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Minovic A, Nozawa M. Evolution of sex-biased genes in Drosophila species with neo-sex chromosomes: Potential contribution to reducing the sexual conflict. Ecol Evol 2024; 14:e11701. [PMID: 39050657 PMCID: PMC11266434 DOI: 10.1002/ece3.11701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2024] [Revised: 06/17/2024] [Accepted: 06/21/2024] [Indexed: 07/27/2024] Open
Abstract
An advantage of sex chromosomes may be the potential to reduce sexual conflict because they provide a basis for selection to operate separately on females and males. However, evaluating the relationship between sex chromosomes and sexual conflict is challenging owing to the difficulty in measuring sexual conflict and substantial divergence between species with and without sex chromosomes. We therefore examined sex-biased gene expression as a proxy for sexual conflict in three sets of Drosophila species with and without young sex chromosomes, the so-called neo-sex chromosomes. In all sets, we detected more sex-biased genes in the species with neo-sex chromosomes than in the species without neo-sex chromosomes in larvae, pupae, and adult somatic tissues but not in gonads. In particular, many unbiased genes became either female- or male-biased after linkage to the neo-sex chromosomes in larvae, despite the low sexual dimorphism. For example, genes involved in metabolism, a key determinant for the rate of development in many animals, were enriched in the genes that acquired sex-biased expression on the neo-sex chromosomes at the larval stage. These genes may be targets of sexually antagonistic selection (i.e., large size and rapid development are selected for in females but selected against in males). These results indicate that acquiring neo-sex chromosomes may have contributed to a reduction in sexual conflict, particularly at the larval stage, in Drosophila..
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Affiliation(s)
- Anika Minovic
- Department of Biological SciencesTokyo Metropolitan UniversityHachiojiJapan
| | - Masafumi Nozawa
- Department of Biological SciencesTokyo Metropolitan UniversityHachiojiJapan
- Research Center for Genomics and BioinformaticsTokyo Metropolitan UniversityHachiojiJapan
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2
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Castellanos MDP, Wickramasinghe CD, Betrán E. The roles of gene duplications in the dynamics of evolutionary conflicts. Proc Biol Sci 2024; 291:20240555. [PMID: 38865605 DOI: 10.1098/rspb.2024.0555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 04/02/2024] [Indexed: 06/14/2024] Open
Abstract
Evolutionary conflicts occur when there is antagonistic selection between different individuals of the same or different species, life stages or between levels of biological organization. Remarkably, conflicts can occur within species or within genomes. In the dynamics of evolutionary conflicts, gene duplications can play a major role because they can bring very specific changes to the genome: changes in protein dose, the generation of novel paralogues with different functions or expression patterns or the evolution of small antisense RNAs. As we describe here, by having those effects, gene duplication might spark evolutionary conflict or fuel arms race dynamics that takes place during conflicts. Interestingly, gene duplication can also contribute to the resolution of a within-locus evolutionary conflict by partitioning the functions of the gene that is under an evolutionary trade-off. In this review, we focus on intraspecific conflicts, including sexual conflict and illustrate the various roles of gene duplications with a compilation of examples. These examples reveal the level of complexity and the differences in the patterns of gene duplications within genomes under different conflicts. These examples also reveal the gene ontologies involved in conflict and the genomic location of the elements of the conflict. The examples provide a blueprint for the direct study of these conflicts or the exploration of the presence of similar conflicts in other lineages.
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Affiliation(s)
| | | | - Esther Betrán
- Department of Biology, University of Texas at Arlington , Arlington, TX 76019, USA
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3
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Brink K, Thomas CL, Jones A, Chan TW, Mallon EB. Exploring the ageing methylome in the model insect, Nasonia vitripennis. BMC Genomics 2024; 25:305. [PMID: 38519892 PMCID: PMC10958858 DOI: 10.1186/s12864-024-10211-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 03/11/2024] [Indexed: 03/25/2024] Open
Abstract
BACKGROUND The ageing process is a multifaceted phenomenon marked by the gradual deterioration of cellular and organismal functions, accompanied by an elevated susceptibility to diseases. The intricate interplay between genetic and environmental factors complicates research, particularly in complex mammalian models. In this context, simple invertebrate organisms have been pivotal, but the current models lack detectable DNA methylation limiting the exploration of this critical epigenetic ageing mechanism. This study introduces Nasonia vitripennis, the jewel wasp, as an innovative invertebrate model for investigating the epigenetics of ageing. Leveraging its advantages as a model organism and possessing a functional DNA methylation system, Nasonia emerges as a valuable addition to ageing research. RESULTS Whole-genome bisulfite sequencing unveiled dynamic alterations in DNA methylation, with differentially methylated CpGs between distinct time points in both male and female wasps. These changes were associated with numerous genes, enriching for functions related to telomere maintenance, histone methylation, and mRNA catabolic processes. Additionally, other CpGs were found to be variably methylated at each timepoint. Sex-specific effects on epigenetic entropy were observed, indicating differential patterns in the loss of epigenetic stability over time. Constructing an epigenetic clock containing 19 CpGs revealed a robust correlation between epigenetic age and chronological age. CONCLUSIONS Nasonia vitripennis emerges as a promising model for investigating the epigenetics of ageing, shedding light on the intricate dynamics of DNA methylation and their implications for age-related processes. This research not only expands the repertoire of ageing models but also opens avenues for deeper exploration of epigenetic mechanisms in the context of ageing.
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Affiliation(s)
- K Brink
- Department of Genetics and Genome Biology, University of Leicester, University Road, Leicester, UK
| | - C L Thomas
- Department of Genetics and Genome Biology, University of Leicester, University Road, Leicester, UK
| | - A Jones
- Institute for Evolution and Biodiversity, University of Muenster, Huefferstrabe, Muenster, Germany
| | - T W Chan
- School of Life Sciences, Gibbet Hill Campus, The University of Warwick, Coventry, UK
| | - E B Mallon
- Department of Genetics and Genome Biology, University of Leicester, University Road, Leicester, UK.
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4
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Tosto NM, Beasley ER, Wong BBM, Mank JE, Flanagan SP. The roles of sexual selection and sexual conflict in shaping patterns of genome and transcriptome variation. Nat Ecol Evol 2023; 7:981-993. [PMID: 36959239 DOI: 10.1038/s41559-023-02019-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 02/21/2023] [Indexed: 03/25/2023]
Abstract
Sexual dimorphism is one of the most prevalent, and often the most extreme, examples of phenotypic variation within species, and arises primarily from genomic variation that is shared between females and males. Many sexual dimorphisms arise through sex differences in gene expression, and sex-biased expression is one way that a single, shared genome can generate multiple, distinct phenotypes. Although many sexual dimorphisms are expected to result from sexual selection, and many studies have invoked the possible role of sexual selection to explain sex-specific traits, the role of sexual selection in the evolution of sexually dimorphic gene expression remains difficult to differentiate from other forms of sex-specific selection. In this Review, we propose a holistic framework for the study of sex-specific selection and transcriptome evolution. We advocate for a comparative approach, across tissues, developmental stages and species, which incorporates an understanding of the molecular mechanisms, including genomic variation and structure, governing gene expression. Such an approach is expected to yield substantial insights into the evolution of genetic variation and have important applications in a variety of fields, including ecology, evolution and behaviour.
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Affiliation(s)
- Nicole M Tosto
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Emily R Beasley
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Bob B M Wong
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
| | - Judith E Mank
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Sarah P Flanagan
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand.
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5
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Cheng JQ, Tao YM, Li J, Chen YZ, Hu HY. Characterization of male-biased fatty acid desaturase in the jewel wasp Nasonia vitripennis and its role in pheromone production. JOURNAL OF EXPERIMENTAL ZOOLOGY. PART B, MOLECULAR AND DEVELOPMENTAL EVOLUTION 2022; 338:421-429. [PMID: 34995007 DOI: 10.1002/jez.b.23120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 12/06/2021] [Accepted: 12/19/2021] [Indexed: 06/14/2023]
Abstract
Linoleic acid is the material for biosynthesis of sex attracting and blocking (postmating) pheromones in Nasonia vitripennis, it is synthesized from oleic acid by a male-biased fatty acid desaturase (SCD5a). In this study, we developed a specific antibody and further characterized the expression patterns of SCD5a in males at different mating stages by western blot. SCD5a was mainly expressed in male heads rather than in abdomens. Along with the aging process (from Day 1 to Day 3), SCD5a increased significantly. Compared with virgin males, mated males showed higher levels of SCD5a. Likewise, abdomen dipping frequency, during which males release attracting pheromone, increased with age and mating. Moreover, real-time quantitative PCR revealed that genes responsible for the first three steps of attracting pheromone biosynthesis were more highly expressed in head than in abdomen, but the final gene for transformation of attracting pheromone was more highly expressed in abdomen than in head. These results suggest that linoleic acid for biosynthesis of attracting pheromones may also originate from the head rather than only synthesized at the rectal vesicles.
