.1038/s41598-020-76139-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 10/07/2020] [Indexed: 12/13/2022] Open
Abstract
The Antarctic midge, Belgica antarctica, is a wingless, non-biting midge endemic to Antarctica. Larval development requires at least 2 years, but adults live only 2 weeks. The nonfeeding adults mate in swarms and females die shortly after oviposition. Eggs are suspended in a gel of unknown composition that is expressed from the female accessory gland. This project characterizes molecular mechanisms underlying reproduction in this midge by examining differential gene expression in whole males, females, and larvae, as well as in male and female accessory glands. Functional studies were used to assess the role of the gel encasing the eggs, as well as the impact of stress on reproductive biology. RNA-seq analyses revealed sex- and development-specific gene sets along with those associated with the accessory glands. Proteomic analyses were used to define the composition of the egg-containing gel, which is generated during multiple developmental stages and derived from both the accessory gland and other female organs. Functional studies indicate the gel provides a larval food source as well as a buffer for thermal and dehydration stress. All of these function are critical to juvenile survival. Larval dehydration stress directly reduces production of storage proteins and key accessory gland components, a feature that impacts adult reproductive success. Modeling reveals that bouts of dehydration may have a significant impact on population growth. This work lays a foundation for further examination of reproduction in midges and provides new information related to general reproduction in dipterans. A key aspect of this work is that reproduction and stress dynamics, currently understudied in polar organisms, are likely to prove critical in determining how climate change will alter their survivability.
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Affiliation(s)
- Geoffrey Finch
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, USA
| | - Sonya Nandyal
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, USA
| | - Carlie Perretta
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, USA
| | - Benjamin Davies
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, USA
| | - Andrew J Rosendale
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, USA
- Department of Biology, Mount St. Joseph University, Cincinnati, OH, USA
| | - Christopher J Holmes
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, USA
| | - J D Gantz
- Department of Biology, Miami University, Oxford, OH, USA
- Department of Biology and Health Science, Hendrix College, Conway, AR, USA
| | - Drew E Spacht
- Departments of Entomology and Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH, USA
| | - Samuel T Bailey
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, USA
| | - Xiaoting Chen
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Kennan Oyen
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, USA
| | - Elise M Didion
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, USA
| | - Souvik Chakraborty
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, USA
| | - Richard E Lee
- Department of Biology, Miami University, Oxford, OH, USA
| | - David L Denlinger
- Departments of Entomology and Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH, USA
| | - Stephen F Matter
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, USA
| | - Geoffrey M Attardo
- Department of Entomology and Nematology, University of California, Davis, Davis, CA, 95616, USA
| | - Matthew T Weirauch
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
- Divisions of Biomedical Informatics and Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, 45267, USA
| | - Joshua B Benoit
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, USA.
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25
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Rocha EM, Katak RDM, Campos de Oliveira J, Araujo MDS, Carlos BC, Galizi R, Tripet F, Marinotti O, Souza-Neto JA. Vector-Focused Approaches to Curb Malaria Transmission in the Brazilian Amazon: An Overview of Current and Future Challenges and Strategies. Trop Med Infect Dis 2020; 5:E161. [PMID: 33092228 PMCID: PMC7709627 DOI: 10.3390/tropicalmed5040161] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 10/10/2020] [Accepted: 10/13/2020] [Indexed: 01/05/2023] Open
Abstract
In Brazil, malaria transmission is mostly confined to the Amazon, where substantial progress has been made towards disease control in the past decade. Vector control has been historically considered a fundamental part of the main malaria control programs implemented in Brazil. However, the conventional vector-control tools have been insufficient to control or eliminate local vector populations due to the complexity of the Amazonian rainforest environment and ecological features of malaria vector species in the Amazon, especially Anopheles darlingi. Malaria elimination in Brazil and worldwide eradication will require a combination of conventional and new approaches that takes into account the regional specificities of vector populations and malaria transmission dynamics. Here we present an overview on both conventional and novel promising vector-focused tools to curb malaria transmission in the Brazilian Amazon. If well designed and employed, vector-based approaches may improve the implementation of malaria-control programs, particularly in remote or difficult-to-access areas and in regions where existing interventions have been unable to eliminate disease transmission. However, much effort still has to be put into research expanding the knowledge of neotropical malaria vectors to set the steppingstones for the optimization of conventional and development of innovative vector-control tools.
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Affiliation(s)
- Elerson Matos Rocha
- Programa de Pós-Graduação em Biotecnologia, Universidade Federal do Amazonas—PPGBIOTEC/UFAM, Manaus 69067-005, Brazil; (E.M.R.); (R.d.M.K.); (J.C.d.O.)
| | - Ricardo de Melo Katak
- Programa de Pós-Graduação em Biotecnologia, Universidade Federal do Amazonas—PPGBIOTEC/UFAM, Manaus 69067-005, Brazil; (E.M.R.); (R.d.M.K.); (J.C.d.O.)
| | - Juan Campos de Oliveira
- Programa de Pós-Graduação em Biotecnologia, Universidade Federal do Amazonas—PPGBIOTEC/UFAM, Manaus 69067-005, Brazil; (E.M.R.); (R.d.M.K.); (J.C.d.O.)
| | - Maisa da Silva Araujo
- Laboratory of Medical Entomology, Oswaldo Cruz Foundation, FIOCRUZ RONDONIA, Porto Velho, RO 76812-245, Brazil;
| | - Bianca Cechetto Carlos
- Department of Bioprocesses and Biotechnology, School of Agricultural Sciences, São Paulo State University (UNESP), Botucatu 18610-034, Brazil;
- Central Multiuser Laboratory, School of Agricultural Sciences, São Paulo State University (UNESP), Botucatu 18610-034, Brazil
| | - Roberto Galizi
- Centre of Applied Entomology and Parasitology, School of Life Sciences, Keele University, Staffordshire ST5 5GB, UK; (R.G.); (F.T.)
| | - Frederic Tripet
- Centre of Applied Entomology and Parasitology, School of Life Sciences, Keele University, Staffordshire ST5 5GB, UK; (R.G.); (F.T.)
| | | | - Jayme A. Souza-Neto
- Department of Bioprocesses and Biotechnology, School of Agricultural Sciences, São Paulo State University (UNESP), Botucatu 18610-034, Brazil;
- Central Multiuser Laboratory, School of Agricultural Sciences, São Paulo State University (UNESP), Botucatu 18610-034, Brazil
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26
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Freitas L, Mesquita RD, Schrago CG. Survey for positively selected coding regions in the genome of the hematophagous tsetse fly Glossina morsitans identifies candidate genes associated with feeding habits and embryonic development. Genet Mol Biol 2020; 43:e20180311. [PMID: 32555940 PMCID: PMC7288665 DOI: 10.1590/1678-4685-gmb-2018-0311] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2018] [Accepted: 08/23/2019] [Indexed: 11/22/2022] Open
Abstract
Tsetse flies are responsible for the transmission of Trypanossoma sp. to vertebrate animals in Africa causing huge health issues and economic loss. The availability of the genome sequence of Glossina morsitans enabled the discovery of several genes related to medically important phenotypes and novel physiological features. However, a genome-wide scan for coding regions that underwent positive selection is still missing, which is surprising given the evolution of traits associated with the hematophagy in this lineage. In this study, we employed an experimental design that controlled for the rate of false positives and we performed a scan of 3,318 G. morsitans genes. We found 145 genes with significant historical signal of positive selection. These genes were categorized into 18 functional classes after careful manual annotation. Based on their attributed functions, we identified candidate genes related with feeding habits and embryonic development. When our results were contrasted with gene expression data, we confirmed that most genes that underwent adaptive molecular evolution were frequently expressed in organs associated with key physiological evolutionary innovations in the G. morsitans lineage, namely, the salivary gland, the midgut, fat body tissue, and in the spermatophore.
