1
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Liao IJY, Lu TM, Chen ME, Luo YJ. Spiralian genomics and the evolution of animal genome architecture. Brief Funct Genomics 2023; 22:498-508. [PMID: 37507111 DOI: 10.1093/bfgp/elad029] [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: 05/05/2023] [Revised: 06/27/2023] [Accepted: 07/07/2023] [Indexed: 07/30/2023] Open
Abstract
Recent developments in sequencing technologies have greatly improved our knowledge of phylogenetic relationships and genomic architectures throughout the tree of life. Spiralia, a diverse clade within Protostomia, is essential for understanding the evolutionary history of parasitism, gene conversion, nervous systems and animal body plans. In this review, we focus on the current hypotheses of spiralian phylogeny and investigate the impact of long-read sequencing on the quality of genome assemblies. We examine chromosome-level assemblies to highlight key genomic features that have driven spiralian evolution, including karyotype, synteny and the Hox gene organization. In addition, we show how chromosome rearrangement has influenced spiralian genomic structures. Although spiralian genomes have undergone substantial changes, they exhibit both conserved and lineage-specific features. We recommend increasing sequencing efforts and expanding functional genomics research to deepen insights into spiralian biology.
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2
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Falcon F, Tanaka EM, Rodriguez-Terrones D. Transposon waves at the water-to-land transition. Curr Opin Genet Dev 2023; 81:102059. [PMID: 37343338 DOI: 10.1016/j.gde.2023.102059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 05/02/2023] [Accepted: 05/15/2023] [Indexed: 06/23/2023]
Abstract
The major transitions in vertebrate evolution are associated with significant genomic reorganizations. In contrast to the evolutionary processes that occurred at the origin of vertebrates or prior to the radiation of teleost fishes, no whole-genome duplication events occurred during the water-to-land transition, and it remains an open question how did genome dynamics contribute to this prominent evolutionary event. Indeed, the recent sequencing of sarcopterygian and amphibian genomes has revealed that the extant lineages immediately preceding and succeeding this transition harbor an exceptional number of transposable elements and it is tempting to speculate that these sequences might have catalyzed the adaptations that enabled vertebrates to venture into land. Here, we review the genome dynamics associated with the major transitions in vertebrate evolution and discuss how the highly repetitive genomic landscapes revealed by recent efforts to characterize the genomes of amphibians and sarcopterygians argue for turbulent genome dynamics occurring before the water-to-land transition and possibly enabling it.
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Affiliation(s)
- Francisco Falcon
- Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Campus Vienna Biocenter, 1030, Vienna, Austria; Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria. https://twitter.com/@FcoJFalcon
| | - Elly M Tanaka
- Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Campus Vienna Biocenter, 1030, Vienna, Austria.
| | - Diego Rodriguez-Terrones
- Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Campus Vienna Biocenter, 1030, Vienna, Austria.
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3
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Mueller RL, Cressler CE, Schwartz RS, Chong RA, Butler M. Metamorphosis Imposes Variable Constraints on Genome Expansion through Effects on Development. Integr Org Biol 2023; 5:obad015. [PMID: 37143961 PMCID: PMC10153748 DOI: 10.1093/iob/obad015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 02/25/2023] [Accepted: 04/14/2023] [Indexed: 05/06/2023] Open
Abstract
Genome size varies ∼100,000-fold across eukaryotes and has long been hypothesized to be influenced by metamorphosis in animals. Transposable element accumulation has been identified as a major driver of increase, but the nature of constraints limiting the size of genomes has remained unclear, even as traits such as cell size and rate of development co-vary strongly with genome size. Salamanders, which possess diverse metamorphic and non-metamorphic life histories, join the lungfish in having the largest vertebrate genomes-3 to 40 times that of humans-as well as the largest range of variation in genome size. We tested 13 biologically-inspired hypotheses exploring how the form of metamorphosis imposes varying constraints on genome expansion in a broadly representative phylogeny containing 118 species of salamanders. We show that metamorphosis during which animals undergo the most extensive and synchronous remodeling imposes the most severe constraint against genome expansion, with the severity of constraint decreasing with reduced extent and synchronicity of remodeling. More generally, our work demonstrates the potential for broader interpretation of phylogenetic comparative analysis in exploring the balance of multiple evolutionary pressures shaping phenotypic evolution.
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Affiliation(s)
| | - C E Cressler
- School of Biological Sciences, University of Nebraska Lincoln, Lincoln, NE 68588, USA
| | - R S Schwartz
- Department of Biological Sciences, University of Rhode Island, Kingston, RI 02881, USA
| | - R A Chong
- School of Life Sciences, University of Hawai'i, Honolulu, HI 96822, USA
| | - M Butler
- School of Life Sciences, University of Hawai'i, Honolulu, HI 96822, USA
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4
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Wang J, Yuan L, Tang J, Liu J, Sun C, Itgen MW, Chen G, Sessions SK, Zhang G, Mueller RL. Transposable element and host silencing activity in gigantic genomes. Front Cell Dev Biol 2023; 11:1124374. [PMID: 36910142 PMCID: PMC9998948 DOI: 10.3389/fcell.2023.1124374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 02/09/2023] [Indexed: 02/26/2023] Open
Abstract
Transposable elements (TEs) and the silencing machinery of their hosts are engaged in a germline arms-race dynamic that shapes TE accumulation and, therefore, genome size. In animal species with extremely large genomes (>10 Gb), TE accumulation has been pushed to the extreme, prompting the question of whether TE silencing also deviates from typical conditions. To address this question, we characterize TE silencing via two pathways-the piRNA pathway and KRAB-ZFP transcriptional repression-in the male and female gonads of Ranodon sibiricus, a salamander species with a ∼21 Gb genome. We quantify 1) genomic TE diversity, 2) TE expression, and 3) small RNA expression and find a significant relationship between the expression of piRNAs and TEs they target for silencing in both ovaries and testes. We also quantified TE silencing pathway gene expression in R. sibiricus and 14 other vertebrates with genome sizes ranging from 1 to 130 Gb and find no association between pathway expression and genome size. Taken together, our results reveal that the gigantic R. sibiricus genome includes at least 19 putatively active TE superfamilies, all of which are targeted by the piRNA pathway in proportion to their expression levels, suggesting comprehensive piRNA-mediated silencing. Testes have higher TE expression than ovaries, suggesting that they may contribute more to the species' high genomic TE load. We posit that apparently conflicting interpretations of TE silencing and genomic gigantism in the literature, as well as the absence of a correlation between TE silencing pathway gene expression and genome size, can be reconciled by considering whether the TE community or the host is currently "on the attack" in the arms race dynamic.
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Affiliation(s)
- Jie Wang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan, China
| | - Liang Yuan
- School of Life Sciences, Xinjiang Normal University, Urumqi, China
| | - Jiaxing Tang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan, China.,College of Life Sciences, Sichuan Normal University, Chengdu, China
| | - Jiongyu Liu
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan, China
| | - Cheng Sun
- College of Life Sciences, Capital Normal University, Beijing, China
| | - Michael W Itgen
- Department of Biology, Colorado State University, Fort Collins, CO, United States
| | - Guiying Chen
- College of Life Sciences, Sichuan Normal University, Chengdu, China
| | | | - Guangpu Zhang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan, China.,College of Life Sciences, Sichuan Normal University, Chengdu, China
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5
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Tanaka EM. Now that We Got There, What Next? Methods Mol Biol 2023; 2562:471-479. [PMID: 36272095 DOI: 10.1007/978-1-0716-2659-7_31] [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] [Indexed: 06/16/2023]
Abstract
As seen in the protocols in this book, the opportunities to pursue work at the cellular and molecular work in salamanders have considerably broadened over the last years. The availability of genomic information and genome editing, and the possibility to image tissues live and other methods enhance the spectrum of biological questions accessible to all researchers. Here I provide a personal perspective on what I consider exciting future questions open for investigation.
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Affiliation(s)
- Elly M Tanaka
- Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria.
