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Arnqvist G, Westerberg I, Galbraith J, Sayadi A, Scofield DG, Olsen RA, Immonen E, Bonath F, Ewels P, Suh A. A chromosome-level assembly of the seed beetle Callosobruchus maculatus genome with annotation of its repetitive elements. G3 (Bethesda) 2024; 14:jkad266. [PMID: 38092066 PMCID: PMC10849321 DOI: 10.1093/g3journal/jkad266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 10/30/2023] [Indexed: 02/09/2024]
Abstract
Callosobruchus maculatus is a major agricultural pest of legume crops worldwide and an established model system in ecology and evolution. Yet, current molecular biological resources for this species are limited. Here, we employ Hi-C sequencing to generate a greatly improved genome assembly and we annotate its repetitive elements in a dedicated in-depth effort where we manually curate and classify the most abundant unclassified repeat subfamilies. We present a scaffolded chromosome-level assembly, which is 1.01 Gb in total length with 86% being contained within the 9 autosomes and the X chromosome. Repetitive sequences accounted for 70% of the total assembly. DNA transposons covered 18% of the genome, with the most abundant superfamily being Tc1-Mariner (9.75% of the genome). This new chromosome-level genome assembly of C. maculatus will enable future genetic and evolutionary studies not only of this important species but of beetles more generally.
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Affiliation(s)
- Göran Arnqvist
- Animal Ecology, Department of Ecology and Genetics, Uppsala University, Uppsala SE75236, Sweden
| | - Ivar Westerberg
- Systematic Biology, Department of Organismal Biology, Uppsala University, Uppsala SE75236, Sweden
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm SE10691, Sweden
| | - James Galbraith
- School of Biological Sciences, University of Adelaide, Adelaide 5005, Australia
- Faculty of Environment, Science and Economy, University of Exeter, Cornwall TR10 9FE, UK
| | - Ahmed Sayadi
- Rheumatology, Department of Medical Sciences, Uppsala University, Uppsala SE75236, Sweden
| | - Douglas G Scofield
- Evolutionary Biology, Department of Ecology and Genetics, Uppsala University, Uppsala SE75236, Sweden
- Uppsala Multidisciplinary Center for Advanced Computational Science, Uppsala University, Uppsala SE75236, Sweden
| | - Remi-André Olsen
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm SE10691, Sweden
| | - Elina Immonen
- Evolutionary Biology, Department of Ecology and Genetics, Uppsala University, Uppsala SE75236, Sweden
| | - Franziska Bonath
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm SE10691, Sweden
| | | | - Alexander Suh
- Systematic Biology, Department of Organismal Biology, Uppsala University, Uppsala SE75236, Sweden
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2
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Kaufmann P, Wiberg RAW, Papachristos K, Scofield DG, Tellgren-Roth C, Immonen E. Y-Linked Copy Number Polymorphism of Target of Rapamycin Is Associated with Sexual Size Dimorphism in Seed Beetles. Mol Biol Evol 2023; 40:msad167. [PMID: 37479678 PMCID: PMC10414808 DOI: 10.1093/molbev/msad167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 07/03/2023] [Accepted: 07/11/2023] [Indexed: 07/23/2023] Open
Abstract
The Y chromosome is theorized to facilitate evolution of sexual dimorphism by accumulating sexually antagonistic loci, but empirical support is scarce. Due to the lack of recombination, Y chromosomes are prone to degenerative processes, which poses a constraint on their adaptive potential. Yet, in the seed beetle, Callosobruchus maculatus segregating Y linked variation affects male body size and thereby sexual size dimorphism (SSD). Here, we assemble C. maculatus sex chromosome sequences and identify molecular differences associated with Y-linked SSD variation. The assembled Y chromosome is largely euchromatic and contains over 400 genes, many of which are ampliconic with a mixed autosomal and X chromosome ancestry. Functional annotation suggests that the Y chromosome plays important roles in males beyond primary reproductive functions. Crucially, we find that, besides an autosomal copy of the gene target of rapamycin (TOR), males carry an additional TOR copy on the Y chromosome. TOR is a conserved regulator of growth across taxa, and our results suggest that a Y-linked TOR provides a male specific opportunity to alter body size. A comparison of Y haplotypes associated with male size difference uncovers a copy number variation for TOR, where the haplotype associated with decreased male size, and thereby increased sexual dimorphism, has two additional TOR copies. This suggests that sexual conflict over growth has been mitigated by autosome to Y translocation of TOR followed by gene duplications. Our results reveal that despite of suppressed recombination, the Y chromosome can harbor adaptive potential as a male-limited supergene.
