1
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Bontonou G, Saint-Leandre B, Kafle T, Baticle T, Hassan A, Sánchez-Alcañiz JA, Arguello JR. Evolution of chemosensory tissues and cells across ecologically diverse Drosophilids. Nat Commun 2024; 15:1047. [PMID: 38316749 PMCID: PMC10844241 DOI: 10.1038/s41467-023-44558-4] [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: 05/10/2023] [Accepted: 12/19/2023] [Indexed: 02/07/2024] Open
Abstract
Chemosensory tissues exhibit significant between-species variability, yet the evolution of gene expression and cell types underlying this diversity remain poorly understood. To address these questions, we conducted transcriptomic analyses of five chemosensory tissues from six Drosophila species and integrated the findings with single-cell datasets. While stabilizing selection predominantly shapes chemosensory transcriptomes, thousands of genes in each tissue have evolved expression differences. Genes that have changed expression in one tissue have often changed in multiple other tissues but at different past epochs and are more likely to be cell type-specific than unchanged genes. Notably, chemosensory-related genes have undergone widespread expression changes, with numerous species-specific gains/losses including novel chemoreceptors expression patterns. Sex differences are also pervasive, including a D. melanogaster-specific excess of male-biased expression in sensory and muscle cells in its forelegs. Together, our analyses provide new insights for understanding evolutionary changes in chemosensory tissues at both global and individual gene levels.
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Affiliation(s)
- Gwénaëlle Bontonou
- Department of Ecology & Evolution, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland.
- Swiss Institute of Bioinformatics, Lausanne, Switzerland.
| | - Bastien Saint-Leandre
- Department of Ecology & Evolution, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland.
- Swiss Institute of Bioinformatics, Lausanne, Switzerland.
| | - Tane Kafle
- Department of Ecology & Evolution, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Tess Baticle
- Department of Ecology & Evolution, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Afrah Hassan
- Department of Ecology & Evolution, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | | | - J Roman Arguello
- Department of Ecology & Evolution, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland.
- Swiss Institute of Bioinformatics, Lausanne, Switzerland.
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK.
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2
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Scanlan JL, Robin C. Phylogenomics of the Ecdysteroid Kinase-like (EcKL) Gene Family in Insects Highlights Roles in Both Steroid Hormone Metabolism and Detoxification. Genome Biol Evol 2024; 16:evae019. [PMID: 38291829 PMCID: PMC10859841 DOI: 10.1093/gbe/evae019] [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: 06/29/2023] [Revised: 11/21/2023] [Accepted: 01/23/2024] [Indexed: 02/01/2024] Open
Abstract
The evolutionary dynamics of large gene families can offer important insights into the functions of their individual members. While the ecdysteroid kinase-like (EcKL) gene family has previously been linked to the metabolism of both steroid molting hormones and xenobiotic toxins, the functions of nearly all EcKL genes are unknown, and there is little information on their evolution across all insects. Here, we perform comprehensive phylogenetic analyses on a manually annotated set of EcKL genes from 140 insect genomes, revealing the gene family is comprised of at least 13 subfamilies that differ in retention and stability. Our results show the only two genes known to encode ecdysteroid kinases belong to different subfamilies and therefore ecdysteroid metabolism functions must be spread throughout the EcKL family. We provide comparative phylogenomic evidence that EcKLs are involved in detoxification across insects, with positive associations between family size and dietary chemical complexity, and we also find similar evidence for the cytochrome P450 and glutathione S-transferase gene families. Unexpectedly, we find that the size of the clade containing a known ecdysteroid kinase is positively associated with host plant taxonomic diversity in Lepidoptera, possibly suggesting multiple functional shifts between hormone and xenobiotic metabolism. Our evolutionary analyses provide hypotheses of function and a robust framework for future experimental studies of the EcKL gene family. They also open promising new avenues for exploring the genomic basis of dietary adaptation in insects, including the classically studied coevolution of butterflies with their host plants.
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Affiliation(s)
- Jack L Scanlan
- School of BioSciences, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Charles Robin
- School of BioSciences, The University of Melbourne, Melbourne, VIC 3010, Australia
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3
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Keesey IW. Sensory neuroecology and multimodal evolution across the genus Drosophila. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.932344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The neural basis and genetic mechanisms for sensory evolution are increasingly being explored in depth across many closely related members of the Drosophila genus. This has, in part, been achieved due to the immense efforts toward adapting gene-editing technologies for additional, non-model species. Studies targeting both peripheral sensory variations, as well as interspecies divergence in coding or neural connectivity, have generated numerous, tangible examples of how and where the evolution of sensory-driven animal behavior has occurred. Here, we review and discuss studies that each aim to identify the neurobiological and genetic components of sensory system evolution to provide a comparative overview of the types of functional variations observed across both perceptual input and behavioral output. In addition, we examined the roles neuroecology and neuroevolution play in speciation events, such as courtship and intraspecies communication, as well as those aspects related to behavioral divergence in host navigation or egg-laying preferences. Through the investigation of comparative, large-scale trends and correlations across diverse, yet closely related species within this highly ecologically variable genus of flies, we can begin to describe the underlying pressures, mechanisms, and constraints that have guided sensory and nervous system evolution within the natural environments of these organisms.
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4
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De Panis D, Dopazo H, Bongcam-Rudloff E, Conesa A, Hasson E. Transcriptional responses are oriented towards different components of the rearing environment in two Drosophila sibling species. BMC Genomics 2022; 23:515. [PMID: 35840900 PMCID: PMC9288027 DOI: 10.1186/s12864-022-08745-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 07/01/2022] [Indexed: 11/26/2022] Open
Abstract
Background The chance to compare patterns of differential gene expression in related ecologically distinct species can be particularly fruitful to investigate the genetics of adaptation and phenotypic plasticity. In this regard, a powerful technique such as RNA-Seq applied to ecologically amenable taxa allows to address issues that are not possible in classic model species. Here, we study gene expression profiles and larval performance of the cactophilic siblings Drosophila buzzatii and D. koepferae reared in media that approximate natural conditions and evaluate both chemical and nutritional components of the diet. These closely related species are complementary in terms of host-plant use since the primary host of one is the secondary of the other. D. koepferae is mainly a columnar cactus dweller while D. buzzatii prefers Opuntia hosts. Results Our comparative study shows that D. buzzatii and D. koepferae have different transcriptional strategies to face the challenges posed by their natural resources. The former has greater transcriptional plasticity, and its response is mainly modulated by alkaloids of its secondary host, while the latter has a more canalized genetic response, and its transcriptional plasticity is associated with the cactus species. Conclusions Our study unveils a complex pleiotropic genetic landscape in both species, with functional links that relate detox responses and redox mechanisms with developmental and neurobiological processes. These results contribute to deepen our understanding of the role of host plant shifts and natural stress driving ecological specialization. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08745-9.
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Affiliation(s)
- D De Panis
- Instituto de Ecología, Genética y Evolución de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de Buenos Aires, Argentina
| | - H Dopazo
- Instituto de Ecología, Genética y Evolución de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de Buenos Aires, Argentina.,Departamento de Ecología, Genética y Evolución, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
| | - E Bongcam-Rudloff
- SLU-Global Bioinformatics Centre, Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - A Conesa
- Microbiology and Cell Science Department, University of Florida, Gainesville, Florida, USA
| | - E Hasson
- Instituto de Ecología, Genética y Evolución de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de Buenos Aires, Argentina. .,Departamento de Ecología, Genética y Evolución, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina.
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5
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Leong JCK, Li Y, Uesaka M, Uchida Y, Omori A, Hao M, Wan W, Dong Y, Ren Y, Zhang S, Zeng T, Wang F, Chen L, Wessel G, Livingston BT, Bradham C, Wang W, Irie N. Derivedness Index for Estimating Degree of Phenotypic Evolution of Embryos: A Study of Comparative Transcriptomic Analyses of Chordates and Echinoderms. Front Cell Dev Biol 2021; 9:749963. [PMID: 34900995 PMCID: PMC8661034 DOI: 10.3389/fcell.2021.749963] [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: 07/30/2021] [Accepted: 11/03/2021] [Indexed: 11/13/2022] Open
Abstract
Species retaining ancestral features, such as species called living fossils, are often regarded as less derived than their sister groups, but such discussions are usually based on qualitative enumeration of conserved traits. This approach creates a major barrier, especially when quantifying the degree of phenotypic evolution or degree of derivedness, since it focuses only on commonly shared traits, and newly acquired or lost traits are often overlooked. To provide a potential solution to this problem, especially for inter-species comparison of gene expression profiles, we propose a new method named "derivedness index" to quantify the degree of derivedness. In contrast to the conservation-based approach, which deals with expressions of commonly shared genes among species being compared, the derivedness index also considers those that were potentially lost or duplicated during evolution. By applying our method, we found that the gene expression profiles of penta-radial phases in echinoderm tended to be more highly derived than those of the bilateral phase. However, our results suggest that echinoderms may not have experienced much larger modifications to their developmental systems than chordates, at least at the transcriptomic level. In vertebrates, we found that the mid-embryonic and organogenesis stages were generally less derived than the earlier or later stages, indicating that the conserved phylotypic period is also less derived. We also found genes that potentially explain less derivedness, such as Hox genes. Finally, we highlight technical concerns that may influence the measured transcriptomic derivedness, such as read depth and library preparation protocols, for further improvement of our method through future studies. We anticipate that this index will serve as a quantitative guide in the search for constrained developmental phases or processes.
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Affiliation(s)
- Jason Cheok Kuan Leong
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Yongxin Li
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Masahiro Uesaka
- RIKEN Center for Biosystems Dynamics Research (BDR), Kobe, Japan
| | - Yui Uchida
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan.,Universal Biology Institute, The University of Tokyo, Tokyo, Japan
| | - Akihito Omori
- Sado Island Center for Ecological Sustainability, Niigata University, Niigata, Japan
| | - Meng Hao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Wenting Wan
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Yang Dong
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Yandong Ren
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Si Zhang
- Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China
| | - Tao Zeng
- Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China
| | - Fayou Wang
- Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China
| | - Luonan Chen
- Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China.,Key Laboratory of Systems Biology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Hangzhou, China
| | - Gary Wessel
- Providence Institute of Molecular Oogenesis, Brown University, Providence, RI, United States
| | - Brian T Livingston
- Department of Biological Sciences, California State University, Long Beach, CA, United States
| | - Cynthia Bradham
- Department of Biology, Boston University, Boston, MA, United States
| | - Wen Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - Naoki Irie
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan.,Universal Biology Institute, The University of Tokyo, Tokyo, Japan
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6
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Maslov DL, Zemskaya NV, Trifonova OP, Lichtenberg S, Balashova EE, Lisitsa AV, Moskalev AA, Lokhov PG. Comparative Metabolomic Study of Drosophila Species with Different Lifespans. Int J Mol Sci 2021; 22:ijms222312873. [PMID: 34884677 PMCID: PMC8657752 DOI: 10.3390/ijms222312873] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 11/18/2021] [Accepted: 11/25/2021] [Indexed: 12/19/2022] Open
Abstract
The increase in life expectancy, leading to a rise in the proportion of older people, is accompanied by a prevalence of age-related disorders among the world population, the fight against which today is one of the leading biomedical challenges. Exploring the biological insights concerning the lifespan is one of the ways to provide a background for designing an effective treatment for the increase in healthy years of life. Untargeted direct injection mass spectrometry-based metabolite profiling of 12 species of Drosophila with significant variations in natural lifespans was conducted in this research. A cross-comparison study of metabolomic profiles revealed lifespan signatures of flies. These signatures indicate that lifespan extension is associated with the upregulation of amino acids, phospholipids, and carbohydrate metabolism. Such information provides a metabolome-level view on longevity and may provide a molecular measure of organism age in age-related studies.
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Affiliation(s)
- Dmitry L. Maslov
- Analytical Branch, Institute of Biomedical Chemistry, 10 Building 8, Pogodinskaya Street, 119121 Moscow, Russia; (O.P.T.); (S.L.); (E.E.B.); (A.V.L.); (P.G.L.)
- Correspondence: ; Tel.: +7-499-246-6980
| | - Nadezhda V. Zemskaya
- Laboratory of Geroprotective and Radioprotective Technologies, Komi Science Center, Institute of Biology, Russian Academy of Sciences, 167982 Syktyvkar, Russia; (N.V.Z.); (A.A.M.)
| | - Oxana P. Trifonova
- Analytical Branch, Institute of Biomedical Chemistry, 10 Building 8, Pogodinskaya Street, 119121 Moscow, Russia; (O.P.T.); (S.L.); (E.E.B.); (A.V.L.); (P.G.L.)
| | - Steven Lichtenberg
- Analytical Branch, Institute of Biomedical Chemistry, 10 Building 8, Pogodinskaya Street, 119121 Moscow, Russia; (O.P.T.); (S.L.); (E.E.B.); (A.V.L.); (P.G.L.)