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6
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Pincheira‐Donoso D, Harvey LP, Johnson JV, Hudson D, Finn C, Goodyear LEB, Guirguis J, Hyland EM, Hodgson DJ. Genome size does not influence extinction risk in the world's amphibians. Funct Ecol 2022. [DOI: 10.1111/1365-2435.14247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
| | - Lilly P. Harvey
- School of Science and Technology Nottingham Trent University Nottingham UK
| | - Jack V. Johnson
- School of Biological Sciences Queen's University Belfast Belfast UK
| | - Dave Hudson
- Centre for Ecology and Conservation, College of Life and Environmental Sciences University of Exeter Penryn UK
| | - Catherine Finn
- School of Biological Sciences Queen's University Belfast Belfast UK
| | | | - Jacinta Guirguis
- School of Biological Sciences Queen's University Belfast Belfast UK
| | - Edel M. Hyland
- School of Biological Sciences Queen's University Belfast Belfast UK
| | - Dave J. Hodgson
- Centre for Ecology and Conservation, College of Life and Environmental Sciences University of Exeter Penryn UK
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7
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Medeiros APM, Santos BA, Betancur-R R. Does genome size increase with water depth in marine fishes? Evolution 2022; 76:1578-1589. [PMID: 35585426 DOI: 10.1111/evo.14510] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 03/10/2022] [Accepted: 03/28/2022] [Indexed: 01/22/2023]
Abstract
A growing body of research suggests that genome size in animals can be affected by ecological factors. Half a century ago, Ebeling et al. proposed that genome size increases with depth in some teleost fish groups and discussed a number of biological mechanisms that may explain this pattern (e.g., passive accumulation, adaptive acclimation). Using phylogenetic comparative approaches, we revisit this hypothesis based on genome size and ecological data from up to 708 marine fish species in combination with a set of large-scale phylogenies, including a newly inferred tree. We also conduct modeling approaches of trait evolution and implement a variety of regression analyses to assess the relationship between genome size and depth. Our reanalysis of Ebeling et al.'s dataset shows a weak association between these variables, but the overall pattern in their data is driven by a single clade. Although new analyses based on our "all-species" dataset resulted in positive correlations, providing some evidence that genome size evolves as a function of depth, only one subclade consistently yielded statistically significant correlations. By contrast, negative correlations are rare and nonsignificant. All in all, we find modest evidence for an increase in genome size along the depth axis in marine fishes. We discuss some mechanistic explanations for the observed trends.
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Affiliation(s)
- Aline P M Medeiros
- Programa de Pós-Graduação em Ciências Biológicas, Universidade Federal da Paraíba, João Pessoa, 58051-900, Brazil.,Department of Biology, The University of Oklahoma, Norman, Oklahoma, 73019
| | - Bráulio A Santos
- Departamento de Sistemática e Ecologia, Centro de Ciências Exatas e da Natureza, Universidade Federal da Paraíba, João Pessoa, 58051-900, Brazil
| | - Ricardo Betancur-R
- Department of Biology, The University of Oklahoma, Norman, Oklahoma, 73019
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8
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Transposable Element Diversity Remains High in Gigantic Genomes. J Mol Evol 2022; 90:332-341. [PMID: 35751655 DOI: 10.1007/s00239-022-10063-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 06/08/2022] [Indexed: 10/17/2022]
Abstract
Transposable elements (TEs) are repetitive sequences of DNA that replicate and proliferate throughout genomes. Taken together, all the TEs in a genome form a diverse community of sequences, which can be studied to draw conclusions about genome evolution. TE diversity can be measured using models for ecological community diversity that consider species richness and evenness. Several models predict TE diversity decreasing as genomes expand because of selection against ectopic recombination and/or competition among TEs to garner host replicative machinery and evade host silencing mechanisms. Salamanders have some of the largest vertebrate genomes and highest TE loads. Salamanders of the genus Plethodon, in particular, have genomes that range in size from 20 to 70 Gb. Here, we use Oxford Nanopore sequencing to generate low-coverage genomic sequences for four species of Plethodon that encompass two independent genome expansion events, one in the eastern clade (Plethodon cinereus, 29.3 Gb vs. Plethodon glutinosus, 38.9 Gb) and one in the western clade (Plethodon vehiculum, 46.4 Gb vs Plethodon idahoensis, 67.0 Gb). We classified the TEs in these genomes and found > 40 TE superfamilies, accounting for 22-27% of the genomes. We calculated Simpson's and Shannon's diversity indices to quantify overall TE diversity. In both pairwise comparisons, the diversity index values for the smaller and larger genome were almost identical. This result indicates that, when genomes reach extremely large sizes, they maintain high levels of TE diversity at the superfamily level, in contrast to predictions made by previous studies on smaller genomes.
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9
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Adams AN, Denton RD, Mueller RL. Gigantic genomes of salamanders indicate that body temperature, not genome size, is the driver of global methylation and 5-methylcytosine deamination in vertebrates. Evolution 2022; 76:1052-1061. [PMID: 35275604 DOI: 10.1111/evo.14468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 12/29/2021] [Accepted: 01/14/2022] [Indexed: 01/21/2023]
Abstract
Transposable elements (TEs) are sequences that replicate and move throughout genomes, and they can be silenced through methylation of cytosines at CpG dinucleotides. TE abundance contributes to genome size, but TE silencing variation across genomes of different sizes remains underexplored. Salamanders include most of the largest C-values - 9 to 120 Gb. We measured CpG methylation levels in salamanders with genomes ranging from 2N = ∼58 Gb to 4N = ∼116 Gb. We compared these levels to results from endo- and ectothermic vertebrates with more typical genomes. Salamander methylation levels are approximately 90%, higher than all endotherms. However, salamander methylation does not differ from other ectotherms, despite an approximately 100-fold difference in nuclear DNA content. Because methylation affects the nucleotide compositional landscape through 5-methylcytosine deamination to thymine, we quantified salamander CpG dinucleotide levels and compared them to other vertebrates. Salamanders and other ectotherms have comparable CpG levels, and ectotherm levels are higher than endotherms. These data show no shift in global methylation at the base of salamanders, despite a dramatic increase in TE load and genome size. This result is reconcilable with previous studies that considered endothermy and ectothermy, which may be more important drivers of methylation in vertebrates than genome size.
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Affiliation(s)
| | - Robert Daniel Denton
- Department of Biology, Marian University, Indianapolis, IN, 46222.,Division of Science and Math, University of Minnesota Morris, Morris, MN, 56267
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10
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Taming, Domestication and Exaptation: Trajectories of Transposable Elements in Genomes. Cells 2021; 10:cells10123590. [PMID: 34944100 PMCID: PMC8700633 DOI: 10.3390/cells10123590] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 11/30/2021] [Accepted: 12/06/2021] [Indexed: 02/06/2023] Open
Abstract
During evolution, several types of sequences pass through genomes. Along with mutations and internal genetic tinkering, they are a useful source of genetic variability for adaptation and evolution. Most of these sequences are acquired by horizontal transfers (HT), but some of them may come from the genomes themselves. If they are not lost or eliminated quickly, they can be tamed, domesticated, or even exapted. Each of these processes results from a series of events, depending on the interactions between these sequences and the host genomes, but also on environmental constraints, through their impact on individuals or population fitness. After a brief reminder of the characteristics of each of these states (taming, domestication, exaptation), the evolutionary trajectories of these new or acquired sequences will be presented and discussed, emphasizing that they are not totally independent insofar as the first can constitute a step towards the second, and the second is another step towards the third.
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11
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Recknagel H, Trontelj P. From Cave Dragons to Genomics: Advancements in the Study of Subterranean Tetrapods. Bioscience 2021; 72:254-266. [PMID: 35241972 PMCID: PMC8888124 DOI: 10.1093/biosci/biab117] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Throughout most of the kingdom Animalia, evolutionary transitions from surface life to a life permanently bound to caves and other subterranean habitats have occurred innumerous times. Not so in tetrapods, where a mere 14 cave-obligate species—all plethodontid and proteid salamanders—are known. We discuss why cave tetrapods are so exceptional and why only salamanders have made the transition. Their evolution follows predictable and convergent, albeit independent pathways. Among the many known changes associated with transitions to subterranean life, eye degeneration, starvation resistance, and longevity are especially relevant to human biomedical research. Recently, sequences of salamander genomes have become available opening up genomic research for cave tetrapods. We discuss new genomic methods that can spur our understanding of the evolutionary mechanisms behind convergent phenotypic change, the relative roles of selective and neutral evolution, cryptic species diversity, and data relevant for conservation such as effective population size and demography.
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Affiliation(s)
- Hans Recknagel
- University of Ljubljana, Slovenia, working, Biotechnical Faculty, Dept. of Biology, Subterranean Biology Lab
| | - Peter Trontelj
- University of Ljubljana, Slovenia, working, Biotechnical Faculty, Dept. of Biology, Subterranean Biology Lab
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12
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Carducci F, Carotti E, Gerdol M, Greco S, Canapa A, Barucca M, Biscotti MA. Investigation of the activity of transposable elements and genes involved in their silencing in the newt Cynops orientalis, a species with a giant genome. Sci Rep 2021; 11:14743. [PMID: 34285310 PMCID: PMC8292531 DOI: 10.1038/s41598-021-94193-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 07/05/2021] [Indexed: 02/06/2023] Open
Abstract
Caudata is an order of amphibians with great variation in genome size, which can reach enormous dimensions in salamanders. In this work, we analysed the activity of transposable elements (TEs) in the transcriptomes obtained from female and male gonads of the Chinese fire-bellied newt, Cynops orientalis, a species with a genome about 12-fold larger than the human genome. We also compared these data with genomes of two basal sarcopterygians, coelacanth and lungfish. In the newt our findings highlighted a major impact of non-LTR retroelements and a greater total TE activity compared to the lungfish Protopterus annectens, an organism also characterized by a giant genome. This difference in TE activity might be due to the presence of young copies in newt in agreement also with the increase in the genome size, an event that occurred independently and later than lungfish. Moreover, the activity of 33 target genes encoding proteins involved in the TE host silencing mechanisms, such as Ago/Piwi and NuRD complex, was evaluated and compared between the three species analysed. These data revealed high transcriptional levels of the target genes in both newt and lungfish and confirmed the activity of NuRD complex genes in adults. Finally, phylogenetic analyses performed on PRDM9 and TRIM28 allowed increasing knowledge about the evolution of these two key genes of the NuRD complex silencing mechanism in vertebrates. Our results confirmed that the gigantism of the newt genomes may be attributed to the activity and accumulation of TEs.
