401
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Trier CN, Hermansen JS, Sætre GP, Bailey RI. Evidence for mito-nuclear and sex-linked reproductive barriers between the hybrid Italian sparrow and its parent species. PLoS Genet 2014; 10:e1004075. [PMID: 24415954 PMCID: PMC3886922 DOI: 10.1371/journal.pgen.1004075] [Citation(s) in RCA: 93] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2013] [Accepted: 11/18/2013] [Indexed: 11/19/2022] Open
Abstract
Studies of reproductive isolation between homoploid hybrid species and their parent species have rarely been carried out. Here we investigate reproductive barriers between a recently recognized hybrid bird species, the Italian sparrow Passer italiae and its parent species, the house sparrow P. domesticus and Spanish sparrow P. hispaniolensis. Reproductive barriers can be difficult to study in hybrid species due to lack of geographical contact between taxa. However, the Italian sparrow lives parapatrically with the house sparrow and both sympatrically and parapatrically with the Spanish sparrow. Through whole-transcriptome sequencing of six individuals of each of the two parent species we identified a set of putatively parent species-diagnostic single nucleotide polymorphism (SNP) markers. After filtering for coverage, genotyping success (>97%) and multiple SNPs per gene, we retained 86 species-informative, genic, nuclear and mitochondrial SNP markers from 84 genes for analysis of 612 male individuals. We show that a disproportionately large number of sex-linked genes, as well as the mitochondria and nuclear genes with mitochondrial function, exhibit sharp clines at the boundaries between the hybrid and the parent species, suggesting a role for mito-nuclear and sex-linked incompatibilities in forming reproductive barriers. We suggest that genomic conflict via interactions between mitochondria and sex-linked genes with mitochondrial function (“mother's curse”) at one boundary and centromeric drive at the other may best explain our findings. Hybrid speciation in the Italian sparrow may therefore be influenced by mechanisms similar to those involved in non-hybrid speciation, but with the formation of two geographically separated species boundaries instead of one. Spanish sparrow alleles at some loci have spread north to form reproductive barriers with house sparrows, while house sparrow alleles at different loci, including some on the same chromosome, have spread in the opposite direction to form barriers against Spanish sparrows. Hybridization between two species has the potential to create a third, hybrid species. However this process, known as hybrid speciation, is thought to be unlikely because it requires reproductive barriers against both parent species to develop despite the barriers between parents being weak enough to allow for the formation of viable, fertile hybrids. The Italian sparrow, which occupies the entire Italian peninsula and some Mediterranean islands, is the product of past hybridization between house and Spanish sparrows and therefore represents one of the few documented cases of vertebrate hybrid speciation in nature. We show that reproductive barriers between Italian sparrows and their parent species exist and that genes on the sex (Z) chromosome and mitochondria are heavily involved. We suggest that speciation in this system may have been driven by dissociation of the sex (Z) chromosome into blocks of different parent species-specific genes, which have shifted alongside mitochondrial genes to form reproductive barriers where the hybrid now meets each of its parent species.
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Affiliation(s)
- Cassandra N. Trier
- Centre for Ecological and Evolutionary Synthesis, Department of Biology, University of Oslo, Oslo, Norway
| | - Jo S. Hermansen
- Centre for Ecological and Evolutionary Synthesis, Department of Biology, University of Oslo, Oslo, Norway
| | - Glenn-Peter Sætre
- Centre for Ecological and Evolutionary Synthesis, Department of Biology, University of Oslo, Oslo, Norway
- * E-mail:
| | - Richard I. Bailey
- Centre for Ecological and Evolutionary Synthesis, Department of Biology, University of Oslo, Oslo, Norway
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402
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Cui J, Zhao W, Huang Z, Jarvis ED, Gilbert MTP, Walker PJ, Holmes EC, Zhang G. Low frequency of paleoviral infiltration across the avian phylogeny. Genome Biol 2014; 15:539. [PMID: 25496498 PMCID: PMC4272516 DOI: 10.1186/s13059-014-0539-3] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Accepted: 11/10/2014] [Indexed: 01/30/2023] Open
Abstract
BACKGROUND Mammalian genomes commonly harbor endogenous viral elements. Due to a lack of comparable genome-scale sequence data, far less is known about endogenous viral elements in avian species, even though their small genomes may enable important insights into the patterns and processes of endogenous viral element evolution. RESULTS Through a systematic screening of the genomes of 48 species sampled across the avian phylogeny we reveal that birds harbor a limited number of endogenous viral elements compared to mammals, with only five viral families observed: Retroviridae, Hepadnaviridae, Bornaviridae, Circoviridae, and Parvoviridae. All nonretroviral endogenous viral elements are present at low copy numbers and in few species, with only endogenous hepadnaviruses widely distributed, although these have been purged in some cases. We also provide the first evidence for endogenous bornaviruses and circoviruses in avian genomes, although at very low copy numbers. A comparative analysis of vertebrate genomes revealed a simple linear relationship between endogenous viral element abundance and host genome size, such that the occurrence of endogenous viral elements in bird genomes is 6- to 13-fold less frequent than in mammals. CONCLUSIONS These results reveal that avian genomes harbor relatively small numbers of endogenous viruses, particularly those derived from RNA viruses, and hence are either less susceptible to viral invasions or purge them more effectively.