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Affiliation(s)
- Philipp Kaufmann
- Department of Ecology and Genetics (Evolutionary Biology program), Uppsala University, Uppsala, Sweden
| | - R Axel W Wiberg
- Department of Ecology and Genetics (Evolutionary Biology program), Uppsala University, Uppsala, Sweden
- Ecology Division, Department of Zoology, Stockholm University, Stockholm, Sweden
| | | | - Douglas G Scofield
- Uppsala Multidisciplinary Center for Advanced Computational Science, Uppsala University, Uppsala, Sweden
| | - Christian Tellgren-Roth
- National Genomics Infrastructure, Uppsala Genome Center, SciLifeLab, BioMedical Centre, Uppsala University, Uppsala, Sweden
| | - Elina Immonen
- Department of Ecology and Genetics (Evolutionary Biology program), Uppsala University, Uppsala, Sweden
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3
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Boman J, Arnqvist G. Larger genomes show improved buffering of adult fitness against environmental stress in seed beetles. Biol Lett 2023; 19:20220450. [PMID: 36693428 PMCID: PMC9873469 DOI: 10.1098/rsbl.2022.0450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Our general understanding of the evolution of genome size (GS) is incomplete, and it has long been clear that GS does not reflect organismal complexity. Here, we assess the hypothesis that larger genomes may allow organisms to better cope with environmental variation. It is, for example, possible that genome expansion due to proliferation of transposable elements or gene duplications may affect the ability to regulate and fine-tune transcriptional profiles. We used 18 populations of the seed beetle Callosobruchus maculatus, which differ in GS by up to 4.5%, and exposed adults and juveniles to environmental stress in a series of experiments where stage-specific fitness was assayed. We found that populations with larger genomes were indeed better buffered against environmental stress for adult, but not for juvenile, fitness. The genetic correlation across populations between GS and canalization of adult fitness is consistent with a role for natural selection in the evolution of GS.
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Affiliation(s)
- Jesper Boman
- Evolutionary Biology, Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
| | - Göran Arnqvist
- Animal Ecology, Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
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4
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Trabuco Amaral D, Mitani Y, Aparecida Silva Bonatelli I, Cerri R, Ohmiya Y, Viviani V. Genome analysis of Phrixothrix hirtus (Phengodidae) railroad worm shows the expansion of odorant-binding gene families and positive selection on morphogenesis and sex determination genes. Gene X 2022; 850:146917. [PMID: 36174905 DOI: 10.1016/j.gene.2022.146917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 09/14/2022] [Accepted: 09/21/2022] [Indexed: 10/14/2022] Open
Abstract
Among bioluminescent beetles of the Elateroidea superfamily, Phengodidae is the third largest family, with 244 bioluminescent species distributed only in the Americas, but is still the least studied from the phylogenetic and evolutionary points of view. The railroad worm Phrixothrix hirtus is an essential biological model and symbolic species due to its bicolor bioluminescence, being the only organism that produces true red light among bioluminescent terrestrial species. Here, we performed partial genome assembly of P. hirtus, combining short and long reads generated with Illumina sequencing, providing the first source of genomic information and a framework for comparative analyses of the bioluminescent system in Elateroidea. This is the largest genome described in the Elateroidea superfamily, with an estimated size of ∼3.4 Gb, displaying 32 % GC content, and 67 % transposable elements. Comparative genomic analyses showed a positive selection of genes and gene family expansion events of growths and morphogenesis gene products, which could be associated with the atypical anatomical development and morphogenesis found in paedomorphic females and underdeveloped males. We also observed gene family expansion among distinct odorant-binding receptors, which could be associated with the pheromone communication system typical of these beetles, and retrotransposable elements. Common genes putatively regulating bioluminescence production and control, including two luciferase genes corresponding to lateral lanterns green-emitting and head lanterns red-emitting luciferases with 7 exons and 6 introns, and genes potentially involved in luciferin biosynthesis were found, indicating that there are no clear differences about the presence or absence of gene families associated with bioluminescence in Elateroidea.
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Affiliation(s)
- Danilo Trabuco Amaral
- Programa de Pós-Graduação em Biotecnociência, Centro de Ciências Naturais e Humanas. Universidade Federal do ABC (UFABC), Santo André, Brazil
| | - Yasuo Mitani
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo, Japan
| | | | - Ricardo Cerri
- Department of Computational Science, Universidade Federal de São Carlos (UFSCar), São Carlos, Brazil
| | - Yoshihiro Ohmiya
- Biomedical Research Institute, AIST, Ikeda-Osaka, Japan; Osaka Institute of Technology, OIT, Osaka, Japan
| | - Vadim Viviani
- Graduate Program of Evolutive Genetics and Molecular Biology, Federal University of São Carlos (UFSCar), São Carlos, Brazil; Graduate Program of Biotechnology and Environmental Monitoring, Federal University of São Carlos (UFSCar), Sorocaba, Brazil.
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5
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Wang S, Liu X, Liu Z, Wang Y, Guo A, Huang W, Wang Q, Zhang S, Zhu G, Luo X, Zhu XQ, Cai X. The genome of the thin-necked bladder worm Taenia hydatigena reveals evolutionary strategies for helminth survival. Commun Biol 2021; 4:1004. [PMID: 34429506 DOI: 10.1038/s42003-021-02536-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 08/09/2021] [Indexed: 11/08/2022] Open
Abstract
Taenia hydatigena is a widespread gastrointestinal helminth that causes significant health problems in livestock industry. This parasite can survive in a remarkably wide range of intermediate hosts and affects the transmission dynamics of zoonotic parasites. T. hydatigena is therefore of particular interest to researchers interested in studying zoonotic diseases and the evolutionary strategies of parasites. Herein we report a high-quality draft genome for this tapeworm, characterized by some hallmarks (e.g., expanded genome size, wide integrations of viral-like sequences and extensive alternative splicing during development), and specialized adaptations related to its parasitic fitness (e.g., adaptive evolutions for teguments and lipid metabolism). Importantly, in contrast with the evolutionarily close trematodes, which achieve gene diversification associated with immunosuppression by gene family expansions, in T. hydatigena and other cestodes, this is accomplished by alternative splicing and gene loss. This indicates that these two classes have evolved different mechanisms for survival. In addition, molecular targets for diagnosis and intervention were identified to facilitate the development of control interventions. Overall, this work uncovers new strategies by which helminths evolved to interact with their hosts.
