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Cornman RS. A genomic hotspot of diversifying selection and structural change in the hoary bat ( Lasiurus cinereus). PeerJ 2024; 12:e17482. [PMID: 38832043 PMCID: PMC11146322 DOI: 10.7717/peerj.17482] [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: 11/29/2023] [Accepted: 05/07/2024] [Indexed: 06/05/2024] Open
Abstract
Background Previous work found that numerous genes positively selected within the hoary bat (Lasiurus cinereus) lineage are physically clustered in regions of conserved synteny. Here I further validate and expand on those finding utilizing an updated L. cinereus genome assembly and additional bat species as well as other tetrapod outgroups. Methods A chromosome-level assembly was generated by chromatin-contact mapping and made available by DNAZoo (www.dnazoo.org). The genomic organization of orthologous genes was extracted from annotation data for multiple additional bat species as well as other tetrapod clades for which chromosome-level assemblies were available from the National Center for Biotechnology Information (NCBI). Tests of branch-specific positive selection were performed for L. cinereus using PAML as well as with the HyPhy package for comparison. Results Twelve genes exhibiting significant diversifying selection in the L. cinereus lineage were clustered within a 12-Mb genomic window; one of these (Trpc4) also exhibited diversifying selection in bats generally. Ten of the 12 genes are landmarks of two distinct blocks of ancient synteny that are not linked in other tetrapod clades. Bats are further distinguished by frequent structural rearrangements within these synteny blocks, which are rarely observed in other Tetrapoda. Patterns of gene order and orientation among bat taxa are incompatible with phylogeny as presently understood, implying parallel evolution or subsequent reversals. Inferences of positive selection were found to be robust to alternative phylogenetic topologies as well as a strong shift in background nucleotide composition in some taxa. Discussion This study confirms and further localizes a genomic hotspot of protein-coding divergence in the hoary bat, one that also exhibits an increased tempo of structural change in bats compared with other mammals. Most genes in the two synteny blocks have elevated expression in brain tissue in humans and model organisms, and genetic studies implicate the selected genes in cranial and neurological development, among other functions.
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Affiliation(s)
- Robert S. Cornman
- U.S. Geological Survey, Fort Collins Science Center, Fort Collins, Colorado, United States
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2
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Ferguson S, Jones A, Murray K, Andrew R, Schwessinger B, Borevitz J. Plant genome evolution in the genus Eucalyptus is driven by structural rearrangements that promote sequence divergence. Genome Res 2024; 34:606-619. [PMID: 38589251 PMCID: PMC11146599 DOI: 10.1101/gr.277999.123] [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: 04/19/2023] [Accepted: 03/22/2024] [Indexed: 04/10/2024]
Abstract
Genomes have a highly organized architecture (nonrandom organization of functional and nonfunctional genetic elements within chromosomes) that is essential for many biological functions, particularly gene expression and reproduction. Despite the need to conserve genome architecture, a high level of structural variation has been observed within species. As species separate and diverge, genome architecture also diverges, becoming increasingly poorly conserved as divergence time increases. However, within plant genomes, the processes of genome architecture divergence are not well described. Here we use long-read sequencing and de novo assembly of 33 phylogenetically diverse, wild and naturally evolving Eucalyptus species, covering 1-50 million years of diverging genome evolution to measure genome architectural conservation and describe architectural divergence. The investigation of these genomes revealed that following lineage divergence, genome architecture is highly fragmented by rearrangements. As genomes continue to diverge, the accumulation of mutations and the subsequent divergence beyond recognition of rearrangements become the primary driver of genome divergence. The loss of syntenic regions also contribute to genome divergence but at a slower pace than that of rearrangements. We hypothesize that duplications and translocations are potentially the greatest contributors to Eucalyptus genome divergence.
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Affiliation(s)
- Scott Ferguson
- Research School of Biology, Australian National University, Canberra, Australian Capital Territory, 2601, Australia;
| | - Ashley Jones
- Research School of Biology, Australian National University, Canberra, Australian Capital Territory, 2601, Australia;
| | - Kevin Murray
- Research School of Biology, Australian National University, Canberra, Australian Capital Territory, 2601, Australia
- Weigel Department, Max Planck Institute for Biology Tübingen, 72076 Tübingen, Germany
| | - Rose Andrew
- Botany & N.C.W. Beadle Herbarium, School of Environmental and Rural Science, University of New England, Armidale, New South Wales 2351, Australia
| | - Benjamin Schwessinger
- Research School of Biology, Australian National University, Canberra, Australian Capital Territory, 2601, Australia
| | - Justin Borevitz
- Research School of Biology, Australian National University, Canberra, Australian Capital Territory, 2601, Australia
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3
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Thiébaut A, Altenhoff AM, Campli G, Glover N, Dessimoz C, Waterhouse RM. DrosOMA: the Drosophila Orthologous Matrix browser. F1000Res 2024; 12:936. [PMID: 38434623 PMCID: PMC10905159 DOI: 10.12688/f1000research.135250.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/12/2024] [Indexed: 03/05/2024] Open
Abstract
Background Comparative genomic analyses to delineate gene evolutionary histories inform the understanding of organismal biology by characterising gene and gene family origins, trajectories, and dynamics, as well as enabling the tracing of speciation, duplication, and loss events, and facilitating the transfer of gene functional information across species. Genomic data are available for an increasing number of species from the genus Drosophila, however, a dedicated resource exploiting these data to provide the research community with browsable results from genus-wide orthology delineation has been lacking. Methods Using the OMA Orthologous Matrix orthology inference approach and browser deployment framework, we catalogued orthologues across a selected set of Drosophila species with high-quality annotated genomes. We developed and deployed a dedicated instance of the OMA browser to facilitate intuitive exploration, visualisation, and downloading of the genus-wide orthology delineation results. Results DrosOMA - the Drosophila Orthologous Matrix browser, accessible from https://drosoma.dcsr.unil.ch/ - presents the results of orthology delineation for 36 drosophilids from across the genus and four outgroup dipterans. It enables querying and browsing of the orthology data through a feature-rich web interface, with gene-view, orthologous group-view, and genome-view pages, including comprehensive gene name and identifier cross-references together with available functional annotations and protein domain architectures, as well as tools to visualise local and global synteny conservation. Conclusions The DrosOMA browser demonstrates the deployability of the OMA browser framework for building user-friendly orthology databases with dense sampling of a selected taxonomic group. It provides the Drosophila research community with a tailored resource of browsable results from genus-wide orthology delineation.
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Affiliation(s)
- Antonin Thiébaut
- Department of Ecology and Evolution, SIB Swiss Institute of Bioinformatics, University of Lausanne, Lausanne, Switzerland
| | - Adrian M. Altenhoff
- Department of Computer Science, SIB Swiss Institute of Bioinformatics, ETH Zurich, Zurich, Switzerland
| | - Giulia Campli
- Department of Ecology and Evolution, SIB Swiss Institute of Bioinformatics, University of Lausanne, Lausanne, Switzerland
| | - Natasha Glover
- Department of Computational Biology, SIB Swiss Institute of Bioinformatics, University of Lausanne, Lausanne, Switzerland
| | - Christophe Dessimoz
- Department of Computational Biology, SIB Swiss Institute of Bioinformatics, University of Lausanne, Lausanne, Switzerland
| | - Robert M. Waterhouse
- Department of Ecology and Evolution, SIB Swiss Institute of Bioinformatics, University of Lausanne, Lausanne, Switzerland
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4
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Miller DE, Dorador AP, Van Vaerenberghe K, Li A, Grantham EK, Cerbin S, Cummings C, Barragan M, Egidy RR, Scott AR, Hall KE, Perera A, Gilliland WD, Hawley RS, Blumenstiel JP. Off-target piRNA gene silencing in Drosophila melanogaster rescued by a transposable element insertion. PLoS Genet 2023; 19:e1010598. [PMID: 36809339 PMCID: PMC9983838 DOI: 10.1371/journal.pgen.1010598] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 03/03/2023] [Accepted: 01/04/2023] [Indexed: 02/23/2023] Open
Abstract
Transposable elements (TE) are selfish genetic elements that can cause harmful mutations. In Drosophila, it has been estimated that half of all spontaneous visible marker phenotypes are mutations caused by TE insertions. Several factors likely limit the accumulation of exponentially amplifying TEs within genomes. First, synergistic interactions between TEs that amplify their harm with increasing copy number are proposed to limit TE copy number. However, the nature of this synergy is poorly understood. Second, because of the harm posed by TEs, eukaryotes have evolved systems of small RNA-based genome defense to limit transposition. However, as in all immune systems, there is a cost of autoimmunity and small RNA-based systems that silence TEs can inadvertently silence genes flanking TE insertions. In a screen for essential meiotic genes in Drosophila melanogaster, a truncated Doc retrotransposon within a neighboring gene was found to trigger the germline silencing of ald, the Drosophila Mps1 homolog, a gene essential for proper chromosome segregation in meiosis. A subsequent screen for suppressors of this silencing identified a new insertion of a Hobo DNA transposon in the same neighboring gene. Here we describe how the original Doc insertion triggers flanking piRNA biogenesis and local gene silencing. We show that this local gene silencing occurs in cis and is dependent on deadlock, a component of the Rhino-Deadlock-Cutoff (RDC) complex, to trigger dual-strand piRNA biogenesis at TE insertions. We further show how the additional Hobo insertion leads to de-silencing by reducing flanking piRNA biogenesis triggered by the original Doc insertion. These results support a model of TE-mediated gene silencing by piRNA biogenesis in cis that depends on local determinants of transcription. This may explain complex patterns of off-target gene silencing triggered by TEs within populations and in the laboratory. It also provides a mechanism of sign epistasis among TE insertions, illuminates the complex nature of their interactions and supports a model in which off-target gene silencing shapes the evolution of the RDC complex.
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Affiliation(s)
- Danny E. Miller
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
- Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, Kansas, United States of America
- Division of Genetic Medicine, Department of Pediatrics, University of Washington and Seattle Children’s Hospital, Seattle, Washington, United States of America
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America
| | - Ana P. Dorador
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas, United States of America
| | - Kelley Van Vaerenberghe
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas, United States of America
- Division of Biological Sciences, University of Montana, Missoula, Montana, United States of America
| | - Angela Li
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas, United States of America
| | - Emily K. Grantham
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas, United States of America
| | - Stefan Cerbin
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas, United States of America
| | - Celeste Cummings
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas, United States of America
| | - Marilyn Barragan
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas, United States of America
| | - Rhonda R. Egidy
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
| | - Allison R. Scott
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
| | - Kate E. Hall
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
| | - Anoja Perera
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
| | - William D. Gilliland
- Department of Biological Sciences, DePaul University, Chicago, Illinois, United States of America
| | - R. Scott Hawley
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
- Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, Kansas, United States of America
| | - Justin P. Blumenstiel
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas, United States of America
- * E-mail:
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Babišová K, Mentelová L, Geisseová TK, Beňová-Liszeková D, Beňo M, Chase BA, Farkaš R. Apocrine secretion in the salivary glands of Drosophilidae and other dipterans is evolutionarily conserved. Front Cell Dev Biol 2023; 10:1088055. [PMID: 36712974 PMCID: PMC9880899 DOI: 10.3389/fcell.2022.1088055] [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: 11/03/2022] [Accepted: 12/15/2022] [Indexed: 01/15/2023] Open
Abstract
Apocrine secretion is a transport and secretory mechanism that remains only partially characterized, even though it is evolutionarily conserved among all metazoans, including humans. The excellent genetic model organism Drosophila melanogaster holds promise for elucidating the molecular mechanisms regulating this fundamental metazoan process. Two prerequisites for such investigations are to clearly define an experimental system to investigate apocrine secretion and to understand the evolutionarily and functional contexts in which apocrine secretion arose in that system. To this end, we recently demonstrated that, in D. melanogaster, the prepupal salivary glands utilize apocrine secretion prior to pupation to deliver innate immune and defense components to the exuvial fluid that lies between the metamorphosing pupae and its chitinous case. This finding provided a unique opportunity to appraise how this novel non-canonical and non-vesicular transport and secretory mechanism is employed in different developmental and evolutionary contexts. Here we demonstrate that this apocrine secretion, which is mechanistically and temporarily separated from the exocytotic mechanism used to produce the massive salivary glue secretion (Sgs), is shared across Drosophilidae and two unrelated dipteran species. Screening more than 30 species of Drosophila from divergent habitats across the globe revealed that apocrine secretion is a widespread and evolutionarily conserved cellular mechanism used to produce exuvial fluid. Species with longer larval and prepupal development than D. melanogaster activate apocrine secretion later, while smaller and more rapidly developing species activate it earlier. In some species, apocrine secretion occurs after the secretory material is first concentrated in cytoplasmic structures of unknown origin that we name "collectors." Strikingly, in contrast to the widespread use of apocrine secretion to provide exuvial fluid, not all species use exocytosis to produce the viscid salivary glue secretion that is seen in D. melanogaster. Thus, apocrine secretion is the conserved mechanism used to realize the major function of the salivary gland in fruitflies and related species: it produces the pupal exuvial fluid that provides an active defense against microbial invasion during pupal metamorphosis.