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Affiliation(s)
- Federica Carducci
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, Via Brecce Bianche, 60131, Ancona, Italy
| | - Elisa Carotti
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, Via Brecce Bianche, 60131, Ancona, Italy
| | - Marco Gerdol
- Dipartimento di Scienze della Vita, Università degli Studi di Trieste, Via L. Giorgieri, 5, 34127, Trieste, Italy
| | - Samuele Greco
- Dipartimento di Scienze della Vita, Università degli Studi di Trieste, Via L. Giorgieri, 5, 34127, Trieste, Italy
| | - Adriana Canapa
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, Via Brecce Bianche, 60131, Ancona, Italy
| | - Marco Barucca
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, Via Brecce Bianche, 60131, Ancona, Italy.
| | - Maria Assunta Biscotti
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, Via Brecce Bianche, 60131, Ancona, Italy
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13
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Ishikawa K, Taguchi Y, Kobayashi R, Anzai W, Hayashi T, Tokita M. Cranial skeletogenesis of one of the largest amphibians, Andrias japonicus, provides insight into ontogenetic adaptations for feeding in salamanders. Zool J Linn Soc 2021. [DOI: 10.1093/zoolinnean/zlab038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
Skeletal development in salamanders is greatly influenced by their complex life history. Although the relationship between skull development and life history has been investigated in a variety of salamander species, few studies have compared skull development among lineages. Here, we describe the cranial skeletogenesis of the Japanese giant salamander, Andrias japonicus (family Cryptobranchidae), for the first time. To conduct interspecific comparisons, we also describe the cranial skeletogenesis of Hynobius nebulosus (Hynobiidae), Pleurodeles waltl (Salamandridae) and Ambystoma mexicanum (Ambystomatidae). Our comparative analyses reveal interspecific differences in cranial skeletogenesis, particularly in the timing of the onset of ossification, the direction of ossification (e.g. from anterior to posterior) and the ossification pattern of the hyobranchial skeleton. The early onset of jaw ossification, posterior extension of the maxilla and posterolateral inclination of the squamosal in An. japonicus might be adaptations that allow An. japonicus to gulp feed, primarily using the suction force generated by opening the mouth wide, while also supplementing that force by depressing the hyobranchial skeleton. Multivariate regression of skull shape on log10-transformed centroid size revealed that the unique skull shape of adult and subadult An. japonicus forms through hypermorphosis.
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Affiliation(s)
- Kaoru Ishikawa
- Department of Biology, Faculty of Science, Toho University, 2-2-1 Miyama, Funabashi, Chiba, 274-8510, Japan
| | - Yuki Taguchi
- Hiroshima City Asa Zoological Park, Doubutsuen, Asa-cho, Asakita-ku, Hiroshima, Hiroshima, 731-3355, Japan
| | - Ryomei Kobayashi
- Department of Biology, Faculty of Science, Toho University, 2-2-1 Miyama, Funabashi, Chiba, 274-8510, Japan
| | - Wataru Anzai
- Hiroshima City Asa Zoological Park, Doubutsuen, Asa-cho, Asakita-ku, Hiroshima, Hiroshima, 731-3355, Japan
| | - Toshinori Hayashi
- Amphibian Research Center, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-8526, Japan
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-8526, Japan
| | - Masayoshi Tokita
- Department of Biology, Faculty of Science, Toho University, 2-2-1 Miyama, Funabashi, Chiba, 274-8510, Japan
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14
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Lamichhaney S, Catullo R, Keogh JS, Clulow S, Edwards SV, Ezaz T. A bird-like genome from a frog: Mechanisms of genome size reduction in the ornate burrowing frog, Platyplectrum ornatum. Proc Natl Acad Sci U S A 2021; 118:e2011649118. [PMID: 33836564 PMCID: PMC7980411 DOI: 10.1073/pnas.2011649118] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The diversity of genome sizes across the tree of life is of key interest in evolutionary biology. Various correlates of variation in genome size, such as accumulation of transposable elements (TEs) or rate of DNA gain and loss, are well known, but the underlying molecular mechanisms driving or constraining genome size are poorly understood. Here, we study one of the smallest genomes among frogs characterized thus far, that of the ornate burrowing frog (Platyplectrum ornatum) from Australia, and compare it to other published frog and vertebrate genomes to examine the forces driving reduction in genome size. At ∼1.06 gigabases (Gb), the P. ornatum genome is like that of birds, revealing four major mechanisms underlying TE dynamics: reduced abundance of all major classes of TEs; increased net deletion bias in TEs; drastic reduction in intron lengths; and expansion via gene duplication of the repertoire of TE-suppressing Piwi genes, accompanied by increased expression of Piwi-interacting RNA (piRNA)-based TE-silencing pathway genes in germline cells. Transcriptomes from multiple tissues in both sexes corroborate these results and provide insight into sex-differentiation pathways in Platyplectrum Genome skimming of two closely related frog species (Lechriodus fletcheri and Limnodynastes fletcheri) confirms a reduction in TEs as a major driver of genome reduction in Platyplectrum and supports a macroevolutionary scenario of small genome size in frogs driven by convergence in life history, especially rapid tadpole development and tadpole diet. The P. ornatum genome offers a model for future comparative studies on mechanisms of genome size reduction in amphibians and vertebrates generally.
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Affiliation(s)
- Sangeet Lamichhaney
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138
- Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138
| | - Renee Catullo
- Division of Ecology and Evolution, Research School of Biology, Australian National University, Acton, ACT, Australia 2601
- Australian National Insect Collection and Future Science Platform Environomics, Commonwealth Scientific and Industrial Research Organization, Acton, ACT, Australia 2601
| | - J Scott Keogh
- Division of Ecology and Evolution, Research School of Biology, Australian National University, Acton, ACT, Australia 2601
| | - Simon Clulow
- Department of Biological Sciences, Macquarie University, Sydney, NSW, Australia 2109
| | - Scott V Edwards
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138;
- Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138
| | - Tariq Ezaz
- Institute for Applied Ecology, Faculty of Science and Technology, University of Canberra, Canberra, ACT, Australia 2617
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15
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Wang J, Itgen MW, Wang H, Gong Y, Jiang J, Li J, Sun C, Sessions SK, Mueller RL. Gigantic Genomes Provide Empirical Tests of Transposable Element Dynamics Models. GENOMICS PROTEOMICS & BIOINFORMATICS 2021; 19:123-139. [PMID: 33677107 PMCID: PMC8498967 DOI: 10.1016/j.gpb.2020.11.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 11/29/2020] [Accepted: 11/30/2020] [Indexed: 12/12/2022]
Abstract
Transposable elements (TEs) are a major determinant of eukaryotic genome size. The collective properties of a genomic TE community reveal the history of TE/host evolutionary dynamics and impact present-day host structure and function, from genome to organism levels. In rare cases, TE community/genome size has greatly expanded in animals, associated with increased cell size and changes to anatomy and physiology. Here, we characterize the TE landscape of the genome and transcriptome in an amphibian with a giant genome — the caecilianIchthyophis bannanicus, which we show has a genome size of 12.2 Gb. Amphibians are an important model system because the clade includes independent cases of genomic gigantism. The I. bannanicus genome differs compositionally from other giant amphibian genomes, but shares a low rate of ectopic recombination-mediated deletion. We examine TE activity using expression and divergence plots; TEs account for 15% of somatic transcription, and most superfamilies appear active. We quantify TE diversity in the caecilian, as well as other vertebrates with a range of genome sizes, using diversity indices commonly applied in community ecology. We synthesize previous models that integrate TE abundance, diversity, and activity, and test whether the caecilian meets model predictions for genomes with high TE abundance. We propose thorough, consistent characterization of TEs to strengthen future comparative analyses. Such analyses will ultimately be required to reveal whether the divergent TE assemblages found across convergent gigantic genomes reflect fundamental shared features of TE/host genome evolutionary dynamics.