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7
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Glazier DS. Genome Size Covaries More Positively with Propagule Size than Adult Size: New Insights into an Old Problem. Biology (Basel) 2021; 10:270. [PMID: 33810583 PMCID: PMC8067107 DOI: 10.3390/biology10040270] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 03/18/2021] [Accepted: 03/23/2021] [Indexed: 12/17/2022]
Abstract
The body size and (or) complexity of organisms is not uniformly related to the amount of genetic material (DNA) contained in each of their cell nuclei ('genome size'). This surprising mismatch between the physical structure of organisms and their underlying genetic information appears to relate to variable accumulation of repetitive DNA sequences, but why this variation has evolved is little understood. Here, I show that genome size correlates more positively with egg size than adult size in crustaceans. I explain this and comparable patterns observed in other kinds of animals and plants as resulting from genome size relating strongly to cell size in most organisms, which should also apply to single-celled eggs and other reproductive propagules with relatively few cells that are pivotal first steps in their lives. However, since body size results from growth in cell size or number or both, it relates to genome size in diverse ways. Relationships between genome size and body size should be especially weak in large organisms whose size relates more to cell multiplication than to cell enlargement, as is generally observed. The ubiquitous single-cell 'bottleneck' of life cycles may affect both genome size and composition, and via both informational (genotypic) and non-informational (nucleotypic) effects, many other properties of multicellular organisms (e.g., rates of growth and metabolism) that have both theoretical and practical significance.
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Amiri A, Bandani AR. Facultative deuterotokous parthenogenesis in Callosobruchus maculatus. ZOOL ANZ 2021. [DOI: 10.1016/j.jcz.2021.01.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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9
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Grzywacz B, Skórka P. Genome size versus geographic range size in birds. PeerJ 2021; 9:e10868. [PMID: 33614292 PMCID: PMC7881720 DOI: 10.7717/peerj.10868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 01/10/2021] [Indexed: 11/20/2022] Open
Abstract
Why do some species occur in small, restricted areas, while others are distributed globally? Environmental heterogeneity increases with area and so does the number of species. Hence, diverse biotic and abiotic conditions across large ranges may lead to specific adaptations that are often linked to a species' genome size and chromosome number. Therefore, a positive association between genome size and geographic range is anticipated. Moreover, high cognitive ability in organisms would be favored by natural selection to cope with the dynamic conditions within large geographic ranges. Here, we tested these hypotheses in birds-the most mobile terrestrial vertebrates-and accounted for the effects of various confounding variables, such as body mass, relative brain mass, and geographic latitude. Using phylogenetic generalized least squares and phylogenetic confirmatory path analysis, we demonstrated that range size is positively associated with bird genome size but probably not with chromosome number. Moreover, relative brain mass had no effect on range size, whereas body mass had a possible weak and negative effect, and range size was larger at higher geographic latitudes. However, our models did not fully explain the overall variation in range size. Hence, natural selection may impose larger genomes in birds with larger geographic ranges, although there may be additional explanations for this phenomenon.
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Affiliation(s)
- Beata Grzywacz
- Institute of Systematics and Evolution of Animals, Polish Academy of Sciences, Kraków, Poland
| | - Piotr Skórka
- Institute of Nature Conservation, Polish Academy of Sciences, Kraków, Poland
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10
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Abstract
Genome size (GS) variation is a fundamental biological characteristic; however, its evolutionary causes and consequences are the topic of ongoing debate. Whether GS is a neutral trait or one subject to selective pressures, and how strong these selective pressures are, may remain open questions. Fundamentally, the genomic sequences responsible for this variation directly impact the potential evolutionary outcomes and, equally, are the targets of different evolutionary pressures. For example, duplications and deletions of genic regions (large or small) can have immediate and drastic phenotypic effects, while an expansion or contraction of non-coding DNA is less likely to cause catastrophic phenotypic effects. However, in the long term, the accumulation or deletion of ncDNA is likely to have larger effects. Modern sequencing technologies are allowing for the dissection of these proximate causes, but a combination of these new technologies with more traditional evolutionary experiments and approaches could revolutionize this debate and potentially resolve many of these arguments. Here, I discuss an ambitious way forward for GS research, putting it in context of historical debates, theories and sometimes contradictory evidence, and highlighting the promise of combining new sequencing technologies and analytical developments with more traditional experimental evolution approaches.