- Metabometrics Inc., 651 N Broad Street, Suite 205 #1370, Middletown, DE 19709, USA
| | - Elena E. Balashova
- Analytical Branch, Institute of Biomedical Chemistry, 10 Building 8, Pogodinskaya Street, 119121 Moscow, Russia; (O.P.T.); (S.L.); (E.E.B.); (A.V.L.); (P.G.L.)
| | - Andrey V. Lisitsa
- Analytical Branch, Institute of Biomedical Chemistry, 10 Building 8, Pogodinskaya Street, 119121 Moscow, Russia; (O.P.T.); (S.L.); (E.E.B.); (A.V.L.); (P.G.L.)
| | - Alexey A. Moskalev
- Laboratory of Geroprotective and Radioprotective Technologies, Komi Science Center, Institute of Biology, Russian Academy of Sciences, 167982 Syktyvkar, Russia; (N.V.Z.); (A.A.M.)
| | - Petr G. Lokhov
- Analytical Branch, Institute of Biomedical Chemistry, 10 Building 8, Pogodinskaya Street, 119121 Moscow, Russia; (O.P.T.); (S.L.); (E.E.B.); (A.V.L.); (P.G.L.)
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7
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Xia S, Ventura IM, Blaha A, Sgromo A, Han S, Izaurralde E, Long M. Rapid Gene evolution in an ancient post-transcriptional and translational regulatory system compensates for meiotic X chromosomal inactivation. Mol Biol Evol 2021; 39:6385248. [PMID: 34626117 PMCID: PMC8763131 DOI: 10.1093/molbev/msab296] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
It is conventionally assumed that conserved pathways evolve slowly with little participation of gene evolution. Nevertheless, it has been recently observed that young genes can take over fundamental functions in essential biological processes, for example, development and reproduction. It is unclear how newly duplicated genes are integrated into ancestral networks and reshape the conserved pathways of important functions. Here, we investigated origination and function of two autosomal genes that evolved recently in Drosophila: Poseidon and Zeus, which were created by RNA-based duplications from the X-linked CAF40, a subunit of the conserved CCR4–NOT deadenylase complex involved in posttranscriptional and translational regulation. Knockdown and knockout assays show that the two genes quickly evolved critically important functions in viability and male fertility. Moreover, our transcriptome analysis demonstrates that the three genes have a broad and distinct effect in the expression of hundreds of genes, with almost half of the differentially expressed genes being perturbed exclusively by one paralog, but not the others. Co-immunoprecipitation and tethering assays show that the CAF40 paralog Poseidon maintains the ability to interact with the CCR4–NOT deadenylase complex and might act in posttranscriptional mRNA regulation. The rapid gene evolution in the ancient posttranscriptional and translational regulatory system may be driven by evolution of sex chromosomes to compensate for the meiotic X chromosomal inactivation (MXCI) in Drosophila.
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Affiliation(s)
- Shengqian Xia
- Department of Ecology & Evolution, The University of Chicago, Chicago, Illinois, USA
| | - Iuri M Ventura
- Department of Ecology & Evolution, The University of Chicago, Chicago, Illinois, USA.,CAPES Foundation, Ministry of Education of Brazil, Brasília, DF, 70040-020, Brazil
| | - Andreas Blaha
- Department of Biochemistry, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Annamaria Sgromo
- Department of Biochemistry, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Shuaibo Han
- Department of Ecology & Evolution, The University of Chicago, Chicago, Illinois, USA
| | - Elisa Izaurralde
- Department of Biochemistry, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Manyuan Long
- Department of Ecology & Evolution, The University of Chicago, Chicago, Illinois, USA
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8
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Tarikere S, Ylla G, Extavour CG. Distinct gene expression dynamics in germ line and somatic tissue during ovariole morphogenesis in Drosophila melanogaster. G3 (BETHESDA, MD.) 2021; 12:6364899. [PMID: 34849771 PMCID: PMC9210308 DOI: 10.1093/g3journal/jkab305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 07/27/2021] [Indexed: 12/14/2022]
Abstract
The survival and evolution of a species is a function of the number of offspring it can produce. In insects, the number of eggs that an ovary can produce is a major determinant of reproductive capacity. Insect ovaries are made up of tubular egg-producing subunits called ovarioles, whose number largely determines the number of eggs that can be potentially laid. Ovariole number in Drosophila is directly determined by the number of cellular structures called terminal filaments, which are stacks of cells that assemble in the larval ovary. Elucidating the developmental and regulatory mechanisms of terminal filament formation is thus key to understanding the regulation of insect reproduction through ovariole number regulation. We systematically measured mRNA expression of all cells in the larval ovary at the beginning, middle, and end of terminal filament formation. We also separated somatic and germ line cells during these stages and assessed their tissue-specific gene expression during larval ovary development. We found that the number of differentially expressed somatic genes is highest during the late stages of terminal filament formation and includes many signaling pathways that govern ovary development. We also show that germ line tissue, in contrast, shows greater differential expression during early stages of terminal filament formation, and highly expressed germ line genes at these stages largely control cell division and DNA repair. We provide a tissue-specific and temporal transcriptomic dataset of gene expression in the developing larval ovary as a resource to study insect reproduction.
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Affiliation(s)
- Shreeharsha Tarikere
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Guillem Ylla
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Cassandra G Extavour
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA,Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA,Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA,Corresponding author:
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9
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Kamel M, Kastano K, Mier P, Andrade-Navarro MA. REP2: A Web Server to Detect Common Tandem Repeats in Protein Sequences. J Mol Biol 2021; 433:166895. [PMID: 33972020 DOI: 10.1016/j.jmb.2021.166895] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 02/01/2021] [Accepted: 02/21/2021] [Indexed: 12/13/2022]
Abstract
Ensembles of tandem repeats (TRs) in protein sequences expand rapidly to form domains well suited for interactions with proteins. For this reason, they are relatively frequent. Some TRs have known structures and therefore it is advantageous to predict their presence in a protein sequence. However, since most TRs diverge quickly, their detection by classical sequence comparison algorithms is not very accurate. Previously, we developed a method and a web server that used curated profiles and thresholds for the detection of 11 common TRs. Here we present a new web server (REP2) that allows the analysis of TRs in both individual and aligned sequences. We provide currently precomputed analyses for a selection of 78 UniProt reference proteomes. We illustrate how these data can be used to study the evolution of TRs using comparative genomics. REP2 can be accessed at http://cbdm-01.zdv.uni-mainz.de/~munoz/rep/.
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Affiliation(s)
- Mohamed Kamel
- Department of Computer Science, Faculty of Mathematics and Informatics, University of M'sila, 28000 M'sila, Algeria; Faculty of Biology, Johannes Gutenberg University of Mainz, 55128 Mainz, Germany
| | - Kristina Kastano
- Faculty of Biology, Johannes Gutenberg University of Mainz, 55128 Mainz, Germany
| | - Pablo Mier
- Faculty of Biology, Johannes Gutenberg University of Mainz, 55128 Mainz, Germany
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10
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Han X, Guo J, Pang E, Song H, Lin K. Ab Initio Construction and Evolutionary Analysis of Protein-Coding Gene Families with Partially Homologous Relationships: Closely Related Drosophila Genomes as a Case Study. Genome Biol Evol 2021; 12:185-202. [PMID: 32108239 PMCID: PMC7144356 DOI: 10.1093/gbe/evaa041] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/18/2020] [Indexed: 01/05/2023] Open
Abstract
How have genes evolved within a well-known genome phylogeny? Many protein-coding genes should have evolved as a whole at the gene level, and some should have evolved partly through fragments at the subgene level. To comprehensively explore such complex homologous relationships and better understand gene family evolution, here, with de novo-identified modules, the subgene units which could consecutively cover proteins within a set of closely related species, we applied a new phylogeny-based approach that considers evolutionary models with partial homology to classify all protein-coding genes in nine Drosophila genomes. Compared with two other popular methods for gene family construction, our approach improved practical gene family classifications with a more reasonable view of homology and provided a much more complete landscape of gene family evolution at the gene and subgene levels. In the case study, we found that most expanded gene families might have evolved mainly through module rearrangements rather than gene duplications and mainly generated single-module genes through partial gene duplication, suggesting that there might be pervasive subgene rearrangement in the evolution of protein-coding gene families. The use of a phylogeny-based approach with partial homology to classify and analyze protein-coding gene families may provide us with a more comprehensive landscape depicting how genes evolve within a well-known genome phylogeny.
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Affiliation(s)
- Xia Han
- State Key Laboratory of Earth Surface Processes and Resource Ecology, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, China
| | - Jindan Guo
- State Key Laboratory of Earth Surface Processes and Resource Ecology, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, China
| | - Erli Pang
- State Key Laboratory of Earth Surface Processes and Resource Ecology, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, China
| | - Hongtao Song
- State Key Laboratory of Earth Surface Processes and Resource Ecology, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, China
| | - Kui Lin
- State Key Laboratory of Earth Surface Processes and Resource Ecology, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, China
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11
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Reverse and forward engineering of Drosophila corneal nanocoatings. Nature 2020; 585:383-389. [PMID: 32939070 DOI: 10.1038/s41586-020-2707-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 07/09/2020] [Indexed: 11/08/2022]
Abstract
Insect eyes have an anti-reflective coating, owing to nanostructures on the corneal surface creating a gradient of refractive index between that of air and that of the lens material1,2. These nanocoatings have also been shown to provide anti-adhesive functionality3. The morphology of corneal nanocoatings are very diverse in arthropods, with nipple-like structures that can be organized into arrays or fused into ridge-like structures4. This diversity can be attributed to a reaction-diffusion mechanism4 and patterning principles developed by Alan Turing5, which have applications in numerous biological settings6. The nanocoatings on insect corneas are one example of such Turing patterns, and the first known example of nanoscale Turing patterns4. Here we demonstrate a clear link between the morphology and function of the nanocoatings on Drosophila corneas. We find that nanocoatings that consist of individual protrusions have better anti-reflective properties, whereas partially merged structures have better anti-adhesion properties. We use biochemical analysis and genetic modification techniques to reverse engineer the protein Retinin and corneal waxes as the building blocks of the nanostructures. In the context of Turing patterns, these building blocks fulfil the roles of activator and inhibitor, respectively. We then establish low-cost production of Retinin, and mix this synthetic protein with waxes to forward engineer various artificial nanocoatings with insect-like morphology and anti-adhesive or anti-reflective function. Our combined reverse- and forward-engineering approach thus provides a way to economically produce functional nanostructured coatings from biodegradable materials.
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12
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Watada M, Hayashi Y, Watanabe K, Mizutani S, Mure A, Hattori Y, Uemura T. Divergence of Drosophila species: Longevity and reproduction under different nutrient balances. Genes Cells 2020; 25:626-636. [PMID: 32594638 DOI: 10.1111/gtc.12798] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 06/15/2020] [Accepted: 06/18/2020] [Indexed: 02/04/2023]
Abstract
How nutrition impacts growth, reproduction and longevity is complex because relationships between these life events are difficult to disentangle. As a first step in sorting out these processes, we carried out a comparative analysis of related species of Drosophila with distinct feeding habits. In particular, we examined life spans and egg laying of two generalists and three specialists on diets with distinct protein-to-carbohydrate ratios. In contrast to the generalist D. melanogaster, adult males of two specialists, D. sechellia and D. elegans, lived longer on a protein-rich diet. These results and our previous studies collectively show that the diet to which larvae of each specialist species have adapted ensures a longer life span of adult males of that same species. We also found a species-specific sexual dimorphism of life span in the above two specialists regardless of the diets, which was in sharp contrast to D. melanogaster. In D. melanogaster, males lived longer than females, whereas females of D. sechellia and D. elegans were longer-lived than males, and those specialist females were exceedingly low in egg production, relative to the other species. We discuss our findings from perspectives of mechanisms, including a possible contribution of egg production to life span.