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Affiliation(s)
- Jie Cui
- />Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Biological Sciences and Sydney Medical School, The University of Sydney, Sydney, NSW 2006 Australia
- />Program in Emerging Infectious Diseases, Duke-NUS Graduate Medical School, Singapore, 169857 Singapore
| | - Wei Zhao
- />China National GeneBank, BGI-Shenzhen, Shenzhen, 518083 China
| | - Zhiyong Huang
- />China National GeneBank, BGI-Shenzhen, Shenzhen, 518083 China
| | - Erich D Jarvis
- />Howard Hughes Medical Institute, Duke University Medical Center, Department of Neurobiology, Box 3209, Durham, North Carolina 27710 USA
| | - M Thomas P Gilbert
- />Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, DK-1350 Copenhagen, Denmark
- />Trace and Environmental DNA Laboratory, Department of Environment and Agriculture, Curtin University, Perth, Western Australia 6102 Australia
| | - Peter J Walker
- />CSIRO Animal, Food and Health Sciences, Australian Animal Health Laboratory, Geelong, Victoria 3220 Australia
| | - Edward C Holmes
- />Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Biological Sciences and Sydney Medical School, The University of Sydney, Sydney, NSW 2006 Australia
| | - Guojie Zhang
- />China National GeneBank, BGI-Shenzhen, Shenzhen, 518083 China
- />Centre for Social Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen, Denmark
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403
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Weber CC, Boussau B, Romiguier J, Jarvis ED, Ellegren H. Evidence for GC-biased gene conversion as a driver of between-lineage differences in avian base composition. Genome Biol 2014; 15:549. [PMID: 25496599 PMCID: PMC4290106 DOI: 10.1186/s13059-014-0549-1] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Accepted: 11/19/2014] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND While effective population size (Ne) and life history traits such as generation time are known to impact substitution rates, their potential effects on base composition evolution are less well understood. GC content increases with decreasing body mass in mammals, consistent with recombination-associated GC biased gene conversion (gBGC) more strongly impacting these lineages. However, shifts in chromosomal architecture and recombination landscapes between species may complicate the interpretation of these results. In birds, interchromosomal rearrangements are rare and the recombination landscape is conserved, suggesting that this group is well suited to assess the impact of life history on base composition. RESULTS Employing data from 45 newly and 3 previously sequenced avian genomes covering a broad range of taxa, we found that lineages with large populations and short generations exhibit higher GC content. The effect extends to both coding and non-coding sites, indicating that it is not due to selection on codon usage. Consistent with recombination driving base composition, GC content and heterogeneity were positively correlated with the rate of recombination. Moreover, we observed ongoing increases in GC in the majority of lineages. CONCLUSIONS Our results provide evidence that gBGC may drive patterns of nucleotide composition in avian genomes and are consistent with more effective gBGC in large populations and a greater number of meioses per unit time; that is, a shorter generation time. Thus, in accord with theoretical predictions, base composition evolution is substantially modulated by species life history.
