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Flynn JM, Yamashita YM. The implications of satellite DNA instability on cellular function and evolution. Semin Cell Dev Biol 2024; 156:152-159. [PMID: 37852904 DOI: 10.1016/j.semcdb.2023.10.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 09/21/2023] [Accepted: 10/11/2023] [Indexed: 10/20/2023]
Abstract
Abundant tandemly repeated satellite DNA is present in most eukaryotic genomes. Previous limitations including a pervasive view that it was uninteresting junk DNA, combined with challenges in studying it, are starting to dissolve - and recent studies have found important functions for satellite DNAs. The observed rapid evolution and implied instability of satellite DNA now has important significance for their functions and maintenance within the genome. In this review, we discuss the processes that lead to satellite DNA copy number instability, and the importance of mechanisms to manage the potential negative effects of instability. Satellite DNA is vulnerable to challenges during replication and repair, since it forms difficult-to-process secondary structures and its homology within tandem arrays can result in various types of recombination. Satellite DNA instability may be managed by DNA or chromatin-binding proteins ensuring proper nuclear localization and repair, or by proteins that process aberrant structures that satellite DNAs tend to form. We also discuss the pattern of satellite DNA mutations from recent mutation accumulation (MA) studies that have tracked changes in satellite DNA for up to 1000 generations with minimal selection. Finally, we highlight examples of satellite evolution from studies that have characterized satellites across millions of years of Drosophila fruit fly evolution, and discuss possible ways that selection might act on the satellite DNA composition.
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Affiliation(s)
- Jullien M Flynn
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA; Howard Hughes Medical Institute, Cambridge, MA, USA.
| | - Yukiko M Yamashita
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA; Howard Hughes Medical Institute, Cambridge, MA, USA; Massachusetts Institute of Technology, Cambridge, MA, USA.
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2
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Fourreau CJL, Kise H, Santander MD, Pirro S, Maronna MM, Poliseno A, Santos ME, Reimer JD. Genome sizes and repeatome evolution in zoantharians (Cnidaria: Hexacorallia: Zoantharia). PeerJ 2023; 11:e16188. [PMID: 37868064 PMCID: PMC10586311 DOI: 10.7717/peerj.16188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 09/06/2023] [Indexed: 10/24/2023] Open
Abstract
Across eukaryotes, large variations of genome sizes have been observed even between closely related species. Transposable elements as part of the repeated DNA have been proposed and confirmed as one of the most important contributors to genome size variation. However, the evolutionary implications of genome size variation and transposable element dynamics are not well understood. Together with phenotypic traits, they are commonly referred to as the "C-value enigma". The order Zoantharia are benthic cnidarians found from intertidal zones to the deep sea, and some species are particularly abundant in coral reefs. Despite their high ecological relevance, zoantharians have yet to be largely studied from the genomic point of view. This study aims at investigating the role of the repeatome (total content of repeated elements) in genome size variations across the order Zoantharia. To this end, whole-genomes of 32 zoantharian species representing five families were sequenced. Genome sizes were estimated and the abundances of different repeat classes were assessed. In addition, the repeat overlap between species was assessed by a sequence clustering method. The genome sizes in the dataset varied up to 2.4 fold magnitude. Significant correlations between genome size, repeated DNA content and transposable elements, respectively (Pearson's correlation test R2 = 0.47, p = 0.0016; R2 = 0.22, p = 0.05) were found, suggesting their involvement in the dynamics of genome expansion and reduction. In all species, long interspersed nuclear elements and DNA transposons were the most abundant identified elements. These transposable elements also appeared to have had a recent expansion event. This was in contrast to the comparative clustering analysis which revealed species-specific patterns of satellite elements' amplification. In summary, the genome sizes of zoantharians likely result from the complex dynamics of repeated elements. Finally, the majority of repeated elements (up to 70%) could not be annotated to a known repeat class, highlighting the need to further investigate non-model cnidarian genomes. More research is needed to understand how repeated DNA dynamics relate to zoantharian evolution and their biology.
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Affiliation(s)
- Chloé Julie Loïs Fourreau
- Molecular Invertebrate Systematics and Ecology (MISE) Lab, Graduate School of Engineering and Science, University of the Ryukyus, Nishihara, Okinawa, Japan
| | - Hiroki Kise
- Molecular Invertebrate Systematics and Ecology (MISE) Lab, Graduate School of Engineering and Science, University of the Ryukyus, Nishihara, Okinawa, Japan
- AIST Tsukuba Central, Geological Survey of Japan, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki, Japan
| | - Mylena Daiana Santander
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Stacy Pirro
- Iridian Genomes, Bethesda, United States of America
| | - Maximiliano M. Maronna
- Molecular Invertebrate Systematics and Ecology (MISE) Lab, Graduate School of Engineering and Science, University of the Ryukyus, Nishihara, Okinawa, Japan
- Faculdade de Ciências, Universidade Estadual Paulista (UNESP), Bauru, Brazil
| | - Angelo Poliseno
- Molecular Invertebrate Systematics and Ecology (MISE) Lab, Graduate School of Engineering and Science, University of the Ryukyus, Nishihara, Okinawa, Japan
| | - Maria E.A. Santos
- Molecular Invertebrate Systematics and Ecology (MISE) Lab, Graduate School of Engineering and Science, University of the Ryukyus, Nishihara, Okinawa, Japan
- Okinawa Institute of Science and Technology, Onna, Okinawa, Japan
| | - James Davis Reimer
- Molecular Invertebrate Systematics and Ecology (MISE) Lab, Graduate School of Engineering and Science, University of the Ryukyus, Nishihara, Okinawa, Japan
- Tropical Biosphere Research Center, University of the Ryukyus, Nishihara, Okinawa, United States of America
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3
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Leung W, Torosin N, Cao W, Reed LK, Arrigo C, Elgin SCR, Ellison CE. Long-read genome assemblies for the study of chromosome expansion: Drosophila kikkawai, Drosophila takahashii, Drosophila bipectinata, and Drosophila ananassae. G3 (BETHESDA, MD.) 2023; 13:jkad191. [PMID: 37611223 PMCID: PMC10542312 DOI: 10.1093/g3journal/jkad191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 08/01/2023] [Accepted: 08/04/2023] [Indexed: 08/25/2023]
Abstract
Flow cytometry estimates of genome sizes among species of Drosophila show a 3-fold variation, ranging from ∼127 Mb in Drosophila mercatorum to ∼400 Mb in Drosophila cyrtoloma. However, the assembled portion of the Muller F element (orthologous to the fourth chromosome in Drosophila melanogaster) shows a nearly 14-fold variation in size, ranging from ∼1.3 Mb to >18 Mb. Here, we present chromosome-level long-read genome assemblies for 4 Drosophila species with expanded F elements ranging in size from 2.3 to 20.5 Mb. Each Muller element is present as a single scaffold in each assembly. These assemblies will enable new insights into the evolutionary causes and consequences of chromosome size expansion.
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Affiliation(s)
- Wilson Leung
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Nicole Torosin
- Department of Genetics and Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ 08854, USA
| | - Weihuan Cao
- Department of Genetics and Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ 08854, USA
| | - Laura K Reed
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL 35487, USA
| | - Cindy Arrigo
- Department of Biology, New Jersey City University, Jersey City, NJ 07305, USA
| | - Sarah C R Elgin
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Christopher E Ellison
- Department of Genetics and Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ 08854, USA
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4
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Leung W, Torosin N, Cao W, Reed LK, Arrigo C, Elgin SCR, Ellison CE. Long-read genome assemblies for the study of chromosome expansion: Drosophila kikkawai , Drosophila takahashii , Drosophila bipectinata , and Drosophila ananassae. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.22.541758. [PMID: 37292993 PMCID: PMC10245892 DOI: 10.1101/2023.05.22.541758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Flow cytometry estimates of genome sizes among species of Drosophila show a 3-fold variation, ranging from ∼127 Mb in Drosophila mercatorum to ∼400 Mb in Drosophila cyrtoloma . However, the assembled portion of the Muller F Element (orthologous to the fourth chromosome in Drosophila melanogaster ) shows a nearly 14-fold variation in size, ranging from ∼1.3 Mb to > 18 Mb. Here, we present chromosome-level long read genome assemblies for four Drosophila species with expanded F Elements ranging in size from 2.3 Mb to 20.5 Mb. Each Muller Element is present as a single scaffold in each assembly. These assemblies will enable new insights into the evolutionary causes and consequences of chromosome size expansion.
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Affiliation(s)
- Wilson Leung
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Nicole Torosin
- Department of Genetics and Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ 08854, USA
| | - Weihuan Cao
- Department of Genetics and Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ 08854, USA
| | - Laura K Reed
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, Alabama, 35487, USA
| | - Cindy Arrigo
- Department of Biology, New Jersey City University, Jersey City, NJ 07305, USA
| | - Sarah C R Elgin
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Christopher E Ellison
- Department of Genetics and Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ 08854, USA
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Hutang GR, Tong Y, Zhu XG, Gao LZ. Genome size variation and polyploidy prevalence in the genus Eragrostis are associated with the global dispersal in arid area. FRONTIERS IN PLANT SCIENCE 2023; 14:1066925. [PMID: 36993864 PMCID: PMC10040770 DOI: 10.3389/fpls.2023.1066925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 02/28/2023] [Indexed: 06/19/2023]
Abstract
BACKGROUND Biologists have long debated the drivers of the genome size evolution and variation ever since Darwin. Assumptions for the adaptive or maladaptive consequences of the associations between genome sizes and environmental factors have been proposed, but the significance of these hypotheses remains controversial. Eragrostis is a large genus in the grass family and is often used as crop or forage during the dry seasons. The wide range and complex ploidy levels make Eragrostis an excellent model for investigating how the genome size variation and evolution is associated with environmental factors and how these changes can ben interpreted. METHODS We reconstructed the Eragrostis phylogeny and estimated genome sizes through flow cytometric analyses. Phylogenetic comparative analyses were performed to explore how genome size variation and evolution is related to their climatic niches and geographical ranges. The genome size evolution and environmental factors were examined using different models to study the phylogenetic signal, mode and tempo throughout evolutionary history. RESULTS Our results support the monophyly of Eragrostis. The genome sizes in Eragrostis ranged from ~0.66 pg to ~3.80 pg. We found that a moderate phylogenetic conservatism existed in terms of the genome sizes but was absent from environmental factors. In addition, phylogeny-based associations revealed close correlations between genome sizes and precipitation-related variables, indicating that the genome size variation mainly caused by polyploidization may have evolved as an adaptation to various environments in the genus Eragrostis. CONCLUSION This is the first study to take a global perspective on the genome size variation and evolution in the genus Eragrostis. Our results suggest that the adaptation and conservatism are manifested in the genome size variation, allowing the arid species of Eragrostis to spread the xeric area throughout the world.
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Affiliation(s)
- Ge-Ran Hutang
- Germplasm Bank of Wild Species in Southwestern China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yan Tong
- Germplasm Bank of Wild Species in Southwestern China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Xun-Ge Zhu
- Germplasm Bank of Wild Species in Southwestern China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Li-Zhi Gao
- Germplasm Bank of Wild Species in Southwestern China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
- Engineering Research Center for Selecting and Breeding New Tropical Crop Varieties, Ministry of Education, College of Tropical Crops, Hainan University, Haikou, China
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Genome Survey Sequencing of the Mole Cricket Gryllotalpa orientalis. Genes (Basel) 2023; 14:genes14020255. [PMID: 36833184 PMCID: PMC9957284 DOI: 10.3390/genes14020255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 01/05/2023] [Accepted: 01/13/2023] [Indexed: 01/20/2023] Open
Abstract
The mole cricket Gryllotalpa orientalis is an evolutionarily, medicinal, and agriculturally significant insect that inhabits underground environments and is distributed globally. This study measured genome size by flow cytometry and k-mer based on low-coverage sequencing, and nuclear repetitive elements were also identified. The haploid genome size estimate is 3.14 Gb by flow cytometry, 3.17 Gb, and 3.77 Gb-based two k-mer methods, respectively, which is well within the range previously reported for other species of the suborder Ensifera. 56% of repetitive elements were found in G. orientalis, similar to 56.83% in Locusta migratoria. However, the great size of repetitive sequences could not be annotated to specific repeat element families. For the repetitive elements that were annotated, Class I-LINE retrotransposon elements were the most common families and more abundant than satellite and Class I-LTR. These results based on the newly developed genome survey could be used in the taxonomic study and whole genome sequencing to improve the understanding of the biology of G. orientalis.
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Hawlitschek O, Sadílek D, Dey LS, Buchholz K, Noori S, Baez IL, Wehrt T, Brozio J, Trávníček P, Seidel M, Husemann M. New estimates of genome size in Orthoptera and their evolutionary implications. PLoS One 2023; 18:e0275551. [PMID: 36920952 PMCID: PMC10016648 DOI: 10.1371/journal.pone.0275551] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 02/24/2023] [Indexed: 03/16/2023] Open
Abstract
Animal genomes vary widely in size, and much of their architecture and content remains poorly understood. Even among related groups, such as orders of insects, genomes may vary in size by orders of magnitude-for reasons unknown. The largest known insect genomes were repeatedly found in Orthoptera, e.g., Podisma pedestris (1C = 16.93 pg), Stethophyma grossum (1C = 18.48 pg) and Bryodemella holdereri (1C = 18.64 pg). While all these species belong to the suborder of Caelifera, the ensiferan Deracantha onos (1C = 19.60 pg) was recently found to have the largest genome. Here, we present new genome size estimates of 50 further species of Ensifera (superfamilies Gryllidea, Tettigoniidea) and Caelifera (Acrididae, Tetrigidae) based on flow cytometric measurements. We found that Bryodemella tuberculata (Caelifera: Acrididae) has the so far largest measured genome of all insects with 1C = 21.96 pg (21.48 gBp). Species of Orthoptera with 2n = 16 and 2n = 22 chromosomes have significantly larger genomes than species with other chromosome counts. Gryllidea genomes vary between 1C = 0.95 and 2.88 pg, and Tetrigidae between 1C = 2.18 and 2.41, while the genomes of all other studied Orthoptera range in size from 1C = 1.37 to 21.96 pg. Reconstructing ancestral genome sizes based on a phylogenetic tree of mitochondrial genomic data, we found genome size values of >15.84 pg only for the nodes of Bryodemella holdereri / B. tuberculata and Chrysochraon dispar / Euthystira brachyptera. The predicted values of ancestral genome sizes are 6.19 pg for Orthoptera, 5.37 pg for Ensifera, and 7.28 pg for Caelifera. The reasons for the large genomes in Orthoptera remain largely unknown, but a duplication or polyploidization seems unlikely as chromosome numbers do not differ much. Sequence-based genomic studies may shed light on the underlying evolutionary mechanisms.