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Affiliation(s)
- Julie Blommaert
- Department of Organismal Biology, Uppsala University, Uppsala, Sweden
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11
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Hjelmen CE, Parrott JJ, Srivastav SP, McGuane AS, Ellis LL, Stewart AD, Johnston JS, Tarone AM. Effect of Phenotype Selection on Genome Size Variation in Two Species of Diptera. Genes (Basel) 2020; 11:genes11020218. [PMID: 32093067 PMCID: PMC7074110 DOI: 10.3390/genes11020218] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 02/11/2020] [Accepted: 02/15/2020] [Indexed: 11/16/2022] Open
Abstract
Genome size varies widely across organisms yet has not been found to be related to organismal complexity in eukaryotes. While there is no evidence for a relationship with complexity, there is evidence to suggest that other phenotypic characteristics, such as nucleus size and cell-cycle time, are associated with genome size, body size, and development rate. However, what is unknown is how the selection for divergent phenotypic traits may indirectly affect genome size. Drosophila melanogaster were selected for small and large body size for up to 220 generations, while Cochliomyia macellaria were selected for 32 generations for fast and slow development. Size in D. melanogaster significantly changed in terms of both cell-count and genome size in isolines, but only the cell-count changed in lines which were maintained at larger effective population sizes. Larger genome sizes only occurred in a subset of D. melanogaster isolines originated from flies selected for their large body size. Selection for development time did not change average genome size yet decreased the within-population variation in genome size with increasing generations of selection. This decrease in variation and convergence on a similar mean genome size was not in correspondence with phenotypic variation and suggests stabilizing selection on genome size in laboratory conditions.
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Affiliation(s)
- Carl E. Hjelmen
- Department of Entomology, Texas A&M University, College Station, TX 77843, USA; (J.J.P.); (S.P.S.); (A.S.M.); (L.L.E.); (J.S.J.); (A.M.T.)
- Department of Biology, Texas A&M University, College Station, TX 77843, USA
- Correspondence: or
| | - Jonathan J. Parrott
- Department of Entomology, Texas A&M University, College Station, TX 77843, USA; (J.J.P.); (S.P.S.); (A.S.M.); (L.L.E.); (J.S.J.); (A.M.T.)
- School of Mathematical and Natural Sciences, Arizona State University, Glendale, AZ 85306, USA
| | - Satyam P. Srivastav
- Department of Entomology, Texas A&M University, College Station, TX 77843, USA; (J.J.P.); (S.P.S.); (A.S.M.); (L.L.E.); (J.S.J.); (A.M.T.)
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Alexander S. McGuane
- Department of Entomology, Texas A&M University, College Station, TX 77843, USA; (J.J.P.); (S.P.S.); (A.S.M.); (L.L.E.); (J.S.J.); (A.M.T.)
- Harris County Institute of Forensic Sciences, 1861 Old Spanish Trail, Houston, TX 77054, USA
| | - Lisa L. Ellis
- Department of Entomology, Texas A&M University, College Station, TX 77843, USA; (J.J.P.); (S.P.S.); (A.S.M.); (L.L.E.); (J.S.J.); (A.M.T.)
- Department of Biology, Houston Baptist University, Houston, TX 77074, USA
| | | | - J. Spencer Johnston
- Department of Entomology, Texas A&M University, College Station, TX 77843, USA; (J.J.P.); (S.P.S.); (A.S.M.); (L.L.E.); (J.S.J.); (A.M.T.)
| | - Aaron M. Tarone
- Department of Entomology, Texas A&M University, College Station, TX 77843, USA; (J.J.P.); (S.P.S.); (A.S.M.); (L.L.E.); (J.S.J.); (A.M.T.)
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12
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Hjelmen CE, Blackmon H, Holmes VR, Burrus CG, Johnston JS. Genome Size Evolution Differs Between Drosophila Subgenera with Striking Differences in Male and Female Genome Size in Sophophora. G3 (Bethesda) 2019; 9:3167-3179. [PMID: 31358560 PMCID: PMC6778784 DOI: 10.1534/g3.119.400560] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 07/26/2019] [Indexed: 11/29/2022]
Abstract
Genome size varies across the tree of life, with no clear correlation to organismal complexity or coding sequence, but with differences in non-coding regions. Phylogenetic methods have recently been incorporated to further disentangle this enigma, yet most of these studies have focused on widely diverged species. Few have compared patterns of genome size change in closely related species with known structural differences in the genome. As a consequence, the relationship between genome size and differences in chromosome number or inter-sexual differences attributed to XY systems are largely unstudied. We hypothesize that structural differences associated with chromosome number and X-Y chromosome differentiation, should result in differing rates and patterns of genome size change. In this study, we utilize the subgenera within the Drosophila to ask if patterns and rates of genome size change differ between closely related species with differences in chromosome numbers and states of the XY system. Genome sizes for males and females of 152 species are used to answer these questions (with 92 newly added or updated estimates). While we find no relationship between chromosome number and genome size or chromosome number and inter-sexual differences in genome size, we find evidence for differing patterns of genome size change between the subgenera, and increasing rates of change throughout time. Estimated shifts in rates of change in sex differences in genome size occur more often in Sophophora and correspond to known neo-sex events.