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Affiliation(s)
- Claudia C Weber
- />Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden
| | - Bastien Boussau
- />Laboratoire de Biométrie et Biologie Evolutive, Université de Lyon, Université Lyon 1, CNRS, UMR5558 Villeurbanne, France
| | | | - Erich D Jarvis
- />Department of Neurobiology, Howard Hughes Medical Institute, Duke University Medical Center, Durham, NC USA
| | - Hans Ellegren
- />Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden
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404
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Ellegren H. Genome sequencing and population genomics in non-model organisms. Trends Ecol Evol 2014; 29:51-63. [DOI: 10.1016/j.tree.2013.09.008] [Citation(s) in RCA: 392] [Impact Index Per Article: 39.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2013] [Revised: 09/02/2013] [Accepted: 09/16/2013] [Indexed: 12/20/2022]
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405
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Clayton DF, London SE. Advancing avian behavioral neuroendocrinology through genomics. Front Neuroendocrinol 2014; 35:58-71. [PMID: 24113222 DOI: 10.1016/j.yfrne.2013.09.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/16/2013] [Revised: 09/16/2013] [Accepted: 09/18/2013] [Indexed: 12/14/2022]
Abstract
Genome technologies are transforming all areas of biology, including the study of hormones, brain and behavior. Annotated reference genome assemblies are rapidly being produced for many avian species. Here we briefly review the basic concepts and tools used in genomics. We then consider how these are informing the study of avian behavioral neuroendocrinology, focusing in particular on lessons from the study of songbirds. We discuss the impact of having a complete "parts list" for an organism; the transformational potential of studying large sets of genes at once instead one gene at a time; the growing recognition that environmental and behavioral signals trigger massive shifts in gene expression in the brain; and the prospects for using comparative genomics to uncover the genetic roots of behavioral variation. Throughout, we identify promising new directions for bolstering the application of genomic information to further advance the study of avian brain and behavior.
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Affiliation(s)
- David F Clayton
- Biological & Experimental Psychology Division, School of Biological & Chemical Sciences, Queen Mary University of London, London E1 4NS, UK.
| | - Sarah E London
- Department of Psychology, Institute for Mind and Biology, Committee on Neurobiology, University of Chicago, 940 E 57th Street, Chicago, IL, USA.
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406
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Lovell PV, Wirthlin M, Wilhelm L, Minx P, Lazar NH, Carbone L, Warren WC, Mello CV. Conserved syntenic clusters of protein coding genes are missing in birds. Genome Biol 2014; 15:565. [PMID: 25518852 PMCID: PMC4290089 DOI: 10.1186/s13059-014-0565-1] [Citation(s) in RCA: 87] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Accepted: 12/08/2014] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Birds are one of the most highly successful and diverse groups of vertebrates, having evolved a number of distinct characteristics, including feathers and wings, a sturdy lightweight skeleton and unique respiratory and urinary/excretion systems. However, the genetic basis of these traits is poorly understood. RESULTS Using comparative genomics based on extensive searches of 60 avian genomes, we have found that birds lack approximately 274 protein coding genes that are present in the genomes of most vertebrate lineages and are for the most part organized in conserved syntenic clusters in non-avian sauropsids and in humans. These genes are located in regions associated with chromosomal rearrangements, and are largely present in crocodiles, suggesting that their loss occurred subsequent to the split of dinosaurs/birds from crocodilians. Many of these genes are associated with lethality in rodents, human genetic disorders, or biological functions targeting various tissues. Functional enrichment analysis combined with orthogroup analysis and paralog searches revealed enrichments that were shared by non-avian species, present only in birds, or shared between all species. CONCLUSIONS Together these results provide a clearer definition of the genetic background of extant birds, extend the findings of previous studies on missing avian genes, and provide clues about molecular events that shaped avian evolution. They also have implications for fields that largely benefit from avian studies, including development, immune system, oncogenesis, and brain function and cognition. With regards to the missing genes, birds can be considered ‘natural knockouts’ that may become invaluable model organisms for several human diseases.