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Affiliation(s)
- Masayoshi Watada
- Graduate School of Science and Engineering, Ehime University, Matsuyama, Japan
| | - Yusaku Hayashi
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Kaori Watanabe
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Shoko Mizutani
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Ayumi Mure
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Yukako Hattori
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Tadashi Uemura
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan.,Research Center for Dynamic Living Systems, Kyoto University, Kyoto, Japan.,AMED-CREST, AMED, Tokyo, Japan
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13
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Ryan SM, Wildman K, Oceguera-Perez B, Barbee S, Mortimer NT, Vrailas-Mortimer AD. Evolutionarily conserved transcription factors drive the oxidative stress response in Drosophila. J Exp Biol 2020; 223:jeb221622. [PMID: 32532866 PMCID: PMC7391405 DOI: 10.1242/jeb.221622] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 06/03/2020] [Indexed: 12/14/2022]
Abstract
As organisms are constantly exposed to the damaging effects of oxidative stress through both environmental exposure and internal metabolic processes, they have evolved a variety of mechanisms to cope with this stress. One such mechanism is the highly conserved p38 MAPK (p38K) pathway, which is known to be post-translationally activated in response to oxidative stress, resulting in the activation of downstream antioxidant targets. However, little is known about the role of p38K transcriptional regulation in response to oxidative stress. Therefore, we analyzed the p38K gene family across the genus Drosophila to identify conserved regulatory elements. We found that oxidative stress exposure results in increased p38K protein levels in multiple Drosophila species and is associated with increased oxidative stress resistance. We also found that the p38Kb genomic locus includes conserved AP-1 and lola-PT transcription factor consensus binding sites. Accordingly, over-expression of these transcription factors in D. melanogaster is sufficient to induce transcription of p38Kb and enhances resistance to oxidative stress. We further found that the presence of a putative lola-PT binding site in the p38Kb locus of a given species is predictive of the species' survival in response to oxidative stress. Through our comparative genomics approach, we have identified biologically relevant putative transcription factor binding sites that regulate the expression of p38Kb and are associated with resistance to oxidative stress. These findings reveal a novel mode of regulation for p38K genes and suggest that transcription may play as important a role in p38K-mediated stress responses as post-translational modifications.
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Affiliation(s)
- Sarah M Ryan
- University of Denver, Department of Biological Sciences, Denver, CO 80210, USA
| | - Kaitie Wildman
- Illinois State University, School of Biological Sciences, Normal, IL 61790-4120, USA
| | | | - Scott Barbee
- University of Denver, Department of Biological Sciences, Denver, CO 80210, USA
| | - Nathan T Mortimer
- Illinois State University, School of Biological Sciences, Normal, IL 61790-4120, USA
| | - Alysia D Vrailas-Mortimer
- University of Denver, Department of Biological Sciences, Denver, CO 80210, USA
- Illinois State University, School of Biological Sciences, Normal, IL 61790-4120, USA
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14
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Keesey IW, Grabe V, Knaden M, Hansson BS. Divergent sensory investment mirrors potential speciation via niche partitioning across Drosophila. eLife 2020; 9:e57008. [PMID: 32602834 PMCID: PMC7402680 DOI: 10.7554/elife.57008] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 06/30/2020] [Indexed: 12/19/2022] Open
Abstract
The examination of phylogenetic and phenotypic characteristics of the nervous system, such as behavior and neuroanatomy, can be utilized as a means to assess speciation. Recent studies have proposed a fundamental tradeoff between two sensory organs, the eye and the antenna. However, the identification of ecological mechanisms for this observed tradeoff have not been firmly established. Our current study examines several monophyletic species within the obscura group, and asserts that despite their close relatedness and overlapping ecology, they deviate strongly in both visual and olfactory investment. We contend that both courtship and microhabitat preferences support the observed inverse variation in these sensory traits. Here, this variation in visual and olfactory investment seems to provide relaxed competition, a process by which similar species can use a shared environment differently and in ways that help them coexist. Moreover, that behavioral separation according to light gradients occurs first, and subsequently, courtship deviations arise.
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Affiliation(s)
- Ian W Keesey
- Max Planck Institute for Chemical Ecology (MPICE), Department of Evolutionary NeuroethologyJenaGermany
| | - Veit Grabe
- Max Planck Institute for Chemical Ecology (MPICE), Department of Evolutionary NeuroethologyJenaGermany
| | - Markus Knaden
- Max Planck Institute for Chemical Ecology (MPICE), Department of Evolutionary NeuroethologyJenaGermany
| | - Bill S Hansson
- Max Planck Institute for Chemical Ecology (MPICE), Department of Evolutionary NeuroethologyJenaGermany
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15
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Rane RV, Clarke DF, Pearce SL, Zhang G, Hoffmann AA, Oakeshott JG. Detoxification Genes Differ Between Cactus-, Fruit-, and Flower-Feeding Drosophila. J Hered 2020; 110:80-91. [PMID: 30445496 DOI: 10.1093/jhered/esy058] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 11/09/2018] [Indexed: 02/07/2023] Open
Abstract
We use annotated genomes of 14 Drosophila species covering diverse host use phenotypes to test whether 4 gene families that often have detoxification functions are associated with host shifts among species. Bark, slime flux, flower, and generalist necrotic fruit-feeding species all have similar numbers of carboxyl/cholinesterase, glutathione S-transferase, cytochrome P450, and UDP-glucuronosyltransferase genes. However, species feeding on toxic Morinda citrifolia fruit and the fresh fruit-feeding Drosophila suzukii have about 30 and 60 more, respectively. ABC transporters show a different pattern, with the flower-feeding D. elegans and the generalist necrotic fruit and cactus feeder D. hydei having about 20 and >100 more than the other species, respectively. Surprisingly, despite the complex secondary chemistry we find that 3 cactophilic specialists in the mojavensis species cluster have variably fewer genes than any of the other species across all 4 families. We also find 82 positive selection events across the 4 families, with the terminal D. suzukii and M. citrifolia-feeding D. sechellia branches again having the highest number of such events in proportion to their respective branch lengths. Many of the genes involved in these host-use-specific gene number differences or positive selection events lie in specific clades of the gene families that have been recurrently associated with detoxification. Several genes are also found to be involved in multiple duplication and/or positive selection events across the species studied regardless of their host use phenotypes; the most frequently involved are the ABC transporter CG1718, which is not in a specific clade associated with detoxification, and the α-esterase gene cluster, which is.
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Affiliation(s)
- Rahul V Rane
- CSIRO, Acton, ACT, Australia.,School of BioSciences, University of Melbourne, Parkville, VIC, Australia
| | - David F Clarke
- CSIRO, Acton, ACT, Australia.,School of BioSciences, University of Melbourne, Parkville, VIC, Australia
| | | | - Guojie Zhang
- China National GeneBank, BGI-Shenzhen, Shenzhen, China.,Centre for Social Evolution, Department of Biology, University of Copenhagen, København, Denmark
| | - Ary A Hoffmann
- School of BioSciences, University of Melbourne, Parkville, VIC, Australia
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16
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Helfrich‐Förster C, Bertolini E, Menegazzi P. Flies as models for circadian clock adaptation to environmental challenges. Eur J Neurosci 2020; 51:166-181. [PMID: 30269385 PMCID: PMC7027873 DOI: 10.1111/ejn.14180] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 08/14/2018] [Accepted: 08/17/2018] [Indexed: 01/02/2023]
Abstract
Life on earth is assumed to have developed in tropical regions that are characterized by regular 24 hr cycles in irradiance and temperature that remain the same throughout the seasons. All organisms developed circadian clocks that predict these environmental cycles and prepare the organisms in advance for them. A central question in chronobiology is how endogenous clocks changed in order to anticipate very different cyclical environmental conditions such as extremely short and long photoperiods existing close to the poles. Flies of the family Drosophilidae can be found all over the world-from the tropics to subarctic regions-making them unprecedented models for studying the evolutionary processes that underlie the adaptation of circadian clocks to different latitudes. This review summarizes our current understanding of these processes. We discuss evolutionary changes in the clock genes and in the clock network in the brain of different Drosophilids that may have caused behavioural adaptations to high latitudes.
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Affiliation(s)
| | - Enrico Bertolini
- Neurobiology and GeneticsTheodor‐Boveri InstituteBiocentre, University of WürzburgWürzburgGermany
| | - Pamela Menegazzi
- Neurobiology and GeneticsTheodor‐Boveri InstituteBiocentre, University of WürzburgWürzburgGermany
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17
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Martin Anduaga A, Evantal N, Patop IL, Bartok O, Weiss R, Kadener S. Thermosensitive alternative splicing senses and mediates temperature adaptation in Drosophila. eLife 2019; 8:44642. [PMID: 31702556 PMCID: PMC6890466 DOI: 10.7554/elife.44642] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 11/07/2019] [Indexed: 12/31/2022] Open
Abstract
Circadian rhythms are generated by the cyclic transcription, translation, and degradation of clock gene products, including timeless (tim), but how the circadian clock senses and adapts to temperature changes is not completely understood. Here, we show that temperature dramatically changes the splicing pattern of tim in Drosophila. We found that at 18°C, TIM levels are low because of the induction of two cold-specific isoforms: tim-cold and tim-short and cold. At 29°C, another isoform, tim-medium, is upregulated. Isoform switching regulates the levels and activity of TIM as each isoform has a specific function. We found that tim-short and cold encodes a protein that rescues the behavioral defects of tim01 mutants, and that flies in which tim-short and cold is abrogated have abnormal locomotor activity. In addition, miRNA-mediated control limits the expression of some of these isoforms. Finally, data that we obtained using minigenes suggest that tim alternative splicing might act as a thermometer for the circadian clock.
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Affiliation(s)
| | - Naveh Evantal
- Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | | | - Osnat Bartok
- Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Ron Weiss
- Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Sebastian Kadener
- Biology Department, Brandeis University, Waltham, United States.,Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
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18
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Sarikaya DP, Church SH, Lagomarsino LP, Magnacca KN, Montgomery SL, Price DK, Kaneshiro KY, Extavour CG. Reproductive Capacity Evolves in Response to Ecology through Common Changes in Cell Number in Hawaiian Drosophila. Curr Biol 2019; 29:1877-1884.e6. [PMID: 31130459 PMCID: PMC6673671 DOI: 10.1016/j.cub.2019.04.063] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Revised: 02/01/2019] [Accepted: 04/24/2019] [Indexed: 02/07/2023]
Abstract
Lifetime reproductive capacity is a critical fitness component. In insects, female reproductive capacity is largely determined by the number of ovarioles, the egg-producing subunits of the ovary [e.g., 1]. Recent work has provided insights into ovariole number regulation in Drosophila melanogaster. However, whether mechanisms discovered under laboratory conditions explain evolutionary variation in natural populations is an outstanding question. We investigated potential effects of ecology on the developmental processes underlying ovariole number evolution among Hawaiian Drosophila, a large adaptive radiation wherein the highest and lowest ovariole numbers of the family have evolved within 25 million years. Previous studies proposed that ovariole number correlated with oviposition substrate [2-4] but sampled largely one clade of these flies and were limited by a provisional phylogeny and the available comparative methods. We test this hypothesis by applying phylogenetic modeling to an expanded sampling of ovariole numbers and substrate types and show support for these predictions across all major groups of Hawaiian Drosophila, wherein ovariole number variation is best explained by adaptation to specific substrates. Furthermore, we show that oviposition substrate evolution is linked to changes in the allometric relationship between body size and ovariole number. Finally, we provide evidence that the major changes in ovarian cell number that regulate D. melanogaster ovariole number also regulate ovariole number in Hawaiian drosophilids. Thus, we provide evidence that this remarkable adaptive radiation is linked to evolutionary changes in a key reproductive trait regulated at least partly by variation in the same developmental parameters that operate in the model species D. melanogaster.
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Affiliation(s)
- Didem P Sarikaya
- Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford St., Cambridge, MA 02138, USA.
| | - Samuel H Church
- Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford St., Cambridge, MA 02138, USA
| | - Laura P Lagomarsino
- Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA 70803, USA
| | | | | | - Donald K Price
- Biology Department, University of Hawai'i at Hilo, 200 W. Kawili St., Hilo, HI 96720, USA
| | - Kenneth Y Kaneshiro
- Pacific Biosciences Research Center, University of Hawai'i at Manoa, 1993 East-West Rd., Manoa, HI 96822, USA
| | - Cassandra G Extavour
- Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford St., Cambridge, MA 02138, USA; Department of Molecular and Cellular Biology, Harvard University, 52 Oxford St., Cambridge, MA 02138, USA.