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Affiliation(s)
- Klaudia Babišová
- Laboratory of Developmental Genetics, Institute of Experimental Endocrinology, Biomedical Research Center v.v.i., Slovak Academy of Sciences, Bratislava, Slovakia
| | - Lucia Mentelová
- Laboratory of Developmental Genetics, Institute of Experimental Endocrinology, Biomedical Research Center v.v.i., Slovak Academy of Sciences, Bratislava, Slovakia,Department of Genetics, Comenius University, Bratislava, Slovakia
| | - Terézia Klaudia Geisseová
- Laboratory of Developmental Genetics, Institute of Experimental Endocrinology, Biomedical Research Center v.v.i., Slovak Academy of Sciences, Bratislava, Slovakia
| | - Denisa Beňová-Liszeková
- Laboratory of Developmental Genetics, Institute of Experimental Endocrinology, Biomedical Research Center v.v.i., Slovak Academy of Sciences, Bratislava, Slovakia
| | - Milan Beňo
- Laboratory of Developmental Genetics, Institute of Experimental Endocrinology, Biomedical Research Center v.v.i., Slovak Academy of Sciences, Bratislava, Slovakia
| | - Bruce A. Chase
- Department of Biology, University of Nebraska, Omaha, NE, United States
| | - Robert Farkaš
- Laboratory of Developmental Genetics, Institute of Experimental Endocrinology, Biomedical Research Center v.v.i., Slovak Academy of Sciences, Bratislava, Slovakia,*Correspondence: Robert Farkaš,
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6
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De novo metatranscriptomic exploration of gene function in the millipede holobiont. Sci Rep 2022; 12:16173. [PMID: 36171216 PMCID: PMC9519908 DOI: 10.1038/s41598-022-19565-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 08/31/2022] [Indexed: 11/09/2022] Open
Abstract
Invertebrate-microbial associations are widespread in the biosphere and are often related to the function of novel genes, fitness advantages, and even speciation events. Despite ~ 13,000 species of millipedes identified across the world, millipedes and their gut microbiota are markedly understudied compared to other arthropods. Exploring the contribution of individual host-associated microbes is often challenging as many are uncultivable. In this study, we conducted metatranscriptomic profiling of different body segments of a millipede at the holobiont level. This is the first reported transcriptome assembly of a tropical millipede Telodeinopus aoutii (Demange, 1971), as well as the first study on any Myriapoda holobiont. High-throughput RNA sequencing revealed that Telodeinopus aoutii contained > 90% of the core Arthropoda genes. Proteobacteria, Bacteroidetes, Firmicutes, and Euryarchaeota represented dominant and functionally active phyla in the millipede gut, among which 97% of Bacteroidetes and 98% of Firmicutes were present exclusively in the hindgut. A total of 37,831 predicted protein-coding genes of millipede holobiont belonged to six enzyme classes. Around 35% of these proteins were produced by microbiota in the hindgut and 21% by the host in the midgut. Our results indicated that although major metabolic pathways operate at the holobiont level, the involvement of some host and microbial genes are mutually exclusive and microbes predominantly contribute to essential amino acid biosynthesis, short-chain fatty acid metabolism, and fermentation.
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7
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Ko KY, Chen CY, Juan HF, Huang HC. Phylotranscriptomic patterns of network stochasticity and pathway dynamics during embryogenesis. Bioinformatics 2022; 38:763-769. [PMID: 34677580 DOI: 10.1093/bioinformatics/btab735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Revised: 09/30/2021] [Accepted: 10/19/2021] [Indexed: 02/03/2023] Open
Abstract
MOTIVATION The hourglass model is a popular evo-devo model depicting that the developmental constraints in the middle of a developmental process are higher, and hence the phenotypes are evolutionarily more conserved, than those that occur in early and late ontogeny stages. Although this model has been supported by studies analyzing developmental gene expression data, the evolutionary explanation and molecular mechanism behind this phenomenon are not fully understood yet. To approach this problem, Raff proposed a hypothesis and claimed that higher interconnectivity among elements in an organism during organogenesis resulted in the larger constraints at the mid-developmental stage. By employing stochastic network analysis and gene-set pathway analysis, we aim to demonstrate such changes of interconnectivity claimed in Raff's hypothesis. RESULTS We first compared the changes of network randomness among developmental processes in different species by measuring the stochasticity within the biological network in each developmental stage. By tracking the network entropy along each developmental process, we found that the network stochasticity follows an anti-hourglass trajectory, and such a pattern supports Raff's hypothesis in dynamic changes of interconnections among biological modules during development. To understand which biological functions change during the transition of network stochasticity, we sketched out the pathway dynamics along the developmental stages and found that species may activate similar groups of biological processes across different stages. Moreover, higher interspecies correlations are found at the mid-developmental stages. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Kuei-Yueh Ko
- Genome and Systems Biology Degree Program, National Taiwan University, Taipei 106, Taiwan.,Computational Biology and Bioinformatics Program, Duke University, Durham, NC 27710, USA
| | - Cho-Yi Chen
- Institute of Biomedical Informatics, National Yang Ming Chiao Tung University, Taipei 112, Taiwan
| | - Hsueh-Fen Juan
- Genome and Systems Biology Degree Program, National Taiwan University, Taipei 106, Taiwan.,Department of Life Science, Graduate Institute of Biomedical Electronics and Bioinformatics, Center for Computational and Systems Biology, National Taiwan University, Taipei 106, Taiwan
| | - Hsuan-Cheng Huang
- Institute of Biomedical Informatics, National Yang Ming Chiao Tung University, Taipei 112, Taiwan
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Serrato-Capuchina A, D’Agostino ERR, Peede D, Roy B, Isbell K, Wang J, Matute DR. P-elements strengthen reproductive isolation within the Drosophila simulans species complex. Evolution 2021; 75:2425-2440. [PMID: 34463356 PMCID: PMC8772388 DOI: 10.1111/evo.14319] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 04/29/2021] [Accepted: 05/06/2021] [Indexed: 11/28/2022]
Abstract
Determining mechanisms that underlie reproductive isolation (RI) is key to understanding how species boundaries are maintained in nature. Transposable elements (TEs) are ubiquitous across eukaryotic genomes. However, the role of TEs in modulating the strength of RI between species is poorly understood. Several species of Drosophila have been found to harbor P-elements (PEs), yet only D. simulans is known to be currently polymorphic for their presence in wild populations. PEs can cause RI between PE-containing (P) and PE-lacking (M) lineages of the same species. However, it is unclear whether they also contribute to the magnitude of RI between species. Here, we use the simulans species complex to assess whether differences in PE status between D. simulans and its sister species, which do not harbor PEs, contribute to multiple barriers to gene flow between species. We show that crosses involving a P D. simulans father and an M mother from a sister species exhibit lower F1 female fecundity than crosses involving an M D. simulans father and an M sister-species mother. We also find that another TE, I-element, might play a minor role in determining the frequency of dysgenesis between species. Our results suggest that the presence of PEs in a species can strengthen isolation from its sister species, providing evidence that TEs can play a role in RI.
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Affiliation(s)
- Antonio Serrato-Capuchina
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27514
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138
| | - Emmanuel R. R. D’Agostino
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27514
| | - David Peede
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27514
| | - Baylee Roy
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27514
| | - Kristin Isbell
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27514
| | - Jeremy Wang
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27514
| | - Daniel R. Matute
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27514
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Prabh N, Tautz D. Frequent lineage-specific substitution rate changes support an episodic model for protein evolution. G3-GENES GENOMES GENETICS 2021; 11:6372692. [PMID: 34542594 PMCID: PMC8664490 DOI: 10.1093/g3journal/jkab333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 09/13/2021] [Indexed: 12/04/2022]
Abstract
Since the inception of the molecular clock model for sequence evolution, the investigation of protein divergence has revolved around the question of a more or less constant change of amino acid sequences, with specific overall rates for each family. Although anomalies in clock-like divergence are well known, the assumption of a constant decay rate for a given protein family is usually taken as the null model for protein evolution. However, systematic tests of this null model at a genome-wide scale have lagged behind, despite the databases’ enormous growth. We focus here on divergence rate comparisons between very closely related lineages since this allows clear orthology assignments by synteny and reliable alignments, which are crucial for determining substitution rate changes. We generated a high-confidence dataset of syntenic orthologs from four ape species, including humans. We find that despite the appearance of an overall clock-like substitution pattern, several hundred protein families show lineage-specific acceleration and deceleration in divergence rates, or combinations of both in different lineages. Hence, our analysis uncovers a rather dynamic history of substitution rate changes, even between these closely related lineages, implying that one should expect that a large fraction of proteins will have had a history of episodic rate changes in deeper phylogenies. Furthermore, each of the lineages has a separate set of particularly fast diverging proteins. The genes with the highest percentage of branch-specific substitutions are ADCYAP1 in the human lineage (9.7%), CALU in chimpanzees (7.1%), SLC39A14 in the internal branch leading to humans and chimpanzees (4.1%), RNF128 in gorillas (9%), and S100Z in gibbons (15.2%). The mutational pattern in ADCYAP1 suggests a biased mutation process, possibly through asymmetric gene conversion effects. We conclude that a null model of constant change can be problematic for predicting the evolutionary trajectories of individual proteins.
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Affiliation(s)
- Neel Prabh
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, August-Thienemann-Str. 2, 24306 Plön, Germany
| | - Diethard Tautz
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, August-Thienemann-Str. 2, 24306 Plön, Germany
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10
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Saint-Leandre B, Capy P, Hua-Van A, Filée J. piRNA and Transposon Dynamics in Drosophila: A Female Story. Genome Biol Evol 2021; 12:931-947. [PMID: 32396626 PMCID: PMC7337185 DOI: 10.1093/gbe/evaa094] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/06/2020] [Indexed: 12/12/2022] Open
Abstract
The germlines of metazoans contain transposable elements (TEs) causing genetic instability and affecting fitness. To protect the germline from TE activity, gonads of metazoans produce TE-derived PIWI-interacting RNAs (piRNAs) that silence TE expression. In Drosophila, our understanding of piRNA biogenesis is mainly based on studies of the Drosophila melanogaster female germline. However, it is not known whether piRNA functions are also important in the male germline or whether and how piRNAs are affected by the global genomic context. To address these questions, we compared genome sequences, transcriptomes, and small RNA libraries extracted from entire testes and ovaries of two sister species: D. melanogaster and Drosophila simulans. We found that most TE-derived piRNAs were produced in ovaries and that piRNA pathway genes were strongly overexpressed in ovaries compared with testes, indicating that the silencing of TEs by the piRNA pathway mainly took place in the female germline. To study the relationship between host piRNAs and TE landscape, we analyzed TE genomic features and how they correlate with piRNA production in the two species. In D. melanogaster, we found that TE-derived piRNAs target recently active TEs. In contrast, although Drosophila simulans TEs do not display any features of recent activity, the host still intensively produced silencing piRNAs targeting old TE relics. Together, our results show that the piRNA silencing response mainly takes place in Drosophila ovaries and indicate that the host piRNA response is implemented following a burst of TE activity and could persist long after the extinction of active TE families.
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Affiliation(s)
- Bastien Saint-Leandre
- Laboratoire Evolution, Génomes, Comportement, Ecologie CNRS, Université Paris-Sud, IRD, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Pierre Capy
- Laboratoire Evolution, Génomes, Comportement, Ecologie CNRS, Université Paris-Sud, IRD, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Aurelie Hua-Van
- Laboratoire Evolution, Génomes, Comportement, Ecologie CNRS, Université Paris-Sud, IRD, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Jonathan Filée
- Laboratoire Evolution, Génomes, Comportement, Ecologie CNRS, Université Paris-Sud, IRD, Université Paris-Saclay, Gif-sur-Yvette, France
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Larkin A, Marygold SJ, Antonazzo G, Attrill H, Dos Santos G, Garapati PV, Goodman JL, Gramates LS, Millburn G, Strelets VB, Tabone CJ, Thurmond J. FlyBase: updates to the Drosophila melanogaster knowledge base. Nucleic Acids Res 2021; 49:D899-D907. [PMID: 33219682 PMCID: PMC7779046 DOI: 10.1093/nar/gkaa1026] [Citation(s) in RCA: 266] [Impact Index Per Article: 88.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 10/13/2020] [Accepted: 10/22/2020] [Indexed: 01/04/2023] Open
Abstract
FlyBase (flybase.org) is an essential online database for researchers using Drosophila melanogaster as a model organism, facilitating access to a diverse array of information that includes genetic, molecular, genomic and reagent resources. Here, we describe the introduction of several new features at FlyBase, including Pathway Reports, paralog information, disease models based on orthology, customizable tables within reports and overview displays ('ribbons') of expression and disease data. We also describe a variety of recent important updates, including incorporation of a developmental proteome, upgrades to the GAL4 search tab, additional Experimental Tool Reports, migration to JBrowse for genome browsing and improvements to batch queries/downloads and the Fast-Track Your Paper tool.