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Affiliation(s)
- Oliver Hawlitschek
- Leibniz Institute for the Analysis of Biodiversity Change (LIB), Museum of Nature, Hamburg, Germany
- * E-mail:
| | - David Sadílek
- Institute of Medical Biochemistry and Laboratory Diagnostics, Centre of Oncocytogenomics, General University Hospital in Prague, Prague, Czech Republic
| | - Lara-Sophie Dey
- Leibniz Institute for the Analysis of Biodiversity Change (LIB), Museum of Nature, Hamburg, Germany
| | - Katharina Buchholz
- Leibniz Institute for the Analysis of Biodiversity Change (LIB), Museum of Nature, Hamburg, Germany
- Department of Biology, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Sajad Noori
- Leibniz Institute for the Analysis of Biodiversity Change (LIB), Museum of Nature, Hamburg, Germany
- Staatliches Museum für Naturkunde Stuttgart, Stuttgart, Germany
| | - Inci Livia Baez
- Leibniz Institute for the Analysis of Biodiversity Change (LIB), Museum of Nature, Hamburg, Germany
- Leibniz Institute for the Analysis of Biodiversity Change (LIB), Museum Koenig, Bonn, Germany
| | - Timo Wehrt
- Leibniz Institute for the Analysis of Biodiversity Change (LIB), Museum of Nature, Hamburg, Germany
| | - Jason Brozio
- Zoologische Staatssammlung München (ZSM-SNSB), München, Germany
| | - Pavel Trávníček
- Czech Academy of Sciences, Institute of Botany, Průhonice, Czech Republic
| | | | - Martin Husemann
- Leibniz Institute for the Analysis of Biodiversity Change (LIB), Museum of Nature, Hamburg, Germany
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Byeon E, Kim MS, Lee Y, Lee YH, Park JC, Hwang UK, Hagiwara A, Lee JS, Park HG. The genome of the freshwater monogonont rotifer Brachionus rubens: Identification of phase I, II, and III detoxification genes. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2022; 42:100979. [PMID: 35245781 DOI: 10.1016/j.cbd.2022.100979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Revised: 02/14/2022] [Accepted: 02/16/2022] [Indexed: 06/14/2023]
Abstract
Monogonont rotifers are common species in aquatic environments and make model species for ecotoxicology studies. Whole genomes of several species of the genus Brachionus have been assembled, but no information on the freshwater rotifer Brachionus rubens has been reported. In this study, the whole-genome sequence of B. rubens was successfully assembled using NextDenovo. The total length of the genome was 132.7 Mb (N50 = 2.51 Mb), including 122 contigs. The GC contents accounted for 29.96% of the genome. Aquatic organisms are always exposed to various external stresses, and a comprehensive genomic analysis is needed to better understand the adverse effects on organisms. This paper focuses on the ecotoxicological aspect and conducted genome analysis of representative gene families involved in detoxification mechanisms against environmental stressors. Specifically, we identified cytochrome P450 genes (CYPs) of phase I, glutathione S-transferase genes (GSTs) of phase II, and ATP-binding cassette transporter genes (ABCs) of phase III in the genome of B. rubens. Gene duplications were found in CYP, GST, and ABC genes, as is the case for other Brachionus rotifers. Our results suggest that these detoxification-related gene families have evolved in a species-specific and/or lineage-specific manner. This paper improves our understanding of how the freshwater Brachionus rotifers respond to environmental stressors in a molecular ecotoxicology context.
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Affiliation(s)
- Eunjin Byeon
- Department of Biological Sciences, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Min-Sub Kim
- Department of Biological Sciences, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Yoseop Lee
- Department of Biological Sciences, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Young Hwan Lee
- Department of Biological Sciences, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Jun Chul Park
- Département des Sciences, Université Sainte-Anne, Church Point, NS B0W 1M0, Canada
| | - Un-Ki Hwang
- Marine Environment Research Division, National Institute of Fisheries Science, Busan 46083, South Korea
| | - Atsushi Hagiwara
- Graduate School of Fisheries and Environmental Sciences, Nagasaki University, Nagasaki 852-8521, Japan; Organization for Marine Science and Technology, Nagasaki University, Nagasaki 852-8521, Japan
| | - Jae-Seong Lee
- Department of Biological Sciences, College of Science, Sungkyunkwan University, Suwon 16419, South Korea.
| | - Heum Gi Park
- Department of Marine Ecology and Environment, College of Life Sciences, Gangneung-Wonju National University, Gangneung 25457, South Korea.
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Yoshida Y, Shaikhutdinov N, Kozlova O, Itoh M, Tagami M, Murata M, Nishiyori-Sueki H, Kojima-Ishiyama M, Noma S, Cherkasov A, Gazizova G, Nasibullina A, Deviatiiarov R, Shagimardanova E, Ryabova A, Yamaguchi K, Bino T, Shigenobu S, Tokumoto S, Miyata Y, Cornette R, Yamada TG, Funahashi A, Tomita M, Gusev O, Kikawada T. High quality genome assembly of the anhydrobiotic midge provides insights on a single chromosome-based emergence of extreme desiccation tolerance. NAR Genom Bioinform 2022; 4:lqac029. [PMID: 35387384 PMCID: PMC8982440 DOI: 10.1093/nargab/lqac029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 03/08/2022] [Accepted: 03/18/2022] [Indexed: 12/13/2022] Open
Abstract
Non-biting midges (Chironomidae) are known to inhabit a wide range of environments, and certain species can tolerate extreme conditions, where the rest of insects cannot survive. In particular, the sleeping chironomid Polypedilum vanderplanki is known for the remarkable ability of its larvae to withstand almost complete desiccation by entering a state called anhydrobiosis. Chromosome numbers in chironomids are higher than in other dipterans and this extra genomic resource might facilitate rapid adaptation to novel environments. We used improved sequencing strategies to assemble a chromosome-level genome sequence for P. vanderplanki for deep comparative analysis of genomic location of genes associated with desiccation tolerance. Using whole genome-based cross-species and intra-species analysis, we provide evidence for the unique functional specialization of Chromosome 4 through extensive acquisition of novel genes. In contrast to other insect genomes, in the sleeping chironomid a uniquely high degree of subfunctionalization in paralogous anhydrobiosis genes occurs in this chromosome, as well as pseudogenization in a highly duplicated gene family. Our findings suggest that the Chromosome 4 in Polypedilum is a site of high genetic turnover, allowing it to act as a 'sandbox' for evolutionary experiments, thus facilitating the rapid adaptation of midges to harsh environments.
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Affiliation(s)
- Yuki Yoshida
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0035, Japan
- Graduate School of Media and Governance, Systems Biology Program, Keio University, Fujisawa, Kanagawa 252-0882, Japan
| | - Nurislam Shaikhutdinov
- Regulatory Genomics Research Center, Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan 420012, Russian Federation
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, 21205, Russian Federation
| | - Olga Kozlova
- Regulatory Genomics Research Center, Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan 420012, Russian Federation
| | - Masayoshi Itoh
- Preventive Medicine & Diagnosis Innovation Program (PMI), RIKEN, Wako, Saitama 351-0198, Japan
- Center for Integrative Medical Sciences, RIKEN, Yokohama, Kanagawa 230-0045, Japan
| | - Michihira Tagami
- Center for Integrative Medical Sciences, RIKEN, Yokohama, Kanagawa 230-0045, Japan
| | - Mitsuyoshi Murata
- Center for Integrative Medical Sciences, RIKEN, Yokohama, Kanagawa 230-0045, Japan
| | | | - Miki Kojima-Ishiyama
- Center for Integrative Medical Sciences, RIKEN, Yokohama, Kanagawa 230-0045, Japan
| | - Shohei Noma
- Center for Integrative Medical Sciences, RIKEN, Yokohama, Kanagawa 230-0045, Japan
| | - Alexander Cherkasov
- Regulatory Genomics Research Center, Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan 420012, Russian Federation
| | - Guzel Gazizova
- Regulatory Genomics Research Center, Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan 420012, Russian Federation
| | - Aigul Nasibullina
- Regulatory Genomics Research Center, Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan 420012, Russian Federation
| | - Ruslan Deviatiiarov
- Regulatory Genomics Research Center, Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan 420012, Russian Federation
| | - Elena Shagimardanova
- Regulatory Genomics Research Center, Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan 420012, Russian Federation
| | - Alina Ryabova
- Regulatory Genomics Research Center, Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan 420012, Russian Federation
| | - Katsushi Yamaguchi
- Functional Genomics Facility, National Institute for Basic Biology, Okazaki, Aichi 444-8585, Japan
| | - Takahiro Bino
- Functional Genomics Facility, National Institute for Basic Biology, Okazaki, Aichi 444-8585, Japan
| | - Shuji Shigenobu
- Functional Genomics Facility, National Institute for Basic Biology, Okazaki, Aichi 444-8585, Japan
| | - Shoko Tokumoto
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8562, Japan
| | - Yugo Miyata
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki 305-8634, Japan
| | - Richard Cornette
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki 305-8634, Japan
| | - Takahiro G Yamada
- Department of Biosciences and Informatics, Keio University, Yokohama, Kanagawa 223-8522, Japan
| | - Akira Funahashi
- Department of Biosciences and Informatics, Keio University, Yokohama, Kanagawa 223-8522, Japan
| | - Masaru Tomita
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0035, Japan
- Graduate School of Media and Governance, Systems Biology Program, Keio University, Fujisawa, Kanagawa 252-0882, Japan
- Faculty of Environment and Information studies, Keio University, Fujisawa, Kanagawa 252-0882, Japan
| | - Oleg Gusev
- Regulatory Genomics Research Center, Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan 420012, Russian Federation
- Center for Integrative Medical Sciences, RIKEN, Yokohama, Kanagawa 230-0045, Japan
- Department of Regulatory Transcriptomics for Medical Genetic Diagnostics, Graduate School of Medicine, Juntendo University, Tokyo 113-8421, Japan
| | - Takahiro Kikawada
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8562, Japan
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki 305-8634, Japan
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10
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Ishikawa Y, Kimura MT, Toda MJ. Biology and ecology of the Oriental flower-breeding Drosophila elegans and related species. Fly (Austin) 2022; 16:207-220. [PMID: 35499147 PMCID: PMC9067466 DOI: 10.1080/19336934.2022.2066953] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Animals adapt to their environments in the course of evolution. One effective approach to elucidate mechanisms of adaptive evolution is to compare closely related species with model organisms in which knowledge of the molecular and physiological bases of various traits has been accumulated. Drosophila elegans and its close relatives, belonging to the same species group as the model organism D. melanogaster, exhibit various unique characteristics such as flower-breeding habit, courtship display, territoriality, sexual dimorphism, and colour polymorphism. Their ease of culturing and availability of genomic information makes them a useful model for understanding mechanisms of adaptive evolution. Here, we review the morphology, distribution, and phylogenetic relationships of D. elegans and related species, as well as their characteristic flower-dependent biology, food habits, and life-history traits. We also describe their unique mating and territorial behaviours and note their distinctive karyotype and the genetic mechanisms of morphological diversity that have recently been revealed.
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Affiliation(s)
- Yuki Ishikawa
- Graduate School of Science, Nagoya University, Nagoya, Japan
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11
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Affiliation(s)
| | - Francisco J. Ruiz-Ruano
- Department of Organismal Biology – Systematic Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
- School of Biological Sciences, Norwich Research Park University of East Anglia, Norwich, UK
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12
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Ward CM, Perry KD, Baker G, Powis K, Heckel DG, Baxter SW. A haploid diamondback moth (Plutella xylostella L.) genome assembly resolves 31 chromosomes and identifies a diamide resistance mutation. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2021; 138:103622. [PMID: 34252570 DOI: 10.1016/j.ibmb.2021.103622] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 07/04/2021] [Accepted: 07/04/2021] [Indexed: 05/21/2023]
Abstract
The diamondback moth, Plutella xylostella (L.), is a highly mobile brassica crop pest with worldwide distribution and can rapidly evolve resistance to insecticides, including group 28 diamides. Reference genomes assembled using Illumina sequencing technology have provided valuable resources to advance our knowledge regarding the biology, origin and movement of diamondback moth, and more recently with its sister species, Plutella australiana. Here we apply a trio binning approach to sequence and annotate a chromosome level reference genome of P. xylostella using PacBio Sequel and Dovetail Hi-C sequencing technology and identify a point mutation that causes resistance to commercial diamides. A P. xylostella population collected from brassica crops in the Lockyer Valley, Australia (LV-R), was reselected for chlorantraniliprole resistance then a single male was crossed to a P. australiana female and a hybrid pupa sequenced. A chromosome level 328 Mb P. xylostella genome was assembled with 98.1% assigned to 30 autosomes and the Z chromosome. The genome was highly complete with 98.4% of BUSCO Insecta genes identified and RNAseq informed protein prediction annotated 19,002 coding genes. The LV-R strain survived recommended field application doses of chlorantraniliprole, flubendiamide and cyclaniliprole. Some hybrids also survived these doses, indicating significant departure from recessivity, which has not been previously documented for diamides. Diamide chemicals modulate insect Ryanodine Receptors (RyR), disrupting calcium homeostasis, and we identified an amino acid substitution (I4790K) recently reported to cause diamide resistance in a strain from Japan. This chromosome level assembly provides a new resource for insect comparative genomics and highlights the emergence of diamide resistance in Australia. Resistance management plans need to account for the fact that resistance is not completely recessive.
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Affiliation(s)
- C M Ward
- School of Biological Sciences, University of Adelaide, 5005, Australia
| | - K D Perry
- South Australian Research and Development Institute, Urrbrae, 5064, Australia
| | - G Baker
- South Australian Research and Development Institute, Urrbrae, 5064, Australia
| | - K Powis
- South Australian Research and Development Institute, Urrbrae, 5064, Australia
| | - D G Heckel
- Department of Entomology, Max Planck Institute for Chemical Ecology, 07745, Jena, Germany
| | - S W Baxter
- Bio21 Institute, School of BioSciences, University of Melbourne, 3052, Australia.