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Affiliation(s)
- Jie Wang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China.
| | - Michael W Itgen
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Huiju Wang
- School of Information and Safety Engineering, Zhongnan University of Economics and Law, Wuhan 430073, China
| | - Yuzhou Gong
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| | - Jianping Jiang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| | - Jiatang Li
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| | - Cheng Sun
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing 100093, China
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16
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Sessions SK, Wake DB. Forever young: Linking regeneration and genome size in salamanders. Dev Dyn 2020; 250:768-778. [DOI: 10.1002/dvdy.279] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 10/21/2020] [Accepted: 11/11/2020] [Indexed: 11/12/2022] Open
Affiliation(s)
| | - David B. Wake
- Department of Integrative Biology and Museum of Vertebrate Zoology University of California Berkeley California USA
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17
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Abstract
Transposable elements (TEs) are mobile DNA sequences that propagate within genomes. Through diverse invasion strategies, TEs have come to occupy a substantial fraction of nearly all eukaryotic genomes, and they represent a major source of genetic variation and novelty. Here we review the defining features of each major group of eukaryotic TEs and explore their evolutionary origins and relationships. We discuss how the unique biology of different TEs influences their propagation and distribution within and across genomes. Environmental and genetic factors acting at the level of the host species further modulate the activity, diversification, and fate of TEs, producing the dramatic variation in TE content observed across eukaryotes. We argue that cataloging TE diversity and dissecting the idiosyncratic behavior of individual elements are crucial to expanding our comprehension of their impact on the biology of genomes and the evolution of species.
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Affiliation(s)
- Jonathan N Wells
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14850; ,
| | - Cédric Feschotte
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14850; ,
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18
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Dorant Y, Cayuela H, Wellband K, Laporte M, Rougemont Q, Mérot C, Normandeau E, Rochette R, Bernatchez L. Copy number variants outperform SNPs to reveal genotype–temperature association in a marine species. Mol Ecol 2020; 29:4765-4782. [DOI: 10.1111/mec.15565] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 07/16/2020] [Accepted: 07/21/2020] [Indexed: 12/12/2022]
Affiliation(s)
- Yann Dorant
- Institut de Biologie Intégrative des Systèmes (IBIS) Université Laval Québec QC Canada
| | - Hugo Cayuela
- Institut de Biologie Intégrative des Systèmes (IBIS) Université Laval Québec QC Canada
| | - Kyle Wellband
- Institut de Biologie Intégrative des Systèmes (IBIS) Université Laval Québec QC Canada
| | - Martin Laporte
- Institut de Biologie Intégrative des Systèmes (IBIS) Université Laval Québec QC Canada
| | - Quentin Rougemont
- Institut de Biologie Intégrative des Systèmes (IBIS) Université Laval Québec QC Canada
| | - Claire Mérot
- Institut de Biologie Intégrative des Systèmes (IBIS) Université Laval Québec QC Canada
| | - Eric Normandeau
- Institut de Biologie Intégrative des Systèmes (IBIS) Université Laval Québec QC Canada
| | - Rémy Rochette
- Department of Biology University of New Brunswick Saint John NB Canada
| | - Louis Bernatchez
- Institut de Biologie Intégrative des Systèmes (IBIS) Université Laval Québec QC Canada
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19
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Canapa A, Biscotti MA, Barucca M, Carducci F, Carotti E, Olmo E. Shedding light upon the complex net of genome size, genome composition and environment in chordates. EUROPEAN ZOOLOGICAL JOURNAL 2020. [DOI: 10.1080/24750263.2020.1747558] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- A. Canapa
- Dipartimento di Scienze della Vita e dell’Ambiente, Università Politecnica delle Marche, Ancona, Italy
| | - M. A. Biscotti
- Dipartimento di Scienze della Vita e dell’Ambiente, Università Politecnica delle Marche, Ancona, Italy
| | - M. Barucca
- Dipartimento di Scienze della Vita e dell’Ambiente, Università Politecnica delle Marche, Ancona, Italy
| | - F. Carducci
- Dipartimento di Scienze della Vita e dell’Ambiente, Università Politecnica delle Marche, Ancona, Italy
| | - E. Carotti
- Dipartimento di Scienze della Vita e dell’Ambiente, Università Politecnica delle Marche, Ancona, Italy
| | - E. Olmo
- Dipartimento di Scienze della Vita e dell’Ambiente, Università Politecnica delle Marche, Ancona, Italy
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20
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Bonett RM, Hess AJ, Ledbetter NM. Facultative Transitions Have Trouble Committing, But Stable Life Cycles Predict Salamander Genome Size Evolution. Evol Biol 2020. [DOI: 10.1007/s11692-020-09497-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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21
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Hopkins WA, DuRant SE, Beck ML, Ray WK, Helm RF, Romero LM. Cortisol is the predominant glucocorticoid in the giant paedomorphic hellbender salamander (Cryptobranchus alleganiensis). Gen Comp Endocrinol 2020; 285:113267. [PMID: 31491375 DOI: 10.1016/j.ygcen.2019.113267] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 08/19/2019] [Accepted: 09/01/2019] [Indexed: 11/20/2022]
Abstract
Corticosterone is widely regarded to be the predominant glucocorticoid produced in amphibians. However, we recently described unusually low baseline and stress-induced corticosterone profiles in eastern hellbenders (Cryptobranchus alleganiensis alleganiensis), a giant, fully aquatic salamander. Here, we hypothesized that hellbenders might also produce cortisol, the predominant glucocorticoid used by fishes and non-rodent mammals. To test our hypothesis, we collected plasma samples in two field experiments and analyzed them using multiple analytical techniques to determine how plasma concentrations of cortisol and corticosterone co-varied after 1) physical restraint and 2) injection with adrenocorticotropic hormone (ACTH), the pituitary hormone responsible for triggering the release of glucocorticoids from amphibian interrenal glands. Using liquid chromatography-mass spectrometry, we found that baseline and restraint-induced plasma concentrations of cortisol were more than five times those of corticosterone. We then demonstrated that plasma concentrations of both glucocorticoids increased in response to ACTH in a dose-dependent manner, but cortisol concentrations were consistently higher (up to 10-fold) than corticosterone. Cortisol and corticosterone concentrations were not correlated with one another at basal or induced conditions. The extremely low plasma concentrations of corticosterone in hellbenders suggests that corticosterone could simply be a byproduct of cortisol production, and raises questions as to whether corticosterone has any distinct physiological function in hellbenders. Our results indicate that hellbenders produce cortisol as their predominant glucocorticoid, supporting a small and inconclusive body of literature indicating that some other amphibians may produce appreciable quantities of cortisol. We hypothesize that the use of cortisol by hellbenders could be an adaptation to their fully aquatic life history due to cortisol's ability to fulfill both mineralocorticoid and glucocorticoid functions, similar to its functions in fishes. Given the large number of amphibian species that are fully aquatic or have aquatic life stages, we suggest that the broadly held assumption that corticosterone is the predominant glucocorticoid in all amphibians requires further scrutiny. Ultimately, multi-species tests of this assumption will reveal the ecological factors that influenced the evolution of endocrine adaptations among amphibian lineages, and may provide insight into convergent evolution of endocrine traits in paedomorphic species.
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Affiliation(s)
- William A Hopkins
- Dept of Fish and Wildlife Conservation, Virginia Tech, Blacksburg, VA 24061, USA.