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Affiliation(s)
- Aoife Larkin
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3DY, UK
| | - Steven J Marygold
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3DY, UK
| | - Giulia Antonazzo
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3DY, UK
| | - Helen Attrill
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3DY, UK
| | - Gilberto Dos Santos
- The Biological Laboratories, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA
| | - Phani V Garapati
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3DY, UK
| | - Joshua L Goodman
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - L Sian Gramates
- The Biological Laboratories, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA
| | - Gillian Millburn
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3DY, UK
| | - Victor B Strelets
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Christopher J Tabone
- The Biological Laboratories, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA
| | - Jim Thurmond
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
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12
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Sackton TB. Studying Natural Selection in the Era of Ubiquitous Genomes. Trends Genet 2020; 36:792-803. [DOI: 10.1016/j.tig.2020.07.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 07/10/2020] [Accepted: 07/13/2020] [Indexed: 01/15/2023]
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13
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Wang YJ, Wang HL, Wang XW, Liu SS. Transcriptome analysis and comparison reveal divergence between the Mediterranean and the greenhouse whiteflies. PLoS One 2020; 15:e0237744. [PMID: 32841246 PMCID: PMC7447059 DOI: 10.1371/journal.pone.0237744] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 07/31/2020] [Indexed: 12/24/2022] Open
Abstract
Both the Mediterranean (MED) species of the Bemisia tabaci whitefly complex and the greenhouse whitefly (Trialeurodes vaporariorum, TV) are important agricultural pests. The two species of whiteflies differ in many aspects such as morphology, geographical distribution, host plant range, plant virus transmission, and resistance to insecticides. However, the molecular basis underlying their differences remains largely unknown. In this study, we analyzed the genetic divergences between the transcriptomes of MED and TV. In total, 2,944 pairs of orthologous genes were identified. The average identity of amino acid sequences between the two species is 93.6%. The average nonsynonymous (Ka) and synonymous (Ks) substitution rates and the ratio of Ka/Ks of the orthologous genes are 0.0389, 2.23 and 0.0204, respectively. The low average Ka/Ks ratio indicates that orthologous genes tend to be under strong purified selection. The most divergent gene classes are related to the metabolisms of xenobiotics, cofactors, vitamins and amino acids, and this divergence may underlie the different biological characteristics between the two species of whiteflies. Genes of differential expression between the two species are enriched in carbohydrate metabolism and regulation of autophagy. These findings provide molecular clues to uncover the biological and molecular differences between the two species of whiteflies.
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Affiliation(s)
- Yu-Jun Wang
- Ministry of Agriculture Key Laboratory of Agricultural Entomology, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Hua-Ling Wang
- Ministry of Agriculture Key Laboratory of Agricultural Entomology, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Xiao-Wei Wang
- Ministry of Agriculture Key Laboratory of Agricultural Entomology, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Shu-Sheng Liu
- Ministry of Agriculture Key Laboratory of Agricultural Entomology, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
- * E-mail:
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14
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Faber-Hammond JJ, Bezault E, Lunt DH, Joyce DA, Renn SCP. The Genomic Substrate for Adaptive Radiation: Copy Number Variation across 12 Tribes of African Cichlid Species. Genome Biol Evol 2020; 11:2856-2874. [PMID: 31504491 DOI: 10.1093/gbe/evz185] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/27/2019] [Indexed: 02/06/2023] Open
Abstract
The initial sequencing of five cichlid genomes revealed an accumulation of genetic variation, including extensive copy number variation in cichlid lineages particularly those that have undergone dramatic evolutionary radiation. Gene duplication has the potential to generate substantial molecular substrate for the origin of evolutionary novelty. We use array-based comparative heterologous genomic hybridization to identify copy number variation events (CNVEs) for 168 samples representing 53 cichlid species including the 5 species for which full genome sequence is available. We identify an average of 50-100 CNVEs per individual. For those species represented by multiple samples, we identify 150-200 total CNVEs suggesting a substantial amount of intraspecific variation. For these species, only ∼10% of the detected CNVEs are fixed. Hierarchical clustering of species according to CNVE data recapitulates phylogenetic relationships fairly well at both the tribe and radiation level. Although CNVEs are detected on all linkage groups, they tend to cluster in "hotspots" and are likely to contain and be flanked by transposable elements. Furthermore, we show that CNVEs impact functional categories of genes with potential roles in adaptive phenotypes that could reasonably promote divergence and speciation in the cichlid clade. These data contribute to a more complete understanding of the molecular basis for adaptive natural selection, speciation, and evolutionary radiation.
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Affiliation(s)
| | - Etienne Bezault
- BOREA Research Unit, MNHN, CNRS 7208, Sorbonne Université, IRD 207, UCN, UA, Paris, France
| | - David H Lunt
- Department of Biological and Marine Sciences, University of Hull, Hull Kingston-Upon-Hull, United Kingdom
| | - Domino A Joyce
- Department of Biological and Marine Sciences, University of Hull, Hull Kingston-Upon-Hull, United Kingdom
| | - Suzy C P Renn
- Department of Biology, Reed College, Portland OR 97202
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15
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Mugal CF, Kutschera VE, Botero-Castro F, Wolf JBW, Kaj I. Polymorphism Data Assist Estimation of the Nonsynonymous over Synonymous Fixation Rate Ratio ω for Closely Related Species. Mol Biol Evol 2020; 37:260-279. [PMID: 31504782 PMCID: PMC6984366 DOI: 10.1093/molbev/msz203] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The ratio of nonsynonymous over synonymous sequence divergence, dN/dS, is a widely used estimate of the nonsynonymous over synonymous fixation rate ratio ω, which measures the extent to which natural selection modulates protein sequence evolution. Its computation is based on a phylogenetic approach and computes sequence divergence of protein-coding DNA between species, traditionally using a single representative DNA sequence per species. This approach ignores the presence of polymorphisms and relies on the indirect assumption that new mutations fix instantaneously, an assumption which is generally violated and reasonable only for distantly related species. The violation of the underlying assumption leads to a time-dependence of sequence divergence, and biased estimates of ω in particular for closely related species, where the contribution of ancestral and lineage-specific polymorphisms to sequence divergence is substantial. We here use a time-dependent Poisson random field model to derive an analytical expression of dN/dS as a function of divergence time and sample size. We then extend our framework to the estimation of the proportion of adaptive protein evolution α. This mathematical treatment enables us to show that the joint usage of polymorphism and divergence data can assist the inference of selection for closely related species. Moreover, our analytical results provide the basis for a protocol for the estimation of ω and α for closely related species. We illustrate the performance of this protocol by studying a population data set of four corvid species, which involves the estimation of ω and α at different time-scales and for several choices of sample sizes.
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Affiliation(s)
- Carina F Mugal
- Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
| | - Verena E Kutschera
- Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden.,Science for Life Laboratory, Stockholm University, Stockholm, Sweden.,Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Fidel Botero-Castro
- Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Planegg-Martinsried, Germany
| | - Jochen B W Wolf
- Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden.,Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Planegg-Martinsried, Germany
| | - Ingemar Kaj
- Department of Mathematics, Uppsala University, Uppsala, Sweden
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16
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Houé V, Gabiane G, Dauga C, Suez M, Madec Y, Mousson L, Marconcini M, Yen PS, de Lamballerie X, Bonizzoni M, Failloux AB. Evolution and biological significance of flaviviral elements in the genome of the arboviral vector Aedes albopictus. Emerg Microbes Infect 2020; 8:1265-1279. [PMID: 31469046 PMCID: PMC6735342 DOI: 10.1080/22221751.2019.1657785] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Since its genome details are publically available, the mosquito Aedes albopictus has become the central stage of attention for deciphering multiple biological and evolutionary aspects at the root of its success as an invasive species. Its genome of 1,967 Mb harbours an unusual high number of non-retroviral integrated RNA virus sequences (NIRVS). NIRVS are enriched in piRNA clusters and produce piRNAs, suggesting an antiviral effect. Here, we investigated the evolutionary history of NIRVS in geographically distant Ae. albopictus populations by comparing genetic variation as derived by neutral microsatellite loci and seven selected NIRVS. We found that the evolution of NIRVS was far to be neutral with variations both in their distribution and sequence polymorphism among Ae. albopictus populations. The Flaviviral elements AlbFlavi2 and AlbFlavi36 were more deeply investigated in their association with dissemination rates of dengue virus (DENV) and chikungunya virus (CHIKV) in Ae. albopictus at both population and individual levels. Our results show a complex association between NIRVS and DENV/CHIKV opening a new avenue for investigating the functional role of NIRVS as antiviral elements shaping vector competence of mosquitoes to arboviruses.
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Affiliation(s)
- Vincent Houé
- Department of Virology, Arboviruses and Insect Vectors, Institut Pasteur , Paris , France.,Sorbonne Université, Collège Doctoral , Paris , France
| | - Gaelle Gabiane
- Department of Virology, Arboviruses and Insect Vectors, Institut Pasteur , Paris , France
| | - Catherine Dauga
- Institut Pasteur, Center for Bioinformatics, BioStatistics and Integrative Biology (C3BI) , Paris , France
| | - Marie Suez
- Institut de Biologie Paris-Seine , Paris , France
| | - Yoann Madec
- Department of Infection and Epidemiology, Institut Pasteur, Epidemiology of Emerging Diseases , Paris , France
| | - Laurence Mousson
- Department of Virology, Arboviruses and Insect Vectors, Institut Pasteur , Paris , France
| | - Michele Marconcini
- Department of Biology and Biotechnology, University of Pavia , Pavia , Italy
| | - Pei-Shi Yen
- Department of Virology, Arboviruses and Insect Vectors, Institut Pasteur , Paris , France
| | - Xavier de Lamballerie
- Aix Marseille Université, IRD French Institute of Research for Development, EHESP French School of Public Health, EPV UMR_D 190 'Emergence des Pathologies Virales' , Marseille , France.,IHU Méditerranée Infection, APHM Public Hospitals of Marseille , Marseille , France
| | | | - Anna-Bella Failloux
- Department of Virology, Arboviruses and Insect Vectors, Institut Pasteur , Paris , France
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17
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Comparative Analysis of Intra- and Inter-Specific Genomic Variability in the Peach Potato Aphid, Myzus persicae. INSECTS 2019; 10:insects10100368. [PMID: 31652640 PMCID: PMC6835256 DOI: 10.3390/insects10100368] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 10/09/2019] [Accepted: 10/17/2019] [Indexed: 12/20/2022]
Abstract
The availability of genomic data in the last decade relating to different aphid species has allowed the analysis of the genomic variability occurring among such species, whereas intra-specific variability has hitherto very largely been neglected. In order to analyse the intra-genomic variability in the peach potato aphid, Myzus persicae, comparative analyses were performed revealing several clone-specific gene duplications, together with numerous deletions/rearrangements. Our comparative approach also allowed us to evaluate the synteny existing between the two M. persicae clones tested and between the peach potato aphid and the pea aphid, Acyrthosiphon pisum. Even if part of the observed rearrangements are related to a low quality of some assembled contigs and/or to the high number of contigs present in these aphid genomes, our evidence reveals that aphid clones are genetically more different than expected. These results suggest that the choice of performing genomes sequencing combining different biotypes/populations, as revealed in the case of the soybean aphid, Aphis glycines, is unlikely to be very informative in aphids. Interestingly, it is possible that the holocentric nature of aphid chromosomes favours genome rearrangements that can be successively inherited transgenerationally via the aphid's apomictic (parthenogenetic) mode of reproduction. Lastly, we evaluated the structure of the cluster of genes coding for the five histones (H1, H2A, H2B, H3 and H4) in order to better understand the quality of the two M. persicae genomes and thereby to improve our knowledge of this functionally important gene family.
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18
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Talla V, Soler L, Kawakami T, Dincă V, Vila R, Friberg M, Wiklund C, Backström N. Dissecting the Effects of Selection and Mutation on Genetic Diversity in Three Wood White (Leptidea) Butterfly Species. Genome Biol Evol 2019; 11:2875-2886. [PMID: 31580421 PMCID: PMC6795238 DOI: 10.1093/gbe/evz212] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/26/2019] [Indexed: 12/12/2022] Open
Abstract
The relative role of natural selection and genetic drift in evolution is a major topic of debate in evolutionary biology. Most knowledge spring from a small group of organisms and originate from before it was possible to generate genome-wide data on genetic variation. Hence, it is necessary to extend to a larger number of taxonomic groups, descriptive and hypothesis-based research aiming at understanding the proximate and ultimate mechanisms underlying both levels of genetic polymorphism and the efficiency of natural selection. In this study, we used data from 60 whole-genome resequenced individuals of three cryptic butterfly species (Leptidea sp.), together with novel gene annotation information and population recombination data. We characterized the overall prevalence of natural selection and investigated the effects of mutation and linked selection on regional variation in nucleotide diversity. Our analyses showed that genome-wide diversity and rate of adaptive substitutions were comparatively low, whereas nonsynonymous to synonymous polymorphism and substitution levels were comparatively high in Leptidea, suggesting small long-term effective population sizes. Still, negative selection on linked sites (background selection) has resulted in reduced nucleotide diversity in regions with relatively high gene density and low recombination rate. We also found a significant effect of mutation rate variation on levels of polymorphism. Finally, there were considerable population differences in levels of genetic diversity and pervasiveness of selection against slightly deleterious alleles, in line with expectations from differences in estimated effective population sizes.