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Affiliation(s)
- Carl E Hjelmen
- Department of Biology and
- Department of Entomology, Texas A&M University, College Station, TX 77843
| | - Heath Blackmon
- Department of Entomology, Texas A&M University, College Station, TX 77843
| | | | - Crystal G Burrus
- Department of Entomology, Texas A&M University, College Station, TX 77843
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13
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Hjelmen CE, Garrett MA, Holmes VR, Mynes M, Piron E, Johnston JS. Genome Size Evolution within and between the Sexes. J Hered 2019; 110:219-228. [PMID: 30476187 DOI: 10.1093/jhered/esy063] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 11/21/2018] [Indexed: 02/02/2023] Open
Abstract
Genome sizes are known to vary between closely related species, but the patterns behind this variation have yet to be fully understood. Although this variation has been evaluated between species and within sexes, unknown is the extent to which this variation is driven by differentiation in sex chromosomes. To address this longstanding question, we examine the mode and tempo of genome size evolution for a total of 87 species of Drosophilidae, estimating and updating male genome size values for 44 of these species. We compare the evolution of genome size within each sex to the evolution of the differences between the sexes. Utilizing comparative phylogenetic methods, we find that male and female genome size evolution is largely a neutral process, reflective of phylogenetic relatedness between species, which supports the newly proposed accordion model for genome size change. When similarly analyzed, the difference between the sexes due to heteromorphic sex chromosomes is a dynamic process; the male-female genome size difference increases with time with or without known neo-Y events or complete loss of the Y. Observed instances of rapid change match theoretical expectations and known neo-Y and Y loss events in individual species.
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Affiliation(s)
- Carl E Hjelmen
- Department of Entomology, Texas A&M University, College Station, TX
| | - Margaret A Garrett
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX
| | - V Renee Holmes
- Department of Entomology, Texas A&M University, College Station, TX
| | - Melissa Mynes
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX
| | - Elizabeth Piron
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX
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14
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Bhattachan P, Dong B. Multivariate analysis of genomic variables, effective population size, and mutation rate. BMC Res Notes 2019; 12:60. [PMID: 30683153 PMCID: PMC6347809 DOI: 10.1186/s13104-019-4097-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 01/19/2019] [Indexed: 11/26/2022] Open
Abstract
Objective The relationship between genomic variables (genome size, gene number, intron size, and intron number) and evolutionary forces has two implications. First, they help to unravel the mechanism underlying genome evolution. Second, they provide a solution to the debate over discrepancy between genome size variation and organismal complexity. Previously, a clear correlation between genomic variables and effective population size and mutation rate (Neu) led to an important hypothesis to consider random genetic drift as a major evolutionary force during evolution of genome size and complexity. But recent reports also support natural selection as the leading evolutionary force. As such, the debate remains unresolved. Results Here, we used a multivariate method to explore the relationship between genomic variables and Neu in order to understand the evolution of genome. Previously reported patterns between genomic variables and Neu were not observed in our multivariate study. We found only one association between intron number and Neu, but no relationships were observed between genome size, intron size, gene number, and Neu, suggesting that Neu of the organisms solely does not influence genome evolution. We, therefore, concluded that Neu influences intron evolution, while it may not be the only force that provides mechanistic insights into genome evolution and complexity. Electronic supplementary material The online version of this article (10.1186/s13104-019-4097-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Punit Bhattachan
- Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, No. 5 Yushan Road, Qingdao, 266003, China
| | - Bo Dong
- Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, No. 5 Yushan Road, Qingdao, 266003, China. .,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China. .,Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China.
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15
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Abstract
With care, it is possible using flow cytometry to create a precise and accurate estimate of the genome size of an insect that is useful for genomics, genetics, molecular/cell biology, or systematics. Genome size estimation is a useful first step in a complete genome sequencing project. The number of sequencing reads required to produce a given level of coverage depends directly upon the 1C amount of DNA per cell, while an even more critical need is an accurate 1C genome size estimate to compare against the final assembly. Here we present a detailed protocol to estimate genome size using flow cytometry. Published genome size estimates should be submitted to genomesize.com so that they are available to all.
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Affiliation(s)
- J Spencer Johnston
- Department of Entomology, Texas A&M University, College Station, TX, USA
| | - Angelina Bernardini
- Interdisciplinary Program in Genetics, Texas A&M University, College Station, TX, USA
| | - Carl E Hjelmen
- Department of Entomology, Texas A&M University, College Station, TX, USA.
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Grover CE, Arick MA, Conover JL, Thrash A, Hu G, Sanders WS, Hsu CY, Naqvi RZ, Farooq M, Li X, Gong L, Mudge J, Ramaraj T, Udall JA, Peterson DG, Wendel JF. Comparative Genomics of an Unusual Biogeographic Disjunction in the Cotton Tribe (Gossypieae) Yields Insights into Genome Downsizing. Genome Biol Evol 2017; 9:3328-3344. [PMID: 29194487 PMCID: PMC5737505 DOI: 10.1093/gbe/evx248] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/27/2017] [Indexed: 12/19/2022] Open
Abstract
Long-distance insular dispersal is associated with divergence and speciation because of founder effects and strong genetic drift. The cotton tribe (Gossypieae) has experienced multiple transoceanic dispersals, generating an aggregate geographic range that encompasses much of the tropics and subtropics worldwide. Two genera in the Gossypieae, Kokia and Gossypioides, exhibit a remarkable geographic disjunction, being restricted to the Hawaiian Islands and Madagascar/East Africa, respectively. We assembled and use de novo genome sequences to address questions regarding the divergence of these two genera from each other and from their sister-group, Gossypium. In addition, we explore processes underlying the genome downsizing that characterizes Kokia and Gossypioides relative to other genera in the tribe. Using 13,000 gene orthologs and synonymous substitution rates, we show that the two disjuncts last shared a common ancestor ∼5 Ma, or half as long ago as their divergence from Gossypium. We report relative stasis in the transposable element fraction. In comparison to Gossypium, there is loss of ∼30% of the gene content in the two disjunct genera and a history of genome-wide accumulation of deletions. In both genera, there is a genome-wide bias toward deletions over insertions, and the number of gene losses exceeds the number of gains by ∼2- to 4-fold. The genomic analyses presented here elucidate genomic consequences of the demographic and biogeographic history of these closest relatives of Gossypium, and enhance their value as phylogenetic outgroups.