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Affiliation(s)
- Jian-Qiu Cheng
- School of Ecology and Environment, Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in Wanjiang Basin Co-founded by Anhui Province and Ministry of Education, Anhui Normal University, Wuhu, Anhui, China
| | - Yu-Mei Tao
- School of Ecology and Environment, Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in Wanjiang Basin Co-founded by Anhui Province and Ministry of Education, Anhui Normal University, Wuhu, Anhui, China
| | - Jing Li
- School of Ecology and Environment, Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in Wanjiang Basin Co-founded by Anhui Province and Ministry of Education, Anhui Normal University, Wuhu, Anhui, China
| | - Yong-Zhuo Chen
- School of Ecology and Environment, Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in Wanjiang Basin Co-founded by Anhui Province and Ministry of Education, Anhui Normal University, Wuhu, Anhui, China
| | - Hao-Yuan Hu
- School of Ecology and Environment, Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in Wanjiang Basin Co-founded by Anhui Province and Ministry of Education, Anhui Normal University, Wuhu, Anhui, China
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6
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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] [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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7
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Wang M, Chen D, Zheng H, Zhao L, Xue X, Yu F, Zhang Y, Cheng C, Niu Q, Wang S, Zhang Y, Wu L. Sex-Specific Development in Haplodiploid Honeybee Is Controlled by the Female-Embryo-Specific Activation of Thousands of Intronic LncRNAs. Front Cell Dev Biol 2021; 9:690167. [PMID: 34422813 PMCID: PMC8377728 DOI: 10.3389/fcell.2021.690167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 07/12/2021] [Indexed: 11/13/2022] Open
Abstract
Embryonic development depends on a highly coordinated shift in transcription programs known as the maternal-to-zygotic transition (MZT). It remains unclear how haploid and diploid embryo coordinate their genomic activation and embryonic development during MZT in haplodiploid animals. Here, we applied a single-embryo RNA-seq approach to characterize the embryonic transcriptome dynamics in haploid males vs. diploid females of the haplodiploid insect honeybee (Apis mellifera). We observed typical zygotic genome activation (ZGA) occurred in three major waves specifically in female honeybee embryos; haploid genome activation was much weaker and occurred later. Strikingly, we also observed three waves of transcriptional activation for thousands of long non-coding transcripts (lncRNA), 73% of which are transcribed from intronic regions and 65% were specific to female honeybee embryos. These findings support a model in which introns encode thousands of lncRNAs that are expressed in a diploid-embryo-specific and ZGA-triggered manner that may have potential functions to regulate gene expression during early embryonic development in the haplodiploid insect honeybee.
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Affiliation(s)
- Miao Wang
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Dong Chen
- ABLife BioBigData Institute, Wuhan, China.,Laboratory for Genome Regulation and Human Health, ABLife Inc., Wuhan, China
| | - Huoqing Zheng
- College of Animal Science, Zhejiang University, Hangzhou, China
| | - Liuwei Zhao
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaofeng Xue
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Fengyun Yu
- Laboratory for Genome Regulation and Human Health, ABLife Inc., Wuhan, China
| | - Yu Zhang
- ABLife BioBigData Institute, Wuhan, China
| | - Chao Cheng
- ABLife BioBigData Institute, Wuhan, China
| | - Qingsheng Niu
- Department of Scientific Research, Jilin Province Institute of Apicultural Science, Jilin, China
| | - Shuai Wang
- College of Animal Science, Zhejiang University, Hangzhou, China
| | - Yi Zhang
- ABLife BioBigData Institute, Wuhan, China.,Laboratory for Genome Regulation and Human Health, ABLife Inc., Wuhan, China
| | - Liming Wu
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, China
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8
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Zhang J, Li Y, Luo S, Cao M, Zhang L, Li X. Differential gene expression patterns during gametophyte development provide insights into sex differentiation in the dioicous kelp Saccharina japonica. BMC PLANT BIOLOGY 2021; 21:335. [PMID: 34261451 PMCID: PMC8278619 DOI: 10.1186/s12870-021-03117-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Accepted: 06/23/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND In brown algae, dioicy is the prevalent sexual system, and phenotypic differences between male and female gametophytes have been found in many dioicous species. Saccharina japonica show remarkable sexual dimorphism in gametophytes before gametogenesis. A higher level of phenotypic differentiation was also found in female and male gametes after gametogenesis. However, the patterns of differential gene expression throughout gametophyte development and how these changes might relate to sex-specific fitness at the gamete stage in S. japonica are not well known. RESULTS In this study, differences in gene expression between male and female gametophytes in different developmental stages were investigated using comparative transcriptome analysis. Among the 20,151 genes expressed in the haploid gametophyte generation, 37.53% were sex-biased. The abundance of sex-biased genes in mature gametophytes was much higher than that in immature gametophytes, and more male-biased than female-biased genes were observed in the mature stage. The predicted functions of most sex-biased genes were closely related to the sex-specific characteristics of gametes, including cell wall biosynthesis, sperm motility, and sperm and egg recognition. In addition, 51 genes were specifically expressed in males in both stages, showing great potential as candidate male sex-determining region (SDR) genes. CONCLUSIONS This study describes a thorough investigation into differential gene expression between male and female gametophytes in the dioicous kelp S. japonica. A large number of sex-biased genes in mature gametophytes may be associated with the divergence of phenotypic traits and physiological functions between female gametes (eggs) and male gametes (sperm) during sexual differentiation. These genes may mainly come from new sex-biased genes that have recently evolved in the S. japonica lineage. The duplication of sex-biased genes was detected, which may increase the number of sex-biased genes after gametogenesis in S. japonica to some extent. The excess of male-biased genes over female-biased genes in the mature stage may reflect the different levels of sexual selection across sexes. This study deepens our understanding of the regulation of sex development and differentiation in the dioicous kelp S. japonica.
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Affiliation(s)
- Jiaxun Zhang
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Yan Li
- National Engineering Science Research & Development Center of Algae and Sea Cucumbers of China, Provincial Key Laboratory of Genetic Improvement & Efficient Culture of Marine Algae of Shandong, Shandong Oriental Ocean Sci-Tech Co., Ltd., Yantai, 264003, China
| | - Shiju Luo
- National Engineering Science Research & Development Center of Algae and Sea Cucumbers of China, Provincial Key Laboratory of Genetic Improvement & Efficient Culture of Marine Algae of Shandong, Shandong Oriental Ocean Sci-Tech Co., Ltd., Yantai, 264003, China
| | - Min Cao
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Linan Zhang
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China.
| | - Xiaojie Li
- National Engineering Science Research & Development Center of Algae and Sea Cucumbers of China, Provincial Key Laboratory of Genetic Improvement & Efficient Culture of Marine Algae of Shandong, Shandong Oriental Ocean Sci-Tech Co., Ltd., Yantai, 264003, China
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9
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A comparative genomic approach using mouse and fruit fly data to discover genes involved in testis function in hymenopterans with a focus on Nasonia vitripennis. BMC Ecol Evol 2021; 21:90. [PMID: 34011283 PMCID: PMC8132408 DOI: 10.1186/s12862-021-01825-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 05/12/2021] [Indexed: 11/18/2022] Open
Abstract
Background Spermatogenesis appears to be a relatively well-conserved process even among distantly related animal taxa such as invertebrates and vertebrates. Although Hymenopterans share many characteristics with other organisms, their complex haplodiploid reproduction system is still relatively unknown. However, they serve as a complementary insect model to Drosophila for studying functional male fertility. In this study, we used a comparative method combining taxonomic, phenotypic data and gene expression to identify candidate genes that could play a significant role in spermatogenesis in hymenopterans. Results Of the 546 mouse genes predominantly or exclusively expressed in the mouse testes, 36% had at least one ortholog in the fruit fly. Of these genes, 68% had at least one ortholog in one of the six hymenopteran species we examined. Based on their gene expression profiles in fruit fly testes, 71 of these genes were hypothesized to play a marked role in testis function. Forty-three of these 71 genes had an ortholog in at least one of the six hymenopteran species examined, and their enriched GO terms were related to the G2/M transition or to cilium organization, assembly, or movement. Second, of the 379 genes putatively involved in male fertility in Drosophila, 224 had at least one ortholog in each of the six Hymenoptera species. Finally, we showed that 199 of these genes were expressed in early pupal testis in Nasonia vitripennis; 86 exhibited a high level of expression, and 54 displayed modulated expression during meiosis. Conclusions In this study combining phylogenetic and experimental approaches, we highlighted genes that may have a major role in gametogenesis in hymenopterans; an essential prerequisite for further research on functional importance of these genes. Supplementary Information The online version contains supplementary material available at 10.1186/s12862-021-01825-6.
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10
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Kollar LM, Kiel S, James AJ, Carnley CT, Scola DN, Clark TN, Khanal T, Rosenstiel TN, Gall ET, Grieshop K, McDaniel SF. The genetic architecture of sexual dimorphism in the moss Ceratodon purpureus. Proc Biol Sci 2021; 288:20202908. [PMID: 33715431 PMCID: PMC7944104 DOI: 10.1098/rspb.2020.2908] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 02/02/2021] [Indexed: 12/12/2022] Open
Abstract
A central problem in evolutionary biology is to identify the forces that maintain genetic variation for fitness in natural populations. Sexual antagonism, in which selection favours different variants in males and females, can slow the transit of a polymorphism through a population or can actively maintain fitness variation. The amount of sexually antagonistic variation to be expected depends in part on the genetic architecture of sexual dimorphism, about which we know relatively little. Here, we used a multivariate quantitative genetic approach to examine the genetic architecture of sexual dimorphism in a scent-based fertilization syndrome of the moss Ceratodon purpureus. We found sexual dimorphism in numerous traits, consistent with a history of sexually antagonistic selection. The cross-sex genetic correlations (rmf) were generally heterogeneous with many values indistinguishable from zero, which typically suggests that genetic constraints do not limit the response to sexually antagonistic selection. However, we detected no differentiation between the female- and male-specific trait (co)variance matrices (Gf and Gm, respectively), meaning the evolution of sexual dimorphism may be constrained. The cross-sex cross-trait covariance matrix B contained both symmetric and asymmetric elements, indicating that the response to sexually antagonistic or sexually concordant selection, and the constraint to sexual dimorphism, are highly dependent on the traits experiencing selection. The patterns of genetic variances and covariances among these fitness components is consistent with partly sex-specific genetic architectures having evolved in order to partially resolve multivariate genetic constraints (i.e. sexual conflict), enabling the sexes to evolve towards their sex-specific multivariate trait optima.