| | - Sarah E DuRant
- Dept of Biological Sciences, University of Arkansas, Fayetteville, AR 72701, USA
| | - Michelle L Beck
- Dept of Fish and Wildlife Conservation, Virginia Tech, Blacksburg, VA 24061, USA; Dept. of Biology, Rivier University, Nashua, NH 03060, USA
| | - W Keith Ray
- Dept of Biochemistry, Virginia Tech, Blacksburg, VA 24061, USA
| | - Richard F Helm
- Dept of Biochemistry, Virginia Tech, Blacksburg, VA 24061, USA
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22
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Itgen MW, Prša P, Janža R, Skubic L, Townsend JH, Kladnik A, Mali LB, Sessions SK. Genome Size Diversification in Central American Bolitoglossine Salamanders (Caudata; Plethodontidae). COPEIA 2019. [DOI: 10.1643/ch-18-156] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- Michael W. Itgen
- Department of Biology, Colorado State University, 200 West Lake Street, 1878 Campus Delivery, Fort Collins, Colorado 80523; . Send reprint requests to this address
| | - Patrik Prša
- Institute of Pathophysiology, Faculty of Medicine, University of Ljubljana, Zaloška 4, Ljubljana, 1000, Slovenia;
| | - Rok Janža
- Department of Organisms and Ecosystems Research, National Institute of Biology, Večna pot 111, Ljubljana, 1000, Slovenia;
| | - Lucijan Skubic
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Zaloška 4, Ljubljana, 1000, Slovenia;
| | - Josiah H. Townsend
- Department of Biology, Indiana University of Pennsylvania, 975 Oakland Avenue, Indiana, Pennsylvania 15701;
| | - Aleš Kladnik
- Department of Biology, Biotechnical faculty, University of Ljubljana, Slovenia; Mailing address: Jamnikarjeva 101, Ljubljana, 1000, Slovenia; (AK) ; and (LBM)
| | - Lilijana Bizjak Mali
- Department of Biology, Biotechnical faculty, University of Ljubljana, Slovenia; Mailing address: Jamnikarjeva 101, Ljubljana, 1000, Slovenia; (AK) ; and (LBM)
| | - Stanley K. Sessions
- Department of Biology, Hartwick College, 1 Hartwick Drive, Oneonta, New York 13820;
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23
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Genomic Data Reveal Conserved Female Heterogamety in Giant Salamanders with Gigantic Nuclear Genomes. G3-GENES GENOMES GENETICS 2019; 9:3467-3476. [PMID: 31439718 PMCID: PMC6778777 DOI: 10.1534/g3.119.400556] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Systems of genetic sex determination and the homology of sex chromosomes in different taxa vary greatly across vertebrates. Much progress remains to be made in understanding systems of genetic sex determination in non-model organisms, especially those with homomorphic sex chromosomes and/or large genomes. We used reduced representation genome sequencing to investigate genetic sex determination systems in the salamander family Cryptobranchidae (genera Cryptobranchus and Andrias), which typifies both of these inherent difficulties. We tested hypotheses of male- or female-heterogamety by sequencing hundreds of thousands of anonymous genomic regions in a panel of known-sex cryptobranchids and characterized patterns of presence/absence, inferred zygosity, and depth of coverage to identify sex-linked regions of these 56 gigabase genomes. Our results strongly support the hypothesis that all cryptobranchid species possess homologous systems of female heterogamety, despite maintenance of homomorphic sex chromosomes over nearly 60 million years. Additionally, we report a robust, non-invasive genetic assay for sex diagnosis in Cryptobranchus and Andrias which may have great utility for conservation efforts with these endangered salamanders. Co-amplification of these W-linked markers in both cryptobranchid genera provides evidence for long-term sex chromosome stasis in one of the most divergent salamander lineages. These findings inform hypotheses about the ancestral mode of sex determination in salamanders, but suggest that comparative data from other salamander families are needed. Our results further demonstrate that massive genomes are not necessarily a barrier to effective genome-wide sequencing and that the resulting data can be highly informative about sex determination systems in taxa with homomorphic sex chromosomes.
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24
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Lertzman-Lepofsky G, Mooers AØ, Greenberg DA. Ecological constraints associated with genome size across salamander lineages. Proc Biol Sci 2019; 286:20191780. [PMID: 31530144 DOI: 10.1098/rspb.2019.1780] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Salamanders have some of the largest, and most variable, genome sizes among the vertebrates. Larger genomes have been associated with larger cell sizes, lower metabolic rates, and longer embryonic and larval durations in many different taxonomic groups. These life-history traits are often important for dictating fitness under different environmental conditions, suggesting that a species' genome size may have the potential to constrain its ecological distribution. We test how genome size varies with the ephemerality of larval habitat across the salamanders, predicting that species with larger genomes will be constrained to more permanent habitats that permit slower development, while species with smaller genomes will be more broadly distributed across the gradient of habitat ephemerality. We found that salamanders with larger genomes are almost exclusively associated with permanent aquatic habitats. In addition, the evolutionary transition rate between permanent and ephemeral larval habitats is much higher in salamander lineages with smaller genome sizes. These patterns suggest that genome size may act as an evolutionary constraint on the ecological habitats of salamanders, restricting those species with large genomes and slower development to habitats with permanent sources of water.
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Affiliation(s)
- Gavia Lertzman-Lepofsky
- Department of Biological Sciences, Simon Fraser University, Burnaby, British Columbia, Canada V5A 1S6
| | - Arne Ø Mooers
- Department of Biological Sciences, Simon Fraser University, Burnaby, British Columbia, Canada V5A 1S6
| | - Dan A Greenberg
- Department of Biological Sciences, Simon Fraser University, Burnaby, British Columbia, Canada V5A 1S6
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25
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Joven A, Elewa A, Simon A. Model systems for regeneration: salamanders. Development 2019; 146:146/14/dev167700. [PMID: 31332037 DOI: 10.1242/dev.167700] [Citation(s) in RCA: 93] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 05/28/2019] [Indexed: 02/03/2023]
Abstract
Salamanders have been hailed as champions of regeneration, exhibiting a remarkable ability to regrow tissues, organs and even whole body parts, e.g. their limbs. As such, salamanders have provided key insights into the mechanisms by which cells, tissues and organs sense and regenerate missing or damaged parts. In this Primer, we cover the evolutionary context in which salamanders emerged. We outline the varieties of mechanisms deployed during salamander regeneration, and discuss how these mechanisms are currently being explored and how they have advanced our understanding of animal regeneration. We also present arguments about why it is important to study closely related species in regeneration research.
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Affiliation(s)
- Alberto Joven
- Karolinska Institute, Department of Cell and Molecular Biology, Biomedicum, Solnavägen 9, 17163 Stockolm, Sweden
| | - Ahmed Elewa
- Karolinska Institute, Department of Cell and Molecular Biology, Biomedicum, Solnavägen 9, 17163 Stockolm, Sweden
| | - András Simon
- Karolinska Institute, Department of Cell and Molecular Biology, Biomedicum, Solnavägen 9, 17163 Stockolm, Sweden
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26
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Kelleher ES, Azevedo RBR, Zheng Y. The Evolution of Small-RNA-Mediated Silencing of an Invading Transposable Element. Genome Biol Evol 2018; 10:3038-3057. [PMID: 30252073 PMCID: PMC6404463 DOI: 10.1093/gbe/evy218] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/24/2018] [Indexed: 12/11/2022] Open
Abstract
Transposable elements (TEs) are genomic parasites that impose fitness costs on their
hosts by producing deleterious mutations and disrupting gametogenesis. Host genomes avoid
these costs by regulating TE activity, particularly in germline cells where new insertions
are heritable and TEs are exceptionally active. However, the capacity of different
TE-associated fitness costs to select for repression in the host, and the role of
selection in the evolution of TE regulation more generally remain controversial. In this
study, we use forward, individual-based simulations to examine the evolution of
small-RNA-mediated TE regulation, a conserved mechanism for TE repression that is employed
by both prokaryotes and eukaryotes. To design and parameterize a biologically realistic
model, we drew on an extensive survey of empirical studies of the transposition and
regulation of P-element DNA transposons in Drosophila
melanogaster. We observed that even under conservative assumptions, where
small-RNA-mediated regulation reduces transposition only, repression evolves rapidly and
adaptively after the genome is invaded by a new TE in simulated populations. We further
show that the spread of repressor alleles through simulated populations is greatly
enhanced by two additional TE-imposed fitness costs: dysgenic sterility and ectopic
recombination. Finally, we demonstrate that the adaptive mutation rate to repression is a
critical parameter that influences both the evolutionary trajectory of host repression and
the associated proliferation of TEs after invasion in simulated populations. Our findings
suggest that adaptive evolution of TE regulation may be stronger and more prevalent than
previously appreciated, and provide a framework for interpreting empirical data.
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Affiliation(s)
- Erin S Kelleher
- Department of Biology and Biochemistry, University of Houston, Houston
| | | | - Yichen Zheng
- Department of Biology and Biochemistry, University of Houston, Houston.,Biodiversitt und Klima Forschungszentrum, Senckenberg Gesellschaft fr Naturforschung, Frankfurt am Main, Germany.,Institute of Genetics, University of Cologne, 50674 Cologne, NRW, Germany
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27
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Liedtke HC, Gower DJ, Wilkinson M, Gomez-Mestre I. Macroevolutionary shift in the size of amphibian genomes and the role of life history and climate. Nat Ecol Evol 2018; 2:1792-1799. [PMID: 30250158 DOI: 10.1038/s41559-018-0674-4] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2017] [Accepted: 08/17/2018] [Indexed: 11/09/2022]
Abstract
The evolution and great diversity of genome size has been of long-standing interest to biologists, but has seldom been investigated on a broad phylogenetic scale. Here we present a comparative quantitative analysis of factors shaping genome size evolution in amphibians, the extant class of vertebrates with the largest variation in genome size. We find that amphibian genomes have undergone saltations in size, although these are rare and the evolutionary history of genome size in amphibians has otherwise been one of gradual, time-dependent variation (that is, Brownian motion). This macroevolutionary homogeneity is remarkable given the evolutionary and ecological diversity of most other aspects of the natural history of amphibians. Contrary to previous claims, we find no evidence for associations between life cycle complexity and genome size despite the high diversity of reproductive modes and the multiple events of independent evolution of divergent life cycles in the group. Climate (temperature and humidity) affects genome size indirectly, at least in frogs, as a consequence of its effect on premetamorphic developmental period, although directionality of the relationship between developmental period and genome size is not unequivocal.