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Affiliation(s)
- Peter V Lovell
- />Department of Behavioral Neuroscience, Oregon Health and Science University, Portland, OR USA
| | - Morgan Wirthlin
- />Department of Behavioral Neuroscience, Oregon Health and Science University, Portland, OR USA
| | - Larry Wilhelm
- />Department of Behavioral Neuroscience, Oregon Health and Science University, Portland, OR USA
- />Oregon National Primate Research Center, West Campus, Oregon Health and Science University, Portland, OR USA
| | - Patrick Minx
- />The Genome Institute, Washington University School of Medicine, St. Louis, MO USA
| | - Nathan H Lazar
- />Oregon National Primate Research Center, West Campus, Oregon Health and Science University, Portland, OR USA
- />Bioinformatics and Computational Biology Division, Oregon Health & Science University, Portland, OR USA
| | - Lucia Carbone
- />Department of Behavioral Neuroscience, Oregon Health and Science University, Portland, OR USA
- />Oregon National Primate Research Center, West Campus, Oregon Health and Science University, Portland, OR USA
| | - Wesley C Warren
- />The Genome Institute, Washington University School of Medicine, St. Louis, MO USA
| | - Claudio V Mello
- />Department of Behavioral Neuroscience, Oregon Health and Science University, Portland, OR USA
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407
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A novel recombinant retrovirus in the genomes of modern birds combines features of avian and mammalian retroviruses. J Virol 2013; 88:2398-405. [PMID: 24352464 DOI: 10.1128/jvi.02863-13] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Endogenous retroviruses (ERVs) represent ancestral sequences of modern retroviruses or their extinct relatives. The majority of ERVs cluster alongside exogenous retroviruses into two main groups based on phylogenetic analyses of the reverse transcriptase (RT) enzyme. Class I includes gammaretroviruses, and class II includes lentiviruses and alpha-, beta-, and deltaretroviruses. However, analyses of the transmembrane subunit (TM) of the envelope glycoprotein (env) gene result in a different topology for some retroviruses, suggesting recombination events in which heterologous env sequences have been acquired. We previously demonstrated that the TM sequences of five of the six genera of orthoretroviruses can be divided into three types, each of which infects a distinct set of vertebrate classes. Moreover, these classes do not always overlap the host range of the associated RT classes. Thus, recombination resulting in acquisition of a heterologous env gene could in theory facilitate cross-species transmissions across vertebrate classes, for example, from mammals to reptiles. Here we characterized a family of class II avian ERVs, "TgERV-F," that acquired a mammalian gammaretroviral env sequence. Although TgERV-F clusters near a sister clade to alpharetroviruses, its genome also has some features of betaretroviruses. We offer evidence that this unusual recombinant has circulated among several avian orders and may still have infectious members. In addition to documenting the infection of a nongalliform avian species by a mammalian retrovirus, TgERV-F also underscores the importance of env sequences in reconstructing phylogenies and supports a possible role for env swapping in allowing cross-species transmissions across wide taxonomic distances. IMPORTANCE Retroviruses can sometimes acquire an envelope gene (env) from a distantly related retrovirus. Since env is a key determinant of host range, such an event affects the host range of the recombinant virus and can lead to the creation of novel retroviral lineages. Retroviruses insert viral DNA into the host DNA during infection, and therefore vertebrate genomes contain a "fossil record" of endogenous retroviral sequences thought to represent past infections of germ cells. We examined endogenous retroviral sequences in avian genomes for evidence of recombination events involving env. Although cross-species transmissions of retroviruses between vertebrate classes (from mammals to birds, for example) are thought to be rare, we here characterized a group of avian retroviruses that acquired an env sequence from a mammalian retrovirus. We offer evidence that this unusual recombinant circulated among songbirds 2 to 4 million years ago and has remained active into the recent past.