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Affiliation(s)
- Leslie M. Kollar
- Department of Biology, University of Florida, Gainesville, FL 32611, USA
| | - Scott Kiel
- Center for Life in Extreme Environments, Portland State University, Portland, OR 97207, USA
| | - Ashley J. James
- Department of Biology, University of Florida, Gainesville, FL 32611, USA
| | - Cody T. Carnley
- Department of Biology, University of Florida, Gainesville, FL 32611, USA
| | - Danielle N. Scola
- Department of Biology, University of Florida, Gainesville, FL 32611, USA
| | - Taylor N. Clark
- Department of Biology, University of Florida, Gainesville, FL 32611, USA
| | - Tikahari Khanal
- Department of Biology, University of Florida, Gainesville, FL 32611, USA
| | - Todd N. Rosenstiel
- Center for Life in Extreme Environments, Portland State University, Portland, OR 97207, USA
| | - Elliott T. Gall
- Maseeh College of Engineering and Computer Science, Portland State University, Portland, OR 97207, USA
| | - Karl Grieshop
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Canada
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Stuart F. McDaniel
- Department of Biology, University of Florida, Gainesville, FL 32611, USA
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11
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Bain SA, Marshall H, de la Filia AG, Laetsch DR, Husnik F, Ross L. Sex-specific expression and DNA methylation in a species with extreme sexual dimorphism and paternal genome elimination. Mol Ecol 2021; 30:5687-5703. [PMID: 33629415 DOI: 10.1111/mec.15842] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 12/27/2020] [Accepted: 02/09/2021] [Indexed: 12/16/2022]
Abstract
Phenotypic differences between sexes are often mediated by differential expression and alternative splicing of genes. However, the mechanisms that regulate these expression and splicing patterns remain poorly understood. The mealybug, Planococcus citri, displays extreme sexual dimorphism and exhibits an unusual instance of sex-specific genomic imprinting, paternal genome elimination (PGE), in which the paternal chromosomes in males are highly condensed and eliminated from the sperm. Planococcus citri has no sex chromosomes and both sexual dimorphism and PGE are predicted to be under epigenetic control. We recently showed that P. citri females display a highly unusual DNA methylation profile for an insect species, with the presence of promoter methylation associated with lower levels of gene expression. Here, we therefore decided to explore genome-wide differences in DNA methylation between male and female P. citri using whole-genome bisulphite sequencing. We identified extreme differences in genome-wide levels and patterns between the sexes. Males display overall higher levels of DNA methylation which manifest as more uniform low levels across the genome. Whereas females display more targeted high levels of methylation. We suggest these unique sex-specific differences are due to chromosomal differences caused by PGE and may be linked to possible ploidy compensation. Using RNA-Seq, we identify extensive sex-specific gene expression and alternative splicing, but we find no correlation with cis-acting DNA methylation.
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Affiliation(s)
- Stevie A Bain
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Hollie Marshall
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | | | - Dominik R Laetsch
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Filip Husnik
- Evolution, Cell Biology, and Symbiosis Unit, Okinawa Institute of Science and Technology, Kunigami-gun, Japan
| | - Laura Ross
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
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12
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Leung K, Ras E, Ferguson KB, Ariëns S, Babendreier D, Bijma P, Bourtzis K, Brodeur J, Bruins MA, Centurión A, Chattington SR, Chinchilla‐Ramírez M, Dicke M, Fatouros NE, González‐Cabrera J, Groot TVM, Haye T, Knapp M, Koskinioti P, Le Hesran S, Lyrakis M, Paspati A, Pérez‐Hedo M, Plouvier WN, Schlötterer C, Stahl JM, Thiel A, Urbaneja A, van de Zande L, Verhulst EC, Vet LEM, Visser S, Werren JH, Xia S, Zwaan BJ, Magalhães S, Beukeboom LW, Pannebakker BA. Next-generation biological control: the need for integrating genetics and genomics. Biol Rev Camb Philos Soc 2020; 95:1838-1854. [PMID: 32794644 PMCID: PMC7689903 DOI: 10.1111/brv.12641] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 07/16/2020] [Accepted: 07/20/2020] [Indexed: 12/12/2022]
Abstract
Biological control is widely successful at controlling pests, but effective biocontrol agents are now more difficult to import from countries of origin due to more restrictive international trade laws (the Nagoya Protocol). Coupled with increasing demand, the efficacy of existing and new biocontrol agents needs to be improved with genetic and genomic approaches. Although they have been underutilised in the past, application of genetic and genomic techniques is becoming more feasible from both technological and economic perspectives. We review current methods and provide a framework for using them. First, it is necessary to identify which biocontrol trait to select and in what direction. Next, the genes or markers linked to these traits need be determined, including how to implement this information into a selective breeding program. Choosing a trait can be assisted by modelling to account for the proper agro-ecological context, and by knowing which traits have sufficiently high heritability values. We provide guidelines for designing genomic strategies in biocontrol programs, which depend on the organism, budget, and desired objective. Genomic approaches start with genome sequencing and assembly. We provide a guide for deciding the most successful sequencing strategy for biocontrol agents. Gene discovery involves quantitative trait loci analyses, transcriptomic and proteomic studies, and gene editing. Improving biocontrol practices includes marker-assisted selection, genomic selection and microbiome manipulation of biocontrol agents, and monitoring for genetic variation during rearing and post-release. We conclude by identifying the most promising applications of genetic and genomic methods to improve biological control efficacy.
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Affiliation(s)
- Kelley Leung
- Groningen Institute for Evolutionary Life SciencesUniversity of GroningenPO Box 111039700 CCGroningenThe Netherlands
| | - Erica Ras
- Insect Pest Control Laboratory, Joint FAO/IAEA Division of Nuclear Techniques in Food and AgricultureVienna International CentreP.O. Box 1001400ViennaAustria
| | - Kim B. Ferguson
- Laboratory of GeneticsWageningen University & ResearchDroevendaalsesteeg 16708 PBWageningenThe Netherlands
| | - Simone Ariëns
- Group for Population and Evolutionary Ecology, FB 02, Institute of EcologyUniversity of BremenLeobener Str. 528359BremenGermany
| | | | - Piter Bijma
- Animal Breeding and GenomicsWageningen University & ResearchPO Box 3386700 AHWageningenThe Netherlands
| | - Kostas Bourtzis
- Insect Pest Control Laboratory, Joint FAO/IAEA Division of Nuclear Techniques in Food and AgricultureVienna International CentreP.O. Box 1001400ViennaAustria
| | - Jacques Brodeur
- Institut de Recherche en Biologie VégétaleUniversité de Montréal4101 Sherbrooke EstMontréalQuebecCanadaH1X 2B2
| | - Margreet A. Bruins
- Laboratory of GeneticsWageningen University & ResearchDroevendaalsesteeg 16708 PBWageningenThe Netherlands
| | - Alejandra Centurión
- Group for Population and Evolutionary Ecology, FB 02, Institute of EcologyUniversity of BremenLeobener Str. 528359BremenGermany
| | - Sophie R. Chattington
- Group for Population and Evolutionary Ecology, FB 02, Institute of EcologyUniversity of BremenLeobener Str. 528359BremenGermany
| | - Milena Chinchilla‐Ramírez
- Instituto Valenciano de Investigaciones Agrarias (IVIA), Centro de Protección Vegetal y BiotecnologíaUnidad Mixta Gestión Biotecnológica de Plagas UV‐IVIACarretera CV‐315, Km 10'746113MoncadaValenciaSpain
| | - Marcel Dicke
- Laboratory of EntomologyWageningen University & ResearchDroevendaalsesteeg 16708 PBWageningenThe Netherlands
| | - Nina E. Fatouros
- Biosystematics GroupWageningen University & ResearchDroevendaalsesteeg 16708 PBWageningenThe Netherlands
| | - Joel González‐Cabrera
- Department of Genetics, Estructura de Recerca Interdisciplinar en Biotecnología i Biomedicina (ERI‐BIOTECMED)Unidad Mixta Gestión Biotecnológica de Plagas UV‐IVIA, Universitat de ValènciaDr Moliner 5046100BurjassotValenciaSpain
| | - Thomas V. M. Groot
- Koppert Biological SystemsVeilingweg 142651 BEBerkel en RodenrijsThe Netherlands
| | - Tim Haye
- CABIRue des Grillons 12800DelémontSwitzerland
| | - Markus Knapp
- Koppert Biological SystemsVeilingweg 142651 BEBerkel en RodenrijsThe Netherlands
| | - Panagiota Koskinioti
- Insect Pest Control Laboratory, Joint FAO/IAEA Division of Nuclear Techniques in Food and AgricultureVienna International CentreP.O. Box 1001400ViennaAustria
- Department of Biochemistry and BiotechnologyUniversity of ThessalyBiopolis41500LarissaGreece
| | - Sophie Le Hesran
- Laboratory of EntomologyWageningen University & ResearchDroevendaalsesteeg 16708 PBWageningenThe Netherlands
- Koppert Biological SystemsVeilingweg 142651 BEBerkel en RodenrijsThe Netherlands
| | - Manolis Lyrakis
- Institut für PopulationsgenetikVetmeduni ViennaVeterinärplatz 11210ViennaAustria
- Vienna Graduate School of Population GeneticsVetmeduni ViennaVeterinärplatz 11210ViennaAustria
| | - Angeliki Paspati
- Instituto Valenciano de Investigaciones Agrarias (IVIA), Centro de Protección Vegetal y BiotecnologíaUnidad Mixta Gestión Biotecnológica de Plagas UV‐IVIACarretera CV‐315, Km 10'746113MoncadaValenciaSpain
| | - Meritxell Pérez‐Hedo
- Instituto Valenciano de Investigaciones Agrarias (IVIA), Centro de Protección Vegetal y BiotecnologíaUnidad Mixta Gestión Biotecnológica de Plagas UV‐IVIACarretera CV‐315, Km 10'746113MoncadaValenciaSpain
| | - Wouter N. Plouvier
- INRA, CNRS, UMR 1355‐7254400 Route des ChappesBP 167 06903Sophia Antipolis CedexFrance
| | | | - Judith M. Stahl
- CABIRue des Grillons 12800DelémontSwitzerland