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Affiliation(s)
- H Christoph Liedtke
- Ecology, Evolution and Developmental Group, Department of Wetland Ecology, Estación Biológica de Doñana (CSIC), Sevilla, Spain
| | - David J Gower
- Department of Life Sciences, Natural History Museum, London, UK
| | - Mark Wilkinson
- Department of Life Sciences, Natural History Museum, London, UK
| | - Ivan Gomez-Mestre
- Ecology, Evolution and Developmental Group, Department of Wetland Ecology, Estación Biológica de Doñana (CSIC), Sevilla, Spain.
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28
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Hernández-Gómez O, Briggler JT, Williams RN. Influence of immunogenetics, sex and body condition on the cutaneous microbial communities of two giant salamanders. Mol Ecol 2018; 27:1915-1929. [PMID: 29411437 DOI: 10.1111/mec.14500] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Revised: 01/23/2018] [Accepted: 01/25/2018] [Indexed: 02/06/2023]
Abstract
The complex association between hosts and microbial symbionts requires the implementation of multiple approaches to evaluate variation in host physiology. Within amphibians, heterogeneity in immunogenetic traits and cutaneous microbiota is associated with variation in disease resistance. Ozark (Cryptobranchus alleganiensis bishopi) and eastern hellbenders (C. a. alleganiensis) provide a model system to assess variation in host traits and microbial communities. Ozark hellbenders have experienced declines throughout their range, are federally endangered and experience wound retardation that is absent in the eastern subspecies. Previous microbial investigations indicate differentiation in the composition of the skin microbiota of both hellbender subspecies, but it is not clear whether these patterns are concurrent with diversity in the major histocompatibility complex (MHC) genes. We characterized the MHC IIB and the skin microbiota of hellbenders in Missouri, where both subspecies co-occur though not sympatric. We compared the microbiota composition and MHC diversity between both subspecies and investigated whether individual-level MHC diversity, sex and body condition were associated with microbiota composition. Overall, MHC IIB diversity was lower in Ozark hellbenders compared to the eastern subspecies. Multivariate statistical comparisons identified microbiota differentiation between Ozark and eastern hellbenders. MHC IIB allele presence/absence, allele divergence, body composition and sex defined grouping of hellbender microbiotas within populations. Differentiation of the cutaneous microbiotas and MHC IIB genes between eastern and Ozark hellbenders suggests that differences exist in immunity between the two subspecies. This study demonstrates how simultaneous assessments of host genetic traits and microbiotas can inform patterns of microbial community structure in natural systems.
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Affiliation(s)
- Obed Hernández-Gómez
- Department of Forestry and Natural Resources, Purdue University, West Lafayette, IN, USA
| | | | - Rod N Williams
- Department of Forestry and Natural Resources, Purdue University, West Lafayette, IN, USA
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29
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The axolotl genome and the evolution of key tissue formation regulators. Nature 2018; 554:50-55. [PMID: 29364872 DOI: 10.1038/nature25458] [Citation(s) in RCA: 312] [Impact Index Per Article: 52.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Accepted: 12/13/2017] [Indexed: 02/08/2023]
Abstract
Salamanders serve as important tetrapod models for developmental, regeneration and evolutionary studies. An extensive molecular toolkit makes the Mexican axolotl (Ambystoma mexicanum) a key representative salamander for molecular investigations. Here we report the sequencing and assembly of the 32-gigabase-pair axolotl genome using an approach that combined long-read sequencing, optical mapping and development of a new genome assembler (MARVEL). We observed a size expansion of introns and intergenic regions, largely attributable to multiplication of long terminal repeat retroelements. We provide evidence that intron size in developmental genes is under constraint and that species-restricted genes may contribute to limb regeneration. The axolotl genome assembly does not contain the essential developmental gene Pax3. However, mutation of the axolotl Pax3 paralogue Pax7 resulted in an axolotl phenotype that was similar to those seen in Pax3-/- and Pax7-/- mutant mice. The axolotl genome provides a rich biological resource for developmental and evolutionary studies.
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30
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Evans T, Johnson AD, Loose M. Virtual Genome Walking across the 32 Gb Ambystoma mexicanum genome; assembling gene models and intronic sequence. Sci Rep 2018; 8:618. [PMID: 29330416 PMCID: PMC5766544 DOI: 10.1038/s41598-017-19128-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 12/19/2017] [Indexed: 11/09/2022] Open
Abstract
Large repeat rich genomes present challenges for assembly using short read technologies. The 32 Gb axolotl genome is estimated to contain ~19 Gb of repetitive DNA making an assembly from short reads alone effectively impossible. Indeed, this model species has been sequenced to 20× coverage but the reads could not be conventionally assembled. Using an alternative strategy, we have assembled subsets of these reads into scaffolds describing over 19,000 gene models. We call this method Virtual Genome Walking as it locally assembles whole genome reads based on a reference transcriptome, identifying exons and iteratively extending them into surrounding genomic sequence. These assemblies are then linked and refined to generate gene models including upstream and downstream genomic, and intronic, sequence. Our assemblies are validated by comparison with previously published axolotl bacterial artificial chromosome (BAC) sequences. Our analyses of axolotl intron length, intron-exon structure, repeat content and synteny provide novel insights into the genic structure of this model species. This resource will enable new experimental approaches in axolotl, such as ChIP-Seq and CRISPR and aid in future whole genome sequencing efforts. The assembled sequences and annotations presented here are freely available for download from https://tinyurl.com/y8gydc6n . The software pipeline is available from https://github.com/LooseLab/iterassemble .
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Affiliation(s)
- Teri Evans
- School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
| | - Andrew D Johnson
- School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
| | - Matthew Loose
- School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK.
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31
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Surmounting the Large-Genome “Problem” for Genomic Data Generation in Salamanders. POPULATION GENOMICS 2018. [DOI: 10.1007/13836_2018_36] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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Mueller RL. piRNAs and Evolutionary Trajectories in Genome Size and Content. J Mol Evol 2017; 85:169-171. [PMID: 29110026 DOI: 10.1007/s00239-017-9818-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 10/30/2017] [Indexed: 11/24/2022]
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Zhang S, Kelleher ES. Targeted identification of TE insertions in a Drosophila genome through hemi-specific PCR. Mob DNA 2017; 8:10. [PMID: 28775768 PMCID: PMC5534036 DOI: 10.1186/s13100-017-0092-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Accepted: 07/10/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Transposable elements (TEs) are major components of eukaryotic genomes and drivers of genome evolution, producing intraspecific polymorphism and interspecific differences through mobilization and non-homologous recombination. TE insertion sites are often highly variable within species, creating a need for targeted genome re-sequencing (TGS) methods to identify TE insertion sites. METHODS We present a hemi-specific PCR approach for TGS of P-elements in Drosophila genomes on the Illumina platform. We also present a computational framework for identifying new insertions from TGS reads. Finally, we describe a new method for estimating the frequency of TE insertions from WGS data, which is based precise insertion sites provided by TGS annotations. RESULTS By comparing our results to TE annotations based on whole genome re-sequencing (WGS) data for the same Drosophilamelanogaster strain, we demonstrate that TGS is powerful for identifying true insertions, even in repeat-rich heterochromatic regions. We also demonstrate that TGS offers enhanced annotation of precise insertion sites, which facilitates estimation of TE insertion frequency. CONCLUSIONS TGS by hemi-specific PCR is a powerful approach for identifying TE insertions of particular TE families in species with a high-quality reference genome, at greatly reduced cost as compared to WGS. It may therefore be ideal for population genomic studies of particular TE families. Additionally, TGS and WGS can be used as complementary approaches, with TGS annotations identifying more annotated insertions with greater precision for a target TE family, and WGS data allowing for estimates of TE insertion frequencies, and a broader picture of the location of non-target TEs across the genome.