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19
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Evolution of maternal and zygotic mRNA complements in the early Drosophila embryo. PLoS Genet 2018; 14:e1007838. [PMID: 30557299 PMCID: PMC6312346 DOI: 10.1371/journal.pgen.1007838] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2018] [Revised: 12/31/2018] [Accepted: 11/18/2018] [Indexed: 01/19/2023] Open
Abstract
The earliest stages of animal development are controlled by maternally deposited mRNA transcripts and proteins. Once the zygote is able to transcribe its own genome, maternal transcripts are degraded, in a tightly regulated process known as the maternal to zygotic transition (MZT). While this process has been well-studied within model species, we have little knowledge of how the pools of maternal and zygotic transcripts evolve. To characterize the evolutionary dynamics and functional constraints on early embryonic expression, we created a transcriptomic dataset for 14 Drosophila species spanning over 50 million years of evolution, at developmental stages before and after the MZT, and compared our results with a previously published Aedes aegypti developmental time course. We found deep conservation over 250 million years of a core set of genes transcribed only by the zygote. This select group is highly enriched in transcription factors that play critical roles in early development. However, we also identify a surprisingly high level of change in the transcripts represented at both stages over the phylogeny. While mRNA levels of genes with maternally deposited transcripts are more highly conserved than zygotic genes, those maternal transcripts that are completely degraded at the MZT vary dramatically between species. We also show that hundreds of genes have different isoform usage between the maternal and zygotic genomes. Our work suggests that maternal transcript deposition and early zygotic transcription are remarkably dynamic over evolutionary time, despite the widespread conservation of early developmental processes.
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20
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Nemeth DC, Ammagarahalli B, Layne JE, Rollmann SM. Evolution of coeloconic sensilla in the peripheral olfactory system of Drosophila mojavensis. JOURNAL OF INSECT PHYSIOLOGY 2018; 110:13-22. [PMID: 30107159 DOI: 10.1016/j.jinsphys.2018.08.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Revised: 08/04/2018] [Accepted: 08/05/2018] [Indexed: 06/08/2023]
Abstract
Populations inhabiting habitats with different environmental conditions, such as climate, resource availability, predation, competition, can undergo selection for traits that are adaptive in one habitat and not the other, leading to divergence between populations. Changes in the olfactory systems of insects that rely on different host plants, for example, can occur in response to differences in sensory stimuli between habitats. In this study, we investigate the evolution of host preference by characterizing the coeloconic sensilla in Drosophila mojavensis, a species that breeds on different necrotic cacti across its geographic range. These cactus species differ in the volatile chemicals they emit, a primary sensory cue for host plant discrimination. Analysis of odor-evoked responses identified four coeloconic sensilla that were qualitatively similar to those of Drosophila melanogaster, but varied in the breadth and strength of their olfactory sensory neuron responses to some acids and amines. Variation in responses to certain odorants among D. mojavensis populations was also observed. Compared to D. melanogaster, there was a lack of sensitivity of antennal coeloconic type 3 (ac3) sensilla to primary ligands of OR35a across all populations. Consistent with this result was a lack of detectable Or35a gene expression. Using a comparative approach, we then examined odor specificity of ac3 sensilla for seven additional Drosophila species, and found that OR35a-like sensitivity may be limited to the melanogaster subgroup. The variation in specificity that was observed among species is not clearly attributable to the degree of ecological specialization, nor to the ecological niche.
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Affiliation(s)
- Daniel C Nemeth
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45221, USA
| | - Byrappa Ammagarahalli
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45221, USA
| | - John E Layne
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45221, USA
| | - Stephanie M Rollmann
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45221, USA.
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21
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Beauchamp M, Bertolini E, Deppisch P, Steubing J, Menegazzi P, Helfrich-Förster C. Closely Related Fruit Fly Species Living at Different Latitudes Diverge in Their Circadian Clock Anatomy and Rhythmic Behavior. J Biol Rhythms 2018; 33:602-613. [PMID: 30203704 DOI: 10.1177/0748730418798096] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Recently, we reported differences in the expression pattern of the blue light-sensitive flavoprotein cryptochrome (CRY) and the neuropeptide pigment-dispersing factor (PDF) in the neuronal clock network of high-latitude Drosophila species, belonging to the Drosophila subgenus ( virilis-repleta radiation), compared with cosmopolitan D. melanogaster flies, belonging to the Sophophora subgenus. Alterations in rhythmic patterns of activity due to these differences might have adaptive significance for colonizing high-latitude habitats and, hence, adjusting to long photoperiods. Here, we show that these differing CRY/PDF expression patterns are only present in those species of the virilis-repleta radiation that colonized high latitudes. The cosmopolitan species D. mercatorum and D. hydei have a D. melanogaster-like clock network and behavior despite belonging to the virilis-repleta radiation. Similarly, 2 species of the holotropical Zaprionus genus, more closely related to the Drosophila subgenus than to the Sophophora subgenus, retain a D. melanogaster-like clock network and rhythmic behavior. We therefore suggest that the D. melanogaster-like clock network is the "ancestral fly clock phenotype" and that alterations in the CRY/PDF clock neurochemistry have allowed some species of the virilis-repleta radiation to colonize high-latitude environments.
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Affiliation(s)
- Marta Beauchamp
- Neurobiology and Genetics, Biocenter, University of Würzburg, Würzburg, Germany
| | - Enrico Bertolini
- Neurobiology and Genetics, Biocenter, University of Würzburg, Würzburg, Germany
| | - Peter Deppisch
- Neurobiology and Genetics, Biocenter, University of Würzburg, Würzburg, Germany
| | - Jonathan Steubing
- Neurobiology and Genetics, Biocenter, University of Würzburg, Würzburg, Germany
| | - Pamela Menegazzi
- Neurobiology and Genetics, Biocenter, University of Würzburg, Würzburg, Germany
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22
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Hasson E, De Panis D, Hurtado J, Mensch J. Host Plant Adaptation in Cactophilic Species of theDrosophila buzzatiiCluster: Fitness and Transcriptomics. J Hered 2018; 110:46-57. [DOI: 10.1093/jhered/esy043] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Accepted: 08/07/2018] [Indexed: 01/21/2023] Open
Affiliation(s)
- Esteban Hasson
- IEGEBA (CONICET/UBA), Departamento de Ecología, Genética y Evolución, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria Pab 2, Buenos Aires, Argentina
| | - Diego De Panis
- IEGEBA (CONICET/UBA), Departamento de Ecología, Genética y Evolución, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria Pab 2, Buenos Aires, Argentina
| | - Juan Hurtado
- IEGEBA (CONICET/UBA), Departamento de Ecología, Genética y Evolución, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria Pab 2, Buenos Aires, Argentina
| | - Julián Mensch
- IEGEBA (CONICET/UBA), Departamento de Ecología, Genética y Evolución, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria Pab 2, Buenos Aires, Argentina
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23
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Ma S, Avanesov AS, Porter E, Lee BC, Mariotti M, Zemskaya N, Guigo R, Moskalev AA, Gladyshev VN. Comparative transcriptomics across 14 Drosophila species reveals signatures of longevity. Aging Cell 2018; 17:e12740. [PMID: 29671950 PMCID: PMC6052463 DOI: 10.1111/acel.12740] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/19/2018] [Indexed: 12/14/2022] Open
Abstract
Lifespan varies dramatically among species, but the biological basis is not well understood. Previous studies in model organisms revealed the importance of nutrient sensing, mTOR, NAD/sirtuins, and insulin/IGF1 signaling in lifespan control. By studying life-history traits and transcriptomes of 14 Drosophila species differing more than sixfold in lifespan, we explored expression divergence and identified genes and processes that correlate with longevity. These longevity signatures suggested that longer-lived flies upregulate fatty acid metabolism, downregulate neuronal system development and activin signaling, and alter dynamics of RNA splicing. Interestingly, these gene expression patterns resembled those of flies under dietary restriction and several other lifespan-extending interventions, although on the individual gene level, there was no significant overlap with genes previously reported to have lifespan-extension effects. We experimentally tested the lifespan regulation potential of several candidate genes and found no consistent effects, suggesting that individual genes generally do not explain the observed longevity patterns. Instead, it appears that lifespan regulation across species is modulated by complex relationships at the system level represented by global gene expression.
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Affiliation(s)
- Siming Ma
- Division of GeneticsDepartment of MedicineBrigham and Women's HospitalHarvard Medical SchoolBostonMAUSA
- Genome Institute of SingaporeA*STARSingapore CitySingapore
| | - Andrei S. Avanesov
- Division of GeneticsDepartment of MedicineBrigham and Women's HospitalHarvard Medical SchoolBostonMAUSA
| | - Emily Porter
- Division of GeneticsDepartment of MedicineBrigham and Women's HospitalHarvard Medical SchoolBostonMAUSA
| | - Byung Cheon Lee
- Division of GeneticsDepartment of MedicineBrigham and Women's HospitalHarvard Medical SchoolBostonMAUSA
- College of Life Sciences and BiotechnologyKorea UniversitySeoulSouth Korea
| | - Marco Mariotti
- Division of GeneticsDepartment of MedicineBrigham and Women's HospitalHarvard Medical SchoolBostonMAUSA
- Bioinformatics and Genomics ProgramCentre for Genomic Regulation and Universitat Pompeu FabraBarcelonaSpain
| | - Nadezhda Zemskaya
- Institute of BiologyKomi Science CenterRussian Academy of SciencesSyktyvkarRussia
| | - Roderic Guigo
- Bioinformatics and Genomics ProgramCentre for Genomic Regulation and Universitat Pompeu FabraBarcelonaSpain
| | - Alexey A. Moskalev
- Institute of BiologyKomi Science CenterRussian Academy of SciencesSyktyvkarRussia
- Moscow Institute of Physics and TechnologyDolgoprudny, Moscow RegionRussia
- Engelhardt Institute of Molecular BiologyRussian Academy of SciencesMoscowRussia
| | - Vadim N. Gladyshev
- Division of GeneticsDepartment of MedicineBrigham and Women's HospitalHarvard Medical SchoolBostonMAUSA
- Belozersky Institute of Physico‐Chemical BiologyMoscow State UniversityMoscowRussia
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24
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Souna DA, Bokonon-Ganta A, Ravallec M, Cusumano A, Pittendrigh BR, Volkoff AN, Tamò M. An Insight in the Reproductive Biology of Therophilus javanus (Hymenoptera, Braconidae, and Agathidinae), a Potential Biological Control Agent against the Legume Pod Borer (Lepidoptera, Crambidae). PSYCHE; A JOURNAL OF ENTOMOLOGY 2017; 2017:3156534. [PMID: 33487760 PMCID: PMC7745108 DOI: 10.1155/2017/3156534] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Accepted: 08/17/2017] [Indexed: 06/12/2023]
Abstract
Therophilus javanus is a koinobiont, solitary larval endoparasitoid currently being considered as a biological control agent against the pod borer Maruca vitrata, a devastating cowpea pest causing 20-80% crop losses in West Africa. We investigated ovary morphology and anatomy, oogenesis, potential fecundity, and egg load in T. javanus, as well as the effect of factors such as age of the female and parasitoid/host size at oviposition on egg load. The number of ovarioles was found to be variable and significantly influenced by the age/size of the M. vitrata caterpillar when parasitized. Egg load also was strongly influenced by both the instar of M. vitrata caterpillar at the moment of parasitism and wasp age. The practical implications of these findings for improving mass rearing of the parasitoid toward successful biological control of M. vitrata are discussed.