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Affiliation(s)
- Lucas Freitas
- Universidade Federal do Rio de Janeiro, Departamento de Genética, Rio de Janeiro, RJ, Brazil.,Universidade Federal do Rio de Janeiro, Instituto de Química, Departamento de Bioquímica, Laboratório de Bioinformática, Rio de Janeiro, RJ, Brazil.,Instituto Nacional de Ciência e Tecnologia em Entomologia Molecular, Rio de Janeiro, RJ, Brazil
| | - Rafael D Mesquita
- Universidade Federal do Rio de Janeiro, Instituto de Química, Departamento de Bioquímica, Laboratório de Bioinformática, Rio de Janeiro, RJ, Brazil.,Instituto Nacional de Ciência e Tecnologia em Entomologia Molecular, Rio de Janeiro, RJ, Brazil
| | - Carlos G Schrago
- Universidade Federal do Rio de Janeiro, Departamento de Genética, Rio de Janeiro, RJ, Brazil
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27
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Londono-Renteria B, Drame PM, Montiel J, Vasquez AM, Tobón-Castaño A, Taylor M, Vizcaino L, Lenhart AE. Identification and Pilot Evaluation of Salivary Peptides from Anopheles albimanus as Biomarkers for Bite Exposure and Malaria Infection in Colombia. Int J Mol Sci 2020; 21:ijms21030691. [PMID: 31973044 PMCID: PMC7037407 DOI: 10.3390/ijms21030691] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 01/16/2020] [Accepted: 01/19/2020] [Indexed: 01/23/2023] Open
Abstract
Insect saliva induces significant antibody responses associated with the intensity of exposure to bites and the risk of disease in humans. Several salivary biomarkers have been characterized to determine exposure intensity to Old World Anopheles mosquito species. However, new tools are needed to quantify the intensity of human exposure to Anopheles bites and understand the risk of malaria in low-transmission areas in the Americas. To address this need, we conducted proteomic and bioinformatic analyses of immunogenic candidate proteins present in the saliva of uninfected Anopheles albimanus from two separate colonies—one originating from Central America (STECLA strain) and one originating from South America (Cartagena strain). A ~65 kDa band was identified by IgG antibodies in serum samples from healthy volunteers living in a malaria endemic area in Colombia, and a total of five peptides were designed from the sequences of two immunogenic candidate proteins that were shared by both strains. ELISA-based testing of human IgG antibody levels against the peptides revealed that the transferrin-derived peptides, TRANS-P1, TRANS-P2 and a salivary peroxidase peptide (PEROX-P3) were able to distinguish between malaria-infected and uninfected groups. Interestingly, IgG antibody levels against PEROX-P3 were significantly lower in people that have never experienced malaria, suggesting that it may be a good marker for mosquito bite exposure in naïve populations such as travelers and deployed military personnel. In addition, the strength of the differences in the IgG levels against the peptides varied according to location, suggesting that the peptides may able to detect differences in intensities of bite exposure according to the mosquito population density. Thus, the An. albimanus salivary peptides TRANS-P1, TRANS-P2, and PEROX-P3 are promising biomarkers that could be exploited in a quantitative immunoassay for determination of human-vector contact and calculation of disease risk.
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Affiliation(s)
- Berlin Londono-Renteria
- Entomology Department, Vector Biology Laboratory, Kansas State University, 1603 Old Claflin Pl, 123 Waters Hall, Manhattan, KS 66506, USA;
- Correspondence: ; Tel.: +1-785-532-2120
| | - Papa M. Drame
- Department of Global Health, Duke University, 310 Trent Drive, Durham, NC 27710, USA;
| | - Jehidys Montiel
- Entomology Department, Vector Biology Laboratory, Kansas State University, 1603 Old Claflin Pl, 123 Waters Hall, Manhattan, KS 66506, USA;
| | - Ana M. Vasquez
- Calle 70 No. 52–21, Malaria Group, Universidad de Antioquia, Medellin, Antioquia 05001, Colombia; (A.M.V.); (A.T.-C.)
| | - Alberto Tobón-Castaño
- Calle 70 No. 52–21, Malaria Group, Universidad de Antioquia, Medellin, Antioquia 05001, Colombia; (A.M.V.); (A.T.-C.)
| | - Marissa Taylor
- Division of Parasitic Diseases and Malaria, Entomology Branch, Centers for Disease Control and Prevention (CDC), Atlanta, GA 30329, USA; (M.T.); (L.V.); (A.E.L.)
| | - Lucrecia Vizcaino
- Division of Parasitic Diseases and Malaria, Entomology Branch, Centers for Disease Control and Prevention (CDC), Atlanta, GA 30329, USA; (M.T.); (L.V.); (A.E.L.)
| | - Audrey E. Lenhart
- Division of Parasitic Diseases and Malaria, Entomology Branch, Centers for Disease Control and Prevention (CDC), Atlanta, GA 30329, USA; (M.T.); (L.V.); (A.E.L.)
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28
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Waterhouse RM, Aganezov S, Anselmetti Y, Lee J, Ruzzante L, Reijnders MJMF, Feron R, Bérard S, George P, Hahn MW, Howell PI, Kamali M, Koren S, Lawson D, Maslen G, Peery A, Phillippy AM, Sharakhova MV, Tannier E, Unger MF, Zhang SV, Alekseyev MA, Besansky NJ, Chauve C, Emrich SJ, Sharakhov IV. Evolutionary superscaffolding and chromosome anchoring to improve Anopheles genome assemblies. BMC Biol 2020; 18:1. [PMID: 31898513 PMCID: PMC6939337 DOI: 10.1186/s12915-019-0728-3] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 11/26/2019] [Indexed: 11/18/2022] Open
Abstract
Background New sequencing technologies have lowered financial barriers to whole genome sequencing, but resulting assemblies are often fragmented and far from ‘finished’. Updating multi-scaffold drafts to chromosome-level status can be achieved through experimental mapping or re-sequencing efforts. Avoiding the costs associated with such approaches, comparative genomic analysis of gene order conservation (synteny) to predict scaffold neighbours (adjacencies) offers a potentially useful complementary method for improving draft assemblies. Results We evaluated and employed 3 gene synteny-based methods applied to 21 Anopheles mosquito assemblies to produce consensus sets of scaffold adjacencies. For subsets of the assemblies, we integrated these with additional supporting data to confirm and complement the synteny-based adjacencies: 6 with physical mapping data that anchor scaffolds to chromosome locations, 13 with paired-end RNA sequencing (RNAseq) data, and 3 with new assemblies based on re-scaffolding or long-read data. Our combined analyses produced 20 new superscaffolded assemblies with improved contiguities: 7 for which assignments of non-anchored scaffolds to chromosome arms span more than 75% of the assemblies, and a further 7 with chromosome anchoring including an 88% anchored Anopheles arabiensis assembly and, respectively, 73% and 84% anchored assemblies with comprehensively updated cytogenetic photomaps for Anopheles funestus and Anopheles stephensi. Conclusions Experimental data from probe mapping, RNAseq, or long-read technologies, where available, all contribute to successful upgrading of draft assemblies. Our evaluations show that gene synteny-based computational methods represent a valuable alternative or complementary approach. Our improved Anopheles reference assemblies highlight the utility of applying comparative genomics approaches to improve community genomic resources.
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Affiliation(s)
- Robert M Waterhouse
- Department of Ecology and Evolution, University of Lausanne, and Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland.