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Affiliation(s)
- Shuo Zhang
- Department of Biology and Biochemistry, University of Houston, 3455 Cullen Blvd. Suite 342, Houston, TX 77204 USA
| | - Erin S. Kelleher
- Department of Biology and Biochemistry, University of Houston, 3455 Cullen Blvd. Suite 342, Houston, TX 77204 USA
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Geng X, Li W, Shang H, Gou Q, Zhang F, Zang X, Zeng B, Li J, Wang Y, Ma J, Guo J, Jian J, Chen B, Qiao Z, Zhou M, Wei H, Fang X, Xu C. A reference gene set construction using RNA-seq of multiple tissues of Chinese giant salamander, Andrias davidianus. Gigascience 2017; 6:1-7. [PMID: 28204480 PMCID: PMC5467019 DOI: 10.1093/gigascience/gix006] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Accepted: 02/07/2017] [Indexed: 01/11/2023] Open
Abstract
Background Chinese giant salamander (CGS) is the largest extant amphibian species in the world. Owing to its evolutionary position and four peculiar phenomenon of life (longevity, starvation tolerance, regenerative ability, and hatch without sunshine), it is an invaluable model species for research. However, lack of genomic resources leads to fewer study progresses in these fields, due to its huge genome of ∼50 GB making it extremely difficult to be assembled. Results We reported the sequenced transcriptome of more than 20 tissues from adult CGS using Illumina Hiseq 2000 technology, and a total of 93 366 no-redundancy transcripts with a mean length of 1326 bp were obtained. We developed for the first time an efficient pipeline to construct a high-quality reference gene set of CGS and obtained 26 135 coding genes. BUSCO and homologous assessment showed that our assembly captured 70.6% of vertebrate universal single-copy orthologs, and this coding gene set had a higher proportion of completeness CDS with comparable quality of the protein sets of Tibetan frog. Conclusions These highest quality data will provide a valuable reference gene set to the subsequent research of CGS. In addition, our strategy of de novo transcriptome assembly and protein identification is applicable to similar studies.
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Affiliation(s)
- Xiaofang Geng
- State Key Laboratory Cultivation Base for Cell Differentiation Regulation, College of Life Science, Henan Normal University, Xinxiang 453007, Henan Province, China.,Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi 830046, China
| | | | - Haitao Shang
- Department of Laboratory Animal Science, College of Basic Medical Sciences, Third Military Medical University, Chongqing 400038, China
| | - Qiang Gou
- Chongqing Kui Xu Biotechnology Incorporated Company, Kaixian Country, Chongqing 405423, China
| | - Fuchun Zhang
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi 830046, China
| | - Xiayan Zang
- State Key Laboratory Cultivation Base for Cell Differentiation Regulation, College of Life Science, Henan Normal University, Xinxiang 453007, Henan Province, China
| | - Benhua Zeng
- Department of Laboratory Animal Science, College of Basic Medical Sciences, Third Military Medical University, Chongqing 400038, China
| | - Jiang Li
- BGI-Shenzhen, Shenzhen 518083, China
| | - Ying Wang
- Chongqing Kui Xu Biotechnology Incorporated Company, Kaixian Country, Chongqing 405423, China
| | - Ji Ma
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi 830046, China
| | - Jianlin Guo
- State Key Laboratory Cultivation Base for Cell Differentiation Regulation, College of Life Science, Henan Normal University, Xinxiang 453007, Henan Province, China
| | | | - Bing Chen
- Chongqing Kui Xu Biotechnology Incorporated Company, Kaixian Country, Chongqing 405423, China
| | - Zhigang Qiao
- State Key Laboratory Cultivation Base for Cell Differentiation Regulation, College of Life Science, Henan Normal University, Xinxiang 453007, Henan Province, China
| | - Minghui Zhou
- Chongqing Kui Xu Biotechnology Incorporated Company, Kaixian Country, Chongqing 405423, China
| | - Hong Wei
- Department of Laboratory Animal Science, College of Basic Medical Sciences, Third Military Medical University, Chongqing 400038, China
| | | | - Cunshuan Xu
- State Key Laboratory Cultivation Base for Cell Differentiation Regulation, College of Life Science, Henan Normal University, Xinxiang 453007, Henan Province, China
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Mohlhenrich ER, Mueller RL. Genetic drift and mutational hazard in the evolution of salamander genomic gigantism. Evolution 2016; 70:2865-2878. [DOI: 10.1111/evo.13084] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2015] [Revised: 09/27/2016] [Accepted: 09/27/2016] [Indexed: 12/25/2022]
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Small RNAs from a Big Genome: The piRNA Pathway and Transposable Elements in the Salamander Species Desmognathus fuscus. J Mol Evol 2016; 83:126-136. [PMID: 27743003 DOI: 10.1007/s00239-016-9759-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 10/06/2016] [Indexed: 01/26/2023]
Abstract
Most of the largest vertebrate genomes are found in salamanders, a clade of amphibians that includes 686 species. Salamander genomes range in size from 14 to 120 Gb, reflecting the accumulation of large numbers of transposable element (TE) sequences from all three TE classes. Although DNA loss rates are slow in salamanders relative to other vertebrates, high levels of TE insertion are also likely required to explain such high TE loads. Across the Tree of Life, novel TE insertions are suppressed by several pathways involving small RNA molecules. In most known animals, TE activity in the germline is primarily regulated by the Piwi-interacting RNA (piRNA) pathway. In this study, we test the hypothesis that salamanders' unusually high TE loads reflect the loss of the ancestral piRNA-mediated TE-silencing machinery. We characterized the small RNA pool in the female and male adult gonads, testing for the presence of small RNA molecules that bear the characteristics of TE-targeting piRNAs. We also analyzed the amino acid sequences of piRNA pathway proteins from salamanders and other vertebrates, testing whether the overall patterns of sequence divergence are consistent with conserved pathway function across the vertebrate clade. Our results do not support the hypothesis of piRNA pathway loss; instead, they suggest that the piRNA pathway is expressed in salamanders. Given these results, we propose hypotheses to explain how the extraordinary TE loads in salamander genomes could have accumulated, despite the expression of TE-silencing machinery.
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McCartney-Melstad E, Mount GG, Shaffer HB. Exon capture optimization in amphibians with large genomes. Mol Ecol Resour 2016; 16:1084-94. [DOI: 10.1111/1755-0998.12538] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Revised: 04/13/2016] [Accepted: 05/06/2016] [Indexed: 11/27/2022]
Affiliation(s)
- Evan McCartney-Melstad
- Department of Ecology and Evolutionary Biology; La Kretz Center for California Conservation Science; Institute of the Environment and Sustainability; University of California; Los Angeles CA 90095 USA
| | - Genevieve G. Mount
- Department of Ecology and Evolutionary Biology; La Kretz Center for California Conservation Science; Institute of the Environment and Sustainability; University of California; Los Angeles CA 90095 USA
- Museum of Natural Science; Louisiana State University; Baton Rouge LA 70803 USA
- Department of Biological Sciences; Louisiana State University; Baton Rouge LA 70803 USA
| | - H. Bradley Shaffer
- Department of Ecology and Evolutionary Biology; La Kretz Center for California Conservation Science; Institute of the Environment and Sustainability; University of California; Los Angeles CA 90095 USA
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38
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Keinath MC, Voss SR, Tsonis PA, Smith JJ. A linkage map for the Newt Notophthalmus viridescens: Insights in vertebrate genome and chromosome evolution. Dev Biol 2016; 426:211-218. [PMID: 27265323 DOI: 10.1016/j.ydbio.2016.05.027] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Revised: 05/23/2016] [Accepted: 05/23/2016] [Indexed: 10/21/2022]
Abstract
Genetic linkage maps are fundamental resources that enable diverse genetic and genomic approaches, including quantitative trait locus (QTL) analyses and comparative studies of genome evolution. It is straightforward to build linkage maps for species that are amenable to laboratory culture and genetic crossing designs, and that have relatively small genomes and few chromosomes. It is more difficult to generate linkage maps for species that do not meet these criteria. Here, we introduce a method to rapidly build linkage maps for salamanders, which are known for their enormous genome sizes. As proof of principle, we developed a linkage map with thousands of molecular markers (N=2349) for the Eastern newt (Notophthalmus viridescens). The map contains 12 linkage groups (152.3-934.7cM), only one more than the number of chromosome pairs. Importantly, this map was generated using RNA isolated from a single wild caught female and her 28 offspring. We used the map to reveal chromosome-scale conservation of synteny among N. viridescens, A. mexicanum (Urodela), and chicken (Amniota), and to identify large conserved segments between N. viridescens and Xenopus tropicalis (Anura). We also show that met1, a major effect QTL that regulates the expression of alternate metamorphic and paedomorphic modes of development in Ambystoma, associates with a chromosomal fusion that is not found in the N. viridescens map. Our results shed new light on the ancestral amphibian karyotype and reveal specific fusion and translocation events that shaped the genomes of three amphibian model taxa. The ability to rapidly build linkage maps for large salamander genomes will enable genetic and genomic analyses within this important vertebrate group, and more generally, empower comparative studies of vertebrate biology and evolution.
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Affiliation(s)
- Melissa C Keinath
- Department of Biology, University of Kentucky, Lexington, KY 40506, USA
| | - S Randal Voss
- Department of Biology, University of Kentucky, Lexington, KY 40506, USA; Spinal Cord and Brain and Injury Research Center, University of Kentucky, Lexington, KY 40506, USA
| | | | - Jeramiah J Smith
- Department of Biology, University of Kentucky, Lexington, KY 40506, USA.