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Affiliation(s)
- Djibril Aboubakar Souna
- UMR DGIMI 1333 INRA, UM, Case Courrier 101, Place Eugène Bataillon, 34 095 Montpellier, France
- International Institute of Tropical Agriculture, Benin Research Station (IITA-Benin), 08 BP 0932 Cotonou, Benin
- Faculté des Sciences Agronomiques (FSA), Université d’Abomey Calavi, 01 BP 526 Cotonou, Benin
| | - Aimé Bokonon-Ganta
- Faculté des Sciences Agronomiques (FSA), Université d’Abomey Calavi, 01 BP 526 Cotonou, Benin
| | - Marc Ravallec
- UMR DGIMI 1333 INRA, UM, Case Courrier 101, Place Eugène Bataillon, 34 095 Montpellier, France
| | - Antonino Cusumano
- Department of Plant Sciences, Wageningen University & Research, Wageningen, Netherlands
| | | | - Anne-Nathalie Volkoff
- UMR DGIMI 1333 INRA, UM, Case Courrier 101, Place Eugène Bataillon, 34 095 Montpellier, France
| | - Manuele Tamò
- International Institute of Tropical Agriculture, Benin Research Station (IITA-Benin), 08 BP 0932 Cotonou, Benin
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25
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Kober KM, Pogson GH. Genome-wide signals of positive selection in strongylocentrotid sea urchins. BMC Genomics 2017; 18:555. [PMID: 28732465 PMCID: PMC5521101 DOI: 10.1186/s12864-017-3944-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 07/13/2017] [Indexed: 12/21/2022] Open
Abstract
Background Comparative genomics studies investigating the signals of positive selection among groups of closely related species are still rare and limited in taxonomic breadth. Such studies show great promise in advancing our knowledge about the proportion and the identity of genes experiencing diversifying selection. However, methodological challenges have led to high levels of false positives in past studies. Here, we use the well-annotated genome of the purple sea urchin, Strongylocentrotus purpuratus, as a reference to investigate the signals of positive selection at 6520 single-copy orthologs from nine sea urchin species belonging to the family Strongylocentrotidae paying careful attention to minimizing false positives. Results We identified 1008 (15.5%) candidate positive selection genes (PSGs). Tests for positive selection along the nine terminal branches of the phylogeny identified 824 genes that showed lineage-specific adaptive diversification (1.67% of branch-sites tests performed). Positively selected codons were not enriched at exon borders or near regions containing missing data, suggesting a limited contribution of false positives caused by alignment or annotation errors. Alignments were validated at 10 loci with re-sequencing using Sanger methods. No differences were observed in the rates of synonymous substitution (dS), GC content, and codon bias between the candidate PSGs and those not showing positive selection. However, the candidate PSGs had 68% higher rates of nonsynonymous substitution (dN) and 33% lower levels of heterozygosity, consistent with selective sweeps and opposite to that expected by a relaxation of selective constraint. Although positive selection was identified at reproductive proteins and innate immunity genes, the strongest signals of adaptive diversification were observed at extracellular matrix proteins, cell adhesion molecules, membrane receptors, and ion channels. Many candidate PSGs have been widely implicated as targets of pathogen binding, inactivation, mimicry, or exploitation in other groups (notably mammals). Conclusions Our study confirmed the widespread action of positive selection across sea urchin genomes and allowed us to reject the possibility that annotation and alignment errors (including paralogs) were responsible for creating false signals of adaptive molecular divergence. The candidate PSGs identified in our study represent promising targets for future research into the selective agents responsible for their adaptive diversification and their contribution to speciation. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3944-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kord M Kober
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, USA. .,Institute for Computational Health Sciences, University of California, San Francisco, USA. .,Present address: Department of Physiological Nursing, University of California, San Francisco, USA.
| | - Grant H Pogson
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, USA
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26
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De Panis DN, Padró J, Furió-Tarí P, Tarazona S, Milla Carmona PS, Soto IM, Dopazo H, Conesa A, Hasson E. Transcriptome modulation during host shift is driven by secondary metabolites in desert Drosophila. Mol Ecol 2016; 25:4534-50. [PMID: 27483442 DOI: 10.1111/mec.13785] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Revised: 07/14/2016] [Accepted: 07/21/2016] [Indexed: 12/20/2022]
Abstract
High-throughput transcriptome studies are breaking new ground to investigate the responses that organisms deploy in alternative environments. Nevertheless, much remains to be understood about the genetic basis of host plant adaptation. Here, we investigate genome-wide expression in the fly Drosophila buzzatii raised in different conditions. This species uses decaying tissues of cactus of the genus Opuntia as primary rearing substrate and secondarily, the necrotic tissues of the columnar cactus Trichocereus terscheckii. The latter constitutes a harmful host, rich in mescaline and other related phenylethylamine alkaloids. We assessed the transcriptomic responses of larvae reared in Opuntia sulphurea and T. terscheckii, with and without the addition of alkaloids extracted from the latter. Whole-genome expression profiles were massively modulated by the rearing environment, mainly by the presence of T. terscheckii alkaloids. Differentially expressed genes were mainly related to detoxification, oxidation-reduction and stress response; however, we also found genes involved in development and neurobiological processes. In conclusion, our study contributes new data onto the role of transcriptional plasticity in response to alternative rearing environments.
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Affiliation(s)
- Diego N De Panis
- IEGEBA-CONICET, UNiversidad de Buenos Aires, FAcultad de Ciencias Exactas y Naturales, Intendente Güiraldes 2160, Ciudad Universitaria (C1428 EHA), CABA, Argentina.
| | - Julián Padró
- IEGEBA-CONICET, UNiversidad de Buenos Aires, FAcultad de Ciencias Exactas y Naturales, Intendente Güiraldes 2160, Ciudad Universitaria (C1428 EHA), CABA, Argentina
| | - Pedro Furió-Tarí
- Genomics of Gene Expression Lab, Centro de Investigación Príncipe Felipe, Eduardo Primo Yúfera 3, Valencia, 46012, Spain
| | - Sonia Tarazona
- Genomics of Gene Expression Lab, Centro de Investigación Príncipe Felipe, Eduardo Primo Yúfera 3, Valencia, 46012, Spain.,Department of Applied Statistics, Operations Research and Quality, Universitat Politècnica de València, Camí de Vera, Valencia, 46022, Spain
| | - Pablo S Milla Carmona
- IEGEBA-CONICET, UNiversidad de Buenos Aires, FAcultad de Ciencias Exactas y Naturales, Intendente Güiraldes 2160, Ciudad Universitaria (C1428 EHA), CABA, Argentina.,Laboratorio de Ecosistemas Marinos Fósiles, Instituto de Estudios Andinos Don Pablo Groeber (CONICET-UBA), Intendente Güiraldes 2160, Ciudad Universitaria (C1428 EHA), CABA, Argentina
| | - Ignacio M Soto
- IEGEBA-CONICET, UNiversidad de Buenos Aires, FAcultad de Ciencias Exactas y Naturales, Intendente Güiraldes 2160, Ciudad Universitaria (C1428 EHA), CABA, Argentina
| | - Hernán Dopazo
- IEGEBA-CONICET, UNiversidad de Buenos Aires, FAcultad de Ciencias Exactas y Naturales, Intendente Güiraldes 2160, Ciudad Universitaria (C1428 EHA), CABA, Argentina
| | - Ana Conesa
- Genomics of Gene Expression Lab, Centro de Investigación Príncipe Felipe, Eduardo Primo Yúfera 3, Valencia, 46012, Spain. .,Microbiology and Cell Science Department, Institute for Food and Agricultural Sciences, University of Florida at Gainesville, Gainesville, FL, 32603, USA.
| | - Esteban Hasson
- IEGEBA-CONICET, UNiversidad de Buenos Aires, FAcultad de Ciencias Exactas y Naturales, Intendente Güiraldes 2160, Ciudad Universitaria (C1428 EHA), CABA, Argentina.
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27
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Abstract
Fruit flies of the genus Drosophila have been an attractive and effective genetic model organism since Thomas Hunt Morgan and colleagues made seminal discoveries with them a century ago. Work with Drosophila has enabled dramatic advances in cell and developmental biology, neurobiology and behavior, molecular biology, evolutionary and population genetics, and other fields. With more tissue types and observable behaviors than in other short-generation model organisms, and with vast genome data available for many species within the genus, the fly's tractable complexity will continue to enable exciting opportunities to explore mechanisms of complex developmental programs, behaviors, and broader evolutionary questions. This primer describes the organism's natural history, the features of sequenced genomes within the genus, the wide range of available genetic tools and online resources, the types of biological questions Drosophila can help address, and historical milestones.
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28
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MacMillan HA, Knee JM, Dennis AB, Udaka H, Marshall KE, Merritt TJS, Sinclair BJ. Cold acclimation wholly reorganizes the Drosophila melanogaster transcriptome and metabolome. Sci Rep 2016; 6:28999. [PMID: 27357258 PMCID: PMC4928047 DOI: 10.1038/srep28999] [Citation(s) in RCA: 119] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Accepted: 06/07/2016] [Indexed: 01/05/2023] Open
Abstract
Cold tolerance is a key determinant of insect distribution and abundance, and thermal acclimation can strongly influence organismal stress tolerance phenotypes, particularly in small ectotherms like Drosophila. However, there is limited understanding of the molecular and biochemical mechanisms that confer such impressive plasticity. Here, we use high-throughput mRNA sequencing (RNA-seq) and liquid chromatography – mass spectrometry (LC-MS) to compare the transcriptomes and metabolomes of D. melanogaster acclimated as adults to warm (rearing) (21.5 °C) or cold conditions (6 °C). Cold acclimation improved cold tolerance and led to extensive biological reorganization: almost one third of the transcriptome and nearly half of the metabolome were differentially regulated. There was overlap in the metabolic pathways identified via transcriptomics and metabolomics, with proline and glutathione metabolism being the most strongly-supported metabolic pathways associated with increased cold tolerance. We discuss several new targets in the study of insect cold tolerance (e.g. dopamine signaling and Na+-driven transport), but many previously identified candidate genes and pathways (e.g. heat shock proteins, Ca2+ signaling, and ROS detoxification) were also identified in the present study, and our results are thus consistent with and extend the current understanding of the mechanisms of insect chilling tolerance.
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Affiliation(s)
- Heath A MacMillan
- Department of Biology, University of Western Ontario, London, ON, Canada
| | - Jose M Knee
- Department of Chemistry and Biochemistry, Laurentian University, Sudbury, ON, Canada
| | - Alice B Dennis
- Landcare Research, Auckland, New Zealand.,Allan Wilson Centre for Molecular Ecology and Evolution, Auckland, New Zealand
| | - Hiroko Udaka
- Department of Biology, University of Western Ontario, London, ON, Canada
| | - Katie E Marshall
- Department of Biology, University of Western Ontario, London, ON, Canada
| | - Thomas J S Merritt
- Department of Chemistry and Biochemistry, Laurentian University, Sudbury, ON, Canada
| | - Brent J Sinclair
- Department of Biology, University of Western Ontario, London, ON, Canada
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29
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Abstract
Drosophila, a dipteran insect, has been found to be the best biological model for different kinds of studies. D melanogaster was first described by Meigen in 1830 , is most extensively studied species of the genus Drosophila and a number of investigations employing this species have been documented in areas such as genetics, behaviour, evolution, development, molecular biology, ecology, population biology, etc. Besides D. melanogaster, a number of other species of the genus Drosophila have also been used for different kinds of investigations. Among these, D. ananassae, a cosmopolitan and domestic species endowed with several unusual genetic features, is noteworthy. Described for the first time from Indonesia (Doleschall 1858), this species is commonly distributed in India. Extensive research work on D. ananassae has been done by numerous researchers pertaining to cytology, genetics, mutagenesis, gene mapping, crossing-over in both sexes, population and evolutionary genetics,behaviour genetics, ecological genetics, sexual isolation, fluctuating asymmetry, trade-offs etc. Genome of D. ananassae has also been sequenced. The status of research on D. ananassae at global level is briefly described in this review. Bibliography on this species from different countries worldwide reveals that maximum contribution is from India.
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Affiliation(s)
- B N Singh
- Genetics Laboratory, Department of Zoology, Banaras Hindu University, Varanasi 221 005, India.
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30
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Reassignment of Drosophila willistoni Genome Scaffolds to Chromosome II Arms. G3-GENES GENOMES GENETICS 2015; 5:2559-66. [PMID: 26438290 PMCID: PMC4683629 DOI: 10.1534/g3.115.021311] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Drosophila willistoni is a geographically widespread Neotropical species. The genome of strain Gd-H4-1 from Guadeloupe Island (Caribbean) was sequenced in 2007 as part of the 12 Drosophila Genomes Project. The assembled scaffolds were joined based on conserved linkage and assigned to polytene chromosomes based on a handful of genetic and physical markers. This paucity of markers was particularly striking in the metacentric chromosome II, comprised two similarly sized arms, IIL and IIR, traditionally considered homologous to Muller elements C and B, respectively. In this paper we present the cytological mapping of 22 new gene markers to increase the number of markers mapped by in situ hybridization and to test the assignment of scaffolds to the polytene chromosome II arms. For this purpose, we generated, by polymerase chain reaction amplification, one or two gene probes from each scaffold assigned to the chromosome II arms and mapped these probes to the Gd-H4-1 strain's polytene chromosomes by nonfluorescent in situ hybridization. Our findings show that chromosome arms IIL and IIR correspond to Muller elements B and C, respectively, directly contrasting the current homology assignments in D. willistoni and constituting a major reassignment of the scaffolds to chromosome II arms.
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31
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Jha AR, Miles CM, Lippert NR, Brown CD, White KP, Kreitman M. Whole-Genome Resequencing of Experimental Populations Reveals Polygenic Basis of Egg-Size Variation in Drosophila melanogaster. Mol Biol Evol 2015; 32:2616-32. [PMID: 26044351 PMCID: PMC4576704 DOI: 10.1093/molbev/msv136] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Complete genome resequencing of populations holds great promise in deconstructing complex polygenic traits to elucidate molecular and developmental mechanisms of adaptation. Egg size is a classic adaptive trait in insects, birds, and other taxa, but its highly polygenic architecture has prevented high-resolution genetic analysis. We used replicated experimental evolution in Drosophila melanogaster and whole-genome sequencing to identify consistent signatures of polygenic egg-size adaptation. A generalized linear-mixed model revealed reproducible allele frequency differences between replicated experimental populations selected for large and small egg volumes at approximately 4,000 single nucleotide polymorphisms (SNPs). Several hundred distinct genomic regions contain clusters of these SNPs and have lower heterozygosity than the genomic background, consistent with selection acting on polymorphisms in these regions. These SNPs are also enriched among genes expressed in Drosophila ovaries and many of these genes have well-defined functions in Drosophila oogenesis. Additional genes regulating egg development, growth, and cell size show evidence of directional selection as genes regulating these biological processes are enriched for highly differentiated SNPs. Genetic crosses performed with a subset of candidate genes demonstrated that these genes influence egg size, at least in the large genetic background. These findings confirm the highly polygenic architecture of this adaptive trait, and suggest the involvement of many novel candidate genes in regulating egg size.