| | - Sergey Aganezov
- Department of Computer Science, Princeton University, Princeton, NJ, 08450, USA.,Department of Computer Science, Johns Hopkins University, Baltimore, MD, 21218, USA
| | | | - Jiyoung Lee
- The Interdisciplinary PhD Program in Genetics, Bioinformatics, and Computational Biology, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA
| | - Livio Ruzzante
- Department of Ecology and Evolution, University of Lausanne, and Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland
| | - Maarten J M F Reijnders
- Department of Ecology and Evolution, University of Lausanne, and Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland
| | - Romain Feron
- Department of Ecology and Evolution, University of Lausanne, and Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland
| | - Sèverine Bérard
- ISEM, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Phillip George
- Department of Entomology, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA
| | - Matthew W Hahn
- Departments of Biology and Computer Science, Indiana University, Bloomington, IN, 47405, USA
| | - Paul I Howell
- Centers for Disease Control and Prevention, Atlanta, GA, 30329, USA
| | - Maryam Kamali
- Department of Entomology, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA.,Department of Medical Entomology and Parasitology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Sergey Koren
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Daniel Lawson
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, UK
| | - Gareth Maslen
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, UK
| | - Ashley Peery
- Department of Entomology, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA
| | - Adam M Phillippy
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Maria V Sharakhova
- Department of Entomology, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA.,Laboratory of Ecology, Genetics and Environmental Protection, Tomsk State University, Tomsk, Russia, 634050
| | - Eric Tannier
- Laboratoire de Biométrie et Biologie Evolutive, Université Lyon 1, Unité Mixte de Recherche 5558 Centre National de la Recherche Scientifique, 69622, Villeurbanne, France.,Institut national de recherche en informatique et en automatique, Montbonnot, 38334, Grenoble, Rhône-Alpes, France
| | - Maria F Unger
- Eck Institute for Global Health and Department of Biological Sciences, University of Notre Dame, Galvin Life Sciences Building, Notre Dame, IN, 46556, USA
| | - Simo V Zhang
- Departments of Biology and Computer Science, Indiana University, Bloomington, IN, 47405, USA
| | - Max A Alekseyev
- Department of Mathematics and Computational Biology Institute, George Washington University, Ashburn, VA, 20147, USA
| | - Nora J Besansky
- Eck Institute for Global Health and Department of Biological Sciences, University of Notre Dame, Galvin Life Sciences Building, Notre Dame, IN, 46556, USA
| | - Cedric Chauve
- Department of Mathematics, Simon Fraser University, Burnaby, British Columbia, V5A 1S6, Canada
| | - Scott J Emrich
- Department of Electrical Engineering and Computer Science, University of Tennessee, Knoxville, TN, 37996, USA
| | - Igor V Sharakhov
- The Interdisciplinary PhD Program in Genetics, Bioinformatics, and Computational Biology, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA. .,Department of Entomology, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA. .,Laboratory of Ecology, Genetics and Environmental Protection, Tomsk State University, Tomsk, Russia, 634050.
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29
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Taxiarchi C, Kranjc N, Kriezis A, Kyrou K, Bernardini F, Russell S, Nolan T, Crisanti A, Galizi R. High-resolution transcriptional profiling of Anopheles gambiae spermatogenesis reveals mechanisms of sex chromosome regulation. Sci Rep 2019; 9:14841. [PMID: 31619757 DOI: 10.1038/s41598-019-51181-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 09/25/2019] [Indexed: 12/20/2022] Open
Abstract
Although of high priority for the development of genetic tools to control malaria-transmitting mosquitoes, only a few germline-specific regulatory regions have been characterised to date and the presence of global regulatory mechanisms, such as dosage compensation and meiotic sex chromosome inactivation (MSCI), are mostly assumed from transcriptomic analyses of reproductive tissues or whole gonads. In such studies, samples include a significant portion of somatic tissues inevitably complicating the reconstruction of a defined transcriptional map of gametogenesis. By exploiting recent advances in transgenic technologies and gene editing tools, combined with fluorescence-activated cell sorting and RNA sequencing, we have separated four distinct cell lineages from the Anopheles gambiae male gonads: premeiotic, meiotic (primary and secondary spermatocytes) and postmeiotic. By comparing the overall expression levels of X-linked and autosomal genes across the four populations, we revealed a striking transcriptional repression of the X chromosome coincident with the meiotic phase, classifiable as MSCI, and highlighted genes that may evade silencing. In addition, chromosome-wide median expression ratios of the premeiotic population confirmed the absence of dosage compensation in the male germline. Applying differential expression analysis, we highlighted genes and transcript isoforms enriched at specific timepoints and reconstructed the expression dynamics of the main biological processes regulating the key stages of sperm development and maturation. We generated the first transcriptomic atlas of A. gambiae spermatogenesis that will expand the available toolbox for the genetic engineering of vector control technologies. We also describe an innovative and multidimensional approach to isolate specific cell lineages that can be used for the targeted analysis of other A. gambiae organs or transferred to other medically relevant species and model organisms.
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30
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Vizán-Rico HI, Mayer C, Petersen M, McKenna DD, Zhou X, Gómez-Zurita J. Patterns and Constraints in the Evolution of Sperm Individualization Genes in Insects, with an Emphasis on Beetles. Genes (Basel) 2019; 10:E776. [PMID: 31590243 PMCID: PMC6826512 DOI: 10.3390/genes10100776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2019] [Revised: 09/20/2019] [Accepted: 10/01/2019] [Indexed: 11/17/2022] Open
Abstract
Gene expression profiles can change dramatically between sexes and sex bias may contribute specific macroevolutionary dynamics for sex-biased genes. However, these dynamics are poorly understood at large evolutionary scales due to the paucity of studies that have assessed orthology and functional homology for sex-biased genes and the pleiotropic effects possibly constraining their evolutionary potential. Here, we explore the correlation of sex-biased expression with macroevolutionary processes that are associated with sex-biased genes, including duplications and accelerated evolutionary rates. Specifically, we examined these traits in a group of 44 genes that orchestrate sperm individualization during spermatogenesis, with both unbiased and sex-biased expression. We studied these genes in the broad evolutionary framework of the Insecta, with a particular focus on beetles (order Coleoptera). We studied data mined from 119 insect genomes, including 6 beetle models, and from 19 additional beetle transcriptomes. For the subset of physically and/or genetically interacting proteins, we also analyzed how their network structure may condition the mode of gene evolution. The collection of genes was highly heterogeneous in duplication status, evolutionary rates, and rate stability, but there was statistical evidence for sex bias correlated with faster evolutionary rates, consistent with theoretical predictions. Faster rates were also correlated with clocklike (insect amino acids) and non-clocklike (beetle nucleotides) substitution patterns in these genes. Statistical associations (higher rates for central nodes) or lack thereof (centrality of duplicated genes) were in contrast to some current evolutionary hypotheses, highlighting the need for more research on these topics.
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Affiliation(s)
- Helena I. Vizán-Rico
- Animal Biodiversity and Evolution, Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), 08003 Barcelona, Spain;
| | - Christoph Mayer
- Center for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, 53113 Bonn, Germany; (C.M.); (M.P.)
| | - Malte Petersen
- Center for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, 53113 Bonn, Germany; (C.M.); (M.P.)
| | - Duane D. McKenna
- Center for Biodiversity Research, Department of Biological Sciences, University of Memphis, Memphis, TN 38152, USA;
| | - Xin Zhou
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing 100193, China;
| | - Jesús Gómez-Zurita
- Animal Biodiversity and Evolution, Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), 08003 Barcelona, Spain;
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31
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Mathers TC, Mugford ST, Percival-Alwyn L, Chen Y, Kaithakottil G, Swarbreck D, Hogenhout SA, van Oosterhout C. Sex-specific changes in the aphid DNA methylation landscape. Mol Ecol 2019; 28:4228-4241. [PMID: 31472081 PMCID: PMC6857007 DOI: 10.1111/mec.15216] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 07/22/2019] [Indexed: 12/15/2022]
Abstract
Aphids present an ideal system to study epigenetics as they can produce diverse, but genetically identical, morphs in response to environmental stimuli. Here, using whole genome bisulphite sequencing and transcriptome sequencing of the green peach aphid (Myzus persicae), we present the first detailed analysis of cytosine methylation in an aphid and investigate differences in the methylation and transcriptional landscapes of male and asexual female morphs. We found that methylation primarily occurs in a CG dinucleotide (CpG) context and that exons are highly enriched for methylated CpGs, particularly at the 3' end of genes. Methylation is positively associated with gene expression, and methylated genes are more stably expressed than unmethylated genes. Male and asexual female morphs have distinct methylation profiles. Strikingly, these profiles are divergent between the sex chromosome and the autosomes; autosomal genes are hypomethylated in males compared to asexual females, whereas genes belonging to the sex chromosome, which is haploid in males, are hypermethylated. Overall, we found correlated changes in methylation and gene expression between males and asexual females, and this correlation was particularly strong for genes located on the sex chromosome. Our results suggest that differential methylation of sex-biased genes plays a role in aphid sexual differentiation.