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Affiliation(s)
- Venkat Talla
- Department of Evolutionary Biology, Evolutionary Biology Centre (EBC), Uppsala University, Sweden
| | - Lucile Soler
- Department of Medical Biochemistry and Microbiology, National Bioinformatics Infrastructure Sweden (NBIS), Science for Life Laboratory, Uppsala, Sweden
| | - Takeshi Kawakami
- Department of Evolutionary Biology, Evolutionary Biology Centre (EBC), Uppsala University, Sweden
| | - Vlad Dincă
- Department of Ecology and Genetics, University of Oulu, Finland
| | - Roger Vila
- Institut de Biologia Evolutiva (CSIC-UPF), Barcelona, Spain
| | - Magne Friberg
- Department of Biology, Biodiversity Unit, Lund University, Sweden
| | - Christer Wiklund
- Department of Zoology, Division of Ecology, Stockholm University, Sweden
| | - Niclas Backström
- Department of Evolutionary Biology, Evolutionary Biology Centre (EBC), Uppsala University, Sweden
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19
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Chapman JR, Hill T, Unckless RL. Balancing Selection Drives the Maintenance of Genetic Variation in Drosophila Antimicrobial Peptides. Genome Biol Evol 2019; 11:2691-2701. [PMID: 31504505 PMCID: PMC6764478 DOI: 10.1093/gbe/evz191] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/29/2019] [Indexed: 12/19/2022] Open
Abstract
Genes involved in immune defense against pathogens provide some of the most well-known examples of both directional and balancing selection. Antimicrobial peptides (AMPs) are innate immune effector genes, playing a key role in pathogen clearance in many species, including Drosophila. Conflicting lines of evidence have suggested that AMPs may be under directional, balancing, or purifying selection. Here, we use both a linear model and control-gene-based approach to show that balancing selection is an important force shaping AMP diversity in Drosophila. In Drosophila melanogaster, this is most clearly observed in ancestral African populations. Furthermore, the signature of balancing selection is even more striking once background selection has been accounted for. Balancing selection also acts on AMPs in Drosophila mauritiana, an isolated island endemic separated from D. melanogaster by about 4 Myr of evolution. This suggests that balancing selection may be broadly acting to maintain adaptive diversity in Drosophila AMPs, as has been found in other taxa.
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Affiliation(s)
| | - Tom Hill
- Department of Molecular Biosciences, University of Kansas
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20
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Guillén Y, Casillas S, Ruiz A. Genome-Wide Patterns of Sequence Divergence of Protein-Coding Genes Between Drosophila buzzatii and D. mojavensis. J Hered 2019; 110:92-101. [PMID: 30124907 DOI: 10.1093/jhered/esy041] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 08/14/2018] [Indexed: 12/15/2022] Open
Abstract
Evolutionary rates for protein-coding genes are determined not only by natural selection but also by multiple genomic factors including mutation rates, recombination, gene expression levels, and chromosomal location. To investigate the joint effects of different genomic determinants on protein evolution, we compared the coding sequences of 9017 single-copy orthologs between 2 cactophilic species from the Drosophila subgenus, Drosophila mojavensis and D. buzzatii, whose genomes have been previously sequenced. We assessed the impact of 7 genomic determinants, that is, chromosome type, recombination, chromosomal inversions, expression breadth, expression level, gene length, and the number of exons, on divergence rates of protein-coding genes to understand patterns of evolutionary variation. Integrative analysis of these factors revealed that 1) X-linked and autosomal genes evolve at significantly different rates in agreement with the faster-X hypothesis, 2) genes located on the dot chromosome and pericentromeric regions have higher divergence rates, 3) genes located at chromosomes with more fixed inversions have higher pairwise divergence than those located at nearly collinear chromosomes, and 4) gene expression patterns can be considered the strongest determinant of protein evolution. In addition, the number of exons and protein length had a significant effect on pairwise divergence at synonymous sites. All in all, our results show the relative importance of each genomic factor on the rates of protein evolution and functional constraint in these 2 cactophilic Drosophila species.
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Affiliation(s)
- Yolanda Guillén
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra (Barcelona), Spain
| | - Sònia Casillas
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra (Barcelona), Spain.,The Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra (Barcelona), Spain
| | - Alfredo Ruiz
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra (Barcelona), Spain
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21
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Abstract
Understanding phylogenetic relationships among taxa is key to designing and implementing comparative analyses. The genus Drosophila, which contains over 1600 species, is one of the most important model systems in the biological sciences. For over a century, one species in this group, Drosophila melanogaster, has been key to studies of animal development and genetics, genome organization and evolution, and human disease. As whole-genome sequencing becomes more cost-effective, there is increasing interest in other members of this morphologically, ecologically, and behaviorally diverse genus. Phylogenetic relationships within Drosophila are complicated, and the goal of this paper is to provide a review of the recent taxonomic changes and phylogenetic relationships in this genus to aid in further comparative studies.
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22
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Thorpe P, Escudero-Martinez CM, Cock PJA, Eves-van den Akker S, Bos JIB. Shared Transcriptional Control and Disparate Gain and Loss of Aphid Parasitism Genes. Genome Biol Evol 2018; 10:2716-2733. [PMID: 30165560 PMCID: PMC6186164 DOI: 10.1093/gbe/evy183] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/23/2018] [Indexed: 12/27/2022] Open
Abstract
Aphids are a diverse group of taxa that contain agronomically important species, which vary in their host range and ability to infest crop plants. The genome evolution underlying agriculturally important aphid traits is not well understood. We generated draft genome assemblies for two aphid species: Myzus cerasi (black cherry aphid) and the cereal specialist Rhopalosiphum padi. Using a de novo gene prediction pipeline on both these, and three additional aphid genome assemblies (Acyrthosiphon pisum, Diuraphis noxia, and Myzus persicae), we show that aphid genomes consistently encode similar gene numbers. We compare gene content, gene duplication, synteny, and putative effector repertoires between these five species to understand the genome evolution of globally important plant parasites. Aphid genomes show signs of relatively distant gene duplication, and substantial, relatively recent, gene birth. Putative effector repertoires, originating from duplicated and other loci, have an unusual genomic organization and evolutionary history. We identify a highly conserved effector pair that is tightly physically linked in the genomes of all aphid species tested. In R. padi, this effector pair is tightly transcriptionally linked and shares an unknown transcriptional control mechanism with a subset of ∼50 other putative effectors and secretory proteins. This study extends our current knowledge on the evolution of aphid genomes and reveals evidence for an as-of-yet unknown shared control mechanism, which underlies effector expression, and ultimately plant parasitism.
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Affiliation(s)
- Peter Thorpe
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
- Dundee Effector Consortium, The James Hutton Institute, Dundee, United Kingdom
| | - Carmen M Escudero-Martinez
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
- Dundee Effector Consortium, The James Hutton Institute, Dundee, United Kingdom
| | - Peter J A Cock
- Dundee Effector Consortium, The James Hutton Institute, Dundee, United Kingdom
- Information and Computational Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Sebastian Eves-van den Akker
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
- Corresponding authors: E-mails: ;
| | - Jorunn I B Bos
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
- Dundee Effector Consortium, The James Hutton Institute, Dundee, United Kingdom
- Division of Plant Sciences, School of Life Sciences, University of Dundee, Dundee, United Kingdom
- Corresponding authors: E-mails: ;
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23
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Bao R, Dia SE, Issa HA, Alhusein D, Friedrich M. Comparative Evidence of an Exceptional Impact of Gene Duplication on the Developmental Evolution of Drosophila and the Higher Diptera. Front Ecol Evol 2018. [DOI: 10.3389/fevo.2018.00063] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
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24
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RNA-Interference Pathways Display High Rates of Adaptive Protein Evolution in Multiple Invertebrates. Genetics 2018; 208:1585-1599. [PMID: 29437826 PMCID: PMC5887150 DOI: 10.1534/genetics.117.300567] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 01/31/2018] [Indexed: 12/30/2022] Open
Abstract
Conflict between organisms can lead to a reciprocal adaptation that manifests as an increased evolutionary rate in genes mediating the conflict. This adaptive signature has been observed in RNA-interference (RNAi) pathway genes involved in the suppression of viruses and transposable elements in Drosophila melanogaster, suggesting that a subset of Drosophila RNAi genes may be locked in an arms race with these parasites. However, it is not known whether rapid evolution of RNAi genes is a general phenomenon across invertebrates, or which RNAi genes generally evolve adaptively. Here we use population genomic data from eight invertebrate species to infer rates of adaptive sequence evolution, and to test for past and ongoing selective sweeps in RNAi genes. We assess rates of adaptive protein evolution across species using a formal meta-analytic framework to combine data across species and by implementing a multispecies generalized linear mixed model of mutation counts. Across species, we find that RNAi genes display a greater rate of adaptive protein substitution than other genes, and that this is primarily mediated by positive selection acting on the genes most likely to defend against viruses and transposable elements. In contrast, evidence for recent selective sweeps is broadly spread across functional classes of RNAi genes and differs substantially among species. Finally, we identify genes that exhibit elevated adaptive evolution across the analyzed insect species, perhaps due to concurrent parasite-mediated arms races.
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25
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Levin TC, Malik HS. Rapidly Evolving Toll-3/4 Genes Encode Male-Specific Toll-Like Receptors in Drosophila. Mol Biol Evol 2017; 34:2307-2323. [PMID: 28541576 PMCID: PMC5850136 DOI: 10.1093/molbev/msx168] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Animal Toll-like receptors (TLRs) have evolved through a pattern of duplication and divergence. Whereas mammalian TLRs directly recognize microbial ligands, Drosophila Tolls bind endogenous ligands downstream of both developmental and immune signaling cascades. Here, we find that most Toll genes in Drosophila evolve slowly with little gene turnover (gains/losses), consistent with their important roles in development and indirect roles in microbial recognition. In contrast, we find that the Toll-3/4 genes have experienced an unusually rapid rate of gene gains and losses, resulting in lineage-specific Toll-3/4s and vastly different gene repertoires among Drosophila species, from zero copies (e.g., D. mojavensis) to nineteen copies (e.g., D. willistoni). In D. willistoni, we find strong evidence for positive selection in Toll-3/4 genes, localized specifically to an extracellular region predicted to overlap with the binding site of Spätzle, the only known ligand of insect Tolls. However, because Spätzle genes are not experiencing similar selective pressures, we hypothesize that Toll-3/4s may be rapidly evolving because they bind to a different ligand, akin to TLRs outside of insects. We further find that most Drosophila Toll-3/4 genes are either weakly expressed or expressed exclusively in males, specifically in the germline. Unlike other Toll genes in D. melanogaster, Toll-3, and Toll-4 have apparently escaped from essential developmental roles, as knockdowns have no substantial effects on viability or male fertility. Based on these findings, we propose that the Toll-3/4 genes represent an exceptionally rapidly evolving lineage of Drosophila Toll genes, which play an unusual, as-yet-undiscovered role in the male germline.
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Affiliation(s)
- Tera C Levin
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Harmit S Malik
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA.,Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, WA
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Positive diversifying selection is a pervasive adaptive force throughout the Drosophila radiation. Mol Phylogenet Evol 2017; 112:230-243. [DOI: 10.1016/j.ympev.2017.04.023] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Revised: 04/26/2017] [Accepted: 04/26/2017] [Indexed: 01/02/2023]
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Mohanty S, Khanna R. Genome-wide comparative analysis of four Indian Drosophila species. Mol Genet Genomics 2017; 292:1197-1208. [DOI: 10.1007/s00438-017-1339-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 06/19/2017] [Indexed: 11/24/2022]
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Vieira GC, Vieira GF, Sinigaglia M, da Silva Valente VL. Linking epigenetic function to electrostatics: The DNMT2 structural model example. PLoS One 2017; 12:e0178643. [PMID: 28575027 PMCID: PMC5456315 DOI: 10.1371/journal.pone.0178643] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Accepted: 05/16/2017] [Indexed: 11/25/2022] Open
Abstract
The amino acid sequence of DNMT2 is very similar to the catalytic domains of bacterial and eukaryotic proteins. However, there is great variability in the region of recognition of the target sequence. While bacterial DNMT2 acts as a DNA methyltransferase, previous studies have indicated low DNA methylation activity in eukaryotic DNMT2, with preference by tRNA methylation. Drosophilids are known as DNMT2-only species and the DNA methylation phenomenon is a not elucidated case yet, as well as the ontogenetic and physiologic importance of DNMT2 for this species group. In addition, more recently study showed that methylation in the genome in Drosophila melanogaster is independent in relation to DNMT2. Despite these findings, Drosophilidae family has more than 4,200 species with great ecological diversity and historical evolution, thus we, therefore, aimed to examine the drosophilids DNMT2 in order to verify its conservation at the physicochemical and structural levels in a functional context. We examined the twenty-six DNMT2 models generated by molecular modelling and five crystallographic structures deposited in the Protein Data Bank (PDB) using different approaches. Our results showed that despite sequence and structural similarity between species close related, we found outstanding differences when they are analyzed in the context of surface distribution of electrostatic properties. The differences found in the electrostatic potentials may be linked with different affinities and processivity of DNMT2 for its different substrates (DNA, RNA or tRNA) and even for interactions with other proteins involved in the epigenetic mechanisms.
