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Luecke D, Luo Y, Krzystek H, Jones C, Kopp A. Highly contiguous genome assembly of Drosophila prolongata-a model for evolution of sexual dimorphism and male-specific innovations. G3 (BETHESDA, MD.) 2024; 14:jkae155. [PMID: 39001868 PMCID: PMC11457088 DOI: 10.1093/g3journal/jkae155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Revised: 05/22/2024] [Accepted: 06/13/2024] [Indexed: 07/15/2024]
Abstract
Drosophila prolongata is a member of the melanogaster species group and rhopaloa subgroup native to the subtropical highlands of Southeast Asia. This species exhibits an array of recently evolved male-specific morphological, physiological, and behavioral traits that distinguish it from its closest relatives, making it an attractive model for studying the evolution of sexual dimorphism and testing theories of sexual selection. The lack of genomic resources has impeded the dissection of the molecular basis of sex-specific development and behavior in this species. To address this, we assembled the genome of D. prolongata using long-read sequencing and Hi-C scaffolding, resulting in a highly complete and contiguous (scaffold N50 2.2 Mb) genome assembly of 220 Mb. The repetitive content of the genome is 24.6%, the plurality of which are long terminal repeats retrotransposons (33.2%). Annotations based on RNA-seq data and homology to related species revealed a total of 19,330 genes, of which 16,170 are protein-coding. The assembly includes 98.5% of Diptera BUSCO genes, including 93.8% present as a single copy. Despite some likely regional duplications, the completeness of this genome suggests that it can be readily used for gene expression, genome-wide association studies (GWAS), and other genomic analyses.
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Affiliation(s)
- David Luecke
- Department of Evolution and Ecology, University of California Davis, One Shields Ave, Davis, CA 95616, USA
- USDA, ARS, PA, US Livestock Insects Research Lab, 2700 Fredericksburg Road, Kerrville, TX 78028, USA
| | - Yige Luo
- Department of Evolution and Ecology, University of California Davis, One Shields Ave, Davis, CA 95616, USA
| | - Halina Krzystek
- Biology Department of the University of North Carolina (UNC), 3159 Genome Sciences Building, 250 Bell Tower Drive, Chapel Hill, NC 27599, USA
| | - Corbin Jones
- Biology Department of the University of North Carolina (UNC), 3159 Genome Sciences Building, 250 Bell Tower Drive, Chapel Hill, NC 27599, USA
| | - Artyom Kopp
- Department of Evolution and Ecology, University of California Davis, One Shields Ave, Davis, CA 95616, USA
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Luecke D, Luo Y, Krzystek H, Jones C, Kopp A. Highly Contiguous Genome Assembly of Drosophila prolongata - a Model for Evolution of Sexual Dimorphism and Male-specific Innovations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.29.577853. [PMID: 38352395 PMCID: PMC10862779 DOI: 10.1101/2024.01.29.577853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/22/2024]
Abstract
Drosophila prolongata is a member of the melanogaster species group and rhopaloa subgroup native to the subtropical highlands of southeast Asia. This species exhibits an array of recently evolved male-specific morphological, physiological, and behavioral traits that distinguish it from its closest relatives, making it an attractive model for studying the evolution of sexual dimorphism and testing theories of sexual selection. The lack of genomic resources has impeded the dissection of the molecular basis of sex-specific development and behavior in this species. To address this, we assembled the genome of D. prolongata using long-read sequencing and Hi-C scaffolding, resulting in a highly complete and contiguous (scaffold N50 2.2Mb) genome assembly of 220Mb. The repetitive content of the genome is 24.6%, the plurality of which are LTR retrotransposons (33.2%). Annotations based on RNA-seq data and homology to related species revealed a total of 19,330 genes, of which 16,170 are protein-coding. The assembly includes 98.5% of Diptera BUSCO genes, including 93.8% present as a single copy. Despite some likely regional duplications, the completeness of this genome suggests that it can be readily used for gene expression, GWAS, and other genomic analyses.