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Affiliation(s)
- Thomas C Mathers
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, UK
| | - Sam T Mugford
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, UK
| | | | - Yazhou Chen
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, UK
| | | | | | - Saskia A Hogenhout
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, UK
| | - Cock van Oosterhout
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
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32
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Attardo GM, Abd-Alla AMM, Acosta-Serrano A, Allen JE, Bateta R, Benoit JB, Bourtzis K, Caers J, Caljon G, Christensen MB, Farrow DW, Friedrich M, Hua-Van A, Jennings EC, Larkin DM, Lawson D, Lehane MJ, Lenis VP, Lowy-Gallego E, Macharia RW, Malacrida AR, Marco HG, Masiga D, Maslen GL, Matetovici I, Meisel RP, Meki I, Michalkova V, Miller WJ, Minx P, Mireji PO, Ometto L, Parker AG, Rio R, Rose C, Rosendale AJ, Rota-Stabelli O, Savini G, Schoofs L, Scolari F, Swain MT, Takáč P, Tomlinson C, Tsiamis G, Van Den Abbeele J, Vigneron A, Wang J, Warren WC, Waterhouse RM, Weirauch MT, Weiss BL, Wilson RK, Zhao X, Aksoy S. Comparative genomic analysis of six Glossina genomes, vectors of African trypanosomes. Genome Biol 2019; 20:187. [PMID: 31477173 PMCID: PMC6721284 DOI: 10.1186/s13059-019-1768-2] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 07/22/2019] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Tsetse flies (Glossina sp.) are the vectors of human and animal trypanosomiasis throughout sub-Saharan Africa. Tsetse flies are distinguished from other Diptera by unique adaptations, including lactation and the birthing of live young (obligate viviparity), a vertebrate blood-specific diet by both sexes, and obligate bacterial symbiosis. This work describes the comparative analysis of six Glossina genomes representing three sub-genera: Morsitans (G. morsitans morsitans, G. pallidipes, G. austeni), Palpalis (G. palpalis, G. fuscipes), and Fusca (G. brevipalpis) which represent different habitats, host preferences, and vectorial capacity. RESULTS Genomic analyses validate established evolutionary relationships and sub-genera. Syntenic analysis of Glossina relative to Drosophila melanogaster shows reduced structural conservation across the sex-linked X chromosome. Sex-linked scaffolds show increased rates of female-specific gene expression and lower evolutionary rates relative to autosome associated genes. Tsetse-specific genes are enriched in protease, odorant-binding, and helicase activities. Lactation-associated genes are conserved across all Glossina species while male seminal proteins are rapidly evolving. Olfactory and gustatory genes are reduced across the genus relative to other insects. Vision-associated Rhodopsin genes show conservation of motion detection/tracking functions and variance in the Rhodopsin detecting colors in the blue wavelength ranges. CONCLUSIONS Expanded genomic discoveries reveal the genetics underlying Glossina biology and provide a rich body of knowledge for basic science and disease control. They also provide insight into the evolutionary biology underlying novel adaptations and are relevant to applied aspects of vector control such as trap design and discovery of novel pest and disease control strategies.
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Affiliation(s)
- Geoffrey M Attardo
- Department of Entomology and Nematology, University of California, Davis, Davis, CA, USA.
| | - Adly M M Abd-Alla
- Insect Pest Control Laboratory, Joint FAO/IAEA Division of Nuclear Techniques in Food & Agriculture, Vienna, Vienna, Austria
| | - Alvaro Acosta-Serrano
- Department of Vector Biology, Liverpool School of Tropical Medicine, Merseyside, Liverpool, UK
| | - James E Allen
- VectorBase, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, Cambridgeshire, UK
| | - Rosemary Bateta
- Department of Biochemistry, Biotechnology Research Institute - Kenya Agricultural and Livestock Research Organization, Kikuyu, Kenya
| | - Joshua B Benoit
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, USA
| | - Kostas Bourtzis
- Insect Pest Control Laboratory, Joint FAO/IAEA Division of Nuclear Techniques in Food & Agriculture, Vienna, Vienna, Austria
| | - Jelle Caers
- Department of Biology - Functional Genomics and Proteomics Group, KU Leuven, Leuven, Belgium
| | - Guy Caljon
- Laboratory of Microbiology, Parasitology and Hygiene, University of Antwerp, Antwerp, Belgium
| | - Mikkel B Christensen
- VectorBase, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, Cambridgeshire, UK
| | - David W Farrow
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, USA
| | - Markus Friedrich
- Department of Biological Sciences, Wayne State University, Detroit, MI, USA
| | - Aurélie Hua-Van
- Laboratoire Evolution, Genomes, Comportement, Ecologie, CNRS, IRD, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Emily C Jennings
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, USA
| | - Denis M Larkin
- Department of Comparative Biomedical Sciences, Royal Veterinary College, London, UK
| | - Daniel Lawson
- Department of Life Sciences, Imperial College London, London, UK
| | - Michael J Lehane
- Department of Vector Biology, Liverpool School of Tropical Medicine, Merseyside, Liverpool, UK
| | - Vasileios P Lenis
- Schools of Medicine and Dentistry, University of Plymouth, Plymouth, UK
| | - Ernesto Lowy-Gallego
- VectorBase, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, Cambridgeshire, UK
| | - Rosaline W Macharia
- Molecular Biology and Bioinformatics Unit, International Center for Insect Physiology and Ecology, Nairobi, Kenya.,Centre for Biotechnology and Bioinformatics, University of Nairobi, Nairobi, Kenya
| | - Anna R Malacrida
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
| | - Heather G Marco
- Department of Biological Sciences, University of Cape Town, Rondebosch, South Africa
| | - Daniel Masiga
- Molecular Biology and Bioinformatics Unit, International Center for Insect Physiology and Ecology, Nairobi, Kenya
| | - Gareth L Maslen
- VectorBase, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, Cambridgeshire, UK
| | - Irina Matetovici
- Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Richard P Meisel
- Department of Biology and Biochemistry, University of Houston, Houston, TX, USA
| | - Irene Meki
- Insect Pest Control Laboratory, Joint FAO/IAEA Division of Nuclear Techniques in Food & Agriculture, Vienna, Vienna, Austria
| | - Veronika Michalkova
- Department of Biological Sciences, Florida International University, Miami, Florida, USA.,Institute of Zoology, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Wolfgang J Miller
- Department of Cell and Developmental Biology, Medical University of Vienna, Vienna, Austria
| | - Patrick Minx
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - Paul O Mireji
- Department of Biochemistry, Biotechnology Research Institute - Kenya Agricultural and Livestock Research Organization, Kikuyu, Kenya.,Centre for Geographic Medicine Research Coast, Kenya Medical Research Institute, Kilifi, Kenya
| | - Lino Ometto
- Department of Sustainable Ecosystems and Bioresources, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, TN, Italy.,Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
| | - Andrew G Parker
- Insect Pest Control Laboratory, Joint FAO/IAEA Division of Nuclear Techniques in Food & Agriculture, Vienna, Vienna, Austria
| | - Rita Rio
- Department of Biology, West Virginia University, Morgantown, WV, USA
| | - Clair Rose
- Department of Vector Biology, Liverpool School of Tropical Medicine, Merseyside, Liverpool, UK
| | - Andrew J Rosendale
- Department of Biology, Mount St. Joseph University, Cincinnati, OH, USA.,Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, USA
| | - Omar Rota-Stabelli
- Department of Sustainable Ecosystems and Bioresources, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, TN, Italy
| | - Grazia Savini
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
| | - Liliane Schoofs
- Department of Biology - Functional Genomics and Proteomics Group, KU Leuven, Leuven, Belgium
| | - Francesca Scolari
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
| | - Martin T Swain
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, Ceredigion, UK
| | - Peter Takáč
- Department of Animal Systematics, Ústav zoológie SAV; Scientica, Ltd, Bratislava, Slovakia
| | - Chad Tomlinson
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - George Tsiamis
- Department of Environmental and Natural Resources Management, University of Patras, Agrinio, Etoloakarnania, Greece
| | | | - Aurelien Vigneron
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Jingwen Wang
- School of Life Sciences, Fudan University, Shanghai, China
| | - Wesley C Warren
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA.,Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
| | - Robert M Waterhouse
- Department of Ecology & Evolution, Swiss Institute of Bioinformatics, University of Lausanne, Lausanne, Switzerland
| | - Matthew T Weirauch
- Center for Autoimmune Genomics and Etiology and Divisions of Biomedical Informatics and Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Brian L Weiss
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Richard K Wilson
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - Xin Zhao
- CAS Center for Influenza Research and Early-warning (CASCIRE), Chinese Academy of Sciences, Beijing, China
| | - Serap Aksoy
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA.