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Affiliation(s)
- Aashish R Jha
- Institute for Genomics and Systems Biology, The University of Chicago Department of Human Genetics, The University of Chicago Department of Ecology and Evolution, The University of Chicago
| | | | | | - Christopher D Brown
- Institute for Genomics and Systems Biology, The University of Chicago Department of Genetics, Perelman School of Medicine, University of Pennsylvania
| | - Kevin P White
- Institute for Genomics and Systems Biology, The University of Chicago Department of Human Genetics, The University of Chicago Department of Ecology and Evolution, The University of Chicago Committee on Genetics, Genomics & Systems Biology, The University of Chicago
| | - Martin Kreitman
- Institute for Genomics and Systems Biology, The University of Chicago Department of Ecology and Evolution, The University of Chicago Committee on Genetics, Genomics & Systems Biology, The University of Chicago
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32
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Simon JC, d'Alencon E, Guy E, Jacquin-Joly E, Jaquiery J, Nouhaud P, Peccoud J, Sugio A, Streiff R. Genomics of adaptation to host-plants in herbivorous insects. Brief Funct Genomics 2015; 14:413-23. [DOI: 10.1093/bfgp/elv015] [Citation(s) in RCA: 96] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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33
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Nadimpalli S, Persikov AV, Singh M. Pervasive variation of transcription factor orthologs contributes to regulatory network evolution. PLoS Genet 2015; 11:e1005011. [PMID: 25748510 PMCID: PMC4351887 DOI: 10.1371/journal.pgen.1005011] [Citation(s) in RCA: 14] [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: 06/13/2014] [Accepted: 01/18/2015] [Indexed: 01/17/2023] Open
Abstract
Differences in transcriptional regulatory networks underlie much of the phenotypic variation observed across organisms. Changes to cis-regulatory elements are widely believed to be the predominant means by which regulatory networks evolve, yet examples of regulatory network divergence due to transcription factor (TF) variation have also been observed. To systematically ascertain the extent to which TFs contribute to regulatory divergence, we analyzed the evolution of the largest class of metazoan TFs, Cys2-His2 zinc finger (C2H2-ZF) TFs, across 12 Drosophila species spanning ~45 million years of evolution. Remarkably, we uncovered that a significant fraction of all C2H2-ZF 1-to-1 orthologs in flies exhibit variations that can affect their DNA-binding specificities. In addition to loss and recruitment of C2H2-ZF domains, we found diverging DNA-contacting residues in ~44% of domains shared between D. melanogaster and the other fly species. These diverging DNA-contacting residues, found in ~70% of the D. melanogaster C2H2-ZF genes in our analysis and corresponding to ~26% of all annotated D. melanogaster TFs, show evidence of functional constraint: they tend to be conserved across phylogenetic clades and evolve slower than other diverging residues. These same variations were rarely found as polymorphisms within a population of D. melanogaster flies, indicating their rapid fixation. The predicted specificities of these dynamic domains gradually change across phylogenetic distances, suggesting stepwise evolutionary trajectories for TF divergence. Further, whereas proteins with conserved C2H2-ZF domains are enriched in developmental functions, those with varying domains exhibit no functional enrichments. Our work suggests that a subset of highly dynamic and largely unstudied TFs are a likely source of regulatory variation in Drosophila and other metazoans.
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Affiliation(s)
- Shilpa Nadimpalli
- Department of Computer Science, Princeton University, Princeton, New Jersey, United States of America
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
| | - Anton V. Persikov
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
| | - Mona Singh
- Department of Computer Science, Princeton University, Princeton, New Jersey, United States of America
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
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34
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Micro-plasticity of genomes as illustrated by the evolution of glutathione transferases in 12 Drosophila species. PLoS One 2014; 9:e109518. [PMID: 25310450 PMCID: PMC4195677 DOI: 10.1371/journal.pone.0109518] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Accepted: 09/03/2014] [Indexed: 12/05/2022] Open
Abstract
Glutathione transferases (GST) are an ancient superfamily comprising a large number of paralogous proteins in a single organism. This multiplicity of GSTs has allowed the copies to diverge for neofunctionalization with proposed roles ranging from detoxication and oxidative stress response to involvement in signal transduction cascades. We performed a comparative genomic analysis using FlyBase annotations and Drosophila melanogaster GST sequences as templates to further annotate the GST orthologs in the 12 Drosophila sequenced genomes. We found that GST genes in the Drosophila subgenera have undergone repeated local duplications followed by transposition, inversion, and micro-rearrangements of these copies. The colinearity and orientations of the orthologous GST genes appear to be unique in many of the species which suggests that genomic rearrangement events have occurred multiple times during speciation. The high micro-plasticity of the genomes appears to have a functional contribution utilized for evolution of this gene family.
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35
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Lang M, Polihronakis Richmond M, Acurio AE, Markow TA, Orgogozo V. Radiation of the Drosophila nannoptera species group in Mexico. J Evol Biol 2014; 27:575-84. [PMID: 26227897 DOI: 10.1111/jeb.12325] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Revised: 12/20/2013] [Accepted: 12/24/2013] [Indexed: 10/25/2022]
Abstract
The Drosophila nannoptera species group, a taxon of Mexican cactophilic flies, is an excellent model system to study the influence of abiotic and biotic factors on speciation, the genetic causes of ecological specialization and the evolution of unusual reproductive characters. However, the phylogenetic relationships in the nannoptera species group and its position within the virilis-repleta phylogeny have not been thoroughly investigated. Using a multilocus data set of gene coding regions of eight nuclear and three mitochondrial genes, we found that the four described nannoptera group species diverged rapidly, with very short internodes between divergence events. Phylogenetic analysis of repleta group lineages revealed that D. inca and D. canalinea are sister to all other repleta group species, whereas the annulimana species D. aracataca and D. pseudotalamancana are sister to the nannoptera and bromeliae species groups. Our divergence time estimates suggest that the nannoptera species group radiated following important geological events in Central America. Our results indicate that a single evolutionary transition to asymmetric genitalia and to unusual sperm storage may have occurred during evolution of the nannoptera group.
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Affiliation(s)
- M Lang
- CNRS UMR7592, Institut Jacques Monod, Université Paris Diderot, Paris, France
| | - M Polihronakis Richmond
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California, La Jolla, CA, USA
| | - A E Acurio
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - T A Markow
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California, La Jolla, CA, USA.,Laboratorio Nacional de Genómica de la Biodiversidad, CINVESTAV, Irapuato, Mexico
| | - V Orgogozo
- CNRS UMR7592, Institut Jacques Monod, Université Paris Diderot, Paris, France
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36
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Kim J, Lee J, Lee S, Lee B, Kim-Ha J. Phylogenetic comparison of oskar mRNA localization signals. Biochem Biophys Res Commun 2014; 444:98-103. [PMID: 24440702 DOI: 10.1016/j.bbrc.2014.01.021] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2013] [Accepted: 01/11/2014] [Indexed: 02/04/2023]
Abstract
As a way to spatially control the expression of genes within cells, RNA localization is being recognized as an important process by which proteins are restricted to specific subcellular domains, which occurs in more diverse types of tissue than previously considered. Although many localized RNAs have been identified, information on cis-acting elements of localization is still limited. As transcripts of oskar (osk) are known to localize to the posterior pole of oocytes, we computationally analyzed a conserved sequence among eight Drosophila species and tested its role as a localization element. Dimerization of osk mRNA did not occur when the motif was deleted, but this did not affect assembly of osk mRNA-containing ribonucleoprotein (RNP) complexes. Without the motif, however, large RNP complex particles accumulated in nurse cells, and only a small fraction of these RNP complexes was transported into oocytes and properly localized to the posterior pole. Therefore, this motif may be required for the early transport of osk mRNA into oocytes. Also, as dimerization of osk mRNA does not seem to be a prerequisite for the assembly of RNP complexes, a dimerization-independent mechanism may also serve to localize osk mRNA to the posterior pole.
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Affiliation(s)
- Jihyun Kim
- Department of Molecular Biology, College of Life Sciences, Sejong University, 98 Kunja-Dong, Kwangjin-ku, Seoul, South Korea
| | - Jiyeon Lee
- Department of Molecular Biology, College of Life Sciences, Sejong University, 98 Kunja-Dong, Kwangjin-ku, Seoul, South Korea
| | - Sujung Lee
- Department of Molecular Biology, College of Life Sciences, Sejong University, 98 Kunja-Dong, Kwangjin-ku, Seoul, South Korea
| | - Borim Lee
- Department of Molecular Biology, College of Life Sciences, Sejong University, 98 Kunja-Dong, Kwangjin-ku, Seoul, South Korea
| | - Jeongsil Kim-Ha
- Department of Molecular Biology, College of Life Sciences, Sejong University, 98 Kunja-Dong, Kwangjin-ku, Seoul, South Korea.
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37
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Extensive differences in antifungal immune response in two Drosophila species revealed by comparative transcriptome analysis. Int J Genomics 2013; 2013:542139. [PMID: 24151578 PMCID: PMC3782847 DOI: 10.1155/2013/542139] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2013] [Accepted: 08/03/2013] [Indexed: 12/19/2022] Open
Abstract
The innate immune system of Drosophila is activated by ingestion of microorganisms. D. melanogaster breeds on fruits fermented by Saccharomyces cerevisiae, whereas D. virilis breeds on slime flux and decaying bark of tree housing a variety of bacteria, yeasts, and molds. In this study, it is shown that D. virilis has a higher resistance to oral infection of a species of filamentous fungi belonging to the genus Penicillium compared to D. melanogaster. In response to the fungal infection, a transcriptome profile of immune-related genes was considerably different between D. melanogaster and D. virilis: the genes encoding antifungal peptides, Drosomycin and Metchnikowin, were highly expressed in D. melanogaster whereas, the genes encoding Diptericin and Defensin were highly expressed in D. virilis. On the other hand, the immune-induced molecule (IM) genes showed contrary expression patterns between the two species: they were induced by the fungal infection in D. melanogaster but tended to be suppressed in D. virilis. Our transcriptome analysis also showed newly predicted immune-related genes in D. virilis. These results suggest that the innate immune system has been extensively differentiated during the evolution of these Drosophila species.
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38
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Wissler L, Gadau J, Simola DF, Helmkampf M, Bornberg-Bauer E. Mechanisms and dynamics of orphan gene emergence in insect genomes. Genome Biol Evol 2013; 5:439-55. [PMID: 23348040 PMCID: PMC3590893 DOI: 10.1093/gbe/evt009] [Citation(s) in RCA: 101] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Orphan genes are defined as genes that lack detectable similarity to genes in other species and therefore no clear signals of common descent (i.e., homology) can be inferred. Orphans are an enigmatic portion of the genome because their origin and function are mostly unknown and they typically make up 10% to 30% of all genes in a genome. Several case studies demonstrated that orphans can contribute to lineage-specific adaptation. Here, we study orphan genes by comparing 30 arthropod genomes, focusing in particular on seven recently sequenced ant genomes. This setup allows analyzing a major metazoan taxon and a comparison between social Hymenoptera (ants and bees) and nonsocial Diptera (flies and mosquitoes). First, we find that recently split lineages undergo accelerated genomic reorganization, including the rapid gain of many orphan genes. Second, between the two insect orders Hymenoptera and Diptera, orphan genes are more abundant and emerge more rapidly in Hymenoptera, in particular, in leaf-cutter ants. With respect to intragenomic localization, we find that ant orphan genes show little clustering, which suggests that orphan genes in ants are scattered uniformly over the genome and between nonorphan genes. Finally, our results indicate that the genetic mechanisms creating orphan genes—such as gene duplication, frame-shift fixation, creation of overlapping genes, horizontal gene transfer, and exaptation of transposable elements—act at different rates in insects, primates, and plants. In Formicidae, the majority of orphan genes has their origin in intergenic regions, pointing to a high rate of de novo gene formation or generalized gene loss, and support a recently proposed dynamic model of frequent gene birth and death.