- Kearney Agricultural Research and Extension CenterUniversity of California Berkeley9240 South Riverbend AvenueParlierCA93648USA
| | - Andra Thiel
- Group for Population and Evolutionary Ecology, FB 02, Institute of EcologyUniversity of BremenLeobener Str. 528359BremenGermany
| | - Alberto Urbaneja
- Instituto Valenciano de Investigaciones Agrarias (IVIA), Centro de Protección Vegetal y BiotecnologíaUnidad Mixta Gestión Biotecnológica de Plagas UV‐IVIACarretera CV‐315, Km 10'746113MoncadaValenciaSpain
| | - Louis van de Zande
- Groningen Institute for Evolutionary Life SciencesUniversity of GroningenPO Box 111039700 CCGroningenThe Netherlands
| | - Eveline C. Verhulst
- Laboratory of EntomologyWageningen University & ResearchDroevendaalsesteeg 16708 PBWageningenThe Netherlands
| | - Louise E. M. Vet
- Laboratory of EntomologyWageningen University & ResearchDroevendaalsesteeg 16708 PBWageningenThe Netherlands
- Netherlands Institute of Ecology (NIOO‐KNAW)Droevendaalsesteeg 106708 PBWageningenThe Netherlands
| | - Sander Visser
- Institute of EntomologyBiology Centre CASBranišovská 31370 05České BudějoviceCzech Republic
- Faculty of ScienceUniversity of South BohemiaBranišovská 1760370 05České BudějoviceCzech Republic
| | - John H. Werren
- Department of BiologyUniversity of RochesterRochesterNY14627USA
| | - Shuwen Xia
- Animal Breeding and GenomicsWageningen University & ResearchPO Box 3386700 AHWageningenThe Netherlands
| | - Bas J. Zwaan
- Laboratory of GeneticsWageningen University & ResearchDroevendaalsesteeg 16708 PBWageningenThe Netherlands
| | - Sara Magalhães
- cE3c: Centre for Ecology, Evolution, and Environmental ChangesFaculdade de Ciências da Universidade de LisboaEdifício C2, Campo Grande1749‐016LisbonPortugal
| | - Leo W. Beukeboom
- Groningen Institute for Evolutionary Life SciencesUniversity of GroningenPO Box 111039700 CCGroningenThe Netherlands
| | - Bart A. Pannebakker
- Laboratory of GeneticsWageningen University & ResearchDroevendaalsesteeg 16708 PBWageningenThe Netherlands
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Lin ZJ, Wang X, Wang J, Tan Y, Tang X, Werren JH, Zhang D, Wang X. Comparative analysis reveals the expansion of mitochondrial DNA control region containing unusually high G-C tandem repeat arrays in Nasonia vitripennis. Int J Biol Macromol 2020; 166:1246-1257. [PMID: 33159940 DOI: 10.1016/j.ijbiomac.2020.11.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Revised: 11/01/2020] [Accepted: 11/02/2020] [Indexed: 11/25/2022]
Abstract
Insect mitochondrial DNA (mtDNA) ranges from 14 to 19 kbp, and the size difference is attributed to the AT-rich control region. Jewel wasps have a parasitoid lifestyle, which may affect mitochondria function and evolution. We sequenced, assembled, and annotated mitochondrial genomes in Nasonia and outgroup species. Gene composition and order are conserved within Nasonia, but they differ from other parasitoids by two large inversion events that were not reported before. We observed a much higher substitution rate relative to the nuclear genome and mitochondrial introgression between N. giraulti and N. oneida, which is consistent with previous studies. Most strikingly, N. vitripennis mtDNA has an extremely long control region (7665 bp), containing twenty-nine 217 bp tandem repeats and can fold into a super-cruciform structure. In contrast to tandem repeats commonly found in other mitochondria, these high-copy repeats are highly conserved (98.7% sequence identity), much longer in length (approximately 8 Kb), extremely GC-rich (50.7%), and CpG-rich (percent CpG 19.4% vs. 1.1% in coding region), resulting in a 23 kbp mtDNA beyond the typical size range in insects. These N. vitripennis-specific mitochondrial repeats are not related to any known sequences in insect mitochondria. Their evolutionary origin and functional consequences warrant further investigations.
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Affiliation(s)
- Zi Jie Lin
- Department of Chemistry, Columbus State University, Columbus, GA 31909, United States of America
| | - Xiaozhu Wang
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, AL 36849, United States of America
| | - Jinbin Wang
- Institute of Biotechnology Research, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China
| | - Yongjun Tan
- Department of Biology, College of Arts & Sciences, Saint Louis University, St. Louis, MO 63103, United States of America
| | - Xueming Tang
- Institute of Biotechnology Research, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China
| | - John H Werren
- Department of Biology, University of Rochester, Rochester, NY 14627, United States of America
| | - Dapeng Zhang
- Department of Biology, College of Arts & Sciences, Saint Louis University, St. Louis, MO 63103, United States of America
| | - Xu Wang
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, AL 36849, United States of America; HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, United States of America; Alabama Agricultural Experiment Station, Auburn University, Auburn, AL 36849, United States of America; Department of Entomology and Plant Pathology, Auburn University, Auburn, AL 36849, United States of America.
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14
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Wang X, Kelkar YD, Xiong X, Martinson EO, Lynch J, Zhang C, Werren JH, Wang X. Genome Report: Whole Genome Sequence and Annotation of the Parasitoid Jewel Wasp Nasonia giraulti Laboratory Strain RV2X[u]. G3 (BETHESDA, MD.) 2020; 10:2565-2572. [PMID: 32571804 PMCID: PMC7407473 DOI: 10.1534/g3.120.401200] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Accepted: 06/16/2020] [Indexed: 12/23/2022]
Abstract
Jewel wasps in the genus of Nasonia are parasitoids with haplodiploidy sex determination, rapid development and are easy to culture in the laboratory. They are excellent models for insect genetics, genomics, epigenetics, development, and evolution. Nasonia vitripennis (Nv) and N. giraulti (Ng) are closely-related species that can be intercrossed, particularly after removal of the intracellular bacterium Wolbachia, which serve as a powerful tool to map and positionally clone morphological, behavioral, expression and methylation phenotypes. The Nv reference genome was assembled using Sanger, PacBio and Nanopore approaches and annotated with extensive RNA-seq data. In contrast, Ng genome is only available through low coverage resequencing. Therefore, de novo Ng assembly is in urgent need to advance this system. In this study, we report a high-quality Ng assembly using 10X Genomics linked-reads with 670X sequencing depth. The current assembly has a genome size of 259,040,977 bp in 3,160 scaffolds with 38.05% G-C and a 98.6% BUSCO completeness score. 97% of the RNA reads are perfectly aligned to the genome, indicating high quality in contiguity and completeness. A total of 14,777 genes are annotated in the Ng genome, and 72% of the annotated genes have a one-to-one ortholog in the Nv genome. We reported 5 million Ng-Nv SNPs which will facility mapping and population genomic studies in Nasonia In addition, 42 Ng-specific genes were identified by comparing with Nv genome and annotation. This is the first de novo assembly for this important species in the Nasonia model system, providing a useful new genomic toolkit.
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Affiliation(s)
- Xiaozhu Wang
- Department of Pathobiology, Auburn University, AL 36849
| | | | - Xiao Xiong
- Department of Pathobiology, Auburn University, AL 36849
- Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, China
| | - Ellen O Martinson
- Department of Biology, University of New Mexico, Albuquerque, NM 87131
| | - Jeremy Lynch
- Department of Biological Science, University of Illinois at Chicago, IL 60607
| | - Chao Zhang
- Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, China
| | - John H Werren
- Department of Biology, University of Rochester, NY 14627
| | - Xu Wang
- Department of Pathobiology, Auburn University, AL 36849,
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806
- Alabama Agricultural Experiment Station, Auburn, AL 36849, and
- Department of Entomology and Plant Pathology, Auburn University, AL 36849
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15
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Liu PC, Hao DJ, Hu HY, Wei JR. Sexual dimorphism and sex-biased gene expression in an egg parasitoid species, Anastatus disparis. BMC Genomics 2020; 21:492. [PMID: 32682391 PMCID: PMC7368684 DOI: 10.1186/s12864-020-06903-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Accepted: 07/10/2020] [Indexed: 11/10/2022] Open
Abstract
Background Differences in the expression of genes present in both sexes are assumed to contribute to sex differences including behavioural, physiological and morphological dimorphisms. For enriching our knowledge of gender differences in an important egg parasitoid wasp, Anastatus disparis (Hymenoptera: Eupelmidae), sex-biased differences in gene expression were investigated using Illumina-based transcriptomic analysis. Results A total of 15,812 resulting unigenes were annotated, and a large set of genes accounting for 50.09% of the total showed sex-biased expression and included 630 sex-specific genes. Gene Ontology (GO) enrichment analyses showed that the functional categories associated with sex-biased genes were mainly related to reproduction. In addition, the transcriptome data provided evidence that sex pheromones in A. disparis are produced by the female, and activity of Δ12-desaturases appear to have been replaced by Δ9-desaturases playing roles in sex pheromone production. The large set of sex-biased genes identified in this study provide a molecular background for sexually dimorphic traits such as flyability, longevity, and aggression in this species and suggests candidate venom proteins expressed only in females that could be used for biological control. Conclusions This study provides comprehensive insight into sexually dimorphic traits of a parasitoid wasp and can inform future research into the molecular mechanisms underlying such traits and the application of parasitoids to the biological control of pest species.