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33
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Attardo GM, Abd-Alla AMM, Acosta-Serrano A, Allen JE, Bateta R, Benoit JB, Bourtzis K, Caers J, Caljon G, Christensen MB, Farrow DW, Friedrich M, Hua-Van A, Jennings EC, Larkin DM, Lawson D, Lehane MJ, Lenis VP, Lowy-Gallego E, Macharia RW, Malacrida AR, Marco HG, Masiga D, Maslen GL, Matetovici I, Meisel RP, Meki I, Michalkova V, Miller WJ, Minx P, Mireji PO, Ometto L, Parker AG, Rio R, Rose C, Rosendale AJ, Rota-Stabelli O, Savini G, Schoofs L, Scolari F, Swain MT, Takáč P, Tomlinson C, Tsiamis G, Van Den Abbeele J, Vigneron A, Wang J, Warren WC, Waterhouse RM, Weirauch MT, Weiss BL, Wilson RK, Zhao X, Aksoy S. Comparative genomic analysis of six Glossina genomes, vectors of African trypanosomes. Genome Biol 2019; 20:187. [PMID: 31477173 DOI: 10.1101/531749] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 07/22/2019] [Indexed: 05/24/2023] Open
Abstract
BACKGROUND Tsetse flies (Glossina sp.) are the vectors of human and animal trypanosomiasis throughout sub-Saharan Africa. Tsetse flies are distinguished from other Diptera by unique adaptations, including lactation and the birthing of live young (obligate viviparity), a vertebrate blood-specific diet by both sexes, and obligate bacterial symbiosis. This work describes the comparative analysis of six Glossina genomes representing three sub-genera: Morsitans (G. morsitans morsitans, G. pallidipes, G. austeni), Palpalis (G. palpalis, G. fuscipes), and Fusca (G. brevipalpis) which represent different habitats, host preferences, and vectorial capacity. RESULTS Genomic analyses validate established evolutionary relationships and sub-genera. Syntenic analysis of Glossina relative to Drosophila melanogaster shows reduced structural conservation across the sex-linked X chromosome. Sex-linked scaffolds show increased rates of female-specific gene expression and lower evolutionary rates relative to autosome associated genes. Tsetse-specific genes are enriched in protease, odorant-binding, and helicase activities. Lactation-associated genes are conserved across all Glossina species while male seminal proteins are rapidly evolving. Olfactory and gustatory genes are reduced across the genus relative to other insects. Vision-associated Rhodopsin genes show conservation of motion detection/tracking functions and variance in the Rhodopsin detecting colors in the blue wavelength ranges. CONCLUSIONS Expanded genomic discoveries reveal the genetics underlying Glossina biology and provide a rich body of knowledge for basic science and disease control. They also provide insight into the evolutionary biology underlying novel adaptations and are relevant to applied aspects of vector control such as trap design and discovery of novel pest and disease control strategies.
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Affiliation(s)
- Geoffrey M Attardo
- Department of Entomology and Nematology, University of California, Davis, Davis, CA, USA.
| | - Adly M M Abd-Alla
- Insect Pest Control Laboratory, Joint FAO/IAEA Division of Nuclear Techniques in Food & Agriculture, Vienna, Vienna, Austria
| | - Alvaro Acosta-Serrano
- Department of Vector Biology, Liverpool School of Tropical Medicine, Merseyside, Liverpool, UK
| | - James E Allen
- VectorBase, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, Cambridgeshire, UK
| | - Rosemary Bateta
- Department of Biochemistry, Biotechnology Research Institute - Kenya Agricultural and Livestock Research Organization, Kikuyu, Kenya
| | - Joshua B Benoit
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, USA
| | - Kostas Bourtzis
- Insect Pest Control Laboratory, Joint FAO/IAEA Division of Nuclear Techniques in Food & Agriculture, Vienna, Vienna, Austria
| | - Jelle Caers
- Department of Biology - Functional Genomics and Proteomics Group, KU Leuven, Leuven, Belgium
| | - Guy Caljon
- Laboratory of Microbiology, Parasitology and Hygiene, University of Antwerp, Antwerp, Belgium
| | - Mikkel B Christensen
- VectorBase, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, Cambridgeshire, UK
| | - David W Farrow
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, USA
| | - Markus Friedrich
- Department of Biological Sciences, Wayne State University, Detroit, MI, USA
| | - Aurélie Hua-Van
- Laboratoire Evolution, Genomes, Comportement, Ecologie, CNRS, IRD, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Emily C Jennings
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, USA
| | - Denis M Larkin
- Department of Comparative Biomedical Sciences, Royal Veterinary College, London, UK
| | - Daniel Lawson
- Department of Life Sciences, Imperial College London, London, UK
| | - Michael J Lehane
- Department of Vector Biology, Liverpool School of Tropical Medicine, Merseyside, Liverpool, UK
| | - Vasileios P Lenis
- Schools of Medicine and Dentistry, University of Plymouth, Plymouth, UK
| | - Ernesto Lowy-Gallego
- VectorBase, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, Cambridgeshire, UK
| | - Rosaline W Macharia
- Molecular Biology and Bioinformatics Unit, International Center for Insect Physiology and Ecology, Nairobi, Kenya
- Centre for Biotechnology and Bioinformatics, University of Nairobi, Nairobi, Kenya
| | - Anna R Malacrida
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
| | - Heather G Marco
- Department of Biological Sciences, University of Cape Town, Rondebosch, South Africa
| | - Daniel Masiga
- Molecular Biology and Bioinformatics Unit, International Center for Insect Physiology and Ecology, Nairobi, Kenya
| | - Gareth L Maslen
- VectorBase, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, Cambridgeshire, UK
| | - Irina Matetovici
- Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Richard P Meisel
- Department of Biology and Biochemistry, University of Houston, Houston, TX, USA
| | - Irene Meki
- Insect Pest Control Laboratory, Joint FAO/IAEA Division of Nuclear Techniques in Food & Agriculture, Vienna, Vienna, Austria
| | - Veronika Michalkova
- Department of Biological Sciences, Florida International University, Miami, Florida, USA
- Institute of Zoology, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Wolfgang J Miller
- Department of Cell and Developmental Biology, Medical University of Vienna, Vienna, Austria
| | - Patrick Minx
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - Paul O Mireji
- Department of Biochemistry, Biotechnology Research Institute - Kenya Agricultural and Livestock Research Organization, Kikuyu, Kenya
- Centre for Geographic Medicine Research Coast, Kenya Medical Research Institute, Kilifi, Kenya
| | - Lino Ometto
- Department of Sustainable Ecosystems and Bioresources, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, TN, Italy
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
| | - Andrew G Parker
- Insect Pest Control Laboratory, Joint FAO/IAEA Division of Nuclear Techniques in Food & Agriculture, Vienna, Vienna, Austria
| | - Rita Rio
- Department of Biology, West Virginia University, Morgantown, WV, USA
| | - Clair Rose
- Department of Vector Biology, Liverpool School of Tropical Medicine, Merseyside, Liverpool, UK
| | - Andrew J Rosendale
- Department of Biology, Mount St. Joseph University, Cincinnati, OH, USA
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, USA
| | - Omar Rota-Stabelli
- Department of Sustainable Ecosystems and Bioresources, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, TN, Italy
| | - Grazia Savini
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
| | - Liliane Schoofs
- Department of Biology - Functional Genomics and Proteomics Group, KU Leuven, Leuven, Belgium
| | - Francesca Scolari
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
| | - Martin T Swain
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, Ceredigion, UK
| | - Peter Takáč
- Department of Animal Systematics, Ústav zoológie SAV; Scientica, Ltd, Bratislava, Slovakia
| | - Chad Tomlinson
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - George Tsiamis
- Department of Environmental and Natural Resources Management, University of Patras, Agrinio, Etoloakarnania, Greece
| | | | - Aurelien Vigneron
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Jingwen Wang
- School of Life Sciences, Fudan University, Shanghai, China
| | - Wesley C Warren
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
- Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
| | - Robert M Waterhouse
- Department of Ecology & Evolution, Swiss Institute of Bioinformatics, University of Lausanne, Lausanne, Switzerland
| | - Matthew T Weirauch
- Center for Autoimmune Genomics and Etiology and Divisions of Biomedical Informatics and Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Brian L Weiss
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Richard K Wilson
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - Xin Zhao
- CAS Center for Influenza Research and Early-warning (CASCIRE), Chinese Academy of Sciences, Beijing, China
| | - Serap Aksoy
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA.