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Affiliation(s)
- David Luecke
- Department of Evolution and Ecology, University of California Davis, One Shields Ave Davis CA 95616
| | - Yige Luo
- Department of Evolution and Ecology, University of California Davis, One Shields Ave Davis CA 95616
| | - Halina Krzystek
- Biology Department of the University of North Carolina (UNC), 3159 Genome Sciences Building. 250 Bell Tower Drive. Chapel Hill, NC 27599
| | - Corbin Jones
- Biology Department of the University of North Carolina (UNC), 3159 Genome Sciences Building. 250 Bell Tower Drive. Chapel Hill, NC 27599
| | - Artyom Kopp
- Department of Evolution and Ecology, University of California Davis, One Shields Ave Davis CA 95616
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Bachem K, Li X, Ceolin S, Mühling B, Hörl D, Harz H, Leonhardt H, Arnoult L, Weber S, Matarlo B, Prud’homme B, Gompel N. Regulatory evolution tuning pigmentation intensity quantitatively in Drosophila. SCIENCE ADVANCES 2024; 10:eadl2616. [PMID: 38266088 PMCID: PMC10807792 DOI: 10.1126/sciadv.adl2616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Accepted: 12/21/2023] [Indexed: 01/26/2024]
Abstract
Quantitative variation in attributes such as color, texture, or stiffness dominates morphological diversification. It results from combinations of alleles at many Mendelian loci. Here, we identify an additional source of quantitative variation among species, continuous evolution in a gene regulatory region. Specifically, we examined the modulation of wing pigmentation in a group of fly species and showed that inter-species variation correlated with the quantitative expression of the pigmentation gene yellow. This variation results from an enhancer of yellow determining darkness through species-specific activity. We mapped the divergent activities between two sister species and found the changes to be broadly distributed along the enhancer. Our results demonstrate that enhancers can act as dials fueling quantitative morphological diversification by modulating trait properties.
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Affiliation(s)
- Katharina Bachem
- Department of Evolutionary Ecology, Ludwig-Maximilians Universität München, München 82152, Germany
| | - Xinyi Li
- Department of Evolutionary Ecology, Ludwig-Maximilians Universität München, München 82152, Germany
| | - Stefano Ceolin
- Department of Evolutionary Ecology, Ludwig-Maximilians Universität München, München 82152, Germany
| | - Bettina Mühling
- Department of Evolutionary Ecology, Ludwig-Maximilians Universität München, München 82152, Germany
| | - David Hörl
- Human Biology and Bioimaging, Ludwig-Maximilians Universität München, München 82152, Germany
| | - Hartmann Harz
- Human Biology and Bioimaging, Ludwig-Maximilians Universität München, München 82152, Germany
| | - Heinrich Leonhardt
- Human Biology and Bioimaging, Ludwig-Maximilians Universität München, München 82152, Germany
| | - Laurent Arnoult
- Institut de Biologie du Développement de Marseille, Aix-Marseille Université, Marseille 13288, France
| | - Sabrina Weber
- Department of Evolutionary Ecology, Ludwig-Maximilians Universität München, München 82152, Germany
| | - Blair Matarlo
- Department of Evolutionary Ecology, Ludwig-Maximilians Universität München, München 82152, Germany
| | - Benjamin Prud’homme
- Institut de Biologie du Développement de Marseille, Aix-Marseille Université, Marseille 13288, France
| | - Nicolas Gompel
- Department of Evolutionary Ecology, Ludwig-Maximilians Universität München, München 82152, Germany
- Bonn Institute for Organismic Biology, University of Bonn, Bonn 53115, Germany
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Robinson CD, Hale MD, Wittman TN, Cox CL, John-Alder HB, Cox RM. Species differences in hormonally mediated gene expression underlie the evolutionary loss of sexually dimorphic coloration in Sceloporus lizards. J Hered 2023; 114:637-653. [PMID: 37498153 DOI: 10.1093/jhered/esad046] [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: 04/19/2023] [Accepted: 07/24/2023] [Indexed: 07/28/2023] Open
Abstract