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Affiliation(s)
- Peng-Cheng Liu
- The College of Ecology and Environment, Anhui Normal University, Wuhu, Anhui Province, China.
| | - De-Jun Hao
- The College of Forestry, Nanjing Forestry University, Nanjing, Jiangsu Province, China
| | - Hao-Yuan Hu
- The College of Ecology and Environment, Anhui Normal University, Wuhu, Anhui Province, China
| | - Jian-Rong Wei
- The College of Life Science, Hebei University, Baoding, Hebei Province, China
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16
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Rago A, Werren JH, Colbourne JK. Sex biased expression and co-expression networks in development, using the hymenopteran Nasonia vitripennis. PLoS Genet 2020; 16:e1008518. [PMID: 31986136 PMCID: PMC7004391 DOI: 10.1371/journal.pgen.1008518] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 02/06/2020] [Accepted: 11/13/2019] [Indexed: 12/17/2022] Open
Abstract
Sexual dimorphism requires regulation of gene expression in developing organisms. These developmental differences are caused by differential expression of genes and isoforms. The effect of expressing a gene is also influenced by which other genes are simultaneously expressed (functional interactions). However, few studies have described how these processes change across development. We compare the dynamics of differential expression, isoform switching and functional interactions in the sexual development of the model parasitoid wasp Nasonia vitripennis, a system that permits genome wide analysis of sex bias from early embryos to adults. We find relatively little sex-bias in embryos and larvae at the gene level, but several sub-networks show sex-biased functional interactions in early developmental stages. These networks provide new candidates for hymenopteran sex determination, including histone modification. In contrast, sex-bias in pupae and adults is driven by the differential expression of genes. We observe sex-biased isoform switching consistently across development, but mostly in genes that are already differentially expressed. Finally, we discover that sex-biased networks are enriched by genes specific to the Nasonia clade, and that those genes possess the topological properties of key regulators. These findings suggest that regulators in sex-biased networks evolve more rapidly than regulators of other developmental networks.
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Affiliation(s)
- Alfredo Rago
- School of Biosciences, The University of Birmingham, Birmingham, United Kingdom
| | - John H. Werren
- Department of Biology, University of Rochester, Rochester, NY, United States of America
| | - John K. Colbourne
- School of Biosciences, The University of Birmingham, Birmingham, United Kingdom
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17
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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] [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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18
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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] [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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19
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Mair MM, Ruther J. Chemical Ecology of the Parasitoid Wasp Genus Nasonia (Hymenoptera, Pteromalidae). Front Ecol Evol 2019. [DOI: 10.3389/fevo.2019.00184] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
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20
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Semmelmann F, Kabeya N, Malcicka M, Bruckmann A, Broschwitz B, Straub K, Merkl R, Monroig O, Sterner R, Ruther J, Ellers J. Functional characterisation of two Δ12-desaturases demonstrates targeted production of linoleic acid as pheromone precursor in Nasonia. ACTA ACUST UNITED AC 2019; 222:jeb.201038. [PMID: 31019064 DOI: 10.1242/jeb.201038] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 04/18/2019] [Indexed: 01/08/2023]
Abstract
Insect pheromones are often derived from fatty acid metabolism. Fatty acid desaturases, enzymes introducing double bonds into fatty acids, are crucial for the biosynthesis of these chemical signals. Δ12-desaturases catalyse the biosynthesis of linoleic acid by introducing a second double bond into oleic acid, but have been identified in only a few animal species. Here, we report the functional characterisation of two Δ12-desaturases, Nvit_D12a and Nvit_D12b, from the parasitic wasp Nasonia vitripennis. We demonstrate that Nvit_D12a is expressed in the rectal vesicle of males where they produce a linoleic acid-derived sex pheromone to attract virgin females. 13C-labelling experiments with Urolepis rufipes, a closely related species belonging to the 'Nasonia group', revealed that females, but not males, are able to synthesise linoleic acid. U. rufipes males produce an isoprenoid sex pheromone in the same gland and do not depend on linoleic acid for pheromone production. This suggests that Δ12-desaturases are common in the 'Nasonia group', but acquired a specialised function in chemical communication of those species that use linoleic acid as a pheromone precursor. Phylogenetic analysis suggests that insect Δ12-desaturases have evolved repeatedly from Δ9-desaturases in different insect taxa. Hence, insects have developed a way to produce linoleic acid independent of the omega desaturase subfamily which harbours all of the eukaryotic Δ12-desaturases known so far.
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Affiliation(s)
- Florian Semmelmann
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, Universitätsstraße 31, 93053 Regensburg, Germany
| | - Naoki Kabeya
- Department of Aquatic Bioscience, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, 113-8657 Tokyo, Japan
| | - Miriama Malcicka
- Department of Ecological Sciences, Vrije Universiteit, Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands
| | - Astrid Bruckmann
- Institute of Biochemistry, Genetics and Microbiology, University of Regensburg, Universitätsstraße 31, 93053 Regensburg, Germany
| | - Bastian Broschwitz
- Institute of Zoology, University of Regensburg, Universitätsstraße 31, 93053 Regensburg, Germany
| | - Kristina Straub
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, Universitätsstraße 31, 93053 Regensburg, Germany
| | - Rainer Merkl
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, Universitätsstraße 31, 93053 Regensburg, Germany
| | - Oscar Monroig
- Instituto de Acuicultura Torre de la Sal, Consejo Superior de Investigaciones Científicas (IATS-CSIC), Ribera de Cabanes 12595, Spain
| | - Reinhard Sterner
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, Universitätsstraße 31, 93053 Regensburg, Germany
| | - Joachim Ruther
- Institute of Zoology, University of Regensburg, Universitätsstraße 31, 93053 Regensburg, Germany
| | - Jacintha Ellers
- Department of Ecological Sciences, Vrije Universiteit, Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands
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Liu PC, Tian S, Hao DJ. Sexual Transcription Differences in Brachymeria lasus (Hymenoptera: Chalcididae), a Pupal Parasitoid Species of Lymantria dispar (Lepidoptera: Lymantriidae). Front Genet 2019; 10:172. [PMID: 30891067 PMCID: PMC6411638 DOI: 10.3389/fgene.2019.00172] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 02/18/2019] [Indexed: 12/11/2022] Open
Abstract
Sex differences in gene expression have been extensively documented, but little is known about these differences in parasitoid species that are widely applied to control pests. Brachymeria lasus is a solitary parasitoid species and has been evaluated as a potential candidate for release to control Lymantria dispar. In this study, gender differences in B. lasus were investigated using Illumina-based transcriptomic analysis. The resulting 37,453 unigene annotations provided a large amount of useful data for molecular studies of B. lasus. A total of 1416 differentially expressed genes were identified between females and males, and the majority of the sex-biased genes were female biased. Gene Ontology (GO) and Pathway enrichment analyses showed that (1) the functional categories DNA replication, fatty acid biosynthesis, and metabolism were enhanced in females and that (2) the only pathway enriched in males was phototransduction, while the GO subcategories enriched in males were those involved in membrane and ion transport. In addition, thirteen genes involving transient receptor potential (TRP) channels were annotated in B. lasus. We further explored and discussed the functions of TRPs in sensory signaling of light and temperature. In general, this study provides new molecular insights into the biological and sexually dimorphic traits of parasitoids, which may improve the application of these insects to the biological control of pests.
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Affiliation(s)
- Peng-Cheng Liu
- Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
- The College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Shuo Tian
- Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
- The College of Forestry, Nanjing Forestry University, Nanjing, China
| | - De-Jun Hao
- Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
- The College of Forestry, Nanjing Forestry University, Nanjing, China
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22
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Whittle CA, Extavour CG. Selection shapes turnover and magnitude of sex-biased expression in Drosophila gonads. BMC Evol Biol 2019; 19:60. [PMID: 30786879 PMCID: PMC6383255 DOI: 10.1186/s12862-019-1377-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 01/23/2019] [Indexed: 12/18/2022] Open
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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23
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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] [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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24
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Shirk PD, Furlong RB, Dolan A, Werren JH. Functional characterization of the transcriptional regulatory elements of three highly expressed constitutive genes in the jewel wasp, Nasonia vitripennis. INSECT MOLECULAR BIOLOGY 2017; 26:743-751. [PMID: 28753244 DOI: 10.1111/imb.12333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The jewel wasp, Nasonia vitripennis Ashmead (Hymenoptera: Pteromalidae), is an easily reared parasitoid that is providing an ever increasingly malleable model for examining the biology and genetics of Hymenoptera. Utilizing genomic and transcriptome resources, 5' upstream transcriptional regulatory sequences (TREs) from three highly expressed genes were identified and cloned. Criteria for TRE selection included the presence of an adjacent gene 5' of the translation initiation site. One gene was methylated whereas the other two were nonmethylated. Each TRE, heat-shock protein 70 (hsp70), activator of 90 kDa hsp ATPase protein 1 (hsp90A), and lipid storage droplet surface-binding protein 1 (lsdp) was linked with enhanced green fluorescent protein (EGFP) coding sequence and cloned into both pDP9e somatic and piggyBac germline transformation vectors. EGFP expression patterns under control of each TRE were compared with patterns of DsRed fluorescence produced from the transformation vector cassette. Functional activity of each TRE was observed in cultured Spodoptera frugiperda 9 (Sf9) cells and Drosophila melanogaster as well as in N. vitripennis embryos demonstrating that all three sequences had functional transcriptional regulatory activity in three different insect orders. Identification and functional characterization of these three TREs will provide critical and necessary resources for further genetic analyses of N. vitripennis, Hymenoptera and other insects.