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34
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Abstract
The heterochromatic genome compartment mediates strictly conserved cellular processes such as chromosome segregation, telomere integrity, and genome stability. Paradoxically, heterochromatic DNA sequence is wildly unconserved. Recent reports that many hybrid incompatibility genes encode heterochromatin proteins, together with the observation that interspecies hybrids suffer aberrant heterochromatin-dependent processes, suggest that heterochromatic DNA packaging requires species-specific innovations. Testing this model of coevolution between fast-evolving heterochromatic DNA and its packaging proteins begins with defining the latter. Here we describe many such candidates encoded by the Heterochromatin Protein 1 (HP1) gene family across Diptera, an insect Order that encompasses dramatic episodes of heterochromatic sequence turnover. Using BLAST, synteny analysis, and phylogenetic tree building across 64 Diptera genomes, we discovered a staggering 121 HP1 duplication events. In contrast, we observed virtually no gene duplication in gene families that share a common “chromodomain” with HP1s, including Polycomb and Su(var)3-9. The remarkably high number of Dipteran HP1 paralogs arises from distant clades undergoing convergent HP1 family amplifications. These independently derived, young HP1s span diverse ages, domain structures, and rates of molecular evolution, including episodes of positive selection. Moreover, independently derived HP1s exhibit convergent expression evolution. While ancient HP1 parent genes are transcribed ubiquitously, young HP1 paralogs are transcribed primarily in male germline tissue, a pattern typical of young genes. Pervasive gene youth, rapid evolution, and germline specialization implicate heterochromatin-encoded selfish elements driving recurrent HP1 gene family expansions. The 121 young genes offer valuable experimental traction for elucidating the germline processes shaped by Diptera’s many dramatic episodes of heterochromatin turnover.
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Affiliation(s)
- Quentin Helleu
- Department of Biology, Epigenetics Institute, University of Pennsylvania, Philadelphia, PA
| | - Mia T Levine
- Department of Biology, Epigenetics Institute, University of Pennsylvania, Philadelphia, PA
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35
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Abstract
BACKGROUND Sex-biased gene expression is thought to drive the phenotypic differences in males and females in metazoans. Drosophila has served as a primary model for studying male-female differences in gene expression, and its effects on protein sequence divergence. However, the forces shaping evolution of sex-biased expression remain largely unresolved, including the roles of selection and pleiotropy. Research on sex organs in Drosophila, employing original approaches and multiple-species contrasts, provides a means to gain insights into factors shaping the turnover and magnitude (fold-bias) of sex-biased expression. RESULTS Here, using recent RNA-seq data, we studied sex-biased gonadal expression in 10,740 protein coding sequences in four species of Drosophila, D. melanogaster, D. simulans, D. yakuba and D. ananassae (5 to 44 My divergence). Using an approach wherein we identified genes with lineage-specific transitions (LSTs) in sex-biased status (amongst testis-biased, ovary-biased and unbiased; thus, six transition types) standardized to the number of genes with the ancestral state (S-LSTs), and those with clade-wide expression bias status, we reveal several key findings. First, the six categorical types of S-LSTs in sex-bias showed disparate rates of turnover, consistent with differential selection pressures. Second, the turnover in sex-biased status was largely unrelated to cross-tissue expression breadth, suggesting pleiotropy does not restrict evolution of sex-biased expression. Third, the fold-sex-biased expression, for both testis-biased and ovary-biased genes, evolved directionally over time toward higher values, a crucial finding that could be interpreted as a selective advantage of greater sex-bias, and sexual antagonism. Fourth, in terms of protein divergence, genes with LSTs to testis-biased expression exhibited weak signals of elevated rates of evolution (than ovary-biased) in as little as 5 My, which strengthened over time. Moreover, genes with clade-wide testis-specific expression (44 My), a status not observed for any ovary-biased genes, exhibited striking acceleration of protein divergence, which was linked to low pleiotropy. CONCLUSIONS By studying LSTs and clade-wide sex-biased gonadal expression in a multi-species clade of Drosophila, we describe evidence that interspecies turnover and magnitude of sex-biased expression have been influenced by selection. Further, whilst pleiotropy was not connected to turnover in sex-biased gonadal expression, it likely explains protein sequence divergence.
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Affiliation(s)
- Carrie A Whittle
- Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA, 02138, USA
| | - Cassandra G Extavour
- Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA, 02138, USA.
- Department of Molecular and Cellular Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA, 02138, USA.
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36
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Kandul NP, Liu J, Sanchez C HM, Wu SL, Marshall JM, Akbari OS. Transforming insect population control with precision guided sterile males with demonstration in flies. Nat Commun 2019; 10:84. [PMID: 30622266 PMCID: PMC6325135 DOI: 10.1038/s41467-018-07964-7] [Citation(s) in RCA: 93] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 12/05/2018] [Indexed: 01/03/2023] Open
Abstract
The sterile insect technique (SIT) is an environmentally safe and proven technology to suppress wild populations. To further advance its utility, a novel CRISPR-based technology termed precision guided SIT (pgSIT) is described. PgSIT mechanistically relies on a dominant genetic technology that enables simultaneous sexing and sterilization, facilitating the release of eggs into the environment ensuring only sterile adult males emerge. Importantly, for field applications, the release of eggs will eliminate burdens of manually sexing and sterilizing males, thereby reducing overall effort and increasing scalability. Here, to demonstrate efficacy, we systematically engineer multiple pgSIT systems in Drosophila which consistently give rise to 100% sterile males. Importantly, we demonstrate that pgSIT-generated sterile males are fit and competitive. Using mathematical models, we predict pgSIT will induce substantially greater population suppression than can be achieved by currently-available self-limiting suppression technologies. Taken together, pgSIT offers to potentially transform our ability to control insect agricultural pests and disease vectors.
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Affiliation(s)
- Nikolay P Kandul
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA 92093, California, USA
| | - Junru Liu
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA 92093, California, USA
| | - Hector M Sanchez C
- Division of Biostatistics and Epidemiology, School of Public Health, University of California, Berkeley, CA 94720, California, USA
| | - Sean L Wu
- Division of Biostatistics and Epidemiology, School of Public Health, University of California, Berkeley, CA 94720, California, USA
| | - John M Marshall
- Division of Biostatistics and Epidemiology, School of Public Health, University of California, Berkeley, CA 94720, California, USA
| | - Omar S Akbari
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA 92093, California, USA.
- Tata Institute for Genetics and Society, University of California, San Diego, La Jolla, CA 92093, California, USA.
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37
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Izquierdo A, Fahrenberger M, Persampieri T, Benedict MQ, Giles T, Catteruccia F, Emes RD, Dottorini T. Evolution of gene expression levels in the male reproductive organs of Anopheles mosquitoes. Life Sci Alliance 2019; 2:e201800191. [PMID: 30623175 PMCID: PMC6315087 DOI: 10.26508/lsa.201800191] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 12/21/2018] [Accepted: 12/21/2018] [Indexed: 12/31/2022] Open
Abstract
Modifications in gene expression determine many of the phenotypic differentiations between closely related species. This is particularly evident in reproductive tissues, where evolution of genes is more rapid, facilitating the appearance of distinct reproductive characteristics which may lead to species isolation and phenotypic variation. Large-scale, comparative analyses of transcript expression levels have been limited until recently by lack of inter-species data mining solutions. Here, by combining expression normalisation across lineages, multivariate statistical analysis, evolutionary rate, and protein-protein interaction analysis, we investigate ortholog transcripts in the male accessory glands and testes across five closely related species in the Anopheles gambiae complex. We first demonstrate that the differentiation by transcript expression is consistent with the known Anopheles phylogeny. Then, through clustering, we discover groups of transcripts with tissue-dependent expression patterns conserved across lineages, or lineage-dependent patterns conserved across tissues. The strongest associations with reproductive function, transcriptional regulatory networks, protein-protein subnetworks, and evolutionary rate are found for the groups of transcripts featuring large expression differences in lineage or tissue-conserved patterns.