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Affiliation(s)
- Corrinne E Grover
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA
| | - Mark A Arick
- Institute for Genomics, Biocomputing, and Biotechnology, Mississippi State University, Mississippi State, MS
| | - Justin L Conover
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA
| | - Adam Thrash
- Institute for Genomics, Biocomputing, and Biotechnology, Mississippi State University, Mississippi State, MS
| | - Guanjing Hu
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA
| | - William S Sanders
- Institute for Genomics, Biocomputing, and Biotechnology, Mississippi State University, Mississippi State, MS
- Department of Computer Science & Engineering, Mississippi State University, Mississippi State, MS
- The Jackson Laboratory, Connecticut, Farmington, CT
| | - Chuan-Yu Hsu
- Institute for Genomics, Biocomputing, and Biotechnology, Mississippi State University, Mississippi State, MS
| | - Rubab Zahra Naqvi
- National Institute for Biotechnology and Genetic Engineering, Faisalabad, Punjab, Pakistan
| | - Muhammad Farooq
- National Institute for Biotechnology and Genetic Engineering, Faisalabad, Punjab, Pakistan
| | - Xiaochong Li
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, P.R. China
| | - Lei Gong
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, P.R. China
| | - Joann Mudge
- National Center for Genome Resources, Santa Fe, New Mexico
| | | | - Joshua A Udall
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo
| | - Daniel G Peterson
- Institute for Genomics, Biocomputing, and Biotechnology, Mississippi State University, Mississippi State, MS
| | - Jonathan F Wendel
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA
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17
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Talla V, Suh A, Kalsoom F, Dincă V, Vila R, Friberg M, Wiklund C, Backström N. Rapid Increase in Genome Size as a Consequence of Transposable Element Hyperactivity in Wood-White (Leptidea) Butterflies. Genome Biol Evol 2017; 9:2491-2505. [PMID: 28981642 PMCID: PMC5737376 DOI: 10.1093/gbe/evx163] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/22/2016] [Indexed: 12/14/2022] Open
Abstract
Characterizing and quantifying genome size variation among organisms and understanding if genome size evolves as a consequence of adaptive or stochastic processes have been long-standing goals in evolutionary biology. Here, we investigate genome size variation and association with transposable elements (TEs) across lepidopteran lineages using a novel genome assembly of the common wood-white (Leptidea sinapis) and population re-sequencing data from both L. sinapis and the closely related L. reali and L. juvernica together with 12 previously available lepidopteran genome assemblies. A phylogenetic analysis confirms established relationships among species, but identifies previously unknown intraspecific structure within Leptidea lineages. The genome assembly of L. sinapis is one of the largest of any lepidopteran taxon so far (643 Mb) and genome size is correlated with abundance of TEs, both in Lepidoptera in general and within Leptidea where L. juvernica from Kazakhstan has considerably larger genome size than any other Leptidea population. Specific TE subclasses have been active in different Lepidoptera lineages with a pronounced expansion of predominantly LINEs, DNA elements, and unclassified TEs in the Leptidea lineage after the split from other Pieridae. The rate of genome expansion in Leptidea in general has been in the range of four Mb/Million year (My), with an increase in a particular L. juvernica population to 72 Mb/My. The considerable differences in accumulation rates of specific TE classes in different lineages indicate that TE activity plays a major role in genome size evolution in butterflies and moths.