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Affiliation(s)
- Gilberto Cavalheiro Vieira
- Programa de Pós Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
- * E-mail:
| | - Gustavo Fioravanti Vieira
- Programa de Pós Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
- Núcleo de Bioinformática do Laboratório de Imunogenética, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Marialva Sinigaglia
- Programa de Pós Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
- Instituto do Câncer Infantil, Porto Alegre, RS, Brazil
| | - Vera Lúcia da Silva Valente
- Programa de Pós Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
- Programa de Pós Graduação em Biologia Animal, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
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Blumenstiel JP, Erwin AA, Hemmer LW. What Drives Positive Selection in the Drosophila piRNA Machinery? The Genomic Autoimmunity Hypothesis. THE YALE JOURNAL OF BIOLOGY AND MEDICINE 2016; 89:499-512. [PMID: 28018141 PMCID: PMC5168828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
In animals, PIWI-interacting RNAs (piRNAs) play a crucial role in genome defense. Moreover, because piRNAs can be maternally transmitted, they contribute to the epigenetic profile of inheritance. Multiple studies, especially in Drosophila, have demonstrated that the machinery of piRNA biogenesis is often the target of positive selection. Because transposable elements (TEs) are a form of genetic parasite, positive selection in the piRNA machinery is often explained by analogy to the signatures of positive selection commonly observed in genes that play a role in host-parasite dynamics. However, the precise mechanisms that drive positive selection in the piRNA machinery are not known. In this review, we outline several mechanistic models that might explain pervasive positive selection in the piRNA machinery of Drosophila species. We propose that recurrent positive selection in the piRNA machinery can be partly explained by an ongoing tension between selection for sensitivity required by genome defense and selection for specificity to avoid the off-target effects of maladaptive genic silencing by piRNA.
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Affiliation(s)
| | - Alexandra A. Erwin
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS
| | - Lucas W. Hemmer
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS
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Nürnberger B, Lohse K, Fijarczyk A, Szymura JM, Blaxter ML. Para-allopatry in hybridizing fire-bellied toads (Bombina bombina and B. variegata): Inference from transcriptome-wide coalescence analyses. Evolution 2016; 70:1803-18. [PMID: 27282112 PMCID: PMC5129456 DOI: 10.1111/evo.12978] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Revised: 05/18/2016] [Accepted: 05/27/2016] [Indexed: 12/26/2022]
Abstract
Ancient origins, profound ecological divergence, and extensive hybridization make the fire‐bellied toads Bombina bombina and B. variegata (Anura: Bombinatoridae) an intriguing test case of ecological speciation. Previous modeling has proposed that the narrow Bombina hybrid zones represent strong barriers to neutral introgression. We test this prediction by inferring the rate of gene exchange between pure populations on either side of the intensively studied Kraków transect. We developed a method to extract high confidence sets of orthologous genes from de novo transcriptome assemblies, fitted a range of divergence models to these data and assessed their relative support with analytic likelihood calculations. There was clear evidence for postdivergence gene flow, but, as expected, no perceptible signal of recent introgression via the nearby hybrid zone. The analysis of two additional Bombina taxa (B. v. scabra and B. orientalis) validated our parameter estimates against a larger set of prior expectations. Despite substantial cumulative introgression over millions of years, adaptive divergence of the hybridizing taxa is essentially unaffected by their lack of reproductive isolation. Extended distribution ranges also buffer them against small‐scale environmental perturbations that have been shown to reverse the speciation process in other, more recent ecotypes.
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Affiliation(s)
- Beate Nürnberger
- Institute of Evolutionary Biology, University of Edinburgh, Ashworth Laboratories, Charlotte Auerbach Road, Edinburgh, EH9 3FL, United Kingdom. .,Current Address: Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, Brno, Czech Republic.
| | - Konrad Lohse
- Institute of Evolutionary Biology, University of Edinburgh, Ashworth Laboratories, Charlotte Auerbach Road, Edinburgh, EH9 3FL, United Kingdom
| | - Anna Fijarczyk
- Institute of Evolutionary Biology, University of Edinburgh, Ashworth Laboratories, Charlotte Auerbach Road, Edinburgh, EH9 3FL, United Kingdom.,Department of Comparative Anatomy, Institute of Zoology, Jagiellonian University, Gronostajowa 9, 30-387, Kraków, Poland.,Current Address: Institute of Environmental Sciences, Jagiellonian University, Gronostajowa 7, 30-387, Kraków, Poland
| | - Jacek M Szymura
- Department of Comparative Anatomy, Institute of Zoology, Jagiellonian University, Gronostajowa 9, 30-387, Kraków, Poland
| | - Mark L Blaxter
- Institute of Evolutionary Biology, University of Edinburgh, Ashworth Laboratories, Charlotte Auerbach Road, Edinburgh, EH9 3FL, United Kingdom
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Homaei A, Lavajoo F, Sariri R. Development of marine biotechnology as a resource for novel proteases and their role in modern biotechnology. Int J Biol Macromol 2016; 88:542-52. [DOI: 10.1016/j.ijbiomac.2016.04.023] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Revised: 03/09/2016] [Accepted: 04/10/2016] [Indexed: 10/22/2022]
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Macharia R, Mireji P, Murungi E, Murilla G, Christoffels A, Aksoy S, Masiga D. Genome-Wide Comparative Analysis of Chemosensory Gene Families in Five Tsetse Fly Species. PLoS Negl Trop Dis 2016; 10:e0004421. [PMID: 26886411 PMCID: PMC4757090 DOI: 10.1371/journal.pntd.0004421] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Accepted: 01/11/2016] [Indexed: 12/04/2022] Open
Abstract
For decades, odour-baited traps have been used for control of tsetse flies (Diptera; Glossinidae), vectors of African trypanosomes. However, differential responses to known attractants have been reported in different Glossina species, hindering establishment of a universal vector control tool. Availability of full genome sequences of five Glossina species offers an opportunity to compare their chemosensory repertoire and enhance our understanding of their biology in relation to chemosensation. Here, we identified and annotated the major chemosensory gene families in Glossina. We identified a total of 118, 115, 124, and 123 chemosensory genes in Glossina austeni, G. brevipalpis, G. f. fuscipes, G. pallidipes, respectively, relative to 127 reported in G. m. morsitans. Our results show that tsetse fly genomes have fewer chemosensory genes when compared to other dipterans such as Musca domestica (n>393), Drosophila melanogaster (n = 246) and Anopheles gambiae (n>247). We also found that Glossina chemosensory genes are dispersed across distantly located scaffolds in their respective genomes, in contrast to other insects like D. melanogaster whose genes occur in clusters. Further, Glossina appears to be devoid of sugar receptors and to have expanded CO2 associated receptors, potentially reflecting Glossina's obligate hematophagy and the need to detect hosts that may be out of sight. We also identified, in all species, homologs of Ir84a; a Drosophila-specific ionotropic receptor that promotes male courtship suggesting that this is a conserved trait in tsetse flies. Notably, our selection analysis revealed that a total of four gene loci (Gr21a, GluRIIA, Gr28b, and Obp83a) were under positive selection, which confers fitness advantage to species. These findings provide a platform for studies to further define the language of communication of tsetse with their environment, and influence development of novel approaches for control. Chemical sensing is crucial to survival of tsetse flies; the sole cyclical vectors of African trypanosomes that cause the neglected zoonotic tropical disease sleeping sickness in humans. For many years, vector control has been used to mitigate trypanosome infections among rural populations of sub-Saharan Africa. Nevertheless, development of an all-inclusive strategy to control tsetse flies using odour-baited traps has been limited by disparate responses to the odors exhibited by various tsetse species. In this study, proteins that are putatively involved in chemical sensing were identified and compared among five tsetse species and their close relatives with an aim of enhancing our knowledge on tsetse olfaction. Our findings suggest that the chemosensory genes are conserved across tsetse fly species despite their documented differential responses in odours. We found no species-specific sequence variations among the five species to suggest that differential response to odours is due to loss or gain of genes. It could therefore be hypothesized that the observed differences emerge during the downstream processing of odour molecules involving post translational modification of the chemosensory proteins. We thus recommend functional studies on the identified proteins to determine their roles and molecular interactions.
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Affiliation(s)
- Rosaline Macharia
- Molecular Biology and Bioinformatics Unit, International Centre of Insect Physiology and Ecology, Nairobi, Kenya
- South African National Bioinformatics Institute, University of the Western Cape, Cape Town, South Africa
| | - Paul Mireji
- Department of Epidemiology of Microbial Diseases, Yale School of Public Heath, New Haven, Connecticut, United States of America
- Biotechnology Research Institute, Kenya Agricultural and Livestock Research Organization, Kikuyu, Kenya
- * E-mail: (PM); (DM)
| | - Edwin Murungi
- Department of Biochemistry and Molecular Biology, Egerton University, Njoro, Kenya
| | - Grace Murilla
- Biotechnology Research Institute, Kenya Agricultural and Livestock Research Organization, Kikuyu, Kenya
| | - Alan Christoffels
- South African National Bioinformatics Institute, University of the Western Cape, Cape Town, South Africa
| | - Serap Aksoy
- Department of Epidemiology of Microbial Diseases, Yale School of Public Heath, New Haven, Connecticut, United States of America
| | - Daniel Masiga
- Molecular Biology and Bioinformatics Unit, International Centre of Insect Physiology and Ecology, Nairobi, Kenya
- * E-mail: (PM); (DM)
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Tang H, Bomhoff MD, Briones E, Zhang L, Schnable JC, Lyons E. SynFind: Compiling Syntenic Regions across Any Set of Genomes on Demand. Genome Biol Evol 2015; 7:3286-98. [PMID: 26560340 PMCID: PMC4700967 DOI: 10.1093/gbe/evv219] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The identification of conserved syntenic regions enables discovery of predicted
locations for orthologous and homeologous genes, even when no such gene is present.
This capability means that synteny-based methods are far more effective than sequence
similarity-based methods in identifying true-negatives, a necessity for studying gene
loss and gene transposition. However, the identification of syntenic regions requires
complex analyses which must be repeated for pairwise comparisons between any two
species. Therefore, as the number of published genomes increases, there is a growing
demand for scalable, simple-to-use applications to perform comparative genomic
analyses that cater to both gene family studies and genome-scale studies. We
implemented SynFind, a web-based tool that addresses this need. Given one query
genome, SynFind is capable of identifying conserved syntenic regions in any set of
target genomes. SynFind is capable of reporting per-gene information, useful for
researchers studying specific gene families, as well as genome-wide data sets of
syntenic gene and predicted gene locations, critical for researchers focused on
large-scale genomic analyses. Inference of syntenic homologs provides the basis for
correlation of functional changes around genes of interests between related
organisms. Deployed on the CoGe online platform, SynFind is connected to the genomic
data from over 15,000 organisms from all domains of life as well as supporting
multiple releases of the same organism. SynFind makes use of a powerful job execution
framework that promises scalability and reproducibility. SynFind can be accessed at
http://genomevolution.org/CoGe/SynFind.pl. A video tutorial of SynFind
using Phytophthrora as an example is available at http://www.youtube.com/watch?v=2Agczny9Nyc.
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Affiliation(s)
- Haibao Tang
- Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian Province, China School of Plant Sciences, iPlant Collaborative, University of Arizona
| | - Matthew D Bomhoff
- School of Plant Sciences, iPlant Collaborative, University of Arizona
| | - Evan Briones
- School of Plant Sciences, iPlant Collaborative, University of Arizona
| | - Liangsheng Zhang
- Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian Province, China
| | - James C Schnable
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln
| | - Eric Lyons
- School of Plant Sciences, iPlant Collaborative, University of Arizona
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34
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Whittle CA, Extavour CG. Codon and Amino Acid Usage Are Shaped by Selection Across Divergent Model Organisms of the Pancrustacea. G3 (BETHESDA, MD.) 2015; 5:2307-21. [PMID: 26384771 PMCID: PMC4632051 DOI: 10.1534/g3.115.021402] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 08/28/2015] [Indexed: 01/24/2023]
Abstract
In protein-coding genes, synonymous codon usage and amino acid composition correlate to expression in some eukaryotes, and may result from translational selection. Here, we studied large-scale RNA-seq data from three divergent arthropod models, including cricket (Gryllus bimaculatus), milkweed bug (Oncopeltus fasciatus), and the amphipod crustacean Parhyale hawaiensis, and tested for optimization of codon and amino acid usage relative to expression level. We report strong signals of AT3 optimal codons (those favored in highly expressed genes) in G. bimaculatus and O. fasciatus, whereas weaker signs of GC3 optimal codons were found in P. hawaiensis, suggesting selection on codon usage in all three organisms. Further, in G. bimaculatus and O. fasciatus, high expression was associated with lowered frequency of amino acids with large size/complexity (S/C) scores in favor of those with intermediate S/C values; thus, selection may favor smaller amino acids while retaining those of moderate size for protein stability or conformation. In P. hawaiensis, highly transcribed genes had elevated frequency of amino acids with large and small S/C scores, suggesting a complex dynamic in this crustacean. In all species, the highly transcribed genes appeared to favor short proteins, high optimal codon usage, specific amino acids, and were preferentially involved in cell-cycling and protein synthesis. Together, based on examination of 1,680,067, 1,667,783, and 1,326,896 codon sites in G. bimaculatus, O. fasciatus, and P. hawaiensis, respectively, we conclude that translational selection shapes codon and amino acid usage in these three Pancrustacean arthropods.