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Affiliation(s)
- Abril Izquierdo
- School of Veterinary Medicine and Science, Sutton Bonington Campus, University of Nottingham, Leicestershire, UK
| | - Martin Fahrenberger
- School of Veterinary Medicine and Science, Sutton Bonington Campus, University of Nottingham, Leicestershire, UK
| | - Tania Persampieri
- Department of Experimental Medicine, University of Perugia, Perugia, Italy
| | - Mark Q Benedict
- Centers for Disease Control and Prevention, Division of Parasitic Diseases and Malaria, Entomology Branch, Atlanta, GA, USA
| | - Tom Giles
- Advanced Data Analysis Centre, Sutton Bonington Campus, University of Nottingham, Leicestershire, UK
| | - Flaminia Catteruccia
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Richard D Emes
- School of Veterinary Medicine and Science, Sutton Bonington Campus, University of Nottingham, Leicestershire, UK.,Advanced Data Analysis Centre, Sutton Bonington Campus, University of Nottingham, Leicestershire, UK
| | - Tania Dottorini
- School of Veterinary Medicine and Science, Sutton Bonington Campus, University of Nottingham, Leicestershire, UK
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38
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Ruzzante L, Reijnders MJ, Waterhouse RM. Of Genes and Genomes: Mosquito Evolution and Diversity. Trends Parasitol 2019; 35:32-51. [DOI: 10.1016/j.pt.2018.10.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 10/07/2018] [Accepted: 10/08/2018] [Indexed: 12/16/2022]
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39
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Meibers HE, Finch G, Gregg RT, Glenn S, Assani KD, Jennings EC, Davies B, Rosendale AJ, Holmes CJ, Gantz JD, Spacht DE, Lee RE, Denlinger DL, Weirauch MT, Benoit JB. Sex- and developmental-specific transcriptomic analyses of the Antarctic mite, Alaskozetes antarcticus, reveal transcriptional shifts underlying oribatid mite reproduction. Polar Biol 2018. [DOI: 10.1007/s00300-018-2427-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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40
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Ghiselli F, Iannello M, Puccio G, Chang PL, Plazzi F, Nuzhdin SV, Passamonti M. Comparative Transcriptomics in Two Bivalve Species Offers Different Perspectives on the Evolution of Sex-Biased Genes. Genome Biol Evol 2018; 10:1389-1402. [PMID: 29897459 PMCID: PMC6007409 DOI: 10.1093/gbe/evy082] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/19/2018] [Indexed: 12/13/2022] Open
Abstract
Comparative genomics has become a central tool for evolutionary biology, and a better knowledge of understudied taxa represents the foundation for future work. In this study, we characterized the transcriptome of male and female mature gonads in the European clam Ruditapes decussatus, compared with that in the Manila clam Ruditapes philippinarum providing, for the first time in bivalves, information about transcription dynamics and sequence evolution of sex-biased genes. In both the species, we found a relatively low number of sex-biased genes (1,284, corresponding to 41.3% of the orthologous genes between the two species), probably due to the absence of sexual dimorphism, and the transcriptional bias is maintained in only 33% of the orthologs. The dN/dS is generally low, indicating purifying selection, with genes where the female-biased transcription is maintained between the two species showing a significantly higher dN/dS. Genes involved in embryo development, cell proliferation, and maintenance of genome stability show a faster sequence evolution. Finally, we report a lack of clear correlation between transcription level and evolutionary rate in these species, in contrast with studies that reported a negative correlation. We discuss such discrepancy and call into question some methodological approaches and rationales generally used in this type of comparative studies.
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Affiliation(s)
- Fabrizio Ghiselli
- Department of Biological, Geological, and Environmental Sciences, University of Bologna, Italy
| | - Mariangela Iannello
- Department of Biological, Geological, and Environmental Sciences, University of Bologna, Italy
| | - Guglielmo Puccio
- Department of Biological, Geological, and Environmental Sciences, University of Bologna, Italy
| | - Peter L Chang
- Program in Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, USA
| | - Federico Plazzi
- Department of Biological, Geological, and Environmental Sciences, University of Bologna, Italy
| | - Sergey V Nuzhdin
- Program in Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, USA
| | - Marco Passamonti
- Department of Biological, Geological, and Environmental Sciences, University of Bologna, Italy
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41
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Pauletto M, Manousaki T, Ferraresso S, Babbucci M, Tsakogiannis A, Louro B, Vitulo N, Quoc VH, Carraro R, Bertotto D, Franch R, Maroso F, Aslam ML, Sonesson AK, Simionati B, Malacrida G, Cestaro A, Caberlotto S, Sarropoulou E, Mylonas CC, Power DM, Patarnello T, Canario AVM, Tsigenopoulos C, Bargelloni L. Genomic analysis of Sparus aurata reveals the evolutionary dynamics of sex-biased genes in a sequential hermaphrodite fish. Commun Biol 2018; 1:119. [PMID: 30271999 PMCID: PMC6123679 DOI: 10.1038/s42003-018-0122-7] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 07/27/2018] [Indexed: 12/13/2022] Open
Abstract
Sexual dimorphism is a fascinating subject in evolutionary biology and mostly results from sex-biased expression of genes, which have been shown to evolve faster in gonochoristic species. We report here genome and sex-specific transcriptome sequencing of Sparus aurata, a sequential hermaphrodite fish. Evolutionary comparative analysis reveals that sex-biased genes in S. aurata are similar in number and function, but evolved following strikingly divergent patterns compared with gonochoristic species, showing overall slower rates because of stronger functional constraints. Fast evolution is observed only for highly ovary-biased genes due to female-specific patterns of selection that are related to the peculiar reproduction mode of S. aurata, first maturing as male, then as female. To our knowledge, these findings represent the first genome-wide analysis on sex-biased loci in a hermaphrodite vertebrate species, demonstrating how having two sexes in the same individual profoundly affects the fate of a large set of evolutionarily relevant genes.
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Affiliation(s)
- Marianna Pauletto
- Department of Comparative Biomedicine and Food Science, University of Padova, viale dell'Università, 16 35020, Legnaro, Italy
| | - Tereza Manousaki
- Institute of Marine Biology, Biotechnology and Aquaculture ó, Hellenic Centre for Marine Research, Thalassocosmos, Former US Base at Gournes, 715 00, Heraklion, Greece
| | - Serena Ferraresso
- Department of Comparative Biomedicine and Food Science, University of Padova, viale dell'Università, 16 35020, Legnaro, Italy
| | - Massimiliano Babbucci
- Department of Comparative Biomedicine and Food Science, University of Padova, viale dell'Università, 16 35020, Legnaro, Italy
| | - Alexandros Tsakogiannis
- Institute of Marine Biology, Biotechnology and Aquaculture ó, Hellenic Centre for Marine Research, Thalassocosmos, Former US Base at Gournes, 715 00, Heraklion, Greece
| | - Bruno Louro
- CCMAR-Centro de Ciências do Mar, University of Algarve, Campus de Gambelas, 8005-139, Faro, Portugal
| | - Nicola Vitulo
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134, Verona, Italy
| | - Viet Ha Quoc
- Institute of Marine Biology, Biotechnology and Aquaculture ó, Hellenic Centre for Marine Research, Thalassocosmos, Former US Base at Gournes, 715 00, Heraklion, Greece
| | - Roberta Carraro
- Department of Comparative Biomedicine and Food Science, University of Padova, viale dell'Università, 16 35020, Legnaro, Italy
| | - Daniela Bertotto
- Department of Comparative Biomedicine and Food Science, University of Padova, viale dell'Università, 16 35020, Legnaro, Italy
| | - Rafaella Franch
- Department of Comparative Biomedicine and Food Science, University of Padova, viale dell'Università, 16 35020, Legnaro, Italy
| | - Francesco Maroso
- Department of Comparative Biomedicine and Food Science, University of Padova, viale dell'Università, 16 35020, Legnaro, Italy
| | | | | | | | | | - Alessandro Cestaro
- Research and Innovation Centre, Fondazione Edmund Mach, via Edmund Mach 1, 38010, San Michele all'Adige, Trento, Italy
| | - Stefano Caberlotto
- Valle Cà Zuliani Società Agricola Srl, Via Timavo 76, 34074, Monfalcone, Gorizia, Italy
| | - Elena Sarropoulou
- Institute of Marine Biology, Biotechnology and Aquaculture ó, Hellenic Centre for Marine Research, Thalassocosmos, Former US Base at Gournes, 715 00, Heraklion, Greece
| | - Costantinos C Mylonas
- Institute of Marine Biology, Biotechnology and Aquaculture ó, Hellenic Centre for Marine Research, Thalassocosmos, Former US Base at Gournes, 715 00, Heraklion, Greece
| | - Deborah M Power
- CCMAR-Centro de Ciências do Mar, University of Algarve, Campus de Gambelas, 8005-139, Faro, Portugal
| | - Tomaso Patarnello
- Department of Comparative Biomedicine and Food Science, University of Padova, viale dell'Università, 16 35020, Legnaro, Italy
| | - Adelino V M Canario
- CCMAR-Centro de Ciências do Mar, University of Algarve, Campus de Gambelas, 8005-139, Faro, Portugal
| | - Costas Tsigenopoulos
- Institute of Marine Biology, Biotechnology and Aquaculture ó, Hellenic Centre for Marine Research, Thalassocosmos, Former US Base at Gournes, 715 00, Heraklion, Greece
| | - Luca Bargelloni
- Department of Comparative Biomedicine and Food Science, University of Padova, viale dell'Università, 16 35020, Legnaro, Italy.