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Affiliation(s)
- Venkat Talla
- Department of Evolutionary Biology, Evolutionary Biology Centre (EBC), Uppsala University, Sweden
| | - Alexander Suh
- Department of Evolutionary Biology, Evolutionary Biology Centre (EBC), Uppsala University, Sweden
| | - Faheema Kalsoom
- Department of Evolutionary Biology, Evolutionary Biology Centre (EBC), Uppsala University, Sweden
| | - Vlad Dincă
- Animal Biodiversity and Evolution Program, Institut de Biologia Evolutiva (CSIC-UPF), Barcelona, Spain
| | - Roger Vila
- Animal Biodiversity and Evolution Program, Institut de Biologia Evolutiva (CSIC-UPF), Barcelona, Spain
| | - Magne Friberg
- Department of Plant Ecology and Evolution, Evolutionary Biology Centre (EBC), Uppsala University, Sweden
| | - Christer Wiklund
- Division of Ecology, Department of Zoology, Stockholm University, Sweden
| | - Niclas Backström
- Department of Evolutionary Biology, Evolutionary Biology Centre (EBC), Uppsala University, Sweden
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18
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Lower SS, Johnston JS, Stanger-Hall KF, Hjelmen CE, Hanrahan SJ, Korunes K, Hall D. Genome Size in North American Fireflies: Substantial Variation Likely Driven by Neutral Processes. Genome Biol Evol 2017; 9:1499-1512. [PMID: 28541478 PMCID: PMC5499882 DOI: 10.1093/gbe/evx097] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/24/2017] [Indexed: 12/11/2022] Open
Abstract
Eukaryotic genomes show tremendous size variation across taxa. Proximate explanations for genome size variation include differences in ploidy and amounts of noncoding DNA, especially repetitive DNA. Ultimate explanations include selection on physiological correlates of genome size such as cell size, which in turn influence body size, resulting in the often-observed correlation between body size and genome size. In this study, we examined body size and repetitive DNA elements in relationship to the evolution of genome size in North American representatives of a single beetle family, the Lampyridae (fireflies). The 23 species considered represent an excellent study system because of the greater than 5-fold range of genome sizes, documented here using flow cytometry, and the 3-fold range in body size, measured using pronotum width. We also identified common genomic repetitive elements using low-coverage sequencing. We found a positive relationship between genome size and repetitive DNA, particularly retrotransposons. Both genome size and these elements were evolving as expected given phylogenetic relatedness. We also tested whether genome size varied with body size and found no relationship. Together, our results suggest that genome size is evolving neutrally in fireflies.
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Affiliation(s)
| | | | | | | | | | | | - David Hall
- Department of Genetics, University of Georgia
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19
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Dougherty LR, van Lieshout E, McNamara KB, Moschilla JA, Arnqvist G, Simmons LW. Sexual conflict and correlated evolution between male persistence and female resistance traits in the seed beetle Callosobruchus maculatus. Proc Biol Sci 2017; 284:20170132. [PMID: 28539510 PMCID: PMC5454259 DOI: 10.1098/rspb.2017.0132] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Accepted: 04/25/2017] [Indexed: 11/12/2022] Open
Abstract
Traumatic mating (or copulatory wounding) is an extreme form of sexual conflict whereby male genitalia physically harm females during mating. In such species females are expected to evolve counter-adaptations to reduce male-induced harm. Importantly, female counter-adaptations may include both genital and non-genital traits. In this study, we examine evolutionary associations between harmful male genital morphology and female reproductive tract morphology and immune function across 13 populations of the seed beetle Callosobruchus maculatus We detected positive correlated evolution between the injuriousness of male genitalia and putative female resistance adaptations across populations. Moreover, we found evidence for a negative relationship between female immunity and population productivity, which suggests that investment in female resistance may be costly due to the resource trade-offs that are predicted between immunity and reproduction. Finally, the degree of female tract scarring (harm to females) was greater in those populations with both longer aedeagal spines and a thinner female tract lining. Our results are thus consistent with a sexual arms race, which is only apparent when both male and female traits are taken into account. Importantly, our study provides rare evidence for sexually antagonistic coevolution of male and female traits at the within-species level.
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Affiliation(s)
- Liam R Dougherty
- School of Biological Sciences, Centre for Evolutionary Biology, University of Western Australia, Crawley, WA 6009, Australia
| | - Emile van Lieshout
- School of Biological Sciences, Centre for Evolutionary Biology, University of Western Australia, Crawley, WA 6009, Australia
| | - Kathryn B McNamara
- School of Biological Sciences, Centre for Evolutionary Biology, University of Western Australia, Crawley, WA 6009, Australia
| | - Joe A Moschilla
- School of Biological Sciences, Centre for Evolutionary Biology, University of Western Australia, Crawley, WA 6009, Australia
| | - Göran Arnqvist
- Animal Ecology, Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, Uppsala 75236, Sweden
| | - Leigh W Simmons
- School of Biological Sciences, Centre for Evolutionary Biology, University of Western Australia, Crawley, WA 6009, Australia
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Lefébure T, Morvan C, Malard F, François C, Konecny-Dupré L, Guéguen L, Weiss-Gayet M, Seguin-Orlando A, Ermini L, Sarkissian CD, Charrier NP, Eme D, Mermillod-Blondin F, Duret L, Vieira C, Orlando L, Douady CJ. Less effective selection leads to larger genomes. Genome Res 2017; 27:1016-1028. [PMID: 28424354 PMCID: PMC5453316 DOI: 10.1101/gr.212589.116] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 03/30/2017] [Indexed: 12/18/2022]
Abstract
The evolutionary origin of the striking genome size variations found in eukaryotes remains enigmatic. The effective size of populations, by controlling selection efficacy, is expected to be a key parameter underlying genome size evolution. However, this hypothesis has proved difficult to investigate using empirical data sets. Here, we tested this hypothesis using 22 de novo transcriptomes and low-coverage genomes of asellid isopods, which represent 11 independent habitat shifts from surface water to resource-poor groundwater. We show that these habitat shifts are associated with higher transcriptome-wide [Formula: see text] After ruling out the role of positive selection and pseudogenization, we show that these transcriptome-wide [Formula: see text] increases are the consequence of a reduction in selection efficacy imposed by the smaller effective population size of subterranean species. This reduction is paralleled by an important increase in genome size (25% increase on average), an increase also confirmed in subterranean decapods and mollusks. We also control for an adaptive impact of genome size on life history traits but find no correlation between body size, or growth rate, and genome size. We show instead that the independent increases in genome size measured in subterranean isopods are the direct consequence of increasing invasion rates by repeat elements, which are less efficiently purged out by purifying selection. Contrary to selection efficacy, polymorphism is not correlated to genome size. We propose that recent demographic fluctuations and the difficulty of observing polymorphism variation in polymorphism-poor species can obfuscate the link between effective population size and genome size when polymorphism data are used alone.