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Canapa A, Barucca M, Biscotti MA, Forconi M, Olmo E. Transposons, Genome Size, and Evolutionary Insights in Animals. Cytogenet Genome Res 2016; 147:217-39. [PMID: 26967166 DOI: 10.1159/000444429] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/03/2015] [Indexed: 11/19/2022] Open
Abstract
The relationship between genome size and the percentage of transposons in 161 animal species evidenced that variations in genome size are linked to the amplification or the contraction of transposable elements. The activity of transposable elements could represent a response to environmental stressors. Indeed, although with different trends in protostomes and deuterostomes, comprehensive changes in genome size were recorded in concomitance with particular periods of evolutionary history or adaptations to specific environments. During evolution, genome size and the presence of transposable elements have influenced structural and functional parameters of genomes and cells. Changes of these parameters have had an impact on morphological and functional characteristics of the organism on which natural selection directly acts. Therefore, the current situation represents a balance between insertion and amplification of transposons and the mechanisms responsible for their deletion or for decreasing their activity. Among the latter, methylation and the silencing action of small RNAs likely represent the most frequent mechanisms.
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Affiliation(s)
- Adriana Canapa
- Dipartimento di Scienze della Vita e dell'Ambiente, Universitx00E0; Politecnica delle Marche, Ancona, Italy
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Adams RH, Blackmon H, Reyes-Velasco J, Schield DR, Card DC, Andrew AL, Waynewood N, Castoe TA. Microsatellite landscape evolutionary dynamics across 450 million years of vertebrate genome evolution. Genome 2016; 59:295-310. [PMID: 27064176 DOI: 10.1139/gen-2015-0124] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The evolutionary dynamics of simple sequence repeats (SSRs or microsatellites) across the vertebrate tree of life remain largely undocumented and poorly understood. In this study, we analyzed patterns of genomic microsatellite abundance and evolution across 71 vertebrate genomes. The highest abundances of microsatellites exist in the genomes of ray-finned fishes, squamate reptiles, and mammals, while crocodilian, turtle, and avian genomes exhibit reduced microsatellite landscapes. We used comparative methods to infer evolutionary rates of change in microsatellite abundance across vertebrates and to highlight particular lineages that have experienced unusually high or low rates of change in genomic microsatellite abundance. Overall, most variation in microsatellite content, abundance, and evolutionary rate is observed among major lineages of reptiles, yet we found that several deeply divergent clades (i.e., squamate reptiles and mammals) contained relatively similar genomic microsatellite compositions. Archosauromorph reptiles (turtles, crocodilians, and birds) exhibit reduced genomic microsatellite content and the slowest rates of microsatellite evolution, in contrast to squamate reptile genomes that have among the highest rates of microsatellite evolution. Substantial branch-specific shifts in SSR content in primates, monotremes, rodents, snakes, and fish are also evident. Collectively, our results support multiple major shifts in microsatellite genomic landscapes among vertebrates.
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Affiliation(s)
- Richard H Adams
- a Department of Biology, 501 S. Nedderman Dr., University of Texas at Arlington, TX 76019, USA
| | - Heath Blackmon
- b Department of Ecology, Evolution & Behavior, 1987 Upper Buford Cir., University of Minnesota, Saint Paul, MN 55108-6097, USA
| | - Jacobo Reyes-Velasco
- a Department of Biology, 501 S. Nedderman Dr., University of Texas at Arlington, TX 76019, USA
| | - Drew R Schield
- a Department of Biology, 501 S. Nedderman Dr., University of Texas at Arlington, TX 76019, USA
| | - Daren C Card
- a Department of Biology, 501 S. Nedderman Dr., University of Texas at Arlington, TX 76019, USA
| | - Audra L Andrew
- a Department of Biology, 501 S. Nedderman Dr., University of Texas at Arlington, TX 76019, USA
| | - Nyimah Waynewood
- a Department of Biology, 501 S. Nedderman Dr., University of Texas at Arlington, TX 76019, USA
| | - Todd A Castoe
- a Department of Biology, 501 S. Nedderman Dr., University of Texas at Arlington, TX 76019, USA
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Keinath MC, Timoshevskiy VA, Timoshevskaya NY, Tsonis PA, Voss SR, Smith JJ. Initial characterization of the large genome of the salamander Ambystoma mexicanum using shotgun and laser capture chromosome sequencing. Sci Rep 2015; 5:16413. [PMID: 26553646 PMCID: PMC4639759 DOI: 10.1038/srep16413] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2015] [Accepted: 10/14/2015] [Indexed: 12/22/2022] Open
Abstract
Vertebrates exhibit substantial diversity in genome size, and some of the largest genomes exist in species that uniquely inform diverse areas of basic and biomedical research. For example, the salamander Ambystoma mexicanum (the Mexican axolotl) is a model organism for studies of regeneration, development and genome evolution, yet its genome is ~10× larger than the human genome. As part of a hierarchical approach toward improving genome resources for the species, we generated 600 Gb of shotgun sequence data and developed methods for sequencing individual laser-captured chromosomes. Based on these data, we estimate that the A. mexicanum genome is ~32 Gb. Notably, as much as 19 Gb of the A. mexicanum genome can potentially be considered single copy, which presumably reflects the evolutionary diversification of mobile elements that accumulated during an ancient episode of genome expansion. Chromosome-targeted sequencing permitted the development of assemblies within the constraints of modern computational platforms, allowed us to place 2062 genes on the two smallest A. mexicanum chromosomes and resolves key events in the history of vertebrate genome evolution. Our analyses show that the capture and sequencing of individual chromosomes is likely to provide valuable information for the systematic sequencing, assembly and scaffolding of large genomes.
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Affiliation(s)
- Melissa C Keinath
- Department of Biology, University of Kentucky, Lexington, KY, 40506, USA
| | | | | | | | - S Randal Voss
- Department of Biology, University of Kentucky, Lexington, KY, 40506, USA.,Spinal Cord and Brain and Injury Research Center, University of Kentucky, Lexington, KY, 40506, USA
| | - Jeramiah J Smith
- Department of Biology, University of Kentucky, Lexington, KY, 40506, USA
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Frahry MB, Sun C, Chong RA, Mueller RL. Low levels of LTR retrotransposon deletion by ectopic recombination in the gigantic genomes of salamanders. J Mol Evol 2015; 80:120-9. [PMID: 25608479 DOI: 10.1007/s00239-014-9663-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Accepted: 12/30/2014] [Indexed: 11/25/2022]
Abstract
Across the tree of life, species vary dramatically in nuclear genome size. Mutations that add or remove sequences from genomes-insertions or deletions, or indels-are the ultimate source of this variation. Differences in the tempo and mode of insertion and deletion across taxa have been proposed to contribute to evolutionary diversity in genome size. Among vertebrates, most of the largest genomes are found within the salamanders, an amphibian clade with genome sizes ranging from ~14 to ~120 Gb. Salamander genomes have been shown to experience slower rates of DNA loss through small (i.e., <30 bp) deletions than do other vertebrate genomes. However, no studies have addressed DNA loss from salamander genomes resulting from larger deletions. Here, we focus on one type of large deletion-ectopic-recombination-mediated removal of LTR retrotransposon sequences. In ectopic recombination, double-strand breaks are repaired using a "wrong" (i.e., ectopic, or non-allelic) template sequence-typically another locus of similar sequence. When breaks occur within the LTR portions of LTR retrotransposons, ectopic-recombination-mediated repair can produce deletions that remove the internal transposon sequence and the equivalent of one of the two LTR sequences. These deletions leave a signature in the genome-a solo LTR sequence. We compared levels of solo LTRs in the genomes of four salamander species with levels present in five vertebrates with smaller genomes. Our results demonstrate that salamanders have low levels of solo LTRs, suggesting that ectopic-recombination-mediated deletion of LTR retrotransposons occurs more slowly than in other vertebrates with smaller genomes.
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Affiliation(s)
- Matthew Blake Frahry
- Department of Biology, Colorado State University, Fort Collins, CO, 80523-1878, USA
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Abstract
Regeneration is studied in a few model species of salamanders, but the ten families of salamanders show considerable variation, and this has implications for our understanding of salamander biology. The most recent classification of the families identifies the cryptobranchoidea as the basal group which diverged in the early Jurassic. Variation in the sizes of genomes is particularly obvious, and reflects a major contribution from transposable elements which is already present in the basal group.Limb development has been a focus for evodevo studies, in part because of the variable property of pre-axial dominance which distinguishes salamanders from other tetrapods. This is thought to reflect the selective pressures that operate on a free-living aquatic larva, and might also be relevant for the evolution of limb regeneration. Recent fossil evidence suggests that both pre-axial dominance and limb regeneration were present 300 million years ago in larval temnospondyl amphibians that lived in mountain lakes. A satisfying account of regeneration in salamanders may need to address all these different aspects in the future.
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