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Affiliation(s)
- Lothar Wissler
- Institute for Evolution and Biodiversity, University of Muenster, Muenster, Germany
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Gilbert JDJ, Acquisti C, Martinson HM, Elser JJ, Kumar S, Fagan WF. GRASP [Genomic Resource Access for Stoichioproteomics]: comparative explorations of the atomic content of 12 Drosophila proteomes. BMC Genomics 2013; 14:599. [PMID: 24007337 PMCID: PMC3844568 DOI: 10.1186/1471-2164-14-599] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2012] [Accepted: 06/05/2013] [Indexed: 12/05/2022] Open
Abstract
BACKGROUND "Stoichioproteomics" relates the elemental composition of proteins and proteomes to variation in the physiological and ecological environment. To help harness and explore the wealth of hypotheses made possible under this framework, we introduce GRASP (http://www.graspdb.net), a public bioinformatic knowledgebase containing information on the frequencies of 20 amino acids and atomic composition of their side chains. GRASP integrates comparative protein composition data with annotation data from multiple public databases. Currently, GRASP includes information on proteins of 12 sequenced Drosophila (fruit fly) proteomes, which will be expanded to include increasingly diverse organisms over time. In this paper we illustrate the potential of GRASP for testing stoichioproteomic hypotheses by conducting an exploratory investigation into the composition of 12 Drosophila proteomes, testing the prediction that protein atomic content is associated with species ecology and with protein expression levels. RESULTS Elements varied predictably along multivariate axes. Species were broadly similar, with the D. willistoni proteome a clear outlier. As expected, individual protein atomic content within proteomes was influenced by protein function and amino acid biochemistry. Evolution in elemental composition across the phylogeny followed less predictable patterns, but was associated with broad ecological variation in diet. Using expression data available for D. melanogaster, we found evidence consistent with selection for efficient usage of elements within the proteome: as expected, nitrogen content was reduced in highly expressed proteins in most tissues, most strongly in the gut, where nutrients are assimilated, and least strongly in the germline. CONCLUSIONS The patterns identified here using GRASP provide a foundation on which to base future research into the evolution of atomic composition in Drosophila and other taxa.
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Affiliation(s)
- James D J Gilbert
- A08 Heydon-Lawrence Bdg, University of Sydney, Sydney NSW 2006, Australia
- University of Maryland, College Park, MD 20742, USA
| | - Claudia Acquisti
- WWU Munster, Institute for Evolution and Biodiversity, Hufferstr. 1, Munster 48149, Germany
- Center for Evolutionary Medicine and Informatics, Biodesign Institute, Arizona State University, Tempe, AZ 85287-5301, USA
- School of Life Sciences, Arizona State University, Tempe, AZ 85287-4501, USA
| | | | - James J Elser
- School of Life Sciences, Arizona State University, Tempe, AZ 85287-4501, USA
| | - Sudhir Kumar
- Center for Evolutionary Medicine and Informatics, Biodesign Institute, Arizona State University, Tempe, AZ 85287-5301, USA
- School of Life Sciences, Arizona State University, Tempe, AZ 85287-4501, USA
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Rytz R, Croset V, Benton R. Ionotropic receptors (IRs): chemosensory ionotropic glutamate receptors in Drosophila and beyond. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2013; 43:888-97. [PMID: 23459169 DOI: 10.1016/j.ibmb.2013.02.007] [Citation(s) in RCA: 285] [Impact Index Per Article: 25.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2012] [Revised: 01/30/2013] [Accepted: 02/13/2013] [Indexed: 05/20/2023]
Abstract
Ionotropic Receptors (IRs) are a recently characterized family of olfactory receptors in the fruit fly, Drosophila melanogaster. IRs are not related to insect Odorant Receptors (ORs), but rather have evolved from ionotropic glutamate receptors (iGluRs), a conserved family of synaptic ligand-gated ion channels. Here, we review the expression and function of IRs in Drosophila, highlighting similarities and differences with iGluRs. We also briefly describe the organization of the neuronal circuits in which IRs function, comparing and contrasting them with the sensory pathways expressing ORs. Finally, we summarize the bioinformatic identification and initial characterization of IRs in other species, which imply an evolutionarily conserved role for these receptors in chemosensation in insects and other protostomes.
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Affiliation(s)
- Raphael Rytz
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, CH-1015 Lausanne, Switzerland
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Eldon J, Price JP, Magnacca K, Price DK. Patterns and processes in complex landscapes: testing alternative biogeographical hypotheses through integrated analysis of phylogeography and community ecology in Hawai'i. Mol Ecol 2013; 22:3613-28. [PMID: 23683316 DOI: 10.1111/mec.12326] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2012] [Revised: 03/12/2013] [Accepted: 03/14/2013] [Indexed: 11/28/2022]
Abstract
The Island of Hawai'i is a dynamic assemblage of five volcanoes with wet forest habitat currently existing in four distinct natural regions that vary in area, age and geographical isolation. In this complex landscape, alternative assumptions of the relative importance of specific habitat characteristics on evolutionary and ecological processes predict strikingly different general patterns of local diversity and regional similarity. In this study, we compare alternative a priori hypotheses against observed patterns within two distinct biological systems and scales: community composition of wet forest vascular plant species and mitochondrial and nuclear genes of Drosophila sproati, a wet-forest-restricted endemic. All observed patterns display strong and similar regional structuring, with the greatest local diversity found in Kohala and the windward side of Mauna Loa, the least in Ka'ū and Kona, and a distinctive pattern of regional similarity that probably reflects the historical development of this habitat on the island. These observations largely corroborate a biogeographical model that integrates multiple lines of evidence, including climatic reconstruction, over those relying on single measures, such as current habitat configuration or substrate age. This method of testing alternative hypotheses across biological systems and scales is an innovative approach for understanding complex landscapes and should prove valuable in diverse biogeographical systems.
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Affiliation(s)
- Jon Eldon
- Tropical Conservation Biology and Environmental Science Graduate Program, University of Hawai'i, Hilo, HI 96720, USA.
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Austin CJ, Moehring AJ. Optimal temperature range of a plastic species, Drosophila simulans. J Anim Ecol 2013; 82:663-72. [PMID: 23360477 DOI: 10.1111/1365-2656.12041] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2012] [Accepted: 11/24/2012] [Indexed: 11/29/2022]
Abstract
1. When a species experiences a new climate, it can adapt in two main ways: become genetically adapted to the new temperature, or adopt a plastic approach that allows it to survive at a range of temperatures. 2. The constraint on fitness for genetically adapted populations that are exposed to a new temperature has been well studied, but the range of optimal temperatures and their effect on fitness has never been examined across the worldwide distribution of a plastic species. 3. Here, we determined the optimum temperature range of 11 populations of the phenotypically plastic species Drosophila simulans. We measured the influence of temperature on eggs, larvae and adults at six temperatures that span the natural range the flies experience during their primary breeding season. We found no correlation between optimum temperature and native temperature, an effect that is not likely due to laboratory maintenance, suggesting that the species has not locally adapted to temperature. 4. We also found that this species had equal survival and reproductive success at most of the temperatures and life stages that we tested, regardless of the native temperature where the flies originated. 5. Thus, this genetically plastic species has an optimum fitness at a surprisingly wide range of temperatures, and is the first example of a cosmopolitan species exhibiting this large amount of plasticity across its sampling distribution.
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Affiliation(s)
- Christopher J Austin
- Department of Biology, The University of Western Ontario, London, N6A 5B7, ON, Canada
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Kayserili MA, Gerrard DT, Tomancak P, Kalinka AT. An excess of gene expression divergence on the X chromosome in Drosophila embryos: implications for the faster-X hypothesis. PLoS Genet 2012; 8:e1003200. [PMID: 23300473 PMCID: PMC3531489 DOI: 10.1371/journal.pgen.1003200] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2012] [Accepted: 11/19/2012] [Indexed: 12/26/2022] Open
Abstract
The X chromosome is present as a single copy in the heterogametic sex, and this hemizygosity is expected to drive unusual patterns of evolution on the X relative to the autosomes. For example, the hemizgosity of the X may lead to a lower chromosomal effective population size compared to the autosomes, suggesting that the X might be more strongly affected by genetic drift. However, the X may also experience stronger positive selection than the autosomes, because recessive beneficial mutations will be more visible to selection on the X where they will spend less time being masked by the dominant, less beneficial allele--a proposal known as the faster-X hypothesis. Thus, empirical studies demonstrating increased genetic divergence on the X chromosome could be indicative of either adaptive or non-adaptive evolution. We measured gene expression in Drosophila species and in D. melanogaster inbred strains for both embryos and adults. In the embryos we found that expression divergence is on average more than 20% higher for genes on the X chromosome relative to the autosomes; but in contrast, in the inbred strains, gene expression variation is significantly lower on the X chromosome. Furthermore, expression divergence of genes on Muller's D element is significantly greater along the branch leading to the obscura sub-group, in which this element segregates as a neo-X chromosome. In the adults, divergence is greatest on the X chromosome for males, but not for females, yet in both sexes inbred strains harbour the lowest level of gene expression variation on the X chromosome. We consider different explanations for our results and conclude that they are most consistent within the framework of the faster-X hypothesis.
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Affiliation(s)
- Melek A. Kayserili
- Max Planck Institute for Molecular Cell Biology and Genetics, Dresden, Germany
| | - Dave T. Gerrard
- Faculty of Life Sciences, The University of Manchester, Manchester, United Kingdom
| | - Pavel Tomancak
- Max Planck Institute for Molecular Cell Biology and Genetics, Dresden, Germany
| | - Alex T. Kalinka
- Max Planck Institute for Molecular Cell Biology and Genetics, Dresden, Germany
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Seetharam A, Stuart GW. Whole genome phylogenies for multiple Drosophila species. BMC Res Notes 2012; 5:670. [PMID: 23210901 PMCID: PMC3531268 DOI: 10.1186/1756-0500-5-670] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2012] [Accepted: 11/27/2012] [Indexed: 11/23/2022] Open
Abstract
Background Reconstructing the evolutionary history of organisms using traditional phylogenetic methods may suffer from inaccurate sequence alignment. An alternative approach, particularly effective when whole genome sequences are available, is to employ methods that don’t use explicit sequence alignments. We extend a novel phylogenetic method based on Singular Value Decomposition (SVD) to reconstruct the phylogeny of 12 sequenced Drosophila species. SVD analysis provides accurate comparisons for a high fraction of sequences within whole genomes without the prior identification of orthologs or homologous sites. With this method all protein sequences are converted to peptide frequency vectors within a matrix that is decomposed to provide simplified vector representations for each protein of the genome in a reduced dimensional space. These vectors are summed together to provide a vector representation for each species, and the angle between these vectors provides distance measures that are used to construct species trees. Results An unfiltered whole genome analysis (193,622 predicted proteins) strongly supports the currently accepted phylogeny for 12 Drosophila species at higher dimensions except for the generally accepted but difficult to discern sister relationship between D. erecta and D. yakuba. Also, in accordance with previous studies, many sequences appear to support alternative phylogenies. In this case, we observed grouping of D. erecta with D. sechellia when approximately 55% to 95% of the proteins were removed using a filter based on projection values or by reducing resolution by using fewer dimensions. Similar results were obtained when just the melanogaster subgroup was analyzed. Conclusions These results indicate that using our novel phylogenetic method, it is possible to consult and interpret all predicted protein sequences within multiple whole genomes to produce accurate phylogenetic estimations of relatedness between Drosophila species. Furthermore, protein filtering can be effectively applied to reduce incongruence in the dataset as well as to generate alternative phylogenies.
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Affiliation(s)
- Arun Seetharam
- Department of Biology, Indiana State University, Terre Haute, Indiana 47809, USA
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Bartoletti M, Rubin T, Chalvet F, Netter S, Dos Santos N, Poisot E, Paces-Fessy M, Cumenal D, Peronnet F, Pret AM, Théodore L. Genetic basis for developmental homeostasis of germline stem cell niche number: a network of Tramtrack-Group nuclear BTB factors. PLoS One 2012. [PMID: 23185495 PMCID: PMC3503823 DOI: 10.1371/journal.pone.0049958] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The potential to produce new cells during adult life depends on the number of stem cell niches and the capacity of stem cells to divide, and is therefore under the control of programs ensuring developmental homeostasis. However, it remains generally unknown how the number of stem cell niches is controlled. In the insect ovary, each germline stem cell (GSC) niche is embedded in a functional unit called an ovariole. The number of ovarioles, and thus the number of GSC niches, varies widely among species. In Drosophila, morphogenesis of ovarioles starts in larvae with the formation of terminal filaments (TFs), each made of 8–10 cells that pile up and sort in stacks. TFs constitute organizers of individual germline stem cell niches during larval and early pupal development. In the Drosophila melanogaster subgroup, the number of ovarioles varies interspecifically from 8 to 20. Here we show that pipsqueak, Trithorax-like, batman and the bric-à-brac (bab) locus, all encoding nuclear BTB/POZ factors of the Tramtrack Group, are involved in limiting the number of ovarioles in D. melanogaster. At least two different processes are differentially perturbed by reducing the function of these genes. We found that when the bab dose is reduced, sorting of TF cells into TFs was affected such that each TF contains fewer cells and more TFs are formed. In contrast, psq mutants exhibited a greater number of TF cells per ovary, with a normal number of cells per TF, thereby leading to formation of more TFs per ovary than in the wild type. Our results indicate that two parallel genetic pathways under the control of a network of nuclear BTB factors are combined in order to negatively control the number of germline stem cell niches.