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Affiliation(s)
- Carrie A Whittle
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138
| | - Cassandra G Extavour
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138 Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138
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Keane M, Semeiks J, Webb AE, Li YI, Quesada V, Craig T, Madsen LB, van Dam S, Brawand D, Marques PI, Michalak P, Kang L, Bhak J, Yim HS, Grishin NV, Nielsen NH, Heide-Jørgensen MP, Oziolor EM, Matson CW, Church GM, Stuart GW, Patton JC, George JC, Suydam R, Larsen K, López-Otín C, O'Connell MJ, Bickham JW, Thomsen B, de Magalhães JP. Insights into the evolution of longevity from the bowhead whale genome. Cell Rep 2015; 10:112-22. [PMID: 25565328 PMCID: PMC4536333 DOI: 10.1016/j.celrep.2014.12.008] [Citation(s) in RCA: 215] [Impact Index Per Article: 23.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2014] [Revised: 11/21/2014] [Accepted: 12/03/2014] [Indexed: 01/01/2023] Open
Abstract
The bowhead whale (Balaena mysticetus) is estimated to live over 200 years and is possibly the longest-living mammal. These animals should possess protective molecular adaptations relevant to age-related diseases, particularly cancer. Here, we report the sequencing and comparative analysis of the bowhead whale genome and two transcriptomes from different populations. Our analysis identifies genes under positive selection and bowhead-specific mutations in genes linked to cancer and aging. In addition, we identify gene gain and loss involving genes associated with DNA repair, cell-cycle regulation, cancer, and aging. Our results expand our understanding of the evolution of mammalian longevity and suggest possible players involved in adaptive genetic changes conferring cancer resistance. We also found potentially relevant changes in genes related to additional processes, including thermoregulation, sensory perception, dietary adaptations, and immune response. Our data are made available online (http://www.bowhead-whale.org) to facilitate research in this long-lived species.
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Affiliation(s)
- Michael Keane
- Integrative Genomics of Ageing Group, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Jeremy Semeiks
- Howard Hughes Medical Institute and Departments of Biophysics and Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390-9050, USA
| | - Andrew E Webb
- Bioinformatics and Molecular Evolution Group, School of Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Yang I Li
- MRC Functional Genomics Unit, University of Oxford, Oxford OX1 3QX, UK
| | - Víctor Quesada
- Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología (IUOPA), Universidad de Oviedo, 33006 Oviedo, Spain
| | - Thomas Craig
- Integrative Genomics of Ageing Group, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Lone Bruhn Madsen
- Department of Molecular Biology and Genetics, Aarhus University, 8830 Tjele, Denmark
| | - Sipko van Dam
- Integrative Genomics of Ageing Group, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - David Brawand
- MRC Functional Genomics Unit, University of Oxford, Oxford OX1 3QX, UK
| | - Patrícia I Marques
- Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología (IUOPA), Universidad de Oviedo, 33006 Oviedo, Spain
| | - Pawel Michalak
- Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA 24061, USA
| | - Lin Kang
- Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA 24061, USA
| | - Jong Bhak
- Personal Genomics Institute, Genome Research Foundation, Suwon 443-270, Republic of Korea
| | - Hyung-Soon Yim
- KIOST, Korea Institute of Ocean Science and Technology, Ansan 426-744, Republic of Korea
| | - Nick V Grishin
- Howard Hughes Medical Institute and Departments of Biophysics and Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390-9050, USA
| | | | | | - Elias M Oziolor
- Department of Environmental Science, Center for Reservoir and Aquatic Systems Research (CRASR) and Institute for Biomedical Studies, Baylor University, Waco, TX 76798, USA
| | - Cole W Matson
- Department of Environmental Science, Center for Reservoir and Aquatic Systems Research (CRASR) and Institute for Biomedical Studies, Baylor University, Waco, TX 76798, USA
| | - George M Church
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Gary W Stuart
- The Center for Genomic Advocacy (TCGA) and Department of Biology, Indiana State University, Terre Haute, IN 47809, USA
| | - John C Patton
- Department of Forestry and Natural Resources, Purdue University, West Lafayette, IN 47907, USA
| | - J Craig George
- North Slope Borough, Department of Wildlife Management, Barrow, AK 99723, USA
| | - Robert Suydam
- North Slope Borough, Department of Wildlife Management, Barrow, AK 99723, USA
| | - Knud Larsen
- Department of Molecular Biology and Genetics, Aarhus University, 8830 Tjele, Denmark
| | - Carlos López-Otín
- Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología (IUOPA), Universidad de Oviedo, 33006 Oviedo, Spain
| | - Mary J O'Connell
- Bioinformatics and Molecular Evolution Group, School of Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - John W Bickham
- Battelle Memorial Institute, Houston, TX 77079, USA; Department of Wildlife and Fisheries Sciences, Texas A&M University, College Station, TX 77843, USA
| | - Bo Thomsen
- Department of Molecular Biology and Genetics, Aarhus University, 8830 Tjele, Denmark
| | - João Pedro de Magalhães
- Integrative Genomics of Ageing Group, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK.
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Heras J, McClintock K, Sunagawa S, Aguilar A. Gonadal transcriptomics elucidate patterns of adaptive evolution within marine rockfishes (Sebastes). BMC Genomics 2015; 16:656. [PMID: 26329285 PMCID: PMC4557894 DOI: 10.1186/s12864-015-1870-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Accepted: 08/20/2015] [Indexed: 12/12/2022] Open
Abstract
Background The genetic mechanisms of speciation and adaptation in the marine environment are not well understood. The rockfish genus Sebastes provides a unique model system for studying adaptive evolution because of the extensive diversity found within this group, which includes morphology, ecology, and a broad range of life spans. Examples of adaptive radiations within marine ecosystems are considered an anomaly due to the absence of geographical barriers and the presence of gene flow. Using marine rockfishes, we identified signatures of natural selection from transcriptomes developed from gonadal tissue of two rockfish species (Sebastes goodei and S. saxicola). We predicted orthologous transcript pairs, and estimated their distributions of nonsynonymous (Ka) and synonymous (Ks) substitution rates. Results We identified 144 genes out of 1079 orthologous pairs under positive selection, of which 11 are functionally annotated to reproduction based on gene ontologies (GOs). One orthologous pair of the zona pellucida gene family, which is known for its role in the selection of sperm by oocytes, out of ten was identified to be evolving under positive selection. In addition to our results in the protein coding-regions of transcripts, we found substitution rates in 3’ and 5’ UTRs to be significantly lower than Ks substitution rates implying negative selection in these regions. Conclusions We were able to identify a series of candidate genes that are useful for the assessment of the critical genes that diverged and are responsible for the radiation within this genus. Genes associated with longevity hold potential for understanding the molecular mechanisms that have contributed to the radiation within this genus. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1870-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Joseph Heras
- Department of Ecology and Evolutionary Biology, University of California Irvine, 321 Steinhaus Hall, Irvine, CA, 92697, USA.
| | - Kelly McClintock
- School of Natural Sciences and Graduate Group in Quantitative and Systems Biology, University of California Merced, 5200 N Lake Rd, Merced, CA, 95344, USA.
| | - Shinichi Sunagawa
- European Molecular Biology Laboratory, Meyerhofstr 1, 69117, Heidelberg, Germany.
| | - Andres Aguilar
- Department of Biological Sciences, California State University Los Angeles, 5151 State University Dr, Los Angeles, CA, 90032, USA.
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37
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Castillo DM, Moyle LC. Intraspecific sperm competition genes enforce post-mating species barriers in Drosophila. Proc Biol Sci 2015; 281:rspb.2014.2050. [PMID: 25355478 DOI: 10.1098/rspb.2014.2050] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Sexual selection and sexual conflict are considered important drivers of speciation, based on both theoretical models and empirical correlations between sexually selected traits and diversification. However, whether reproductive isolation between species evolves directly as a consequence of intrapopulation sexual dynamics remains empirically unresolved, in part because knowledge of the genetic mechanisms (if any) connecting these processes is limited. Here, we provide evidence of a direct mechanistic link between intraspecies sexual selection and reproductive isolation. We examined genes with known roles in intraspecific sperm competition (ISC) in D. melanogaster and assayed their impact on conspecific sperm precedence (CSP). We found that two such genes (Acp36DE and CG9997) contribute to both offensive sperm competition and CSP; null/knockdown lines both had lower competitive ability against D. melanogaster conspecifics and were no longer able to displace heterospecific D. simulans sperm in competitive matings. In comparison, Sex Peptide (Acp70A)-another locus essential for ISC-does not contribute to CSP. These data indicate that two loci important for sperm competitive interactions have an additional role in similar interactions that enforce post-mating reproductive isolation between species, and show that sexual selection and sexual isolation can act on the same molecular targets in a gene-specific manner.
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Affiliation(s)
- Dean M Castillo
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Leonie C Moyle
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
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Singh J, Mukhopadhyay CS, Arora JS, Kaur S. Biocomputational characterization and evolutionary analysis of bubaline dicer1 enzyme. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2015; 28:876-87. [PMID: 25925065 PMCID: PMC4412985 DOI: 10.5713/ajas.14.0767] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Revised: 11/24/2014] [Accepted: 12/19/2014] [Indexed: 12/19/2022]
Abstract
Dicer, an ribonuclease type III type endonuclease, is the key enzyme involved in biogenesis of microRNAs (miRNAs) and small interfering RNAs (siRNAs), and thus plays a critical role in RNA interference through post transcriptional regulation of gene expression. This enzyme has not been well studied in the Indian water buffalo, an important species known for disease resistance and high milk production. In this study, the primary coding sequence (5,778 bp) of bubaline dicer (GenBank: AB969677.1) was determined and the bubaline Dicer1 biocomputationally characterized to determine the phylogenetic signature among higher eukaryotes. The evolutionary tree revealed that all the transcript variants of Dicer1 belonging to a specific species were within the same node and the sequences belonging to primates, rodents and lagomorphs, avians and reptiles formed independent clusters. The bubaline dicer1 is closely related to that of cattle and other ruminants and significantly divergent from dicer of lower species such as tapeworm, sea urchin and fruit fly. Evolutionary divergence analysis conducted using MEGA6 software indicated that dicer has undergone purifying selection over the time. Seventeen divergent sequences, representing each of the families/taxa were selected to study the specific regions of positive vis-à-vis negative selection using different models like single likelihood ancestor counting, fixed effects likelihood, and random effects likelihood of Datamonkey server. Comparative analysis of the domain structure revealed that Dicer1 is conserved across mammalian species while variation both in terms of length of Dicer enzyme and presence or absence of domain is evident in the lower organisms.
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Affiliation(s)
- Jasdeep Singh
- School of Animal Biotechnology, Post Graduate Institute of Veterinary Education and Research, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana, Punjab 141004, India
| | - Chandra Sekhar Mukhopadhyay
- School of Animal Biotechnology, Post Graduate Institute of Veterinary Education and Research, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana, Punjab 141004, India
| | - Jaspreet Singh Arora
- School of Animal Biotechnology, Post Graduate Institute of Veterinary Education and Research, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana, Punjab 141004, India
| | - Simarjeet Kaur
- Department of Animal Genetics and Breeding, College of Veterinary Sciences, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana, Punjab 141004, India
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Kliethermes CL. Conservation of the Ethanol-Induced Locomotor Stimulant Response among Arthropods. BRAIN, BEHAVIOR AND EVOLUTION 2015; 85:37-46. [DOI: 10.1159/000370099] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Accepted: 11/20/2014] [Indexed: 11/19/2022]
Abstract
Ethanol-induced locomotor stimulation has been variously described as reflective of the disinhibitory, euphoric, or reinforcing effects of ethanol and is commonly used as an index of acute ethanol sensitivity in rodents. The fruit fly Drosophila melanogaster also shows a locomotor stimulant response to ethanol that is believed to occur via conserved, ethanol-sensitive neurobiological mechanisms, but it is currently unknown whether this response is conserved among arthropod species or is idiosyncratic to D. melanogaster. The current experiments surveyed locomotor responses to ethanol in a phylogenetically diverse panel of insects and other arthropod species. A clear ethanol-induced locomotor stimulant response was seen in 9 of 13 Drosophilidae species tested, in 8 of 10 other species of insects, and in an arachnid (wolf spider) and a myriapod (millipede) species. Given the diverse phylogenies of the species that showed the response, these experiments support the hypothesis that locomotor stimulation is a conserved behavioral response to ethanol among arthropod species. Further comparative studies are needed to determine whether the specific neurobiological mechanisms known to underlie the stimulant response in D. melanogaster are conserved among arthropod and vertebrate species.