Phenotypic sexual dimorphism often involves the hormonal regulation of sex-biased expression for underlying genes. However, it is generally unknown whether the evolution of hormonally mediated sexual dimorphism occurs through upstream changes in tissue sensitivity to hormone signals, downstream changes in responsiveness of target genes, or both. Here, we use comparative transcriptomics to explore these possibilities in 2 species of Sceloporus lizards exhibiting different patterns of sexual dichromatism. Sexually dimorphic S. undulatus develops blue and black ventral coloration in response to testosterone, while sexually monomorphic S. virgatus does not, despite exhibiting similar sex differences in circulating testosterone levels. We administered testosterone implants to juveniles of each species and used RNAseq to quantify gene expression in ventral skin. Transcriptome-wide responses to testosterone were stronger in S. undulatus than in S. virgatus, suggesting species differences in tissue sensitivity to this hormone signal. Species differences in the expression of genes for androgen metabolism and sex hormone-binding globulin were consistent with this idea, but expression of the androgen receptor gene was higher in S. virgatus, complicating this interpretation. Downstream of androgen signaling, we found clear species differences in hormonal responsiveness of genes related to melanin synthesis, which were upregulated by testosterone in S. undulatus, but not in S. virgatus. Collectively, our results indicate that hormonal regulation of melanin synthesis pathways contributes to the development of sexual dimorphism in S. undulatus, and that changes in the hormonal responsiveness of these genes in S. virgatus contribute to the evolutionary loss of ventral coloration.
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Affiliation(s)
| | - Matthew D Hale
- University of Virginia, Department of Biology, Charlottesville, VA, United States
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States
- Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD, United States
| | - Tyler N Wittman
- University of Virginia, Department of Biology, Charlottesville, VA, United States
| | - Christian L Cox
- Florida International University, Department of Biological Sciences and Institute of Environment, Miami, FL, United States
| | - Henry B John-Alder
- Rutgers University, Department of Ecology, Evolution, and Natural Resources, New Brunswick, NJ, United States
| | - Robert M Cox
- University of Virginia, Department of Biology, Charlottesville, VA, United States
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Kopp A, Barmina O. Interspecific variation in sex-specific gustatory organs in Drosophila. J Comp Neurol 2022; 530:2439-2450. [PMID: 35603778 PMCID: PMC9339527 DOI: 10.1002/cne.25340] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 04/26/2022] [Accepted: 04/28/2022] [Indexed: 11/08/2022]
Abstract
Drosophila males use leg gustatory bristles to discriminate between male and female cuticular pheromones as an important part of courtship behavior. In Drosophila melanogaster, several male-specific gustatory bristles are present on the anterior surface of the first tarsal segment of the prothoracic leg, in addition to a larger set of gustatory bristles found in both sexes. These bristles are thought to be specialized for pheromone detection. Here, we report the number and location of sex-specific gustatory bristles in 27 other Drosophila species. Although some species have a pattern similar to D. melanogaster, others lack anterior male-specific bristles but have many dorsal male-specific gustatory bristles instead. Some species have both anterior and dorsal male-specific bristles, while others lack sexual dimorphism entirely. In several distantly related species, the number of gustatory bristles is much greater in males than in females due to a male-specific transformation of ancestrally mechanosensory bristles to a chemosensory identity. This variation in the extent and pattern of sexual dimorphism may affect the formation and function of neuronal circuits that control Drosophila courtship and contribute to the evolution of mating behavior.
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Affiliation(s)
- Artyom Kopp
- Department of Evolution and Ecology, University of California Davis
| | - Olga Barmina
- Department of Evolution and Ecology, University of California Davis
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