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13
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Hultgren KM, Chak STC, Bjelajac J, Macdonald KS. Correlated evolution of larval development, egg size and genome size across two genera of snapping shrimp. J Evol Biol 2021; 34:1827-1839. [PMID: 34626036 DOI: 10.1111/jeb.13945] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 09/15/2021] [Accepted: 09/27/2021] [Indexed: 01/21/2023]
Abstract
Across plants and animals, genome size is often correlated with life-history traits: large genomes are correlated with larger seeds, slower development, larger body size and slower cell division. Among decapod crustaceans, caridean shrimps are among the most variable both in terms of genome size variation and life-history characteristics such as larval development mode and egg size, but the extent to which these traits are associated in a phylogenetic context is largely unknown. In this study, we examine correlations among egg size, larval development and genome size in two different genera of snapping shrimp, Alpheus and Synalpheus, using phylogenetically informed analyses. In both Alpheus and Synalpheus, egg size is strongly linked to larval development mode: species with abbreviated development had significantly larger eggs than species with extended larval development. We produced the first comprehensive dataset of genome size in Alpheus (n = 37 species) and demonstrated that genome size was strongly and positively correlated with egg size in both Alpheus and Synalpheus. Correlated trait evolution analyses showed that in Alpheus, changes in genome size were clearly dependent on egg size. In Synalpheus, evolutionary path analyses suggest that changes in development mode (from extended to abbreviated) drove increases in egg volume; larger eggs, in turn, resulted in larger genomes. These data suggest that variation in reproductive traits may underpin the high degree of variation in genome size seen in a wide variety of caridean shrimp groups more generally.
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Affiliation(s)
| | - Solomon T C Chak
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, New York, USA.,Biological Sciences Department, SUNY College at Old Westbury, Old Westbury, New York, USA
| | - Jeremy Bjelajac
- Department of Biology, Seattle University, Seattle, Washington, USA
| | - Kenneth S Macdonald
- Laboratories of Analytical Biology, National Museum of Natural History, Smithsonian Institution, Washington, District of Columbia, USA
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14
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Becher H, Powell RF, Brown MR, Metherell C, Pellicer J, Leitch IJ, Twyford AD. The nature of intraspecific and interspecific genome size variation in taxonomically complex eyebrights. ANNALS OF BOTANY 2021; 128:639-651. [PMID: 34318876 PMCID: PMC8422891 DOI: 10.1093/aob/mcab102] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 07/27/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND AND AIMS Genome size varies considerably across the diversity of plant life. Although genome size is, by definition, affected by genetic presence/absence variants, which are ubiquitous in population sequencing studies, genome size is often treated as an intrinsic property of a species. Here, we studied intra- and interspecific genome size variation in taxonomically complex British eyebrights (Euphrasia, Orobanchaceae). Our aim is to document genome size diversity and investigate underlying evolutionary processes shaping variation between individuals, populations and species. METHODS We generated genome size data for 192 individuals of diploid and tetraploid Euphrasia and analysed genome size variation in relation to ploidy, taxonomy, population affiliation and geography. We further compared the genomic repeat content of 30 samples. KEY RESULTS We found considerable intraspecific genome size variation, and observed isolation-by-distance for genome size in outcrossing diploids. Tetraploid Euphrasia showed contrasting patterns, with genome size increasing with latitude in outcrossing Euphrasia arctica, but with little genome size variation in the highly selfing Euphrasia micrantha. Interspecific differences in genome size and the genomic proportions of repeat sequences were small. CONCLUSIONS We show the utility of treating genome size as the outcome of polygenic variation. Like other types of genetic variation, such as single nucleotide polymorphisms, genome size variation may be affected by ongoing hybridization and the extent of population subdivision. In addition to selection on associated traits, genome size is predicted to be affected indirectly by selection due to pleiotropy of the underlying presence/absence variants.
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Affiliation(s)
- Hannes Becher
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | | | - Max R Brown
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
- Wellcome Trust Genome Campus, Hinxton, Saffron Walden, UK
| | - Chris Metherell
- Botanical Society of Britain and Ireland, Harpenden, Hertfordshire, UK
| | - Jaume Pellicer
- Royal Botanic Gardens, Kew, Richmond, Surrey, UK
- Institut Botànic de Barcelona (IBB, CSIC-Ajuntament de Barcelona), Barcelona, Spain
| | | | - Alex D Twyford
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
- Royal Botanic Garden Edinburgh, Edinburgh, UK
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15
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Paule J, von Döhren J, Sagorny C, Nilsson MA. Genome Size Dynamics in Marine Ribbon Worms (Nemertea, Spiralia). Genes (Basel) 2021; 12:1347. [PMID: 34573329 PMCID: PMC8468679 DOI: 10.3390/genes12091347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 08/26/2021] [Accepted: 08/26/2021] [Indexed: 11/28/2022] Open
Abstract
Nemertea is a phylum consisting of 1300 mostly marine species. Nemertea is distinguished by an eversible muscular proboscis, and most of the species are venomous. Genomic resources for this phylum are scarce despite their value in understanding biodiversity. Here, we present genome size estimates of Nemertea based on flow cytometry and their relationship to different morphological and developmental traits. Ancestral genome size estimations were done across the nemertean phylogeny. The results increase the available genome size estimates for Nemertea three-fold. Our analyses show that Nemertea has a narrow genome size range (0.43-3.89 pg) compared to other phyla in Lophotrochozoa. A relationship between genome size and evolutionary rate, developmental modes, and habitat was found. Trait analyses show that the highest evolutionary rate of genome size is found in upper intertidal, viviparous species with direct development. Despite previous findings, body size in nemerteans was not correlated with genome size. A relatively small genome (1.18 pg) is assumed for the most recent common ancestor of all extant nemerteans. The results provide an important basis for future studies in nemertean genomics, which will be instrumental to understanding the evolution of this enigmatic and often neglected phylum.
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Affiliation(s)
- Juraj Paule
- Department of Botany and Molecular Evolution, Senckenberg Research Institute and Natural History Museum Frankfurt, Senckenberganlage 25, D-60325 Frankfurt am Main, Germany;
| | - Jörn von Döhren
- Institute of Evolutionary Biology and Ecology, University of Bonn, An der Immenburg 1, D-53121 Bonn, Germany; (J.v.D.); (C.S.)
| | - Christina Sagorny
- Institute of Evolutionary Biology and Ecology, University of Bonn, An der Immenburg 1, D-53121 Bonn, Germany; (J.v.D.); (C.S.)
| | - Maria A. Nilsson
- Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage 25, D-60325 Frankfurt am Main, Germany
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberganlage 25, D-60325 Frankfurt am Main, Germany
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16
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Kuhn GCS, Heringer P, Dias GB. Structure, Organization, and Evolution of Satellite DNAs: Insights from the Drosophila repleta and D. virilis Species Groups. PROGRESS IN MOLECULAR AND SUBCELLULAR BIOLOGY 2021; 60:27-56. [PMID: 34386871 DOI: 10.1007/978-3-030-74889-0_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The fact that satellite DNAs (satDNAs) in eukaryotes are abundant genomic components, can perform functional roles, but can also change rapidly across species while being homogenous within a species, makes them an intriguing and fascinating genomic component to study. It is also becoming clear that satDNAs represent an important piece in genome architecture and that changes in their structure, organization, and abundance can affect the evolution of genomes and species in many ways. Since the discovery of satDNAs more than 50 years ago, species from the Drosophila genus have continuously been used as models to study several aspects of satDNA biology. These studies have been largely concentrated in D. melanogaster and closely related species from the Sophophora subgenus, even though the vast majority of all Drosophila species belong to the Drosophila subgenus. This chapter highlights some studies on the satDNA structure, organization, and evolution in two species groups from the Drosophila subgenus: the repleta and virilis groups. We also discuss and review the classification of other abundant tandem repeats found in these species in the light of the current information available.
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Affiliation(s)
- Gustavo C S Kuhn
- Departamento de Genética, Ecologia e Evolução, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG, Brazil.
| | - Pedro Heringer
- Departamento de Genética, Ecologia e Evolução, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG, Brazil
| | - Guilherme Borges Dias
- Department of Genetics and Institute of Bioinformatics, University of Georgia, Athens, GA, USA
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17
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Zhao L, Wang H, Li P, Sun K, Guan DL, Xu SQ. Genome Size Estimation and Full-Length Transcriptome of Sphingonotus tsinlingensis: Genetic Background of a Drought-Adapted Grasshopper. Front Genet 2021; 12:678625. [PMID: 34322153 PMCID: PMC8313316 DOI: 10.3389/fgene.2021.678625] [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] [Received: 03/12/2021] [Accepted: 06/14/2021] [Indexed: 11/25/2022] Open
Abstract
Sphingonotus Fieber, 1852 (Orthoptera: Acrididae), is a grasshopper genus comprising approximately 170 species, all of which prefer dry environments such as deserts, steppes, and stony benchlands. In this study, we aimed to examine the adaptation of grasshopper species to arid environments. The genome size of Sphingonotus tsinlingensis was estimated using flow cytometry, and the first high-quality full-length transcriptome of this species was produced. The genome size of S. tsinlingensis is approximately 12.8 Gb. Based on 146.98 Gb of PacBio sequencing data, 221.47 Mb full-length transcripts were assembled. Among these, 88,693 non-redundant isoforms were identified with an N50 value of 2,726 bp, which was markedly longer than previous grasshopper transcriptome assemblies. In total, 48,502 protein-coding sequences were identified, and 37,569 were annotated using public gene function databases. Moreover, 36,488 simple tandem repeats, 12,765 long non-coding RNAs, and 414 transcription factors were identified. According to gene functions, 61 cytochrome P450 (CYP450) and 66 heat shock protein (HSP) genes, which may be associated with drought adaptation of S. tsinlingensis, were identified. We compared the transcriptomes of S. tsinlingensis and two other grasshopper species which were less tolerant to drought, namely Mongolotettix japonicus and Gomphocerus licenti. We observed the expression of CYP450 and HSP genes in S. tsinlingensis were higher. We produced the first full-length transcriptome of a Sphingonotus species that has an ultra-large genome. The assembly characteristics were better than those of all known grasshopper transcriptomes. This full-length transcriptome may thus be used to understand the genetic background and evolution of grasshoppers.
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Affiliation(s)
- Lu Zhao
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Hang Wang
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Ping Li
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Kuo Sun
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - De-Long Guan
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Sheng-Quan Xu
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
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18
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Park JC, Kim DH, Kim MS, Hagiwara A, Lee JS. The genome of the euryhaline rotifer Brachionus paranguensis: Potential use in molecular ecotoxicology. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2021; 39:100836. [PMID: 33940320 DOI: 10.1016/j.cbd.2021.100836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 04/03/2021] [Accepted: 04/07/2021] [Indexed: 10/21/2022]
Abstract
Brachionus spp. rotifers have been proposed as model organisms for ecotoxicological studies. We analyzed the whole-genome sequence of B. paranguensis through NextDenovo, resulting in a total length of 106.2 Mb and 71 contigs. The N50 and the GC content were 4.13 Mb and 28%, respectively. A total of 18,501 genes were predicted within the genome of B. paranguensis. Prominent detoxification-related gene families of phase I and II detoxifications have been investigated. In parallel with other Brachionus rotifers, high gene expansion was observed in CYP clan 3 and GST sigma class in B. paranguensis. Moreover, species-specific expansion of sulfotransferase (SULTs) and gain of UDP-glucuronosyltransferases (UGTs) through horizontal gene transfer has been specifically found within B. plicatilis complex. This whole-genome analysis of B. paranguensis provides a basis for molecular ecotoxicological studies and provides useful information for comparative studies of the evolution of detoxification mechanisms in Brachionus spp.
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Affiliation(s)
- Jun Chul Park
- Department of Biological Sciences, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Duck-Hyun Kim
- Department of Biological Sciences, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Min-Sub Kim
- Department of Biological Sciences, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Atsushi Hagiwara
- Graduate School of Fisheries and Environmental Sciences, Nagasaki University, Nagasaki 852-8521, Japan; Organization for Marine Science and Technology, Nagasaki University, Nagasaki 852-8521, Japan
| | - Jae-Seong Lee
- Department of Biological Sciences, College of Science, Sungkyunkwan University, Suwon 16419, South Korea.
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19
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Glazier DS. Genome Size Covaries More Positively with Propagule Size than Adult Size: New Insights into an Old Problem. BIOLOGY 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] [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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20
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Flynn JM, Long M, Wing RA, Clark AG. Evolutionary Dynamics of Abundant 7-bp Satellites in the Genome of Drosophila virilis. Mol Biol Evol 2021; 37:1362-1375. [PMID: 31960929 DOI: 10.1093/molbev/msaa010] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The factors that drive the rapid changes in abundance of tandem arrays of highly repetitive sequences, known as satellite DNA, are not well understood. Drosophila virilis has one of the highest relative amounts of simple satellites of any organism that has been studied, with an estimated >40% of its genome composed of a few related 7-bp satellites. Here, we use D. virilis as a model to understand technical biases affecting satellite sequencing and the evolutionary processes that drive satellite composition. By analyzing sequencing data from Illumina, PacBio, and Nanopore platforms, we identify platform-specific biases and suggest best practices for accurate characterization of satellites by sequencing. We use comparative genomics and cytogenetics to demonstrate that the highly abundant AAACTAC satellite family arose from a related satellite in the branch leading to the virilis phylad 4.5-11 Ma before exploding in abundance in some species of the clade. The most abundant satellite is conserved in sequence and location in the pericentromeric region but has diverged widely in abundance among species, whereas the satellites nearest the centromere are rapidly turning over in sequence composition. By analyzing multiple strains of D. virilis, we saw that the abundances of two centromere-proximal satellites are anticorrelated along a geographical gradient, which we suggest could be caused by ongoing conflicts at the centromere. In conclusion, we illuminate several key attributes of satellite evolutionary dynamics that we hypothesize to be driven by processes including selection, meiotic drive, and constraints on satellite sequence and abundance.
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Affiliation(s)
- Jullien M Flynn
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY
| | - Manyuan Long
- Department of Ecology and Evolution, University of Chicago, Chicago, IL
| | - Rod A Wing
- School of Plant Sciences, Arizona Genomics Institute, University of Arizona, Tucson, AZ
| | - Andrew G Clark
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY
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21
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Smukowski Heil C, Patterson K, Hickey ASM, Alcantara E, Dunham MJ. Transposable Element Mobilization in Interspecific Yeast Hybrids. Genome Biol Evol 2021; 13:6141023. [PMID: 33595639 PMCID: PMC7952228 DOI: 10.1093/gbe/evab033] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/11/2021] [Indexed: 12/13/2022] Open
Abstract
Barbara McClintock first hypothesized that interspecific hybridization could provide a “genomic shock” that leads to the mobilization of transposable elements (TEs). This hypothesis is based on the idea that regulation of TE movement is potentially disrupted in hybrids. However, the handful of studies testing this hypothesis have yielded mixed results. Here, we set out to identify if hybridization can increase transposition rate and facilitate colonization of TEs in Saccharomyces cerevisiae × Saccharomyces uvarum interspecific yeast hybrids. Saccharomyces cerevisiae have a small number of active long terminal repeat retrotransposons (Ty elements), whereas their distant relative S. uvarum have lost the Ty elements active in S. cerevisiae. Although the regulation system of Ty elements is known in S. cerevisiae, it is unclear how Ty elements are regulated in other Saccharomyces species, and what mechanisms contributed to the loss of most classes of Ty elements in S. uvarum. Therefore, we first assessed whether TEs could insert in the S. uvarum sub-genome of a S. cerevisiae × S. uvarum hybrid. We induced transposition to occur in these hybrids and developed a sequencing technique to show that Ty elements insert readily and nonrandomly in the S. uvarum genome. We then used an in vivo reporter construct to directly measure transposition rate in hybrids, demonstrating that hybridization itself does not alter rate of mobilization. However, we surprisingly show that species-specific mitochondrial inheritance can change transposition rate by an order of magnitude. Overall, our results provide evidence that hybridization can potentially facilitate the introduction of TEs across species boundaries and alter transposition via mitochondrial transmission, but that this does not lead to unrestrained proliferation of TEs suggested by the genomic shock theory.