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Affiliation(s)
- Mathieu Bartoletti
- Centre de Génétique Moléculaire, Unité Propre de Recherche 3404 du Centre National de la Recherche Scientifique, Gif-sur-Yvette, France
- Departement de Biologie, University of Versailles St-Quentin, Versailles, France
- Laboratoire de Génétique et Biologie Cellulaire, Equipe Associée 4589, University of Versailles St-Quentin, Versailles, France
| | - Thomas Rubin
- Departement de Biologie, University of Versailles St-Quentin, Versailles, France
- Laboratoire de Génétique et Biologie Cellulaire, Equipe Associée 4589, University of Versailles St-Quentin, Versailles, France
| | - Fabienne Chalvet
- Centre de Génétique Moléculaire, Unité Propre de Recherche 3404 du Centre National de la Recherche Scientifique, Gif-sur-Yvette, France
- Laboratoire de Génétique et Biologie Cellulaire, Equipe Associée 4589, University of Versailles St-Quentin, Versailles, France
- Departement de Biologie, University of Paris-Sud, Orsay, France
| | - Sophie Netter
- Centre de Génétique Moléculaire, Unité Propre de Recherche 3404 du Centre National de la Recherche Scientifique, Gif-sur-Yvette, France
- Departement de Biologie, University of Versailles St-Quentin, Versailles, France
- Laboratoire de Génétique et Biologie Cellulaire, Equipe Associée 4589, University of Versailles St-Quentin, Versailles, France
| | - Nicolas Dos Santos
- Departement de Biologie, University of Versailles St-Quentin, Versailles, France
- Laboratoire de Génétique et Biologie Cellulaire, Equipe Associée 4589, University of Versailles St-Quentin, Versailles, France
| | - Emilie Poisot
- Departement de Biologie, University of Versailles St-Quentin, Versailles, France
- Laboratoire de Génétique et Biologie Cellulaire, Equipe Associée 4589, University of Versailles St-Quentin, Versailles, France
| | - Mélanie Paces-Fessy
- Departement de Biologie, University of Versailles St-Quentin, Versailles, France
- Laboratoire de Génétique et Biologie Cellulaire, Equipe Associée 4589, University of Versailles St-Quentin, Versailles, France
- Biologie du Développement Unité Mixte de Recherche 7622, Centre National de la Recherche Scientifique et Université Pierre et Marie Curie, Paris, France
| | - Delphine Cumenal
- Biologie du Développement Unité Mixte de Recherche 7622, Centre National de la Recherche Scientifique et Université Pierre et Marie Curie, Paris, France
| | - Frédérique Peronnet
- Biologie du Développement Unité Mixte de Recherche 7622, Centre National de la Recherche Scientifique et Université Pierre et Marie Curie, Paris, France
| | - Anne-Marie Pret
- Centre de Génétique Moléculaire, Unité Propre de Recherche 3404 du Centre National de la Recherche Scientifique, Gif-sur-Yvette, France
- Departement de Biologie, University of Versailles St-Quentin, Versailles, France
| | - Laurent Théodore
- Centre de Génétique Moléculaire, Unité Propre de Recherche 3404 du Centre National de la Recherche Scientifique, Gif-sur-Yvette, France
- Laboratoire de Génétique et Biologie Cellulaire, Equipe Associée 4589, University of Versailles St-Quentin, Versailles, France
- Departement de Biologie, University of Paris-Sud, Orsay, France
- * E-mail:
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Green DA, Extavour CG. Convergent evolution of a reproductive trait through distinct developmental mechanisms in Drosophila. Dev Biol 2012; 372:120-30. [PMID: 23022298 DOI: 10.1016/j.ydbio.2012.09.014] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2012] [Revised: 09/08/2012] [Accepted: 09/16/2012] [Indexed: 11/18/2022]
Abstract
Convergent morphologies often arise due to similar selective pressures in independent lineages. It is poorly understood whether the same or different developmental genetic mechanisms underlie such convergence. Here we show that independent evolution of a reproductive trait, ovariole number, has resulted from changes in distinct developmental mechanisms, each of which may have a different underlying genetic basis in Drosophila. Ovariole number in Drosophila is species-specific, highly variable, and largely under genetic control. Convergent changes in Drosophila ovariole number have evolved independently within and between species. We previously showed that the number of a specific ovarian cell type, terminal filament (TF) cells, determines ovariole number. Here we examine TF cell development in different Drosophila lineages that independently evolved a significantly lower ovariole number than the D. melanogaster Oregon R strain. We show that in these Drosophila lineages, reduction in ovariole number occurs primarily through variations in one of two different developmental mechanisms: (1) reduced number of somatic gonad precursors (SGP cells) specified during embryogenesis; or (2) alterations of somatic gonad cell morphogenesis and differentiation in larval life. Mutations in the D. melanogaster Insulin Receptor (InR) alter SGP cell number but not ovarian morphogenesis, while targeted loss of function of bric-à-brac 2 (bab2) affects morphogenesis without changing SGP cell number. Thus, evolution can produce similar ovariole numbers through distinct developmental mechanisms, likely controlled by different genetic mechanisms.
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Affiliation(s)
- Delbert A Green
- Department of Molecular and Cellular Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA
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Makino T, Kawata M. Habitat variability correlates with duplicate content of Drosophila genomes. Mol Biol Evol 2012; 29:3169-79. [PMID: 22586328 PMCID: PMC3457775 DOI: 10.1093/molbev/mss133] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
The factors limiting the habitat range of species are crucial in understanding their biodiversity and response to environmental change. Yet the genetic and genomic architectures that produce genetic variation to enable environmental adaptation have remained poorly understood. Here we show that the proportion of duplicated genes (PD) in the whole genomes of fully sequenced Drosophila species is significantly correlated with environmental variability within the habitats measured by the climatic envelope and habitat diversity. Furthermore, species with a low PD tend to lose the duplicated genes owing to their faster evolution. These results indicate that the rapid relaxation of functional constraints on duplicated genes resulted in a low PD for species with lower habitat diversity, and suggest that the maintenance of duplicated genes gives organisms an ecological advantage during evolution. We therefore propose that the PD in a genome is related to adaptation to environmental variation.
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Affiliation(s)
- Takashi Makino
- Department of Ecology and Evolutionary Biology, Graduate School of Life Sciences, Tohoku University, Sendai, Japan.
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Guillén Y, Ruiz A. Gene alterations at Drosophila inversion breakpoints provide prima facie evidence for natural selection as an explanation for rapid chromosomal evolution. BMC Genomics 2012; 13:53. [PMID: 22296923 PMCID: PMC3355041 DOI: 10.1186/1471-2164-13-53] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2011] [Accepted: 02/01/2012] [Indexed: 01/17/2023] Open
Abstract
Background Chromosomal inversions have been pervasive during the evolution of the genus Drosophila, but there is significant variation between lineages in the rate of rearrangement fixation. D. mojavensis, an ecological specialist adapted to a cactophilic niche under extreme desert conditions, is a chromosomally derived species with ten fixed inversions, five of them not present in any other species. Results In order to explore the causes of the rapid chromosomal evolution in D. mojavensis, we identified and characterized all breakpoints of seven inversions fixed in chromosome 2, the most dynamic one. One of the inversions presents unequivocal evidence for its generation by ectopic recombination between transposon copies and another two harbor inverted duplications of non-repetitive DNA at the two breakpoints and were likely generated by staggered single-strand breaks and repair by non-homologous end joining. Four out of 14 breakpoints lay in the intergenic region between preexisting duplicated genes, suggesting an adaptive advantage of separating previously tightly linked duplicates. Four out of 14 breakpoints are associated with transposed genes, suggesting these breakpoints are fragile regions. Finally two inversions contain novel genes at their breakpoints and another three show alterations of genes at breakpoints with potential adaptive significance. Conclusions D. mojavensis chromosomal inversions were generated by multiple mechanisms, an observation that does not provide support for increased mutation rate as explanation for rapid chromosomal evolution. On the other hand, we have found a number of gene alterations at the breakpoints with putative adaptive consequences that directly point to natural selection as the cause of D. mojavensis rapid chromosomal evolution.
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Affiliation(s)
- Yolanda Guillén
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, 08193 Bellaterra (Barcelona), Spain
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Lavagnino N, Serra F, Arbiza L, Dopazo H, Hasson E. Evolutionary Genomics of Genes Involved in Olfactory Behavior in the Drosophila melanogaster Species Group. Evol Bioinform Online 2012; 8:89-104. [PMID: 22346339 PMCID: PMC3273929 DOI: 10.4137/ebo.s8484] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Previous comparative genomic studies of genes involved in olfactory behavior in Drosophila focused only on particular gene families such as odorant receptor and/or odorant binding proteins. However, olfactory behavior has a complex genetic architecture that is orchestrated by many interacting genes. In this paper, we present a comparative genomic study of olfactory behavior in Drosophila including an extended set of genes known to affect olfactory behavior. We took advantage of the recent burst of whole genome sequences and the development of powerful statistical tools to analyze genomic data and test evolutionary and functional hypotheses of olfactory genes in the six species of the Drosophila melanogaster species group for which whole genome sequences are available. Our study reveals widespread purifying selection and limited incidence of positive selection on olfactory genes. We show that the pace of evolution of olfactory genes is mostly independent of the life cycle stage, and of the number of life cycle stages, in which they participate in olfaction. However, we detected a relationship between evolutionary rates and the position that the gene products occupy in the olfactory system, genes occupying central positions tend to be more constrained than peripheral genes. Finally, we demonstrate that specialization to one host does not seem to be associated with bursts of adaptive evolution in olfactory genes in D. sechellia and D. erecta, the two specialists species analyzed, but rather different lineages have idiosyncratic evolutionary histories in which both historical and ecological factors have been involved.
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Affiliation(s)
- Nicolás Lavagnino
- Departamento de Ecología, Genética y Evolución; Facultad de Ciencias Exactas y Naturales; Universidad de Buenos Aires; Buenos Aires; Argentina
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Sarikaya DP, Belay AA, Ahuja A, Dorta A, Green DA, Extavour CG. The roles of cell size and cell number in determining ovariole number in Drosophila. Dev Biol 2011; 363:279-89. [PMID: 22200592 DOI: 10.1016/j.ydbio.2011.12.017] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2011] [Revised: 12/09/2011] [Accepted: 12/10/2011] [Indexed: 11/19/2022]
Abstract
All insect ovaries are composed of functional units called ovarioles, which contain sequentially developing egg chambers. The number of ovarioles varies between and within species. Ovariole number is an important determinant of fecundity and thus affects individual fitness. Although Drosophila oogenesis has been intensively studied, the genetic and cellular basis for determination of ovariole number remains unknown. Ovariole formation begins during larval development with the morphogenesis of terminal filament cells (TFCs) into stacks called terminal filaments (TFs). We induced changes in ovariole number in Drosophila melanogaster by genetically altering cell size and cell number in the TFC population, and analyzed TF morphogenesis in these ovaries to understand the cellular basis for the changes in ovariole number. Increasing TFC size contributed to higher ovariole number by increasing TF number. Similarly, increasing total TFC number led to higher ovariole number via an increase in TF number. By analyzing ovarian morphogenesis in another Drosophila species we showed that TFC number regulation is a target of evolutionary change that affects ovariole number. In contrast, temperature-dependent plasticity in ovariole number was due to changes in cell-cell sorting during TF morphogenesis, rather than changes in cell size or cell number. We have thus identified two distinct developmental processes that regulate ovariole number: establishment of total TFC number, and TFC sorting during TF morphogenesis. Our data suggest that the genetic changes underlying species-specific ovariole number may alter the total number of TFCs available to contribute to TF formation. This work provides for the first time specific and quantitative developmental tools to investigate the evolution of a highly conserved reproductive structure.
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Affiliation(s)
- Didem Pelin Sarikaya
- Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA
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