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Affiliation(s)
- P D Shirk
- USDA-ARS Center for Medical Agricultural and Veterinary Entomology, Gainesville, FL, USA
| | - R B Furlong
- USDA-ARS Center for Medical Agricultural and Veterinary Entomology, Gainesville, FL, USA
| | - A Dolan
- Department of Biology, University of Rochester, Rochester, NY, USA
| | - J H Werren
- Department of Biology, University of Rochester, Rochester, NY, USA
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25
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Papa F, Windbichler N, Waterhouse RM, Cagnetti A, D'Amato R, Persampieri T, Lawniczak MKN, Nolan T, Papathanos PA. Rapid evolution of female-biased genes among four species of Anopheles malaria mosquitoes. Genome Res 2017; 27:1536-1548. [PMID: 28747381 PMCID: PMC5580713 DOI: 10.1101/gr.217216.116] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Accepted: 07/18/2017] [Indexed: 01/09/2023]
Abstract
Understanding how phenotypic differences between males and females arise from the sex-biased expression of nearly identical genomes can reveal important insights into the biology and evolution of a species. Among Anopheles mosquito species, these phenotypic differences include vectorial capacity, as it is only females that blood feed and thus transmit human malaria. Here, we use RNA-seq data from multiple tissues of four vector species spanning the Anopheles phylogeny to explore the genomic and evolutionary properties of sex-biased genes. We find that, in these mosquitoes, in contrast to what has been found in many other organisms, female-biased genes are more rapidly evolving in sequence, expression, and genic turnover than male-biased genes. Our results suggest that this atypical pattern may be due to the combination of sex-specific life history challenges encountered by females, such as blood feeding. Furthermore, female propensity to mate only once in nature in male swarms likely diminishes sexual selection of post-reproductive traits related to sperm competition among males. We also develop a comparative framework to systematically explore tissue- and sex-specific splicing to document its conservation throughout the genus and identify a set of candidate genes for future functional analyses of sex-specific isoform usage. Finally, our data reveal that the deficit of male-biased genes on the X Chromosomes in Anopheles is a conserved feature in this genus and can be directly attributed to chromosome-wide transcriptional regulation that de-masculinizes the X in male reproductive tissues.
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Affiliation(s)
- Francesco Papa
- Section of Genomics and Genetics, Department of Experimental Medicine, University of Perugia, 06132 Perugia, Italy
| | - Nikolai Windbichler
- Department of Life Sciences, Imperial College London, SW7 2AZ London, United Kingdom
| | - Robert M Waterhouse
- University of Geneva Medical School and Swiss Institute of Bioinformatics, 1211 Geneva, Switzerland
- Massachusetts Institute of Technology and the Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02139, USA
- Department of Ecology and Evolution, University of Lausanne, CH-1015 Lausanne, Switzerland
| | - Alessia Cagnetti
- Section of Genomics and Genetics, Department of Experimental Medicine, University of Perugia, 06132 Perugia, Italy
- Polo d'Innovazione di Genomica, Genetica e Biologia, 06132 Perugia, Italy
| | - Rocco D'Amato
- Section of Genomics and Genetics, Department of Experimental Medicine, University of Perugia, 06132 Perugia, Italy
| | - Tania Persampieri
- Section of Genomics and Genetics, Department of Experimental Medicine, University of Perugia, 06132 Perugia, Italy
- Polo d'Innovazione di Genomica, Genetica e Biologia, 06132 Perugia, Italy
| | | | - Tony Nolan
- Department of Life Sciences, Imperial College London, SW7 2AZ London, United Kingdom
| | - Philippos Aris Papathanos
- Section of Genomics and Genetics, Department of Experimental Medicine, University of Perugia, 06132 Perugia, Italy
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26
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Lucas ER, Romiguier J, Keller L. Gene expression is more strongly influenced by age than caste in the ant Lasius niger. Mol Ecol 2017; 26:5058-5073. [DOI: 10.1111/mec.14256] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Revised: 06/20/2017] [Accepted: 06/28/2017] [Indexed: 12/20/2022]
Affiliation(s)
- Eric R. Lucas
- Department of Ecology and Evolution; Biophore, University of Lausanne; Lausanne Switzerland
- Department of Vector Biology; Liverpool School of Tropical Medicine; Liverpool UK
| | - Jonathan Romiguier
- Department of Ecology and Evolution; Biophore, University of Lausanne; Lausanne Switzerland
| | - Laurent Keller
- Department of Ecology and Evolution; Biophore, University of Lausanne; Lausanne Switzerland
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27
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Guo D, Luo J, Zhou Y, Xiao H, He K, Yin C, Xu J, Li F. ACE: an efficient and sensitive tool to detect insecticide resistance-associated mutations in insect acetylcholinesterase from RNA-Seq data. BMC Bioinformatics 2017; 18:330. [PMID: 28693417 PMCID: PMC5504734 DOI: 10.1186/s12859-017-1741-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Accepted: 06/22/2017] [Indexed: 01/11/2023] Open
Abstract
Background Insecticide resistance is a substantial problem in controlling agricultural and medical pests. Detecting target site mutations is crucial to manage insecticide resistance. Though PCR-based methods have been widely used in this field, they are time-consuming and inefficient, and typically have a high false positive rate. Acetylcholinesterases (Ace) is the neural target of the widely used organophosphate (OP) and carbamate insecticides. However, there is not any software available to detect insecticide resistance associated mutations in RNA-Seq data at present. Results A computational pipeline ACE was developed to detect resistance mutations of ace in insect RNA-Seq data. Known ace resistance mutations were collected and used as a reference. We constructed a Web server for ACE, and the standalone software in both Linux and Windows versions is available for download. ACE was used to analyse 971 RNA-Seq data from 136 studies in 7 insect pests. The mutation frequency of each RNA-Seq dataset was calculated. The results indicated that the resistance frequency was 30%–44% in an eastern Ugandan Anopheles population, thus suggesting this resistance-conferring mutation has reached high frequency in these mosquitoes in Uganda. Analyses of RNA-Seq data from the diamondback moth Plutella xylostella indicated that the G227A mutation was positively related with resistance levels to organophosphate or carbamate insecticides. The wasp Nasonia vitripennis had a low frequency of resistant reads (<5%), but the agricultural pests Chilo suppressalis and Bemisia tabaci had a high resistance frequency. All ace reads in the 30 B. tabaci RNA-Seq data were resistant reads, suggesting that insecticide resistance has spread to very high frequency in B. tabaci. Conclusions To the best of our knowledge, the ACE pipeline is the first tool to detect resistance mutations from RNA-Seq data, and it facilitates the full utilization of large-scale genetic data obtained by using next-generation sequencing. Electronic supplementary material The online version of this article (doi:10.1186/s12859-017-1741-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Dianhao Guo
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Science, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China.,Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jiapeng Luo
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Science, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China.,College of Computer Science and Technology, Nanjing Normal University, Nanjing, 210023, China
| | - Yuenan Zhou
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Science, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Huamei Xiao
- College of Life Sciences and Resource Environment, Yichun University, Yichun, 336000, China
| | - Kang He
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Science, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Chuanlin Yin
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Science, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Jianhua Xu
- College of Life Sciences and Resource Environment, Yichun University, Yichun, 336000, China
| | - Fei Li
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Science, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China.
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28
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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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29
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Hatching enzymes disrupt aberrant gonadal degeneration by the autophagy/apoptosis cell fate decision. Sci Rep 2017; 7:3183. [PMID: 28600501 PMCID: PMC5466654 DOI: 10.1038/s41598-017-03314-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 04/25/2017] [Indexed: 11/19/2022] Open
Abstract
Environmental stressors, gonadal degenerative diseases and tumour development can significantly alter the oocyte physiology, and species fertility and fitness. To expand the molecular understanding about oocyte degradation, we isolated several spliced variants of Japanese anchovy hatching enzymes (AcHEs; ovastacin homologue) 1 and 2, and analysed their potential in oocyte sustenance. Particularly, AcHE1b, an ovary-specific, steroid-regulated, methylation-dependent, stress-responsive isoform, was neofunctionalized to regulate autophagic oocyte degeneration. AcHE1a and 2 triggered apoptotic degeneration in vitellogenic and mature oocytes, respectively. Progesterone, starvation, and high temperature elevated the total degenerating oocyte population and AcHE1b transcription by hyper-demethylation. Overexpression, knockdown and intracellular zinc ion chelation study confirmed the functional significance of AcHE1b in autophagy induction, possibly to mitigate the stress effects in fish, via ion-homeostasis. Our finding chronicles the importance of AcHEs in stress-influenced apoptosis/autophagy cell fate decision and may prove significant in reproductive failure assessments, gonadal health maintenance and ovarian degenerative disease therapy.