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Affiliation(s)
- Caiti Smukowski Heil
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Kira Patterson
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | | | - Erica Alcantara
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Maitreya J Dunham
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
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22
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Verberk WC, Atkinson D, Hoefnagel KN, Hirst AG, Horne CR, Siepel H. Shrinking body sizes in response to warming: explanations for the temperature-size rule with special emphasis on the role of oxygen. Biol Rev Camb Philos Soc 2021; 96:247-268. [PMID: 32959989 PMCID: PMC7821163 DOI: 10.1111/brv.12653] [Citation(s) in RCA: 93] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 08/28/2020] [Accepted: 08/28/2020] [Indexed: 01/04/2023]
Abstract
Body size is central to ecology at levels ranging from organismal fecundity to the functioning of communities and ecosystems. Understanding temperature-induced variations in body size is therefore of fundamental and applied interest, yet thermal responses of body size remain poorly understood. Temperature-size (T-S) responses tend to be negative (e.g. smaller body size at maturity when reared under warmer conditions), which has been termed the temperature-size rule (TSR). Explanations emphasize either physiological mechanisms (e.g. limitation of oxygen or other resources and temperature-dependent resource allocation) or the adaptive value of either a large body size (e.g. to increase fecundity) or a short development time (e.g. in response to increased mortality in warm conditions). Oxygen limitation could act as a proximate factor, but we suggest it more likely constitutes a selective pressure to reduce body size in the warm: risks of oxygen limitation will be reduced as a consequence of evolution eliminating genotypes more prone to oxygen limitation. Thus, T-S responses can be explained by the 'Ghost of Oxygen-limitation Past', whereby the resulting (evolved) T-S responses safeguard sufficient oxygen provisioning under warmer conditions, reflecting the balance between oxygen supply and demands experienced by ancestors. T-S responses vary considerably across species, but some of this variation is predictable. Body-size reductions with warming are stronger in aquatic taxa than in terrestrial taxa. We discuss whether larger aquatic taxa may especially face greater risks of oxygen limitation as they grow, which may be manifested at the cellular level, the level of the gills and the whole-organism level. In contrast to aquatic species, terrestrial ectotherms may be less prone to oxygen limitation and prioritize early maturity over large size, likely because overwintering is more challenging, with concomitant stronger end-of season time constraints. Mechanisms related to time constraints and oxygen limitation are not mutually exclusive explanations for the TSR. Rather, these and other mechanisms may operate in tandem. But their relative importance may vary depending on the ecology and physiology of the species in question, explaining not only the general tendency of negative T-S responses but also variation in T-S responses among animals differing in mode of respiration (e.g. water breathers versus air breathers), genome size, voltinism and thermally associated behaviour (e.g. heliotherms).
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Affiliation(s)
- Wilco C.E.P. Verberk
- Department of Animal Ecology and Physiology, Institute for Water and Wetland ResearchRadboud UniversityHeyendaalseweg 1356525 AJNijmegenThe Netherlands
| | - David Atkinson
- Department of Evolution, Ecology and BehaviourUniversity of LiverpoolLiverpoolL69 7ZBU.K.
| | - K. Natan Hoefnagel
- Department of Animal Ecology and Physiology, Institute for Water and Wetland ResearchRadboud UniversityHeyendaalseweg 1356525 AJNijmegenThe Netherlands
- Faculty of Science and Engineering, Ocean Ecosystems — Energy and Sustainability Research Institute GroningenUniversity of GroningenNijenborgh 79747 AGGroningenThe Netherlands
| | - Andrew G. Hirst
- School of Environmental SciencesUniversity of LiverpoolLiverpoolL69 3GPU.K.
- Centre for Ocean Life, DTU AquaTechnical University of DenmarkLyngbyDenmark
| | - Curtis R. Horne
- School of Environmental SciencesUniversity of LiverpoolLiverpoolL69 3GPU.K.
| | - Henk Siepel
- Department of Animal Ecology and Physiology, Institute for Water and Wetland ResearchRadboud UniversityHeyendaalseweg 1356525 AJNijmegenThe Netherlands
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The genome of the marine monogonont rotifer Brachionus rotundiformis and insight into species-specific detoxification components in Brachionus spp. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2020; 36:100714. [PMID: 32784096 DOI: 10.1016/j.cbd.2020.100714] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 07/22/2020] [Accepted: 07/26/2020] [Indexed: 11/20/2022]
Abstract
The monogonont rotifer Brachionus spp. have been widely used for ecotoxicological studies because of their advantages as one of the most suitable laboratory experimental species. In the present study, we obtained and assembled the whole genome sequence of the rotifer Brachionus rotundiformis, consisting of 13,612 annotated genes with 213 scaffolds and 58 Mb in total length. Focusing on ecotoxicological aspects, we conducted a comparative genome analysis on the gene families involved in detoxification, including four to six sulfotransferase gene families, seven uridine 5'-diphospho-glucuronosyltransferase gene families, and 58, 61, or 70 ATP-binding cassette genes in the genus Brachionus including Brachionus koreanus and Brachionus plicatilis. Our results suggest that these gene families have undergone a species- and/or lineage-specific evolution in response to the surrounding environmental pressure. Our genome resource for B. rotundiformis would be highly useful for future ecotoxicological studies and also provides a better understanding on the view of evolutionary mechanism of detoxification in the genus Brachionus spp.
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Moura MN, Cardoso DC, Lima Baldez BC, Cristiano MP. Intraspecific variation in the karyotype length and genome size of fungus-farming ants (genus Mycetophylax), with remarks on procedures for the estimation of genome size in the Formicidae by flow cytometry. PLoS One 2020; 15:e0237157. [PMID: 32760102 PMCID: PMC7410318 DOI: 10.1371/journal.pone.0237157] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 07/20/2020] [Indexed: 11/19/2022] Open
Abstract
Ants (Formicidae) present considerable diversity in chromosome numbers, which vary from n = 1 to n = 60, although this variation is not proportional to that in genome size, for which estimates range from 0.18 pg to 0.77 pg. Intraspecific variation in the chromosome number and karyotype structure has been reported among species, although the variation among populations of the same species has received much less attention, and there are few data on genome size. Here, we studied the karyotype length and genome size of different populations of the fungus-farming ants Mycetophylax conformis (Mayr, 1884) and Mycetophylax morschi (Emery, 1888). We also provide remarks on procedure for the estimation of ant genome size by Flow Cytometry (FCM) analysis. Chromosome number and morphology did not vary among the populations of M. conformis or the cytotypes of M. morschi, but karyotype length and genome size were significantly distinct among the populations of these ants. Our results on the variation in karyotype length and genome size among M. morschi and M. conformis populations reveal considerable diversity that would be largely overlooked by more traditional descriptions of karyotypes, which were also supported by the estimates of genome size obtained using flow cytometry. Changes in the amount of DNA reflect variation in the fine structure of the chromosomes, which may represent the first steps of karyotype evolution and may occur previously to any changes in the chromosome number.
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Affiliation(s)
- Mariana Neves Moura
- Programa de Pós-graduação em Ecologia, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Danon Clemes Cardoso
- Departamento de Biodiversidade, Evolução e Meio Ambiente/ICEB, Universidade Federal de Ouro Preto, Ouro Preto, Minas Gerais, Brazil
| | - Brenda Carla Lima Baldez
- Programa de Pós-graduação em Ecologia de Biomas Tropicais, Universidade Federal de Ouro Preto, Ouro Preto, Minas Gerais, Brazil
| | - Maykon Passos Cristiano
- Departamento de Biodiversidade, Evolução e Meio Ambiente/ICEB, Universidade Federal de Ouro Preto, Ouro Preto, Minas Gerais, Brazil
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Near-chromosome level genome assembly of the fruit pest Drosophila suzukii using long-read sequencing. Sci Rep 2020; 10:11227. [PMID: 32641717 PMCID: PMC7343843 DOI: 10.1038/s41598-020-67373-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Accepted: 06/02/2020] [Indexed: 12/31/2022] Open
Abstract
Over the past decade, the spotted wing Drosophila, Drosophila suzukii, has invaded Europe and America and has become a major agricultural pest in these areas, thereby prompting intense research activities to better understand its biology. Two draft genome assemblies already exist for this species but contain pervasive assembly errors and are highly fragmented, which limits their values. Our purpose here was to improve the assembly of the D. suzukii genome and to annotate it in a way that facilitates comparisons with D. melanogaster. For this, we generated PacBio long-read sequencing data and assembled a novel, high-quality D. suzukii genome assembly. It is one of the largest Drosophila genomes, notably because of the expansion of its repeatome. We found that despite 16 rounds of full-sib crossings the D. suzukii strain that we sequenced has maintained high levels of polymorphism in some regions of its genome. As a consequence, the quality of the assembly of these regions was reduced. We explored possible origins of this high residual diversity, including the presence of structural variants and a possible heterogeneous admixture pattern of North American and Asian ancestry. Overall, our assembly and annotation constitute a high-quality genomic resource that can be used for both high-throughput sequencing approaches, as well as manipulative genetic technologies to study D. suzukii.
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Jeong CB, Lee BY, Choi BS, Kim MS, Park JC, Kim DH, Wang M, Park HG, Lee JS. The genome of the harpacticoid copepod Tigriopus japonicus: Potential for its use in marine molecular ecotoxicology. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2020; 222:105462. [PMID: 32169740 DOI: 10.1016/j.aquatox.2020.105462] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 02/28/2020] [Accepted: 02/29/2020] [Indexed: 06/10/2023]
Abstract
The copepod Tigriopus japonicus has been widely used as an experimental species in the field of ecotoxicology. We have sequenced and assembled the whole genome of T. japonicus with comparative analysis of gene families that represent detoxification phases in two additional public genomes of Tigriopus spp., namely, T. californicus and T. kingsejongensis. The total length of the T. japonicus assembled genome was 196.6 Mb with an N50 value of 10.65 Mb and consisted of 339 scaffolds and 25,143 annotated genes. The detoxification gene families encoding cytochrome P450s (CYP450s), glutathione S-transferases (GSTs), and ATP-binding cassette (ABC) proteins in Tigriopus spp. have shown species-dependent diversity in several gene sets, suggesting that these genes have undergone a species-specific expansion to increase their fitness to different marine habitats and environmental pressures. Our study will provide a better understanding of the detoxification system in Tigriopus spp. and will contribute to various areas of research, including ecotoxicology.
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Affiliation(s)
- Chang-Bum Jeong
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon 16419, South Korea; Department of Marine Science, College of Natural Sciences, Incheon National University, Incheon 22012, South Korea
| | - Bo-Young Lee
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | | | - Min-Sub Kim
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Jun Chul Park
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Duck-Hyun Kim
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon 16419, South Korea
| | - Minghua Wang
- State Key Laboratory of Marine Environmental Science, College of the Environment & Ecology, Xiamen University, Xiamen 361102, China; Fujian Provincial Key Laboratory for Coastal Ecology and Environmental Studies, Xiamen University, Xiamen 361102, China
| | - Heum Gi Park
- Department of Marine Resource Development, College of Life Sciences, Gangneung-Wonju National University, Gangneung 25457, South Korea
| | - Jae-Seong Lee
- Department of Biological Science, College of Science, Sungkyunkwan University, Suwon 16419, South Korea.
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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] [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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Yu JP, Liu W, Mai CL, Liao WB. Genome size variation is associated with life‐history traits in birds. J Zool (1987) 2019. [DOI: 10.1111/jzo.12755] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- J. P. Yu
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education) China West Normal University Nanchong China
- Key Laboratory of Artificial Propagation and Utilization in Anurans of Nanchong City China West Normal University Nanchong China
- Institute of Eco‐adaptation in Amphibians and Reptiles China West Normal University Nanchong China
| | - W. Liu
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education) China West Normal University Nanchong China
- Key Laboratory of Artificial Propagation and Utilization in Anurans of Nanchong City China West Normal University Nanchong China
- Institute of Eco‐adaptation in Amphibians and Reptiles China West Normal University Nanchong China
| | - C. L. Mai
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education) China West Normal University Nanchong China
- Key Laboratory of Artificial Propagation and Utilization in Anurans of Nanchong City China West Normal University Nanchong China
- Institute of Eco‐adaptation in Amphibians and Reptiles China West Normal University Nanchong China
| | - W. B. Liao
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education) China West Normal University Nanchong China
- Key Laboratory of Artificial Propagation and Utilization in Anurans of Nanchong City China West Normal University Nanchong China
- Institute of Eco‐adaptation in Amphibians and Reptiles China West Normal University Nanchong China
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Silva BSML, Heringer P, Dias GB, Svartman M, Kuhn GCS. De novo identification of satellite DNAs in the sequenced genomes of Drosophila virilis and D. americana using the RepeatExplorer and TAREAN pipelines. PLoS One 2019; 14:e0223466. [PMID: 31856171 PMCID: PMC6922343 DOI: 10.1371/journal.pone.0223466] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 11/26/2019] [Indexed: 01/10/2023] Open
Abstract
Satellite DNAs are among the most abundant repetitive DNAs found in eukaryote genomes, where they participate in a variety of biological roles, from being components of important chromosome structures to gene regulation. Experimental methodologies used before the genomic era were insufficient, too laborious and time-consuming to recover the collection of all satDNAs from a genome. Today, the availability of whole sequenced genomes combined with the development of specific bioinformatic tools are expected to foster the identification of virtually all the "satellitome" of a particular species. While whole genome assemblies are important to obtain a global view of genome organization, most of them are incomplete and lack repetitive regions. We applied short-read sequencing and similarity clustering in order to perform a de novo identification of the most abundant satellite families in two Drosophila species from the virilis group: Drosophila virilis and D. americana, using the Tandem Repeat Analyzer (TAREAN) and RepeatExplorer pipelines. These species were chosen because they have been used as models to understand satDNA biology since the early 70's. We combined the computational approach with data from the literature and chromosome mapping to obtain an overview of the major tandem repeat sequences of these species. The fact that all of the abundant tandem repeats (TRs) we detected were previously identified in the literature allowed us to evaluate the efficiency of TAREAN in correctly identifying true satDNAs. Our results indicate that raw sequencing reads can be efficiently used to detect satDNAs, but that abundant tandem repeats present in dispersed arrays or associated with transposable elements are frequent false positives. We demonstrate that TAREAN with its parent method RepeatExplorer may be used as resources to detect tandem repeats associated with transposable elements and also to reveal families of dispersed tandem repeats.