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42
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Ma WJ, Veltsos P, Toups MA, Rodrigues N, Sermier R, Jeffries DL, Perrin N. Tissue Specificity and Dynamics of Sex-Biased Gene Expression in a Common Frog Population with Differentiated, Yet Homomorphic, Sex Chromosomes. Genes (Basel) 2018; 9:E294. [PMID: 29895802 PMCID: PMC6027210 DOI: 10.3390/genes9060294] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 06/04/2018] [Accepted: 06/11/2018] [Indexed: 02/06/2023] Open
Abstract
Sex-biased genes are central to the study of sexual selection, sexual antagonism, and sex chromosome evolution. We describe a comprehensive de novo assembled transcriptome in the common frog Rana temporaria based on five developmental stages and three adult tissues from both sexes, obtained from a population with karyotypically homomorphic but genetically differentiated sex chromosomes. This allows the study of sex-biased gene expression throughout development, and its effect on the rate of gene evolution while accounting for pleiotropic expression, which is known to negatively correlate with the evolutionary rate. Overall, sex-biased genes had little overlap among developmental stages and adult tissues. Late developmental stages and gonad tissues had the highest numbers of stage- or tissue-specific genes. We find that pleiotropic gene expression is a better predictor than sex bias for the evolutionary rate of genes, though it often interacts with sex bias. Although genetically differentiated, the sex chromosomes were not enriched in sex-biased genes, possibly due to a very recent arrest of XY recombination. These results extend our understanding of the developmental dynamics, tissue specificity, and genomic localization of sex-biased genes.
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Affiliation(s)
- Wen-Juan Ma
- Department of Ecology and Evolution, University of Lausanne, CH 1015 Lausanne, Switzerland.
| | - Paris Veltsos
- Department of Ecology and Evolution, University of Lausanne, CH 1015 Lausanne, Switzerland.
- Department of Biology, Indiana University, Jordan Hall, 1001 East Third Street, Bloomington, IN 47405, USA.
| | - Melissa A Toups
- Department of Ecology and Evolution, University of Lausanne, CH 1015 Lausanne, Switzerland.
- Institute of Science and Technology Austria, Am Campus 1, 3400 Klosterneuburg, Austria.
| | - Nicolas Rodrigues
- Department of Ecology and Evolution, University of Lausanne, CH 1015 Lausanne, Switzerland.
| | - Roberto Sermier
- Department of Ecology and Evolution, University of Lausanne, CH 1015 Lausanne, Switzerland.
| | - Daniel L Jeffries
- Department of Ecology and Evolution, University of Lausanne, CH 1015 Lausanne, Switzerland.
| | - Nicolas Perrin
- Department of Ecology and Evolution, University of Lausanne, CH 1015 Lausanne, Switzerland.
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43
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Congrains C, Campanini EB, Torres FR, Rezende VB, Nakamura AM, de Oliveira JL, Lima ALA, Chahad-Ehlers S, Sobrinho IS, de Brito RA. Evidence of Adaptive Evolution and Relaxed Constraints in Sex-Biased Genes of South American and West Indies Fruit Flies (Diptera: Tephritidae). Genome Biol Evol 2018; 10:380-395. [PMID: 29346618 PMCID: PMC5786236 DOI: 10.1093/gbe/evy009] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/11/2018] [Indexed: 12/29/2022] Open
Abstract
Several studies have demonstrated that genes differentially expressed between sexes (sex-biased genes) tend to evolve faster than unbiased genes, particularly in males. The reason for this accelerated evolution is not clear, but several explanations have involved adaptive and nonadaptive mechanisms. Furthermore, the differences of sex-biased expression patterns of closely related species are also little explored out of Drosophila. To address the evolutionary processes involved with sex-biased expression in species with incipient differentiation, we analyzed male and female transcriptomes of Anastrepha fraterculus and Anastrepha obliqua, a pair of species that have diverged recently, likely in the presence of gene flow. Using these data, we inferred differentiation indexes and evolutionary rates and tested for signals of selection in thousands of genes expressed in head and reproductive transcriptomes from both species. Our results indicate that sex-biased and reproductive-biased genes evolve faster than unbiased genes in both species, which is due to both adaptive pressure and relaxed constraints. Furthermore, among male-biased genes evolving under positive selection, we identified some related to sexual functions such as courtship behavior and fertility. These findings suggest that sex-biased genes may have played important roles in the establishment of reproductive isolation between these species, due to a combination of selection and drift, and unveil a plethora of genetic markers useful for more studies in these species and their differentiation.
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Affiliation(s)
- Carlos Congrains
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, SP, Brazil
| | - Emeline B Campanini
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, SP, Brazil
| | - Felipe R Torres
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, SP, Brazil
| | - Víctor B Rezende
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, SP, Brazil
| | - Aline M Nakamura
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, SP, Brazil
| | | | - André L A Lima
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, SP, Brazil
| | - Samira Chahad-Ehlers
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, SP, Brazil
| | | | - Reinaldo A de Brito
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, SP, Brazil
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44
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Abstract
Males and females exhibit highly dimorphic phenotypes, particularly in their gonads, which is believed to be driven largely by differential gene expression. Typically, the protein sequences of genes upregulated in males, or male-biased genes, evolve rapidly as compared to female-biased and unbiased genes. To date, the specific study of gonad-biased genes remains uncommon in metazoans. Here, we identified and studied a total of 2927, 2013, and 4449 coding sequences (CDS) with ovary-biased, testis-biased, and unbiased expression, respectively, in the yellow fever mosquito Aedes aegypti The results showed that ovary-biased and unbiased CDS had higher nonsynonymous to synonymous substitution rates (dN/dS) and lower optimal codon usage (those codons that promote efficient translation) than testis-biased genes. Further, we observed higher dN/dS in ovary-biased genes than in testis-biased genes, even for genes coexpressed in nonsexual (embryo) tissues. Ovary-specific genes evolved exceptionally fast, as compared to testis- or embryo-specific genes, and exhibited higher frequency of positive selection. Genes with ovary expression were preferentially involved in olfactory binding and reception. We hypothesize that at least two potential mechanisms could explain rapid evolution of ovary-biased genes in this mosquito: (1) the evolutionary rate of ovary-biased genes may be accelerated by sexual selection (including female-female competition or male-mate choice) affecting olfactory genes during female swarming by males, and/or by adaptive evolution of olfactory signaling within the female reproductive system (e.g., sperm-ovary signaling); and/or (2) testis-biased genes may exhibit decelerated evolutionary rates due to the formation of mating plugs in the female after copulation, which limits male-male sperm competition.
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