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40
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Modolo L, Picard F, Lerat E. A new genome-wide method to track horizontally transferred sequences: application to Drosophila. Genome Biol Evol 2015; 6:416-32. [PMID: 24497602 PMCID: PMC3942030 DOI: 10.1093/gbe/evu026] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Because of methodological breakthroughs and the availability of an increasing amount of whole-genome sequence data, horizontal transfers (HTs) in eukaryotes have received much attention recently. Contrary to similar analyses in prokaryotes, most studies in eukaryotes usually investigate particular sequences corresponding to transposable elements (TEs), neglecting the other components of the genome. We present a new methodological framework for the genome-wide detection of all putative horizontally transferred sequences between two species that requires no prior knowledge of the transferred sequences. This method provides a broader picture of HTs in eukaryotes by fully exploiting complete-genome sequence data. In contrast to previous genome-wide approaches, we used a well-defined statistical framework to control for the number of false positives in the results, and we propose two new validation procedures to control for confounding factors. The first validation procedure relies on a comparative analysis with other species of the phylogeny to validate HTs for the nonrepeated sequences detected, whereas the second one built upon the study of the dynamics of the detected TEs. We applied our method to two closely related Drosophila species, Drosophila melanogaster and D. simulans, in which we discovered 10 new HTs in addition to all the HTs previously detected in different studies, which underscores our method’s high sensitivity and specificity. Our results favor the hypothesis of multiple independent HTs of TEs while unraveling a small portion of the network of HTs in the Drosophila phylogeny.
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Affiliation(s)
- Laurent Modolo
- Université de Lyon, France, Université Lyon 1, CNRS, UMR 5558, Laboratoire de Biométrie et Biologie Evolutive, VIlleurbanne, France
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41
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Romiguier J, Lourenco J, Gayral P, Faivre N, Weinert LA, Ravel S, Ballenghien M, Cahais V, Bernard A, Loire E, Keller L, Galtier N. Population genomics of eusocial insects: the costs of a vertebrate-like effective population size. J Evol Biol 2014; 27:593-603. [DOI: 10.1111/jeb.12331] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Revised: 12/27/2013] [Accepted: 01/02/2014] [Indexed: 12/15/2022]
Affiliation(s)
- J. Romiguier
- Institut des Sciences de l'Evolution de Montpellier; Université Montpellier 2; CNRS UMR 5554; Montpellier France
| | - J. Lourenco
- Institut des Sciences de l'Evolution de Montpellier; Université Montpellier 2; CNRS UMR 5554; Montpellier France
| | - P. Gayral
- Institut des Sciences de l'Evolution de Montpellier; Université Montpellier 2; CNRS UMR 5554; Montpellier France
- Institut de Recherches sur la Biologie de l'Insecte; CNRS UMR 7261; Université François-Rabelais; Tours France
| | - N. Faivre
- Institut des Sciences de l'Evolution de Montpellier; Université Montpellier 2; CNRS UMR 5554; Montpellier France
| | - L. A. Weinert
- Institut des Sciences de l'Evolution de Montpellier; Université Montpellier 2; CNRS UMR 5554; Montpellier France
- Department of Veterinary Medicine; University of Cambridge; Cambridge UK
| | - S. Ravel
- Institut des Sciences de l'Evolution de Montpellier; Université Montpellier 2; CNRS UMR 5554; Montpellier France
| | - M. Ballenghien
- Institut des Sciences de l'Evolution de Montpellier; Université Montpellier 2; CNRS UMR 5554; Montpellier France
| | - V. Cahais
- Institut des Sciences de l'Evolution de Montpellier; Université Montpellier 2; CNRS UMR 5554; Montpellier France
| | - A. Bernard
- Institut des Sciences de l'Evolution de Montpellier; Université Montpellier 2; CNRS UMR 5554; Montpellier France
| | - E. Loire
- Institut des Sciences de l'Evolution de Montpellier; Université Montpellier 2; CNRS UMR 5554; Montpellier France
| | - L. Keller
- Department of Ecology and Evolution, Biophore; University of Lausanne; Lausanne Switzerland
| | - N. Galtier
- Institut des Sciences de l'Evolution de Montpellier; Université Montpellier 2; CNRS UMR 5554; Montpellier France
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42
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Morán T, Fontdevila A. Genome-wide dissection of hybrid sterility in Drosophila confirms a polygenic threshold architecture. J Hered 2014; 105:381-96. [PMID: 24489077 DOI: 10.1093/jhered/esu003] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
To date, different studies about the genetic basis of hybrid male sterility (HMS), a postzygotic reproductive barrier thoroughly investigated using Drosophila species, have demonstrated that no single major gene can produce hybrid sterility without the cooperation of several genetic factors. Early work using hybrids between Drosophila koepferae (Dk) and Drosophila buzzatii (Db) was consistent with the idea that HMS requires the cooperation of several genetic factors, supporting a polygenic threshold (PT) model. Here we present a genome-wide mapping strategy to test the PT model, analyzing serially backcrossed fertile and sterile males in which the Dk genome was introgressed into the Db background. We identified 32 Dk-specific markers significantly associated with hybrid sterility. Our results demonstrate 1) a strong correlation between the number of segregated sterility markers and males' degree of sterility, 2) the exchangeability among markers, 3) their tendency to cluster into low-recombining chromosomal regions, and 4) the requirement for a minimum number (threshold) of markers to elicit sterility. Although our findings do not contradict a role for occasional major hybrid-sterility genes, they conform more to the view that HMS primarily evolves by the cumulative action of many interacting genes of minor effect in a complex PT architecture.
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Affiliation(s)
- Tomás Morán
- the Grup de Biologia Evolutiva, Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
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43
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Li YI, Kong L, Ponting CP, Haerty W. Rapid evolution of Beta-keratin genes contribute to phenotypic differences that distinguish turtles and birds from other reptiles. Genome Biol Evol 2013; 5:923-33. [PMID: 23576313 PMCID: PMC3673632 DOI: 10.1093/gbe/evt060] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Sequencing of vertebrate genomes permits changes in distinct protein families, including gene gains and losses, to be ascribed to lineage-specific phenotypes. A prominent example of this is the large-scale duplication of beta-keratin genes in the ancestors of birds, which was crucial to the subsequent evolution of their beaks, claws, and feathers. Evidence suggests that the shell of Pseudomys nelsoni contains at least 16 beta-keratins proteins, but it is unknown whether this is a complete set and whether their corresponding genes are orthologous to avian beak, claw, or feather beta-keratin genes. To address these issues and to better understand the evolution of the turtle shell at a molecular level, we surveyed the diversity of beta-keratin genes from the genome assemblies of three turtles, Chrysemys picta, Pelodiscus sinensis, and Chelonia mydas, which together represent over 160 Myr of chelonian evolution. For these three turtles, we found 200 beta-keratins, which indicate that, as for birds, a large expansion of beta-keratin genes in turtles occurred concomitantly with the evolution of a unique phenotype, namely, their plastron and carapace. Phylogenetic reconstruction of beta-keratin gene evolution suggests that separate waves of gene duplication within a single genomic location gave rise to scales, claws, and feathers in birds, and independently the scutes of the shell in turtles.
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Affiliation(s)
- Yang I Li
- Department of Physiology, Anatomy and Genetics, MRC Functional Genomics Unit, University of Oxford, United Kingdom
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44
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Balakrishnan CN, Chapus C, Brewer MS, Clayton DF. Brain transcriptome of the violet-eared waxbill Uraeginthus granatina and recent evolution in the songbird genome. Open Biol 2013; 3:130063. [PMID: 24004662 PMCID: PMC3787746 DOI: 10.1098/rsob.130063] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Songbirds are important models for the study of social behaviour and communication. To complement the recent genome sequencing of the domesticated zebra finch, we sequenced the brain transcriptome of a closely related songbird species, the violet-eared waxbill (Uraeginthus granatina). Both the zebra finch and violet-eared waxbill are members of the family Estrildidae, but differ markedly in their social behaviour. Using Roche 454 RNA sequencing, we generated an assembly and annotation of 11 084 waxbill orthologues of 17 475 zebra finch genes (64%), with an average transcript length of 1555 bp. We also identified 5985 single nucleotide polymorphisms (SNPs) of potential utility for future population genomic studies. Comparing the two species, we found evidence for rapid protein evolution (ω) and low polymorphism of the avian Z sex chromosome, consistent with prior studies of more divergent avian species. An intriguing outlier was putative chromosome 4A, which showed a high density of SNPs and low evolutionary rate relative to other chromosomes. Genome-wide ω was identical in zebra finch and violet-eared waxbill lineages, suggesting a similar demographic history with efficient purifying natural selection. Further comparisons of these and other estrildid finches may provide insights into the evolutionary neurogenomics of social behaviour.
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45
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Leushkin EV, Bazykin GA, Kondrashov AS. Strong mutational bias toward deletions in the Drosophila melanogaster genome is compensated by selection. Genome Biol Evol 2013; 5:514-24. [PMID: 23395983 PMCID: PMC3622295 DOI: 10.1093/gbe/evt021] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Insertions and deletions (collectively indels) obviously have a major impact on genome evolution. However, before large-scale data on indel polymorphism became available, it was difficult to estimate the strength of selection acting on indel mutations. Here, we analyze indel polymorphism and divergence in different compartments of the Drosophila melanogaster genome: exons, introns of different lengths, and intergenic regions. Data on low-frequency polymorphisms indicate that 0.036–0.039 short (1–30 nt) insertion mutations and 0.085–0.092 short deletion mutations, with mean lengths 3.23 and 4.78, respectively, occur per single-nucleotide substitution. The excess of short deletion over short insertion mutations implies that indel mutations of these lengths should lead to a loss of approximately 0.30 nt per single-nucleotide replacement. However, polymorphism and divergence data show that this deletion bias is almost completely compensated by selection: Negative selection is stronger against deletions, whereas insertions are more likely to be favored by positive selection. Among the inframe low-frequency polymorphic mutations in exons, long introns, and intergenic regions, selection prevents a larger fraction of deletions (80–87%, depending on the type of the compartment) than of insertions (70–82%) or single-nucleotide substitutions (49–73%), from reaching high frequencies. The corresponding fractions were the lowest in short introns: 66%, 47%, and 15%, respectively, consistent with the weakest selective constraint in them. The McDonald–Kreitman test shows that 32–46% of the deletions and 60–73% of the insertions that were fixed in the recent evolution of D. melanogaster are adaptive, whereas this fraction is only 0–29% for single-nucleotide substitutions.
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Affiliation(s)
- Evgeny V Leushkin
- Department of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia.
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46
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Zhou L, Watzlaf V, Abdelhak M. Flexible approaches for teaching computational genomics in a health information management program. PERSPECTIVES IN HEALTH INFORMATION MANAGEMENT 2013; 10:1b. [PMID: 23861672 PMCID: PMC3709875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The astonishing improvement of high-throughput biotechnologies in recent years makes it possible to access a huge amount of genomic data. The association between genomic data and genetic disease has already been and will continue to be applied to personalized healthcare. Health information management (HIM) professionals are the ones who will handle personal genetic information and provide solid evidence to support physicians' diagnoses and personalized treatment strategies, and therefore they will need to have the knowledge and skills to process genomic data. In this paper, we describe flexible approaches for teaching a computational genomics course in the HIM program at the University of Pittsburgh. HIM programs at other universities may choose an appropriate approach to fit into their own curriculum.
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Affiliation(s)
- Leming Zhou
- Department of Health Information Management, University of Pittsburgh, Pittsburgh, PA, USA
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47
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Leushkin EV, Bazykin GA. Short indels are subject to insertion-biased gene conversion. Evolution 2013; 67:2604-13. [PMID: 24033170 DOI: 10.1111/evo.12129] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2013] [Accepted: 04/05/2013] [Indexed: 11/29/2022]
Abstract
Recombination between homologous loci is accompanied by formation of heteroduplexes. Repairing mismatches in heteroduplexes often leads to single nucleotide substitutions in a process known as gene conversion. Gene conversion was shown to be GC-biased in different organisms; that is, a W(A or T)→S(G or C) substitution is more likely in this process than a S→W substitution. Here, we show that the insertion/deletion ratio for short noncoding indels that reach fixation between species is positively correlated with the recombination rate in Drosophila melanogaster, Homo sapiens, and Saccharomyces cerevisiae. This correlation is both due to an increase of the fixation rate of insertions and decrease of the fixation rate of deletions in regions of high recombination. Whole-genome data on indel polymorphism and divergence in D. melanogaster rule out mutation biases and selection as the cause of this trend, pointing to insertion-biased gene conversion as the most likely explanation. The bias toward insertions is the strongest for single-nucleotide indels, and decreases with indel length. In regions of high recombination rate this bias leads to an up to ∼5-fold excess of fixed short insertions over deletions, and substantially affects the evolution of DNA segments.