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Affiliation(s)
- Bráulio S. M. L. Silva
- Departamento de Genética, Ecologia e Evolução, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brasil
| | - Pedro Heringer
- Departamento de Genética, Ecologia e Evolução, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brasil
| | - Guilherme B. Dias
- Departamento de Genética, Ecologia e Evolução, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brasil
| | - Marta Svartman
- Departamento de Genética, Ecologia e Evolução, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brasil
| | - Gustavo C. S. Kuhn
- Departamento de Genética, Ecologia e Evolução, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brasil
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Absence of W Chromosome in Psychidae Moths and Implications for the Theory of Sex Chromosome Evolution in Lepidoptera. Genes (Basel) 2019; 10:genes10121016. [PMID: 31817557 PMCID: PMC6947638 DOI: 10.3390/genes10121016] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 11/29/2019] [Accepted: 12/02/2019] [Indexed: 11/17/2022] Open
Abstract
Moths and butterflies (Lepidoptera) are the largest group with heterogametic females. Although the ancestral sex chromosome system is probably Z0/ZZ, most lepidopteran species have the W chromosome. When and how the W chromosome arose remains elusive. Existing hypotheses place the W origin either at the common ancestor of Ditrysia and Tischeriidae, or prefer independent origins of W chromosomes in these two groups. Due to their phylogenetic position at the base of Ditrysia, bagworms (Psychidae) play an important role in investigating the W chromosome origin. Therefore, we examined the W chromosome status in three Psychidae species, namely Proutia betulina, Taleporia tubulosa, and Diplodoma laichartingella, using both classical and molecular cytogenetic methods such as sex chromatin assay, comparative genomic hybridization (CGH), and male vs. female genome size comparison by flow cytometry. In females of all three species, no sex chromatin was found, no female-specific chromosome regions were revealed by CGH, and a Z-chromosome univalent was observed in pachytene oocytes. In addition, the genome size of females was significantly smaller than males. Overall, our study provides strong evidence for the absence of the W chromosome in Psychidae, thus supporting the hypothesis of two independent W chromosome origins in Tischeriidae and in advanced Ditrysia.
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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, MD.) 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] [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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Karageorgiou C, Gámez-Visairas V, Tarrío R, Rodríguez-Trelles F. Long-read based assembly and synteny analysis of a reference Drosophila subobscura genome reveals signatures of structural evolution driven by inversions recombination-suppression effects. BMC Genomics 2019; 20:223. [PMID: 30885123 PMCID: PMC6423853 DOI: 10.1186/s12864-019-5590-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 03/06/2019] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Drosophila subobscura has long been a central model in evolutionary genetics. Presently, its use is hindered by the lack of a reference genome. To bridge this gap, here we used PacBio long-read technology, together with the available wealth of genetic marker information, to assemble and annotate a high-quality nuclear and complete mitochondrial genome for the species. With the obtained assembly, we performed the first synteny analysis of genome structure evolution in the subobscura subgroup. RESULTS We generated a highly-contiguous ~ 129 Mb-long nuclear genome, consisting of six pseudochromosomes corresponding to the six chromosomes of a female haploid set, and a complete 15,764 bp-long mitogenome, and provide an account of their numbers and distributions of codifying and repetitive content. All 12 identified paracentric inversion differences in the subobscura subgroup would have originated by chromosomal breakage and repair, with some associated duplications, but no evidence of direct gene disruptions by the breakpoints. Between lineages, inversion fixation rates were 10 times higher in continental D. subobscura than in the two small oceanic-island endemics D. guanche and D. madeirensis. Within D. subobscura, we found contrasting ratios of chromosomal divergence to polymorphism between the A sex chromosome and the autosomes. CONCLUSIONS We present the first high-quality, long-read sequencing of a D. subobscura genome. Our findings generally support genome structure evolution in this species being driven indirectly, through the inversions' recombination-suppression effects in maintaining sets of adaptive alleles together in the face of gene flow. The resources developed will serve to further establish the subobscura subgroup as model for comparative genomics and evolutionary indicator of global change.
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Affiliation(s)
- Charikleia Karageorgiou
- Grup de Genòmica, Bioinformàtica i Biologia Evolutiva (GGBE), Departament de Genètica i de Microbiologia, Universitat Autonòma de Barcelona, Bellaterra, Barcelona, Spain
| | - Víctor Gámez-Visairas
- Grup de Genòmica, Bioinformàtica i Biologia Evolutiva (GGBE), Departament de Genètica i de Microbiologia, Universitat Autonòma de Barcelona, Bellaterra, Barcelona, Spain
| | - Rosa Tarrío
- Grup de Genòmica, Bioinformàtica i Biologia Evolutiva (GGBE), Departament de Genètica i de Microbiologia, Universitat Autonòma de Barcelona, Bellaterra, Barcelona, Spain
| | - Francisco Rodríguez-Trelles
- Grup de Genòmica, Bioinformàtica i Biologia Evolutiva (GGBE), Departament de Genètica i de Microbiologia, Universitat Autonòma de Barcelona, Bellaterra, Barcelona, Spain
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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] [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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Zhang S, Gu S, Ni X, Li X. Genome Size Reversely Correlates With Host Plant Range in Helicoverpa Species. Front Physiol 2019; 10:29. [PMID: 30761014 PMCID: PMC6363812 DOI: 10.3389/fphys.2019.00029] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 01/11/2019] [Indexed: 12/02/2022] Open
Abstract
In organisms with very low percentages of transposable elements (TEs), genome size may positively or negatively correlate with host range, depending on whether host adaptation or host modification is the main route to host generalism. To test if this holds true for insect herbivores with greater percentages of TEs, we conducted flow cytometry to measure the endopolyploidy levels and C-values of the host modification (salivary gland and mandibular gland in head), host adaptation (midgut), and host use-independent tissues (male gonad, hemolymph, and Malpighian tubules) of the generalist Helicoverpa armigera and the head of its older specialist sister H. assulta. Larval salivary gland displayed a consecutive chain of endopolyploidy particles from 8Cx to higher than 32Cx and larval head and midgut had endopolyploidy nuclei clusters of 16Cx and 32Cx, whereas larval male gonad, hemolymph, and Malpighian tubules possessed no endopolyploidy nuclei of higher than 8Cx. The estimated genome size of the Solanaceae plant specialist H. assulta is 430 Mb, significantly larger than that of its older generalist sister Heliothis virescens (408 Mb) and those of its two generalist descendants H. armigera (394 Mb) and H. zea (363 Mb). These data not only reveal a negative correlation between host plant range and genome size in this terminal lineage, but also imply that Helicoverpa species appear to depend more on host modification than on host adaptation to achieve polyphagy.
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Affiliation(s)
- Shen Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shaohua Gu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xinzhi Ni
- USDA-ARS Crop Genetics and Breeding Research Unit, Tifton, GA, United States
| | - Xianchun Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China.,Department of Entomology and BIO5 Institute, University of Arizona, Tucson, AZ, United States
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Bourque G, Burns KH, Gehring M, Gorbunova V, Seluanov A, Hammell M, Imbeault M, Izsvák Z, Levin HL, Macfarlan TS, Mager DL, Feschotte C. Ten things you should know about transposable elements. Genome Biol 2018; 19:199. [PMID: 30454069 PMCID: PMC6240941 DOI: 10.1186/s13059-018-1577-z] [Citation(s) in RCA: 591] [Impact Index Per Article: 98.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Transposable elements (TEs) are major components of eukaryotic genomes. However, the extent of their impact on genome evolution, function, and disease remain a matter of intense interrogation. The rise of genomics and large-scale functional assays has shed new light on the multi-faceted activities of TEs and implies that they should no longer be marginalized. Here, we introduce the fundamental properties of TEs and their complex interactions with their cellular environment, which are crucial to understanding their impact and manifold consequences for organismal biology. While we draw examples primarily from mammalian systems, the core concepts outlined here are relevant to a broad range of organisms.
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Affiliation(s)
- Guillaume Bourque
- Department of Human Genetics, McGill University, Montréal, Québec, H3A 0G1, Canada.
- Canadian Center for Computational Genomics, McGill University, Montréal, Québec, H3A 0G1, Canada.
| | - Kathleen H Burns
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Mary Gehring
- Whitehead Institute for Biomedical Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA
| | - Vera Gorbunova
- Department of Biology, University of Rochester, Rochester, NY, 14627, USA
| | - Andrei Seluanov
- Department of Biology, University of Rochester, Rochester, NY, 14627, USA
| | - Molly Hammell
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
| | - Michaël Imbeault
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, UK
| | - Zsuzsanna Izsvák
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125, Berlin, Germany
| | - Henry L Levin
- The Eunice Kennedy Shriver National Institute of Child Health and Human Development, The National Institutes of Health, Bethesda, Maryland, USA
| | - Todd S Macfarlan
- The Eunice Kennedy Shriver National Institute of Child Health and Human Development, The National Institutes of Health, Bethesda, Maryland, USA
| | - Dixie L Mager
- Terry Fox Laboratory, British Columbia Cancer Agency and Department of Medical Genetics, University of BC, Vancouver, BC, V5Z1L3, Canada
| | - Cédric Feschotte
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14850, USA.
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Highly Contiguous Genome Assemblies of 15 Drosophila Species Generated Using Nanopore Sequencing. G3-GENES GENOMES GENETICS 2018; 8:3131-3141. [PMID: 30087105 PMCID: PMC6169393 DOI: 10.1534/g3.118.200160] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The Drosophila genus is a unique group containing a wide range of species that occupy diverse ecosystems. In addition to the most widely studied species, Drosophila melanogaster, many other members in this genus also possess a well-developed set of genetic tools. Indeed, high-quality genomes exist for several species within the genus, facilitating studies of the function and evolution of cis-regulatory regions and proteins by allowing comparisons across at least 50 million years of evolution. Yet, the available genomes still fail to capture much of the substantial genetic diversity within the Drosophila genus. We have therefore tested protocols to rapidly and inexpensively sequence and assemble the genome from any Drosophila species using single-molecule sequencing technology from Oxford Nanopore. Here, we use this technology to present highly contiguous genome assemblies of 15 Drosophila species: 10 of the 12 originally sequenced Drosophila species (ananassae, erecta, mojavensis, persimilis, pseudoobscura, sechellia, simulans, virilis, willistoni, and yakuba), four additional species that had previously reported assemblies (biarmipes, bipectinata, eugracilis, and mauritiana), and one novel assembly (triauraria). Genomes were generated from an average of 29x depth-of-coverage data that after assembly resulted in an average contig N50 of 4.4 Mb. Subsequent alignment of contigs from the published reference genomes demonstrates that our assemblies could be used to close over 60% of the gaps present in the currently published reference genomes. Importantly, the materials and reagents cost for each genome was approximately $1,000 (USD). This study demonstrates the power and cost-effectiveness of long-read sequencing for genome assembly in Drosophila and provides a framework for the affordable sequencing and assembly of additional Drosophila genomes.
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Yashiro T, Lo N, Kobayashi K, Nozaki T, Fuchikawa T, Mizumoto N, Namba Y, Matsuura K. Loss of males from mixed-sex societies in termites. BMC Biol 2018; 16:96. [PMID: 30249269 PMCID: PMC6154949 DOI: 10.1186/s12915-018-0563-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2018] [Accepted: 08/09/2018] [Indexed: 11/13/2022] Open
Abstract
Background Sexual reproduction is the norm in almost all animal species, and in many advanced animal societies, both males and females participate in social activities. To date, the complete loss of males from advanced social animal lineages has been reported only in ants and honey bees (Hymenoptera), whose workers are always female and whose males display no helping behaviors even in normal sexual species. Asexuality has not previously been observed in colonies of another major group of social insects, the termites, where the ubiquitous presence of both male and female workers and soldiers indicate that males play a critical role beyond that of reproduction. Results Here, we report asexual societies in a lineage of the termite Glyptotermes nakajimai. We investigated the composition of mature colonies from ten distinct populations in Japan, finding six asexual populations characterized by a lack of any males in the reproductive, soldier, and worker castes of their colonies, an absence of sperm in the spermathecae of their queens, and the development of unfertilized eggs at a level comparable to that for the development of fertilized eggs in sexual populations of this species. Phylogenetic analyses indicated a single evolutionary origin of the asexual populations, with divergence from sampled sexual populations occurring about 14 million years ago. Asexual colonies differ from sexual colonies in having a more uniform head size in their all-female soldier caste, and fewer soldiers in proportion to other individuals, suggesting increased defensive efficiencies arising from uniform soldier morphology. Such efficiencies may have contributed to the persistence and spread of the asexual lineage. Cooperative colony foundation by multiple queens, the single-site nesting life history common to both the asexual and sexual lineages, and the occasional development of eggs without fertilization even in the sexual lineage are traits likely to have been present in the ancestors of the asexual lineage that may have facilitated the transition to asexuality. Conclusions Our findings demonstrate that completely asexual social lineages can evolve from mixed-sex termite societies, providing evidence that males are dispensable for the maintenance of advanced animal societies in which they previously played an active social role. Electronic supplementary material The online version of this article (10.1186/s12915-018-0563-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Toshihisa Yashiro
- School of Life and Environmental Sciences, Edgeworth David Building A11, University of Sydney, Sydney, NSW, 2006, Australia. .,Laboratory of Insect Ecology, Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan.
| | - Nathan Lo
- School of Life and Environmental Sciences, Edgeworth David Building A11, University of Sydney, Sydney, NSW, 2006, Australia
| | - Kazuya Kobayashi
- Laboratory of Insect Ecology, Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan
| | - Tomonari Nozaki
- Laboratory of Insect Ecology, Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan
| | - Taro Fuchikawa
- Laboratory of Insect Ecology, Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan
| | - Nobuaki Mizumoto
- Laboratory of Insect Ecology, Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan
| | - Yusuke Namba
- Laboratory of Insect Ecology, Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan
| | - Kenji Matsuura
- Laboratory of Insect Ecology, Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan
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Puerma E, Orengo DJ, Cruz F, Gómez-Garrido J, Librado P, Salguero D, Papaceit M, Gut M, Segarra C, Alioto TS, Aguadé M. The High-Quality Genome Sequence of the Oceanic Island Endemic Species Drosophila guanche Reveals Signals of Adaptive Evolution in Genes Related to Flight and Genome Stability. Genome Biol Evol 2018; 10:1956-1969. [PMID: 29947749 PMCID: PMC6101566 DOI: 10.1093/gbe/evy135] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/26/2018] [Indexed: 12/18/2022] Open
Abstract
Drosophila guanche is a member of the obscura group that originated in the Canary Islands archipelago upon its colonization by D. subobscura. It evolved into a new species in the laurisilva, a laurel forest present in wet regions that in the islands have only minor long-term weather fluctuations. Oceanic island endemic species such as D. guanche can become model species to investigate not only the relative role of drift and adaptation in speciation processes but also how population size affects nucleotide variation. Moreover, the previous identification of two satellite DNAs in D. guanche makes this species attractive for studying how centromeric DNA evolves. As a prerequisite for its establishment as a model species suitable to address all these questions, we generated a high-quality D. guanche genome sequence composed of 42 cytologically mapped scaffolds, which are assembled into six super-scaffolds (one per chromosome). The comparative analysis of the D. guanche proteome with that of twelve other Drosophila species identified 151 genes that were subject to adaptive evolution in the D. guanche lineage, with a subset of them being involved in flight and genome stability. For example, the Centromere Identifier (CID) protein, directly interacting with centromeric satellite DNA, shows signals of adaptation in this species. Both genomic analyses and FISH of the two satellites would support an ongoing replacement of centromeric satellite DNA in D. guanche.