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Affiliation(s)
- Tristan Lefébure
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5023, ENTPE, Laboratoire d'Ecologie des Hydrosystèmes Naturels et Anthropisés, F-69622 Villeurbanne, France
| | - Claire Morvan
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5023, ENTPE, Laboratoire d'Ecologie des Hydrosystèmes Naturels et Anthropisés, F-69622 Villeurbanne, France
| | - Florian Malard
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5023, ENTPE, Laboratoire d'Ecologie des Hydrosystèmes Naturels et Anthropisés, F-69622 Villeurbanne, France
| | - Clémentine François
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5023, ENTPE, Laboratoire d'Ecologie des Hydrosystèmes Naturels et Anthropisés, F-69622 Villeurbanne, France
| | - Lara Konecny-Dupré
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5023, ENTPE, Laboratoire d'Ecologie des Hydrosystèmes Naturels et Anthropisés, F-69622 Villeurbanne, France
| | - Laurent Guéguen
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5558, Laboratoire de Biométrie et Biologie Evolutive, F-69622 Villeurbanne, France
| | - Michèle Weiss-Gayet
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5310, INSERM, Institut NeuroMyoGène, F-69622 Villeurbanne, France
| | - Andaine Seguin-Orlando
- Center for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350K Copenhagen, Denmark
| | - Luca Ermini
- Center for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350K Copenhagen, Denmark
| | - Clio Der Sarkissian
- Center for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350K Copenhagen, Denmark
| | - N Pierre Charrier
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5023, ENTPE, Laboratoire d'Ecologie des Hydrosystèmes Naturels et Anthropisés, F-69622 Villeurbanne, France
| | - David Eme
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5023, ENTPE, Laboratoire d'Ecologie des Hydrosystèmes Naturels et Anthropisés, F-69622 Villeurbanne, France
| | - Florian Mermillod-Blondin
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5023, ENTPE, Laboratoire d'Ecologie des Hydrosystèmes Naturels et Anthropisés, F-69622 Villeurbanne, France
| | - Laurent Duret
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5558, Laboratoire de Biométrie et Biologie Evolutive, F-69622 Villeurbanne, France
| | - Cristina Vieira
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5558, Laboratoire de Biométrie et Biologie Evolutive, F-69622 Villeurbanne, France.,Institut Universitaire de France, F-75005 Paris, France
| | - Ludovic Orlando
- Center for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350K Copenhagen, Denmark.,Université de Toulouse, University Paul Sabatier (UPS), CNRS UMR 5288, Laboratoire AMIS, F-31073 Toulouse, France
| | - Christophe Jean Douady
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5023, ENTPE, Laboratoire d'Ecologie des Hydrosystèmes Naturels et Anthropisés, F-69622 Villeurbanne, France.,Institut Universitaire de France, F-75005 Paris, France
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22
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Sayadi A, Immonen E, Bayram H, Arnqvist G. The De Novo Transcriptome and Its Functional Annotation in the Seed Beetle Callosobruchus maculatus. PLoS One 2016; 11:e0158565. [PMID: 27442123 DOI: 10.1371/journal.pone.0158565] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 06/19/2016] [Indexed: 12/25/2022] Open
Abstract
Despite their unparalleled biodiversity, the genomic resources available for beetles (Coleoptera) remain relatively scarce. We present an integrative and high quality annotated transcriptome of the beetle Callosobruchus maculatus, an important and cosmopolitan agricultural pest as well as an emerging model species in ecology and evolutionary biology. Using Illumina sequencing technology, we sequenced 492 million read pairs generated from 51 samples of different developmental stages (larvae, pupae and adults) of C. maculatus. Reads were de novo assembled using the Trinity software, into a single combined assembly as well as into three separate assemblies based on data from the different developmental stages. The combined assembly generated 218,192 transcripts and 145,883 putative genes. Putative genes were annotated with the Blast2GO software and the Trinotate pipeline. In total, 33,216 putative genes were successfully annotated using Blastx against the Nr (non-redundant) database and 13,382 were assigned to 34,100 Gene Ontology (GO) terms. We classified 5,475 putative genes into Clusters of Orthologous Groups (COG) and 116 metabolic pathways maps were predicted based on the annotation. Our analyses suggested that the transcriptional specificity increases with ontogeny. For example, out of 33,216 annotated putative genes, 51 were only expressed in larvae, 63 only in pupae and 171 only in adults. Our study illustrates the importance of including samples from several developmental stages when the aim is to provide an integrative and high quality annotated transcriptome. Our results will represent an invaluable resource for those working with the ecology, evolution and pest control of C. maculatus, as well for comparative studies of the transcriptomics and genomics of beetles more generally.
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