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Affiliation(s)
- Evgeny V Leushkin
- Department of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Leninskye Gory 1-73, Moscow, 119992, Russia; Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), Bolshoi Karetny pereulok, 19, Moscow, 127994, Russia.
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48
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Bradley Shaffer H, Minx P, Warren DE, Shedlock AM, Thomson RC, Valenzuela N, Abramyan J, Amemiya CT, Badenhorst D, Biggar KK, Borchert GM, Botka CW, Bowden RM, Braun EL, Bronikowski AM, Bruneau BG, Buck LT, Capel B, Castoe TA, Czerwinski M, Delehaunty KD, Edwards SV, Fronick CC, Fujita MK, Fulton L, Graves TA, Green RE, Haerty W, Hariharan R, Hernandez O, Hillier LW, Holloway AK, Janes D, Janzen FJ, Kandoth C, Kong L, de Koning APJ, Li Y, Literman R, McGaugh SE, Mork L, O'Laughlin M, Paitz RT, Pollock DD, Ponting CP, Radhakrishnan S, Raney BJ, Richman JM, St John J, Schwartz T, Sethuraman A, Spinks PQ, Storey KB, Thane N, Vinar T, Zimmerman LM, Warren WC, Mardis ER, Wilson RK. The western painted turtle genome, a model for the evolution of extreme physiological adaptations in a slowly evolving lineage. Genome Biol 2013; 14:R28. [PMID: 23537068 PMCID: PMC4054807 DOI: 10.1186/gb-2013-14-3-r28] [Citation(s) in RCA: 228] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2012] [Revised: 03/15/2013] [Accepted: 03/28/2013] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND We describe the genome of the western painted turtle, Chrysemys picta bellii, one of the most widespread, abundant, and well-studied turtles. We place the genome into a comparative evolutionary context, and focus on genomic features associated with tooth loss, immune function, longevity, sex differentiation and determination, and the species' physiological capacities to withstand extreme anoxia and tissue freezing. RESULTS Our phylogenetic analyses confirm that turtles are the sister group to living archosaurs, and demonstrate an extraordinarily slow rate of sequence evolution in the painted turtle. The ability of the painted turtle to withstand complete anoxia and partial freezing appears to be associated with common vertebrate gene networks, and we identify candidate genes for future functional analyses. Tooth loss shares a common pattern of pseudogenization and degradation of tooth-specific genes with birds, although the rate of accumulation of mutations is much slower in the painted turtle. Genes associated with sex differentiation generally reflect phylogeny rather than convergence in sex determination functionality. Among gene families that demonstrate exceptional expansions or show signatures of strong natural selection, immune function and musculoskeletal patterning genes are consistently over-represented. CONCLUSIONS Our comparative genomic analyses indicate that common vertebrate regulatory networks, some of which have analogs in human diseases, are often involved in the western painted turtle's extraordinary physiological capacities. As these regulatory pathways are analyzed at the functional level, the painted turtle may offer important insights into the management of a number of human health disorders.
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Affiliation(s)
- H Bradley Shaffer
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA 90095-1606, USA
- La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, University of California, Los Angeles, Los Angeles, CA 90095-1496, USA
| | - Patrick Minx
- The Genome Institute, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, MO 63108, USA
| | - Daniel E Warren
- Department of Biology, Saint Louis University, St Louis, MO 63103, USA
| | - Andrew M Shedlock
- College of Charleston Biology Department and Grice Marine Laboratory, Charleston, SC 29424, USA
- Medical University of South Carolina College of Graduate Studies and Center for Marine Biomedicine and Environmental Sciences, Charleston, SC 29412, USA
| | - Robert C Thomson
- Department of Biology, University of Hawaii at Manoa, Honolulu, HI 96822, USA
| | - Nicole Valenzuela
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
| | - John Abramyan
- Faculty of Dentistry, Life Sciences Institute University of British Columbia, Vancouver BC, Canada
| | - Chris T Amemiya
- Benaroya Research Institute at Virginia Mason, Seattle, WA 98101 USA
| | - Daleen Badenhorst
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
| | - Kyle K Biggar
- Department of Biology and Institute of Biochemistry, Carleton University, Ottawa, ON, Canada K1S 5B6, Canada
| | - Glen M Borchert
- School of Biological Sciences, Illinois State University, Normal, IL 61790, USA
- Department of Biological Sciences, Life Sciences Building, University of South Alabama, Mobile, AL 36688-0002, USA
| | | | - Rachel M Bowden
- School of Biological Sciences, Illinois State University, Normal, IL 61790, USA
| | - Edward L Braun
- Department of Biology, University of Florida, Gainesville, FL 32611 USA
| | - Anne M Bronikowski
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
| | - Benoit G Bruneau
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA
- Cardiovascular Research Institute and Department of Pediatrics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Leslie T Buck
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada M5S 3G5, Canada
| | - Blanche Capel
- Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA
| | - Todd A Castoe
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA
- Department of Biology, University of Texas at Arlington, Arlington, TX 76019, USA
| | - Mike Czerwinski
- Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA
| | - Kim D Delehaunty
- The Genome Institute, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, MO 63108, USA
| | - Scott V Edwards
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Catrina C Fronick
- The Genome Institute, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, MO 63108, USA
| | - Matthew K Fujita
- Department of Biology, University of Texas at Arlington, Arlington, TX 76019, USA
- Museum of Comparative Zoology and Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Lucinda Fulton
- The Genome Institute, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, MO 63108, USA
| | - Tina A Graves
- The Genome Institute, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, MO 63108, USA
| | - Richard E Green
- Baskin School of Engineering University of California, Santa Cruz Santa Cruz, CA 95064, USA
| | - Wilfried Haerty
- MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, Henry Wellcome Building of Gene Function, University of Oxford, Oxford, OX13PT, UK
| | - Ramkumar Hariharan
- Cancer Research Program, Rajiv Gandhi Centre for Biotechnology, Poojapura, Thycaud P.O, Thiruvananthapuram, Kerala 695014, India
| | - Omar Hernandez
- FUDECI, Fundación para el Desarrollo de las Ciencias Físicas, Matemáticas y Naturales. Av, Universidad, Bolsa a San Francisco, Palacio de Las Academias, Caracas, Venezuela
| | - LaDeana W Hillier
- The Genome Institute, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, MO 63108, USA
| | - Alisha K Holloway
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA
| | - Daniel Janes
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
| | - Fredric J Janzen
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
| | - Cyriac Kandoth
- The Genome Institute, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, MO 63108, USA
| | - Lesheng Kong
- MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, Henry Wellcome Building of Gene Function, University of Oxford, Oxford, OX13PT, UK
| | - AP Jason de Koning
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Yang Li
- MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, Henry Wellcome Building of Gene Function, University of Oxford, Oxford, OX13PT, UK
| | - Robert Literman
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
| | | | - Lindsey Mork
- Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA
| | - Michelle O'Laughlin
- The Genome Institute, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, MO 63108, USA
| | - Ryan T Paitz
- School of Biological Sciences, Illinois State University, Normal, IL 61790, USA
| | - David D Pollock
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Chris P Ponting
- MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, Henry Wellcome Building of Gene Function, University of Oxford, Oxford, OX13PT, UK
| | - Srihari Radhakrishnan
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
- Bioinformatics and Computational Biology Laboratory, Iowa State University, Ames, IA 50011, USA
| | - Brian J Raney
- Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA
| | - Joy M Richman
- Faculty of Dentistry, Life Sciences Institute University of British Columbia, Vancouver BC, Canada
| | - John St John
- Baskin School of Engineering University of California, Santa Cruz Santa Cruz, CA 95064, USA
| | - Tonia Schwartz
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
- Bioinformatics and Computational Biology Laboratory, Iowa State University, Ames, IA 50011, USA
| | - Arun Sethuraman
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
- Bioinformatics and Computational Biology Laboratory, Iowa State University, Ames, IA 50011, USA
| | - Phillip Q Spinks
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA 90095-1606, USA
- La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, University of California, Los Angeles, Los Angeles, CA 90095-1496, USA
| | - Kenneth B Storey
- Department of Biology and Institute of Biochemistry, Carleton University, Ottawa, ON, Canada K1S 5B6, Canada
| | - Nay Thane
- The Genome Institute, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, MO 63108, USA
| | - Tomas Vinar
- Faculty of Mathematics, Physics and Informatics, Comenius University, Mlynska Dolina, Bratislava 84248, Slovakia
| | - Laura M Zimmerman
- School of Biological Sciences, Illinois State University, Normal, IL 61790, USA
| | - Wesley C Warren
- The Genome Institute, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, MO 63108, USA
| | - Elaine R Mardis
- The Genome Institute, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, MO 63108, USA
| | - Richard K Wilson
- The Genome Institute, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, MO 63108, USA
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Vakhrusheva OA, Bazykin GA, Kondrashov AS. Genome-Level Analysis of Selective Constraint without Apparent Sequence Conservation. Genome Biol Evol 2013; 5:532-41. [PMID: 23418180 PMCID: PMC3622294 DOI: 10.1093/gbe/evt023] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Conservation of function can be accompanied by obvious similarity of homologous sequences which may persist for billions of years (Iyer LM, Leipe DD, Koonin EV, Aravind L. 2004. Evolutionary history and higher order classification of AAA+ ATPases. J Struct Biol. 146:11–31.). However, presumably homologous segments of noncoding DNA can also retain their ancestral function even after their sequences diverge beyond recognition (Fisher S, Grice EA, Vinton RM, Bessling SL, McCallion AS. 2006. Conservation of RET regulatory function from human to zebrafish without sequence similarity. Science 312:276–279.). To investigate this phenomenon at the genomic scale, we studied homologous introns in a quartet of insect species, and in a quartet of vertebrate species. Each quartet consisted of two pairs of moderately distant genomes, with a much larger evolutionary distance between the pairs. In both quartets, we found that introns that carry a regulatory segment or a conserved segment in the first pair tend to carry a conserved segment in the second pair, even though no similarity of these segments could be detected between the two pairs. Furthermore, introns from one pair that are preserved in the other pair tend to carry a conserved segment within the first pair, and be longer in the first pair, compared with the introns that were lost between pairs, even though no similarity between pairs could be detected in such preserved introns. These results indicate that selective constraint, presumably caused by conservation of the ancestral function, often persists even after the homologous DNA segments become unalignable.
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Affiliation(s)
- Olga A Vakhrusheva
- Department of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
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50
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Rands CM, Darling A, Fujita M, Kong L, Webster MT, Clabaut C, Emes RD, Heger A, Meader S, Hawkins MB, Eisen MB, Teiling C, Affourtit J, Boese B, Grant PR, Grant BR, Eisen JA, Abzhanov A, Ponting CP. Insights into the evolution of Darwin's finches from comparative analysis of the Geospiza magnirostris genome sequence. BMC Genomics 2013; 14:95. [PMID: 23402223 PMCID: PMC3575239 DOI: 10.1186/1471-2164-14-95] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2012] [Accepted: 01/23/2013] [Indexed: 01/01/2023] Open
Abstract
Background A classical example of repeated speciation coupled with ecological diversification is the evolution of 14 closely related species of Darwin’s (Galápagos) finches (Thraupidae, Passeriformes). Their adaptive radiation in the Galápagos archipelago took place in the last 2–3 million years and some of the molecular mechanisms that led to their diversification are now being elucidated. Here we report evolutionary analyses of genome of the large ground finch, Geospiza magnirostris. Results 13,291 protein-coding genes were predicted from a 991.0 Mb G. magnirostris genome assembly. We then defined gene orthology relationships and constructed whole genome alignments between the G. magnirostris and other vertebrate genomes. We estimate that 15% of genomic sequence is functionally constrained between G. magnirostris and zebra finch. Genic evolutionary rate comparisons indicate that similar selective pressures acted along the G. magnirostris and zebra finch lineages suggesting that historical effective population size values have been similar in both lineages. 21 otherwise highly conserved genes were identified that each show evidence for positive selection on amino acid changes in the Darwin's finch lineage. Two of these genes (Igf2r and Pou1f1) have been implicated in beak morphology changes in Darwin’s finches. Five of 47 genes showing evidence of positive selection in early passerine evolution have cilia related functions, and may be examples of adaptively evolving reproductive proteins. Conclusions These results provide insights into past evolutionary processes that have shaped G. magnirostris genes and its genome, and provide the necessary foundation upon which to build population genomics resources that will shed light on more contemporaneous adaptive and non-adaptive processes that have contributed to the evolution of the Darwin’s finches.
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Affiliation(s)
- Chris M Rands
- Department of Physiology, Anatomy, and Genetics, MRC Functional Genomics Unit, University of Oxford, Oxford, OX1 3PT, UK
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