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Affiliation(s)
- Eva Puerma
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, i Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Spain
| | - Dorcas J Orengo
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, i Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Spain
| | - Fernando Cruz
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Jèssica Gómez-Garrido
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Pablo Librado
- Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen, Denmark.,Laboratoire d'Anthropobiologie Moléculaire et d'Imagerie de Synthèse, CNRS UMR 5288, Université de Toulouse, Université Paul Sabatier, France
| | - David Salguero
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, i Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Spain
| | - Montserrat Papaceit
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, i Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Spain
| | - Marta Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Carmen Segarra
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, i Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Spain
| | - Tyler S Alioto
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Montserrat Aguadé
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, i Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Spain
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Hill T, Betancourt AJ. Extensive exchange of transposable elements in the Drosophila pseudoobscura group. Mob DNA 2018; 9:20. [PMID: 29946370 PMCID: PMC6006672 DOI: 10.1186/s13100-018-0123-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 06/01/2018] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND As species diverge, so does their transposable element (TE) content. Within a genome, TE families may eventually become dormant due to host-silencing mechanisms, natural selection and the accumulation of inactive copies. The transmission of active copies from a TE families, both vertically and horizontally between species, can allow TEs to escape inactivation if it occurs often enough, as it may allow TEs to temporarily escape silencing in a new host. Thus, the contribution of horizontal exchange to TE persistence has been of increasing interest. RESULTS Here, we annotated TEs in five species with sequenced genomes from the D. pseudoobscura species group, and curated a set of TE families found in these species. We found that, compared to host genes, many TE families showed lower neutral divergence between species, consistent with recent transmission of TEs between species. Despite these transfers, there are differences in the TE content between species in the group. CONCLUSIONS The TE content is highly dynamic in the D. pseudoobscura species group, frequently transferring between species, keeping TEs active. This result highlights how frequently transposable elements are transmitted between sympatric species and, despite these transfers, how rapidly species TE content can diverge.
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Affiliation(s)
- Tom Hill
- The Department of Molecular Biosciences, University of Kansas, 4055 Haworth Hall, 1200 Sunnyside Avenue, Lawrence, KS 66045 USA
| | - Andrea J. Betancourt
- Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB UK
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40
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Sessegolo C, Burlet N, Haudry A. Strong phylogenetic inertia on genome size and transposable element content among 26 species of flies. Biol Lett 2017; 12:rsbl.2016.0407. [PMID: 27576524 PMCID: PMC5014035 DOI: 10.1098/rsbl.2016.0407] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2016] [Accepted: 08/08/2016] [Indexed: 01/28/2023] Open
Abstract
While the evolutionary mechanisms driving eukaryote genome size evolution are still debated, repeated element content appears to be crucial. Here, we reconstructed the phylogeny and identified repeats in the genome of 26 Drosophila exhibiting a twofold variation in genome size. The content in transposable elements (TEs) is highly correlated to genome size evolution among these closely related species. We detected a strong phylogenetic signal on the evolution of both genome size and TE content, and a genome contraction in the Drosophila melanogaster subgroup.
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Affiliation(s)
- Camille Sessegolo
- Laboratoire de Biométrie et Biologie Evolutive, Université de Lyon, Université Claude Bernard Lyon 1, CNRS, UMR5558, 69100 Villeurbanne, France
| | - Nelly Burlet
- Laboratoire de Biométrie et Biologie Evolutive, Université de Lyon, Université Claude Bernard Lyon 1, CNRS, UMR5558, 69100 Villeurbanne, France
| | - Annabelle Haudry
- Laboratoire de Biométrie et Biologie Evolutive, Université de Lyon, Université Claude Bernard Lyon 1, CNRS, UMR5558, 69100 Villeurbanne, France
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41
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Liu GC, Dong ZW, He JW, Zhao RP, Wang W, Li XY. Genome size of 14 species of fireflies (Insecta, Coleoptera, Lampyridae). Zool Res 2017; 38:449-458. [PMID: 29280364 PMCID: PMC5767557 DOI: 10.24272/j.issn.2095-8137.2017.078] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 11/01/2017] [Indexed: 12/19/2022] Open
Abstract
Eukaryotic genome size data are important both as the basis for comparative research into genome evolution and as estimators of the cost and difficulty of genome sequencing programs for non-model organisms. In this study, the genome size of 14 species of fireflies (Lampyridae) (two genera in Lampyrinae, three genera in Luciolinae, and one genus in subfamily incertae sedis) were estimated by propidium iodide (PI)-based flow cytometry. The haploid genome sizes of Lampyridae ranged from 0. 42 to 1. 31 pg, a 3. 1-fold span. Genome sizes of the fireflies varied within the tested subfamilies and genera. Lamprigera and Pyrocoelia species had large and small genome sizes, respectively. No correlation was found between genome size and morphological traits such as body length, body width, eye width, and antennal length. Our data provide additional information on genome size estimation of the firefly family Lampyridae. Furthermore, this study will help clarify the cost and difficulty of genome sequencing programs for non-model organisms and will help promote studies on firefly genome evolution.
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Affiliation(s)
- Gui-Chun Liu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming Yunnan 650223, China
- Center for Ecological and Environmental Sciences, Key Laboratory for Space Bioscience & Biotechnology, Northwestern Polytechnical University, Xi'an Shaanxi 710072, China
| | - Zhi-Wei Dong
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming Yunnan 650223, China
| | - Jin-Wu He
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming Yunnan 650223, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ruo-Ping Zhao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming Yunnan 650223, China
| | - Wen Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming Yunnan 650223, China
- Center for Ecological and Environmental Sciences, Key Laboratory for Space Bioscience & Biotechnology, Northwestern Polytechnical University, Xi'an Shaanxi 710072, China
| | - Xue-Yan Li
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming Yunnan 650223, China.
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Leung W, Shaffer CD, Chen EJ, Quisenberry TJ, Ko K, Braverman JM, Giarla TC, Mortimer NT, Reed LK, Smith ST, Robic S, McCartha SR, Perry DR, Prescod LM, Sheppard ZA, Saville KJ, McClish A, Morlock EA, Sochor VR, Stanton B, Veysey-White IC, Revie D, Jimenez LA, Palomino JJ, Patao MD, Patao SM, Himelblau ET, Campbell JD, Hertz AL, McEvilly MF, Wagner AR, Youngblom J, Bedi B, Bettincourt J, Duso E, Her M, Hilton W, House S, Karimi M, Kumimoto K, Lee R, Lopez D, Odisho G, Prasad R, Robbins HL, Sandhu T, Selfridge T, Tsukashima K, Yosif H, Kokan NP, Britt L, Zoellner A, Spana EP, Chlebina BT, Chong I, Friedman H, Mammo DA, Ng CL, Nikam VS, Schwartz NU, Xu TQ, Burg MG, Batten SM, Corbeill LM, Enoch E, Ensign JJ, Franks ME, Haiker B, Ingles JA, Kirkland LD, Lorenz-Guertin JM, Matthews J, Mittig CM, Monsma N, Olson KJ, Perez-Aragon G, Ramic A, Ramirez JR, Scheiber C, Schneider PA, Schultz DE, Simon M, Spencer E, Wernette AC, Wykle ME, Zavala-Arellano E, McDonald MJ, Ostby K, Wendland P, DiAngelo JR, Ceasrine AM, Cox AH, Docherty JEB, Gingras RM, Grieb SM, Pavia MJ, Personius CL, Polak GL, Beach DL, Cerritos HL, Horansky EA, Sharif KA, Moran R, Parrish S, Bickford K, Bland J, Broussard J, Campbell K, Deibel KE, Forka R, Lemke MC, Nelson MB, O'Keeffe C, Ramey SM, Schmidt L, Villegas P, Jones CJ, Christ SL, Mamari S, Rinaldi AS, Stity G, Hark AT, Scheuerman M, Silver Key SC, McRae BD, Haberman AS, Asinof S, Carrington H, Drumm K, Embry T, McGuire R, Miller-Foreman D, Rosen S, Safa N, Schultz D, Segal M, Shevin Y, Svoronos P, Vuong T, Skuse G, Paetkau DW, Bridgman RK, Brown CM, Carroll AR, Gifford FM, Gillespie JB, Herman SE, Holtcamp KL, Host MA, Hussey G, Kramer DM, Lawrence JQ, Martin MM, Niemiec EN, O'Reilly AP, Pahl OA, Quintana G, Rettie EAS, Richardson TL, Rodriguez AE, Rodriguez MO, Schiraldi L, Smith JJ, Sugrue KF, Suriano LJ, Takach KE, Vasquez AM, Velez X, Villafuerte EJ, Vives LT, Zellmer VR, Hauke J, Hauser CR, Barker K, Cannon L, Parsamian P, Parsons S, Wichman Z, Bazinet CW, Johnson DE, Bangura A, Black JA, Chevee V, Einsteen SA, Hilton SK, Kollmer M, Nadendla R, Stamm J, Fafara-Thompson AE, Gygi AM, Ogawa EE, Van Camp M, Kocsisova Z, Leatherman JL, Modahl CM, Rubin MR, Apiz-Saab SS, Arias-Mejias SM, Carrion-Ortiz CF, Claudio-Vazquez PN, Espada-Green DM, Feliciano-Camacho M, Gonzalez-Bonilla KM, Taboas-Arroyo M, Vargas-Franco D, Montañez-Gonzalez R, Perez-Otero J, Rivera-Burgos M, Rivera-Rosario FJ, Eisler HL, Alexander J, Begley SK, Gabbard D, Allen RJ, Aung WY, Barshop WD, Boozalis A, Chu VP, Davis JS, Duggal RN, Franklin R, Gavinski K, Gebreyesus H, Gong HZ, Greenstein RA, Guo AD, Hanson C, Homa KE, Hsu SC, Huang Y, Huo L, Jacobs S, Jia S, Jung KL, Wai-Chee Kong S, Kroll MR, Lee BM, Lee PF, Levine KM, Li AS, Liu C, Liu MM, Lousararian AP, Lowery PB, Mallya AP, Marcus JE, Ng PC, Nguyen HP, Patel R, Precht H, Rastogi S, Sarezky JM, Schefkind A, Schultz MB, Shen D, Skorupa T, Spies NC, Stancu G, Vivian Tsang HM, Turski AL, Venkat R, Waldman LE, Wang K, Wang T, Wei JW, Wu DY, Xiong DD, Yu J, Zhou K, McNeil GP, Fernandez RW, Menzies PG, Gu T, Buhler J, Mardis ER, Elgin SCR. Retrotransposons Are the Major Contributors to the Expansion of the Drosophila ananassae Muller F Element. G3 (BETHESDA, MD.) 2017; 7:2439-2460. [PMID: 28667019 PMCID: PMC5555453 DOI: 10.1534/g3.117.040907] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2017] [Accepted: 04/03/2017] [Indexed: 11/24/2022]
Abstract
The discordance between genome size and the complexity of eukaryotes can partly be attributed to differences in repeat density. The Muller F element (∼5.2 Mb) is the smallest chromosome in Drosophila melanogaster, but it is substantially larger (>18.7 Mb) in D. ananassae To identify the major contributors to the expansion of the F element and to assess their impact, we improved the genome sequence and annotated the genes in a 1.4-Mb region of the D. ananassae F element, and a 1.7-Mb region from the D element for comparison. We find that transposons (particularly LTR and LINE retrotransposons) are major contributors to this expansion (78.6%), while Wolbachia sequences integrated into the D. ananassae genome are minor contributors (0.02%). Both D. melanogaster and D. ananassae F-element genes exhibit distinct characteristics compared to D-element genes (e.g., larger coding spans, larger introns, more coding exons, and lower codon bias), but these differences are exaggerated in D. ananassae Compared to D. melanogaster, the codon bias observed in D. ananassae F-element genes can primarily be attributed to mutational biases instead of selection. The 5' ends of F-element genes in both species are enriched in dimethylation of lysine 4 on histone 3 (H3K4me2), while the coding spans are enriched in H3K9me2. Despite differences in repeat density and gene characteristics, D. ananassae F-element genes show a similar range of expression levels compared to genes in euchromatic domains. This study improves our understanding of how transposons can affect genome size and how genes can function within highly repetitive domains.