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30
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Casola C, Betrán E. The Genomic Impact of Gene Retrocopies: What Have We Learned from Comparative Genomics, Population Genomics, and Transcriptomic Analyses? Genome Biol Evol 2017; 9:1351-1373. [PMID: 28605529 PMCID: PMC5470649 DOI: 10.1093/gbe/evx081] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/18/2017] [Indexed: 02/07/2023] Open
Abstract
Gene duplication is a major driver of organismal evolution. Gene retroposition is a mechanism of gene duplication whereby a gene's transcript is used as a template to generate retroposed gene copies, or retrocopies. Intriguingly, the formation of retrocopies depends upon the enzymatic machinery encoded by retrotransposable elements, genomic parasites occurring in the majority of eukaryotes. Most retrocopies are depleted of the regulatory regions found upstream of their parental genes; therefore, they were initially considered transcriptionally incompetent gene copies, or retropseudogenes. However, examples of functional retrocopies, or retrogenes, have accumulated since the 1980s. Here, we review what we have learned about retrocopies in animals, plants and other eukaryotic organisms, with a particular emphasis on comparative and population genomic analyses complemented with transcriptomic datasets. In addition, these data have provided information about the dynamics of the different "life cycle" stages of retrocopies (i.e., polymorphic retrocopy number variants, fixed retropseudogenes and retrogenes) and have provided key insights into the retroduplication mechanisms, the patterns and evolutionary forces at work during the fixation process and the biological function of retrogenes. Functional genomic and transcriptomic data have also revealed that many retropseudogenes are transcriptionally active and a biological role has been experimentally determined for many. Finally, we have learned that not only non-long terminal repeat retroelements but also long terminal repeat retroelements play a role in the emergence of retrocopies across eukaryotes. This body of work has shown that mRNA-mediated duplication represents a widespread phenomenon that produces an array of new genes that contribute to organismal diversity and adaptation.
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Affiliation(s)
- Claudio Casola
- Department of Ecosystem Science and Management, Texas A&M University, TX
| | - Esther Betrán
- Department of Biology, University of Texas at Arlington, Arlington, TX
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31
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Affiliation(s)
- Sonja Grath
- Department of Biology II, Faculty of Biology, Ludwig-Maximilians-Universität München, 82152 Planegg, Germany; ,
| | - John Parsch
- Department of Biology II, Faculty of Biology, Ludwig-Maximilians-Universität München, 82152 Planegg, Germany; ,
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32
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Rago A, Gilbert DG, Choi JH, Sackton TB, Wang X, Kelkar YD, Werren JH, Colbourne JK. OGS2: genome re-annotation of the jewel wasp Nasonia vitripennis. BMC Genomics 2016; 17:678. [PMID: 27561358 PMCID: PMC5000498 DOI: 10.1186/s12864-016-2886-9] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2015] [Accepted: 07/06/2016] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Nasonia vitripennis is an emerging insect model system with haplodiploid genetics. It holds a key position within the insect phylogeny for comparative, evolutionary and behavioral genetic studies. The draft genomes for N. vitripennis and two sibling species were published in 2010, yet a considerable amount of transcriptiome data have since been produced thereby enabling improvements to the original (OGS1.2) annotated gene set. We describe and apply the EvidentialGene method used to produce an updated gene set (OGS2). We also carry out comparative analyses showcasing the usefulness of the revised annotated gene set. RESULTS The revised annotation (OGS2) now consists of 24,388 genes with supporting evidence, compared to 18,850 for OGS1.2. Improvements include the nearly complete annotation of untranslated regions (UTR) for 97 % of the genes compared to 28 % of genes for OGS1.2. The fraction of RNA-Seq validated introns also grow from 85 to 98 % in this latest gene set. The EST and RNA-Seq expression data provide support for several non-protein coding loci and 7712 alternative transcripts for 4146 genes. Notably, we report 180 alternative transcripts for the gene lola. Nasonia now has among the most complete insect gene set; only 27 conserved single copy orthologs in arthropods are missing from OGS2. Its genome also contains 2.1-fold more duplicated genes and 1.4-fold more single copy genes than the Drosophila melanogaster genome. The Nasonia gene count is larger than those of other sequenced hymenopteran species, owing both to improvements in the genome annotation and to unique genes in the wasp lineage. We identify 1008 genes and 171 gene families that deviate significantly from other hymenopterans in their rates of protein evolution and duplication history, respectively. We also provide an analysis of alternative splicing that reveals that genes with no annotated isoforms are characterized by shorter transcripts, fewer introns, faster protein evolution and higher probabilities of duplication than genes having alternative transcripts. CONCLUSIONS Genome-wide expression data greatly improves the annotation of the N. vitripennis genome, by increasing the gene count, reducing the number of missing genes and providing more comprehensive data on splicing and gene structure. The improved gene set identifies lineage-specific genomic features tied to Nasonia's biology, as well as numerous novel genes. OGS2 and its associated search tools are available at http://arthropods.eugenes.org/EvidentialGene/nasonia/ , www.hymenopteragenome.org/nasonia/ and waspAtlas: www.tinyURL.com/waspAtlas . The EvidentialGene pipeline is available at https://sourceforge.net/projects/evidentialgene/ .
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Affiliation(s)
- Alfredo Rago
- Environmental Genomics Group, School of Biosciences, University of Birmingham, Birmingham, UK
| | | | - Jeong-Hyeon Choi
- Cancer Center, Department of Biostatistics and Epidemiology, Medical College of Georgia, Georgia Regents University, Augusta, USA
| | - Timothy B. Sackton
- Department of Organismic and Evolutionary Biology, and FAS Informatics Group, Harvard University, Cambridge, USA
| | - Xu Wang
- Department of Molecular Biology and Genetics, Cornell Center for Comparative and Population Genomics, Cornell University, Ithaca, USA
| | - Yogeshwar D. Kelkar
- Department of Biostatistics and Computational Biology, University of Rochester Medical School, Rochester, USA
| | - John H. Werren
- Department of Biology, University of Rochester, Rochester, USA
| | - John K. Colbourne
- Environmental Genomics Group, School of Biosciences, University of Birmingham, Birmingham, UK
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33
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Wang X, Werren JH, Clark AG. Allele-Specific Transcriptome and Methylome Analysis Reveals Stable Inheritance and Cis-Regulation of DNA Methylation in Nasonia. PLoS Biol 2016; 14:e1002500. [PMID: 27380029 PMCID: PMC4933354 DOI: 10.1371/journal.pbio.1002500] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2016] [Accepted: 06/03/2016] [Indexed: 11/18/2022] Open
Abstract
Gene expression divergence between closely related species could be attributed to both cis- and trans- DNA sequence changes during evolution, but it is unclear how the evolutionary dynamics of epigenetic marks are regulated. In eutherian mammals, biparental DNA methylation marks are erased and reset during gametogenesis, resulting in paternal or maternal imprints, which lead to genomic imprinting. Whether DNA methylation reprogramming exists in insects is not known. Wasps of the genus Nasonia are non-social parasitoids that are emerging as a model for studies of epigenetic processes in insects. In this study, we quantified allele-specific expression and methylation genome-wide in Nasonia vitripennis and Nasonia giraulti and their reciprocal F1 hybrids. No parent-of-origin effect in allelic expression was found for >8,000 covered genes, suggesting a lack of genomic imprinting in adult Nasonia. As we expected, both significant cis- and trans- effects are responsible for the expression divergence between N. vitripennis and N. giraulti. Surprisingly, all 178 differentially methylated genes are also differentially methylated between the two alleles in F1 hybrid offspring, recapitulating the parental methylation status with nearly 100% fidelity, indicating the presence of strong cis-elements driving the target of gene body methylation. In addition, we discovered that total and allele-specific expression are positively correlated with allele-specific methylation in a subset of the differentially methylated genes. The 100% cis-regulation in F1 hybrids suggests the methylation machinery is conserved and DNA methylation is targeted by cis features in Nasonia. The lack of genomic imprinting and parent-of-origin differentially methylated regions in Nasonia, together with the stable inheritance of methylation status between generations, suggests either a cis-regulatory motif for methylation at the DNA level or highly stable inheritance of an epigenetic signal in Nasonia. RNA-sequencing and whole-genome bisulfite sequencing in the hybrid offspring of two Nasonia parasitoid wasp species revealed strong cis-regulation of methylation and allele-specific expression. No gene was found to display genomic imprinting. The relationship between methylation of genomic DNA and expression of the genes that it encodes—and how this relationship changes during evolution—has been widely studied in mammals, but remains less well understood for insects. Here we analyze the expressed mRNA transcripts and genomic DNA methylation of the hybrid offspring of a pair of Nasonia parasitoid wasp species, producing a wealth of information about the regulation of gene expression. We find that variation in DNA sequence impacts expression on the same strand (called “cis-regulation”), and that cytosine methylation state is also associated in cis with the regulatory consequences of this base alteration. We show that these wasp species lack differential expression dependent on parent-of-origin (called “genomic imprinting”), and that in the hybrids the alleles retain the methylation status of the parental species in a strong cis-regulated fashion. Transcript abundances were also largely driven in a cis-regulated manner, consistent with a correlation between methylation status and expression levels. Despite the many differences between Nasonia and mammals in the impact of genomic DNA methylation, in both groups the use of methylated cytosine has been co-opted in ways that help tune gene expression.
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Affiliation(s)
- Xu Wang
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
- Cornell Center for Comparative and Population Genomics, Cornell University, Ithaca, New York, United States of America
- * E-mail: (XW); (JHW); (AGC)
| | - John H. Werren
- Department of Biology, University of Rochester, Rochester, New York, United States of America
- * E-mail: (XW); (JHW); (AGC)
| | - Andrew G. Clark
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
- Cornell Center for Comparative and Population Genomics, Cornell University, Ithaca, New York, United States of America
- * E-mail: (XW); (JHW); (AGC)
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Perotti MA, Young DK, Braig HR. The ghost sex-life of the paedogenetic beetle Micromalthus debilis. Sci Rep 2016; 6:27364. [PMID: 27270667 PMCID: PMC4895236 DOI: 10.1038/srep27364] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Accepted: 05/12/2016] [Indexed: 02/02/2023] Open
Abstract
Genetic and sexual systems can be evolutionarily dynamic within and among clades. However, identifying the processes responsible for switches between, for instance, sexual and asexual reproduction, or cyclic and non-cyclic life histories remains challenging. When animals evolve parthenogenetic reproduction, information about the sexual mating system becomes lost. Here we report an extraordinary case where we have been able to resurrect sexual adults in a species of beetle that reproduces by parthenogenetic paedogenesis, without the production of adults. Via heat treatment, we were able to artificially induce adult beetles of Micromalthus debilis in order to describe its pre-paedogenetic mating system. Adults showed a highly female biased sex ratio, out-breeding behaviour, and sex-role reversal. Paedogenetic larvae of Micromalthus are infected with the endosymbiotic bacteria Rickettsia and Wolbachia. Clear signs of vestigialization in adults are concurrent with the loss of adults. Our data suggest an ancient female sex ratio bias that predates the loss of adults, perhaps associated with endosymbionts. We propose a model for the transition from a haplodiploid cyclical parthenogenetic life history to parthenogenetic paedogenesis. Paedogenetic development induces a new mechanism of sex ratio bias in midges, wasps and beetles.