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Affiliation(s)
- Wilson Leung
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
| | | | - Elizabeth J Chen
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
| | | | - Kevin Ko
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
| | - John M Braverman
- Department of Biology, Saint Joseph's University, Philadelphia, PA 19131
| | | | - Nathan T Mortimer
- School of Biological Sciences, Illinois State University, Normal, IL 61790
| | - Laura K Reed
- Department of Biological Sciences, University of Alabama, Tuscaloosa, AL 35401
| | - Sheryl T Smith
- Department of Biology, Arcadia University, Glenside, PA 19038
| | - Srebrenka Robic
- Department of Biology, Agnes Scott College, Decatur, GA 30030
| | | | | | | | | | - Ken J Saville
- Department of Biology, Albion College, Albion, MI 49224
| | | | | | | | | | | | - Dennis Revie
- Department of Biology, California Lutheran University, Thousand Oaks, CA 91360
| | - Luis A Jimenez
- Department of Biology, California Lutheran University, Thousand Oaks, CA 91360
| | - Jennifer J Palomino
- Department of Biology, California Lutheran University, Thousand Oaks, CA 91360
| | - Melissa D Patao
- Department of Biology, California Lutheran University, Thousand Oaks, CA 91360
| | - Shane M Patao
- Department of Biology, California Lutheran University, Thousand Oaks, CA 91360
| | - Edward T Himelblau
- Department of Biological Sciences, California Polytechnic State University, San Luis Obispo, CA 93405
| | - Jaclyn D Campbell
- Department of Biological Sciences, California Polytechnic State University, San Luis Obispo, CA 93405
| | - Alexandra L Hertz
- Department of Biological Sciences, California Polytechnic State University, San Luis Obispo, CA 93405
| | - Maddison F McEvilly
- Department of Biological Sciences, California Polytechnic State University, San Luis Obispo, CA 93405
| | - Allison R Wagner
- Department of Biological Sciences, California Polytechnic State University, San Luis Obispo, CA 93405
| | - James Youngblom
- Department of Biology, California State University, Stanislaus, Turlock, CA 95382
| | - Baljit Bedi
- Department of Biology, California State University, Stanislaus, Turlock, CA 95382
| | - Jeffery Bettincourt
- Department of Biology, California State University, Stanislaus, Turlock, CA 95382
| | - Erin Duso
- Department of Biology, California State University, Stanislaus, Turlock, CA 95382
| | - Maiye Her
- Department of Biology, California State University, Stanislaus, Turlock, CA 95382
| | - William Hilton
- Department of Biology, California State University, Stanislaus, Turlock, CA 95382
| | - Samantha House
- Department of Biology, California State University, Stanislaus, Turlock, CA 95382
| | - Masud Karimi
- Department of Biology, California State University, Stanislaus, Turlock, CA 95382
| | - Kevin Kumimoto
- Department of Biology, California State University, Stanislaus, Turlock, CA 95382
| | - Rebekah Lee
- Department of Biology, California State University, Stanislaus, Turlock, CA 95382
| | - Darryl Lopez
- Department of Biology, California State University, Stanislaus, Turlock, CA 95382
| | - George Odisho
- Department of Biology, California State University, Stanislaus, Turlock, CA 95382
| | - Ricky Prasad
- Department of Biology, California State University, Stanislaus, Turlock, CA 95382
| | - Holly Lyn Robbins
- Department of Biology, California State University, Stanislaus, Turlock, CA 95382
| | - Tanveer Sandhu
- Department of Biology, California State University, Stanislaus, Turlock, CA 95382
| | - Tracy Selfridge
- Department of Biology, California State University, Stanislaus, Turlock, CA 95382
| | - Kara Tsukashima
- Department of Biology, California State University, Stanislaus, Turlock, CA 95382
| | - Hani Yosif
- Department of Biology, California State University, Stanislaus, Turlock, CA 95382
| | - Nighat P Kokan
- Department of Natural Sciences, Cardinal Stritch University, Milwaukee, WI 53217
| | - Latia Britt
- Department of Natural Sciences, Cardinal Stritch University, Milwaukee, WI 53217
| | - Alycia Zoellner
- Department of Natural Sciences, Cardinal Stritch University, Milwaukee, WI 53217
| | - Eric P Spana
- Department of Biology, Duke University, Durham, NC 27708
| | - Ben T Chlebina
- Department of Biology, Duke University, Durham, NC 27708
| | - Insun Chong
- Department of Biology, Duke University, Durham, NC 27708
| | | | - Danny A Mammo
- Department of Biology, Duke University, Durham, NC 27708
| | - Chun L Ng
- Department of Biology, Duke University, Durham, NC 27708
| | | | | | - Thomas Q Xu
- Department of Biology, Duke University, Durham, NC 27708
| | - Martin G Burg
- Departments of Biomedical Sciences and Cell and Molecular Biology, Grand Valley State University, Allendale, MI 49401
| | - Spencer M Batten
- Departments of Biomedical Sciences and Cell and Molecular Biology, Grand Valley State University, Allendale, MI 49401
| | - Lindsay M Corbeill
- Departments of Biomedical Sciences and Cell and Molecular Biology, Grand Valley State University, Allendale, MI 49401
| | - Erica Enoch
- Departments of Biomedical Sciences and Cell and Molecular Biology, Grand Valley State University, Allendale, MI 49401
| | - Jesse J Ensign
- Departments of Biomedical Sciences and Cell and Molecular Biology, Grand Valley State University, Allendale, MI 49401
| | - Mary E Franks
- Departments of Biomedical Sciences and Cell and Molecular Biology, Grand Valley State University, Allendale, MI 49401
| | - Breanna Haiker
- Departments of Biomedical Sciences and Cell and Molecular Biology, Grand Valley State University, Allendale, MI 49401
| | - Judith A Ingles
- Departments of Biomedical Sciences and Cell and Molecular Biology, Grand Valley State University, Allendale, MI 49401
| | - Lyndsay D Kirkland
- Departments of Biomedical Sciences and Cell and Molecular Biology, Grand Valley State University, Allendale, MI 49401
| | - Joshua M Lorenz-Guertin
- Departments of Biomedical Sciences and Cell and Molecular Biology, Grand Valley State University, Allendale, MI 49401
| | - Jordan Matthews
- Departments of Biomedical Sciences and Cell and Molecular Biology, Grand Valley State University, Allendale, MI 49401
| | - Cody M Mittig
- Departments of Biomedical Sciences and Cell and Molecular Biology, Grand Valley State University, Allendale, MI 49401
| | - Nicholaus Monsma
- Departments of Biomedical Sciences and Cell and Molecular Biology, Grand Valley State University, Allendale, MI 49401
| | - Katherine J Olson
- Departments of Biomedical Sciences and Cell and Molecular Biology, Grand Valley State University, Allendale, MI 49401
| | - Guillermo Perez-Aragon
- Departments of Biomedical Sciences and Cell and Molecular Biology, Grand Valley State University, Allendale, MI 49401
| | - Alen Ramic
- Departments of Biomedical Sciences and Cell and Molecular Biology, Grand Valley State University, Allendale, MI 49401
| | - Jordan R Ramirez
- Departments of Biomedical Sciences and Cell and Molecular Biology, Grand Valley State University, Allendale, MI 49401
| | - Christopher Scheiber
- Departments of Biomedical Sciences and Cell and Molecular Biology, Grand Valley State University, Allendale, MI 49401
| | - Patrick A Schneider
- Departments of Biomedical Sciences and Cell and Molecular Biology, Grand Valley State University, Allendale, MI 49401
| | - Devon E Schultz
- Departments of Biomedical Sciences and Cell and Molecular Biology, Grand Valley State University, Allendale, MI 49401
| | - Matthew Simon
- Departments of Biomedical Sciences and Cell and Molecular Biology, Grand Valley State University, Allendale, MI 49401
| | - Eric Spencer
- Departments of Biomedical Sciences and Cell and Molecular Biology, Grand Valley State University, Allendale, MI 49401
| | - Adam C Wernette
- Departments of Biomedical Sciences and Cell and Molecular Biology, Grand Valley State University, Allendale, MI 49401
| | - Maxine E Wykle
- Departments of Biomedical Sciences and Cell and Molecular Biology, Grand Valley State University, Allendale, MI 49401
| | - Elizabeth Zavala-Arellano
- Departments of Biomedical Sciences and Cell and Molecular Biology, Grand Valley State University, Allendale, MI 49401
| | - Mitchell J McDonald
- Departments of Biomedical Sciences and Cell and Molecular Biology, Grand Valley State University, Allendale, MI 49401
| | - Kristine Ostby
- Departments of Biomedical Sciences and Cell and Molecular Biology, Grand Valley State University, Allendale, MI 49401
| | - Peter Wendland
- Departments of Biomedical Sciences and Cell and Molecular Biology, Grand Valley State University, Allendale, MI 49401
| | | | | | - Amanda H Cox
- Department of Biology, Hofstra University, Hempstead, NY 11549
| | | | | | | | - Michael J Pavia
- Department of Biology, Hofstra University, Hempstead, NY 11549
| | | | | | - Dale L Beach
- Department of Biological and Environmental Sciences, Longwood University, Farmville, VA 23909
| | - Heaven L Cerritos
- Department of Biological and Environmental Sciences, Longwood University, Farmville, VA 23909
| | - Edward A Horansky
- Department of Biological and Environmental Sciences, Longwood University, Farmville, VA 23909
| | - Karim A Sharif
- Department of Biology, Massasoit Community College, Brockton, MA 02302
| | - Ryan Moran
- Department of Biology, Massasoit Community College, Brockton, MA 02302
| | - Susan Parrish
- Department of Biology, McDaniel College, Westminster, MD 21157
| | | | - Jennifer Bland
- Department of Biology, McDaniel College, Westminster, MD 21157
| | | | - Kerry Campbell
- Department of Biology, McDaniel College, Westminster, MD 21157
| | | | - Richard Forka
- Department of Biology, McDaniel College, Westminster, MD 21157
| | - Monika C Lemke
- Department of Biology, McDaniel College, Westminster, MD 21157
| | - Marlee B Nelson
- Department of Biology, McDaniel College, Westminster, MD 21157
| | | | - S Mariel Ramey
- Department of Biology, McDaniel College, Westminster, MD 21157
| | - Luke Schmidt
- Department of Biology, McDaniel College, Westminster, MD 21157
| | - Paola Villegas
- Department of Biology, McDaniel College, Westminster, MD 21157
| | | | - Stephanie L Christ
- Department of Biological Sciences, Moravian College, Bethlehem, PA 18018
| | - Sami Mamari
- Department of Biological Sciences, Moravian College, Bethlehem, PA 18018
| | - Adam S Rinaldi
- Department of Biological Sciences, Moravian College, Bethlehem, PA 18018
| | - Ghazal Stity
- Department of Biological Sciences, Moravian College, Bethlehem, PA 18018
| | - Amy T Hark
- Department of Biology, Muhlenberg College, Allentown, PA 18104
| | - Mark Scheuerman
- Department of Biology, Muhlenberg College, Allentown, PA 18104
| | - S Catherine Silver Key
- Department of Biological & Biomedical Sciences, North Carolina Central University, Durham, NC 27707
| | - Briana D McRae
- Department of Biological & Biomedical Sciences, North Carolina Central University, Durham, NC 27707
| | | | - Sam Asinof
- Department of Biology, Oberlin College, Oberlin, OH 44074
| | | | - Kelly Drumm
- Department of Biology, Oberlin College, Oberlin, OH 44074
| | - Terrance Embry
- Department of Biology, Oberlin College, Oberlin, OH 44074
| | | | | | - Stella Rosen
- Department of Biology, Oberlin College, Oberlin, OH 44074
| | - Nadia Safa
- Department of Biology, Oberlin College, Oberlin, OH 44074
| | - Darrin Schultz
- Department of Biology, Oberlin College, Oberlin, OH 44074
| | - Matt Segal
- Department of Biology, Oberlin College, Oberlin, OH 44074
| | - Yakov Shevin
- Department of Biology, Oberlin College, Oberlin, OH 44074
| | | | - Tam Vuong
- Department of Biology, Oberlin College, Oberlin, OH 44074
| | - Gary Skuse
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY 14623
| | - Don W Paetkau
- Department of Biology, Saint Mary's College, Notre Dame, IN 46556
| | | | | | - Alicia R Carroll
- Department of Biology, Saint Mary's College, Notre Dame, IN 46556
| | | | | | - Susan E Herman
- Department of Biology, Saint Mary's College, Notre Dame, IN 46556
| | | | - Misha A Host
- Department of Biology, Saint Mary's College, Notre Dame, IN 46556
| | - Gabrielle Hussey
- Department of Biology, Saint Mary's College, Notre Dame, IN 46556
| | | | - Joan Q Lawrence
- Department of Biology, Saint Mary's College, Notre Dame, IN 46556
| | | | - Ellen N Niemiec
- Department of Biology, Saint Mary's College, Notre Dame, IN 46556
| | | | - Olivia A Pahl
- Department of Biology, Saint Mary's College, Notre Dame, IN 46556
| | | | | | | | | | - Mona O Rodriguez
- Department of Biology, Saint Mary's College, Notre Dame, IN 46556
| | - Laura Schiraldi
- Department of Biology, Saint Mary's College, Notre Dame, IN 46556
| | - Joanna J Smith
- Department of Biology, Saint Mary's College, Notre Dame, IN 46556
| | - Kelsey F Sugrue
- Department of Biology, Saint Mary's College, Notre Dame, IN 46556
| | | | - Kaitlyn E Takach
- Department of Biology, Saint Mary's College, Notre Dame, IN 46556
| | | | - Ximena Velez
- Department of Biology, Saint Mary's College, Notre Dame, IN 46556
| | | | - Laura T Vives
- Department of Biology, Saint Mary's College, Notre Dame, IN 46556
| | | | - Jeanette Hauke
- Department of Biology, Simmons College, Boston, MA 02115
| | - Charles R Hauser
- Bioinformatics Program, St. Edward's University, Austin, TX 78704
| | - Karolyn Barker
- Bioinformatics Program, St. Edward's University, Austin, TX 78704
| | - Laurie Cannon
- Bioinformatics Program, St. Edward's University, Austin, TX 78704
| | | | - Samantha Parsons
- Bioinformatics Program, St. Edward's University, Austin, TX 78704
| | | | | | - Diana E Johnson
- Department of Biological Sciences, The George Washington University, Washington, DC 20052
| | - Abubakarr Bangura
- Department of Biological Sciences, The George Washington University, Washington, DC 20052
| | - Jordan A Black
- Department of Biological Sciences, The George Washington University, Washington, DC 20052
| | - Victoria Chevee
- Department of Biological Sciences, The George Washington University, Washington, DC 20052
| | - Sarah A Einsteen
- Department of Biological Sciences, The George Washington University, Washington, DC 20052
| | - Sarah K Hilton
- Department of Biological Sciences, The George Washington University, Washington, DC 20052
| | - Max Kollmer
- Department of Biological Sciences, The George Washington University, Washington, DC 20052
| | - Rahul Nadendla
- Department of Biological Sciences, The George Washington University, Washington, DC 20052
| | - Joyce Stamm
- Department of Biology, University of Evansville, Evansville, IN 47722
| | | | - Amber M Gygi
- Department of Biology, University of Evansville, Evansville, IN 47722
| | - Emmy E Ogawa
- Department of Biology, University of Evansville, Evansville, IN 47722
| | - Matt Van Camp
- Department of Biology, University of Evansville, Evansville, IN 47722
| | - Zuzana Kocsisova
- Department of Biology, University of Evansville, Evansville, IN 47722
| | - Judith L Leatherman
- Department of Biological Sciences, University of Northern Colorado, Greeley, CO 80639
| | - Cassie M Modahl
- Department of Biological Sciences, University of Northern Colorado, Greeley, CO 80639
| | - Michael R Rubin
- Department of Biology, University of Puerto Rico at Cayey, Cayey, PR 00736
| | - Susana S Apiz-Saab
- Department of Biology, University of Puerto Rico at Cayey, Cayey, PR 00736
| | | | | | | | | | | | | | | | | | | | - Joseph Perez-Otero
- Department of Biology, University of Puerto Rico at Cayey, Cayey, PR 00736
| | | | | | - Heather L Eisler
- Department of Biology, University of the Cumberlands, Williamsburg, KY 40769
| | - Jackie Alexander
- Department of Biology, University of the Cumberlands, Williamsburg, KY 40769
| | - Samatha K Begley
- Department of Biology, University of the Cumberlands, Williamsburg, KY 40769
| | - Deana Gabbard
- Department of Biology, University of the Cumberlands, Williamsburg, KY 40769
| | - Robert J Allen
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
| | - Wint Yan Aung
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
| | - William D Barshop
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
| | - Amanda Boozalis
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
| | - Vanessa P Chu
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
| | - Jeremy S Davis
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
| | - Ryan N Duggal
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
| | - Robert Franklin
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
| | - Katherine Gavinski
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
| | - Heran Gebreyesus
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
| | - Henry Z Gong
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
| | - Rachel A Greenstein
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
| | - Averill D Guo
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
| | - Casey Hanson
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
| | - Kaitlin E Homa
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
| | - Simon C Hsu
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
| | - Yi Huang
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
| | - Lucy Huo
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
| | - Sarah Jacobs
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
| | - Sasha Jia
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
| | - Kyle L Jung
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
| | - Sarah Wai-Chee Kong
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
| | - Matthew R Kroll
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
| | - Brandon M Lee
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
| | - Paul F Lee
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
| | - Kevin M Levine
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
| | - Amy S Li
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
| | - Chengyu Liu
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
| | - Max Mian Liu
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
| | - Adam P Lousararian
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
| | - Peter B Lowery
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
| | - Allyson P Mallya
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
| | - Joseph E Marcus
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
| | - Patrick C Ng
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
| | - Hien P Nguyen
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
| | - Ruchik Patel
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
| | - Hashini Precht
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
| | - Suchita Rastogi
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
| | - Jonathan M Sarezky
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
| | - Adam Schefkind
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
| | - Michael B Schultz
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
| | - Delia Shen
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
| | - Tara Skorupa
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
| | - Nicholas C Spies
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
| | - Gabriel Stancu
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
| | | | - Alice L Turski
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
| | - Rohit Venkat
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
| | - Leah E Waldman
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
| | - Kaidi Wang
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
| | - Tracy Wang
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
| | - Jeffrey W Wei
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
| | - Dennis Y Wu
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
| | - David D Xiong
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
| | - Jack Yu
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
| | - Karen Zhou
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
| | - Gerard P McNeil
- Department of Biology, York College / CUNY, Jamaica, NY 11451
| | | | | | - Tingting Gu
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
| | - Jeremy Buhler
- Department of Computer Science and Engineering, Washington University in St. Louis, St. Louis, MO 63130
| | - Elaine R Mardis
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108
| | - Sarah C R Elgin
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
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de Lima LG, Svartman M, Kuhn GCS. Dissecting the Satellite DNA Landscape in Three Cactophilic Drosophila Sequenced Genomes. G3 (BETHESDA, MD.) 2017; 7:2831-2843. [PMID: 28659292 PMCID: PMC5555486 DOI: 10.1534/g3.117.042093] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 06/26/2017] [Indexed: 01/12/2023]
Abstract
Eukaryote genomes are replete with repetitive DNAs. This class includes tandemly repeated satellite DNAs (satDNA) which are among the most abundant, fast evolving (yet poorly studied) genomic components. Here, we used high-throughput sequencing data from three cactophilic Drosophila species, D. buzzatii, D. seriema, and D. mojavensis, to access and study their whole satDNA landscape. In total, the RepeatExplorer software identified five satDNAs, three previously described (pBuM, DBC-150 and CDSTR198) and two novel ones (CDSTR138 and CDSTR130). Only pBuM is shared among all three species. The satDNA repeat length falls within only two classes, between 130 and 200 bp or between 340 and 390 bp. FISH on metaphase and polytene chromosomes revealed the presence of satDNA arrays in at least one of the following genomic compartments: centromeric, telomeric, subtelomeric, or dispersed along euchromatin. The chromosomal distribution ranges from a single chromosome to almost all chromosomes of the complement. Fiber-FISH and sequence analysis of contigs revealed interspersion between pBuM and CDSTR130 in the microchromosomes of D. mojavensis Phylogenetic analyses showed that the pBuM satDNA underwent concerted evolution at both interspecific and intraspecific levels. Based on RNA-seq data, we found transcription activity for pBuM (in D. mojavensis) and CDSTR198 (in D. buzzatii) in all five analyzed developmental stages, most notably in pupae and adult males. Our data revealed that cactophilic Drosophila present the lowest amount of satDNAs (1.9-2.9%) within the Drosophila genus reported so far. We discuss how our findings on the satDNA location, abundance, organization, and transcription activity may be related to functional aspects.
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Affiliation(s)
- Leonardo G de Lima
- Laboratório de Citogenômica Evolutiva, Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais 31270-901, Brazil
| | - Marta Svartman
- Laboratório de Citogenômica Evolutiva, Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais 31270-901, Brazil
| | - Gustavo C S Kuhn
- Laboratório de Citogenômica Evolutiva, Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais 31270-901, Brazil
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44
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Alfsnes K, Leinaas HP, Hessen DO. Genome size in arthropods; different roles of phylogeny, habitat and life history in insects and crustaceans. Ecol Evol 2017; 7:5939-5947. [PMID: 28811889 PMCID: PMC5552920 DOI: 10.1002/ece3.3163] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 05/23/2017] [Indexed: 02/05/2023] Open
Abstract
Despite the major role of genome size for physiology, ecology, and evolution, there is still mixed evidence with regard to proximate and ultimate drivers. The main causes of large genome size are proliferation of noncoding elements and/or duplication events. The relative role and interplay between these proximate causes and the evolutionary patterns shaped by phylogeny, life history traits or environment are largely unknown for the arthropods. Genome size shows a tremendous variability in this group, and it has a major impact on a range of fitness-related parameters such as growth, metabolism, life history traits, and for many species also body size. In this study, we compared genome size in two major arthropod groups, insects and crustaceans, and related this to phylogenetic patterns and parameters affecting ambient temperature (latitude, depth, or altitude), insect developmental mode, as well as crustacean body size and habitat, for species where data were available. For the insects, the genome size is clearly phylogeny-dependent, reflecting primarily their life history and mode of development, while for crustaceans there was a weaker association between genome size and phylogeny, suggesting life cycle strategies and habitat as more important determinants. Maximum observed latitude and depth, and their combined effect, showed positive, and possibly phylogenetic independent, correlations with genome size for crustaceans. This study illustrate the striking difference in genome sizes both between and within these two major groups of arthropods, and that while living in the cold with low developmental rates may promote large genomes in marine crustaceans, there is a multitude of proximate and ultimate drivers of genome size.
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Affiliation(s)
- Kristian Alfsnes
- Department of BiosciencesUniversity of OsloOsloNorway
- Department of Molecular BiologyNorwegian Institute of Public HealthOsloNorway
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45
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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] [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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46
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McCullers TJ, Steiniger M. Transposable elements in Drosophila. Mob Genet Elements 2017; 7:1-18. [PMID: 28580197 PMCID: PMC5443660 DOI: 10.1080/2159256x.2017.1318201] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Revised: 04/07/2017] [Accepted: 04/07/2017] [Indexed: 11/09/2022] Open
Abstract
Transposable elements (TEs) are mobile genetic elements that can mobilize within host genomes. As TEs comprise more than 40% of the human genome and are linked to numerous diseases, understanding their mechanisms of mobilization and regulation is important. Drosophila melanogaster is an ideal model organism for the study of eukaryotic TEs as its genome contains a diverse array of active TEs. TEs universally impact host genome size via transposition and deletion events, but may also adopt unique functional roles in host organisms. There are 2 main classes of TEs: DNA transposons and retrotransposons. These classes are further divided into subgroups of TEs with unique structural and functional characteristics, demonstrating the significant variability among these elements. Despite this variability, D. melanogaster and other eukaryotic organisms utilize conserved mechanisms to regulate TEs. This review focuses on the transposition mechanisms and regulatory pathways of TEs, and their functional roles in D. melanogaster.
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Affiliation(s)
| | - Mindy Steiniger
- Department of Biology, University of Missouri, St. Louis, MO, USA
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47
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Abstract
Long-read sequencing technology promises to greatly enhance de novo assembly of genomes for nonmodel species. Although the error rates of long reads have been a stumbling block, sequencing at high coverage permits the self-correction of many errors. Here, we sequence and de novo assemble the genome of Drosophila serrata, a species from the montium subgroup that has been well-studied for latitudinal clines, sexual selection, and gene expression, but which lacks a reference genome. Using 11 PacBio single-molecule real-time (SMRT cells), we generated 12 Gbp of raw sequence data comprising ∼65 × whole-genome coverage. Read lengths averaged 8940 bp (NRead50 12,200) with the longest read at 53 kbp. We self-corrected reads using the PBDagCon algorithm and assembled the genome using the MHAP algorithm within the PBcR assembler. Total genome length was 198 Mbp with an N50 just under 1 Mbp. Contigs displayed a high degree of chromosome arm-level conservation with the D. melanogaster genome and many could be sensibly placed on the D. serrata physical map. We also provide an initial annotation for this genome using in silico gene predictions that were supported by RNA-seq data.
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48
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Hjelmen CE, Johnston JS. The mode and tempo of genome size evolution in the subgenus Sophophora. PLoS One 2017; 12:e0173505. [PMID: 28267812 PMCID: PMC5340367 DOI: 10.1371/journal.pone.0173505] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Accepted: 02/21/2017] [Indexed: 01/05/2023] Open
Abstract
Genome size varies widely across organisms, with no apparent tie to organismal complexity. While genome size is inherited, there is no established evolutionary model for this trait. Hypotheses have been postulated for the observed variation in genome sizes across species, most notably the effective population size hypothesis, the mutational equilibrium hypothesis, and the adaptive hypothesis. While much data has been collected on genome size, the above hypotheses have largely ignored impacts from phylogenetic relationships. In order to test these competing hypotheses, genome sizes of 87 Sophophora species were analyzed in a comparative phylogenetic approach using Pagel’s parameters of evolution, Blomberg’s K, Abouheif’s Cmean and Moran’s I. In addition to testing the mode and rate of genome size evolution in Sophophora species, the effect of number of taxa on detection of phylogenetic signal was analyzed for each of these comparative phylogenetic methods. Sophophora genome size was found to be dependent on the phylogeny, indicating that evolutionary time was important for predicting the variation among species. Genome size was found to evolve gradually on branches of the tree, with a rapid burst of change early in the phylogeny. These results suggest that Sophophora genome size has experienced gradual changes, which support the largely theoretical mutational equilibrium hypothesis. While some methods (Abouheif’s Cmean and Moran’s I) were found to be affected by increasing taxa numbers, more commonly used methods (λ and Blomberg’s K) were found to have increasing reliability with increasing taxa number, with significantly more support with fifteen or more taxa. Our results suggest that these comparative phylogenetic methods, with adequate taxon sampling, can be a powerful way to uncover the enigma that is genome size variation through incorporation of phylogenetic relationships.
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Affiliation(s)
- Carl E. Hjelmen
- Department of Entomology, Texas A&M University, College Station, Texas, United States of America
- * E-mail:
| | - J. Spencer Johnston
- Department of Entomology, Texas A&M University, College Station, Texas, United States of America
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Gokhman VE, Kuhn KL, Woolley JB, Hopper KR. Variation in genome size and karyotype among closely related aphid parasitoids (Hymenoptera, Aphelinidae). COMPARATIVE CYTOGENETICS 2017; 11:97-117. [PMID: 28919952 PMCID: PMC5599701 DOI: 10.3897/compcytogen.v11i1.10872] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 01/04/2017] [Indexed: 05/28/2023]
Abstract
Genome sizes were measured and determined for the karyotypes of nine species of aphid parasitoids in the genus Aphelinus Dalman,1820. Large differences in genome size and karyotype were found between Aphelinus species, which is surprising given the similarity in their morphology and life history. Genome sizes estimated from flow cytometry were larger for species in the Aphelinus mali (Haldeman, 1851) complex than those for the species in the Aphelinus daucicola Kurdjumov, 1913 and Aphelinus varipes (Förster,1841) complexes. Haploid karyotypes of the Aphelinus daucicola and Aphelinus mali complexes comprised five metacentric chromosomes of similar size, whereas those of the Aphelinus varipes complex had four chromosomes, including a larger and a smaller metacentric chromosome and two small acrocentric chromosomes or a large metacentric and three smaller acrocentric chromosomes. Total lengths of female haploid chromosome sets correlated with genome sizes estimated from flow cytometry. Phylogenetic analysis of karyotypic variation revealed a chromosomal fusion together with pericentric inversions in the common ancestor of the Aphelinus varipes complex and further pericentric inversions in the clade comprising Aphelinus kurdjumovi Mercet, 1930 and Aphelinus hordei Kurdjumov, 1913. Fluorescence in situ hybridization with a 28S ribosomal DNA probe revealed a single site on chromosomes of the haploid karyotype of Aphelinus coreae Hopper & Woolley, 2012. The differences in genome size and total chromosome length between species complexes matched the phylogenetic divergence between them.
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Affiliation(s)
| | - Kristen L. Kuhn
- Beneficial Insects Introduction Research Unit, ARS-USDA, 501 South Chapel Street, Newark, Delaware, United States of America
| | - James B. Woolley
- Department of Entomology, Texas A&M University, College Station, Texas, United States of America
| | - Keith R. Hopper
- Beneficial Insects Introduction Research Unit, ARS-USDA, 501 South Chapel Street, Newark, Delaware, United States of America
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