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Affiliation(s)
| | - Daniel K. Young
- Department of Entomology, 1630 Linden Drive, University of Wisconsin, Madison, WI 53706, USA
| | - Henk R. Braig
- School of Biological Sciences, Bangor University, Bangor, LL57 2UW, UK
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Martinson EO, Martinson VG, Edwards R, Mrinalini, Werren JH. Laterally Transferred Gene Recruited as a Venom in Parasitoid Wasps. Mol Biol Evol 2016; 33:1042-52. [PMID: 26715630 PMCID: PMC5013869 DOI: 10.1093/molbev/msv348] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Parasitoid wasps use venom to manipulate the immunity and metabolism of their host insects in a variety of ways to provide resources for their offspring. Yet, how genes are recruited and evolve to perform venom functions remain open questions. A recently recognized source of eukaryotic genome innovation is lateral gene transfer (LGT). Glycoside hydrolase family 19 (GH19) chitinases are widespread in bacteria, microsporidia, and plants where they are used in nutrient acquisition or defense, but have previously not been known in metazoans. In this study, a GH19 chitinase LGT is described from the unicellular microsporidia/Rozella clade into parasitoid wasps of the superfamily Chalcidoidea, where it has become recruited as a venom protein. The GH19 chitinase is present in 15 species of chalcidoid wasps representing four families, and phylogenetic analysis indicates that it was laterally transferred near or before the origin of Chalcidoidea (∼95 Ma). The GH19 chitinase gene is highly expressed in the venom gland of at least seven species, indicating a role in the complex host manipulations performed by parasitoid wasp venom. RNAi knockdown in the model parasitoid Nasonia vitripennis reveals that-following envenomation-the GH19 chitinase induces fly hosts to upregulate genes involved in an immune response to fungi. A second, independent LGT of GH19 chitinase from microsporidia into mosquitoes was also found, also supported by phylogenetic reconstructions. Besides these two LGT events, GH19 chitinase is not found in any other sequenced animal genome, or in any fungi outside the microsporidia/Rozella clade.
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Affiliation(s)
| | | | | | - Mrinalini
- Biology Department, University of Rochester
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Remnant EJ, Ashe A, Young PE, Buchmann G, Beekman M, Allsopp MH, Suter CM, Drewell RA, Oldroyd BP. Parent-of-origin effects on genome-wide DNA methylation in the Cape honey bee (Apis mellifera capensis) may be confounded by allele-specific methylation. BMC Genomics 2016; 17:226. [PMID: 26969617 PMCID: PMC4788913 DOI: 10.1186/s12864-016-2506-8] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Accepted: 02/19/2016] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Intersexual genomic conflict sometimes leads to unequal expression of paternal and maternal alleles in offspring, resulting in parent-of-origin effects. In honey bees reciprocal crosses can show strong parent-of-origin effects, supporting theoretical predictions that genomic imprinting occurs in this species. Mechanisms behind imprinting in honey bees are unclear but differential DNA methylation in eggs and sperm suggests that DNA methylation could be involved. Nonetheless, because DNA methylation is multifunctional, it is difficult to separate imprinting from other roles of methylation. Here we use a novel approach to investigate parent-of-origin DNA methylation in honey bees. In the subspecies Apis mellifera capensis, reproduction of females occurs either sexually by fertilization of eggs with sperm, or via thelytokous parthenogenesis, producing female embryos derived from two maternal genomes. RESULTS We compared genome-wide methylation patterns of sexually-produced, diploid embryos laid by a queen, with parthenogenetically-produced diploid embryos laid by her daughters. Thelytokous embryos inheriting two maternal genomes had fewer hypermethylated genes compared to fertilized embryos, supporting the prediction that fertilized embryos have increased methylation due to inheritance of a paternal genome. However, bisulfite PCR and sequencing of a differentially methylated gene, Stan (GB18207) showed strong allele-specific methylation that was maintained in both fertilized and thelytokous embryos. For this gene, methylation was associated with haplotype, not parent of origin. CONCLUSIONS The results of our study are consistent with predictions from the kin theory of genomic imprinting. However, our demonstration of allele-specific methylation based on sequence shows that genome-wide differential methylation studies can potentially confound imprinting and allele-specific methylation. It further suggests that methylation patterns are heritable or that specific sequence motifs are targets for methylation in some genes.
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Affiliation(s)
- Emily J. Remnant
- />Behavior and Genetics of Social Insects Laboratory, School of Life and Environmental Sciences A12, University of Sydney, Room 248, Macleay Building (A12), Sydney, NSW 2006 Australia
| | - Alyson Ashe
- />School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006 Australia
| | - Paul E. Young
- />Victor Chang Cardiac Research Institute, Lowy Packer Building, 405 Liverpool Street, Darlinghurst, NSW 2010 Australia
- />University of New South Wales, Kensington, NSW 2033 Australia
| | - Gabriele Buchmann
- />Behavior and Genetics of Social Insects Laboratory, School of Life and Environmental Sciences A12, University of Sydney, Room 248, Macleay Building (A12), Sydney, NSW 2006 Australia
| | - Madeleine Beekman
- />Behavior and Genetics of Social Insects Laboratory, School of Life and Environmental Sciences A12, University of Sydney, Room 248, Macleay Building (A12), Sydney, NSW 2006 Australia
| | - Michael H. Allsopp
- />Honey Bee Research Section, ARC-Plant Protection Research Institute, Private Bag X5017, Stellenbosch, South Africa
| | - Catherine M. Suter
- />Victor Chang Cardiac Research Institute, Lowy Packer Building, 405 Liverpool Street, Darlinghurst, NSW 2010 Australia
- />University of New South Wales, Kensington, NSW 2033 Australia
| | - Robert A. Drewell
- />Biology Department, Clark University, 950 Main Street, Worcester, MA 01610 USA
| | - Benjamin P. Oldroyd
- />Behavior and Genetics of Social Insects Laboratory, School of Life and Environmental Sciences A12, University of Sydney, Room 248, Macleay Building (A12), Sydney, NSW 2006 Australia
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Identification of Genes Uniquely Expressed in the Germ-Line Tissues of the Jewel Wasp Nasonia vitripennis. G3-GENES GENOMES GENETICS 2015; 5:2647-53. [PMID: 26464360 PMCID: PMC4683638 DOI: 10.1534/g3.115.021386] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The jewel wasp Nasonia vitripennis is a rising model organism for the study of haplo-diploid reproduction characteristic of hymenopteran insects, which include all wasps, bees, and ants. We performed transcriptional profiling of the ovary, the female soma, and the male soma of N. vitripennis to complement a previously existing transcriptome of the wasp testis. These data were deposited into an open-access genome browser for visualization of transcripts relative to their gene models. We used these data to identify the assemblies of genes uniquely expressed in the germ-line tissues. We found that 156 protein-coding genes are expressed exclusively in the wasp testis compared with only 22 in the ovary. Of the testis-specific genes, eight are candidates for male-specific DNA packaging proteins known as protamines. We found very similar expression patterns of centrosome associated genes in the testis and ovary, arguing that de novo centrosome formation, a key process for development of unfertilized eggs into males, likely does not rely on large-scale transcriptional differences between these tissues. In contrast, a number of meiosis-related genes show a bias toward testis-specific expression, despite the lack of true meiosis in N. vitripennis males. These patterns may reflect an unexpected complexity of male gamete production in the haploid males of this organism. Broadly, these data add to the growing number of genomic and genetic tools available in N. vitripennis for addressing important biological questions in this rising insect model organism.
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Davies NJ, Tauber E. WaspAtlas: a Nasonia vitripennis gene database and analysis platform. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2015; 2015:bav103. [PMID: 26452372 PMCID: PMC4599445 DOI: 10.1093/database/bav103] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2015] [Accepted: 09/18/2015] [Indexed: 12/27/2022]
Abstract
Nasonia vitripennis is a parasitoid wasp which is becoming an important model organism for parasitism, epigenetics, evolutionary and developmental genetics. WaspAtlas is a new gene database in which we have compiled annotation data from all available N. vitripennis releases along with a wealth of transcriptomic data, methylation data and original analyses and annotations to form a comprehensive resource to aid the study of Nasonia. WaspAtlas allows users to explore gene structure and function, to compare expression data across sexes, tissues, developmental stages and conditions, and to explore published data relating to gene(s) of interest. WaspAtlas is easy to navigate and the database is easily searchable through the web interface. Detailed illustrations are provided for splice variants, protein domain predictions and the results of analyses. The website also functions as an analysis platform analysis for Nasonia, providing a set of tools designed to perform common analyses including GO term overrepresentation and RNAi off-target prediction. WaspAtlas will act as a hub for published data relating to Nasonia genes, and will be continually updated with new data to reflect the state of Nasonia-omics research. Database URL: http://waspatlas.com
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Affiliation(s)
- Nathaniel J Davies
- Department of Genetics, University of Leicester, University Road, Leicester LE1 7RH, UK
| | - Eran Tauber
- Department of Genetics, University of Leicester, University Road, Leicester LE1 7RH, UK
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