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408
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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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409
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Bonoan R, Clodius F, Dawson A, Caetano S, Yeung E, Paz-y-Miño-C. G. Dominance hierarchy formation in a model organism, the zebra finch (Taeniopygia guttata), and its potential application to laboratory research. ACTA ACUST UNITED AC 2013. [DOI: 10.1893/0005-3155-84.4.201] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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410
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Sheng G. Day-1 chick development. Dev Dyn 2013; 243:357-67. [DOI: 10.1002/dvdy.24087] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2013] [Revised: 10/22/2013] [Accepted: 10/22/2013] [Indexed: 02/04/2023] Open
Affiliation(s)
- Guojun Sheng
- Laboratory for Early Embryogenesis; RIKEN Center for Developmental Biology; Kobe Hyogo Japan
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411
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Suh A, Brosius J, Schmitz J, Kriegs JO. The genome of a Mesozoic paleovirus reveals the evolution of hepatitis B viruses. Nat Commun 2013; 4:1791. [PMID: 23653203 DOI: 10.1038/ncomms2798] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2012] [Accepted: 03/26/2013] [Indexed: 12/26/2022] Open
Abstract
Paleovirology involves the identification of ancient endogenous viral elements within eukaryotic genomes. The evolutionary origins of the reverse-transcribing hepatitis B viruses, however, remain elusive, due to the small number of endogenized sequences present in host genomes. Here we report a comprehensively dated genomic record of hepatitis B virus endogenizations that spans bird evolution from >82 to <12.1 million years ago. The oldest virus relic extends over a 99% complete hepatitis B virus genome sequence and constitutes the first discovery of a Mesozoic paleovirus genome. We show that Hepadnaviridae are >63 million years older than previously known and provide direct evidence for coexistence of hepatitis B viruses and birds during the Mesozoic and Cenozoic Eras. Finally, phylogenetic analyses and distribution of hepatitis B virus relics suggest that birds potentially are the ancestral hosts of Hepadnaviridae and mammalian hepatitis B viruses probably emerged after a bird-mammal host switch. Our study reveals previously undiscovered and multi-faceted insights into prehistoric hepatitis B virus evolution and provides valuable resources for future studies, such as in-vitro resurrection of Mesozoic hepadnaviruses.
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Affiliation(s)
- Alexander Suh
- Institute of Experimental Pathology (ZMBE), University of Münster, Von-Esmarch-Straße 56, D-48149 Münster, Germany.
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412
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Affiliation(s)
- Hans Ellegren
- Department of Evolutionary Biology, Evolutionary Biology Center, Uppsala University, SE-752 36 Uppsala, Sweden;
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413
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Ishige T, Hara H, Hirano T, Kono T, Hanzawa K. Basic characterization of avian NK-lysin (NKL) from the Japanese quail, Coturnix japonica. Anim Sci J 2013; 85:90-5. [PMID: 24206178 DOI: 10.1111/asj.12138] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Accepted: 08/15/2013] [Indexed: 11/28/2022]
Abstract
We identified an antimicrobial cationic peptide that was expressed in the natural killer cells and cytotoxic T-lymphocytes of Japanese quail. The gene, designated CjNKL, was located downstream of AEBP1L and POLD2 in a region syntenic with the chicken genome. CjNKL comprised four exons, as does chicken GgNKL. The coding sequence in CjNKL was 411 bp long and exon 3 of CjNKL lacked 9 bp when compared to chicken GgNKL, but CjNKL and GgNKL were 81% identical at the nucleic acid level. The saposin like type-B domain of CjNKL contained the six essential cysteines, one proline, 15 cationic amino acids residues, and an antibacterial region that are characteristic of NKL proteins. The 5' flanking region of CjNKL contained positive regulatory elements, an activator protein-1 binding site and two nuclear factor (NF)-κB binding sites, and a negative regulatory element, CAAT/enhancer binding protein β (C/EBPβ) binding site. However, the number of NF-κB sites and C/EBPβ sites within CjNKL are fewer than the number within GgNKL. Additionally, we confirmed that CjNKL was transcribed in at least 18 tissues, including immune and digestive tissues. These data indicated that transcriptional activation of CjNKL differed slightly from those of GgNKL.
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Affiliation(s)
- Taichiro Ishige
- Genome Research Center, Tokyo University of Agriculture, Tokyo, Japan
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414
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Cuperus T, Coorens M, van Dijk A, Haagsman HP. Avian host defense peptides. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2013; 41:352-369. [PMID: 23644014 DOI: 10.1016/j.dci.2013.04.019] [Citation(s) in RCA: 136] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2013] [Accepted: 04/24/2013] [Indexed: 06/02/2023]
Abstract
Host defense peptides (HDPs) are important effector molecules of the innate immune system of vertebrates. These antimicrobial peptides are also present in invertebrates, plants and fungi. HDPs display broad-spectrum antimicrobial activities and fulfill an important role in the first line of defense of many organisms. It is becoming increasingly clear that in the animal kingdom the functions of HDPs are not confined to direct antimicrobial actions. Research in mammals has indicated that HDPs have many immunomodulatory functions and are also involved in other physiological processes ranging from development to wound healing. During the past five years our knowledge about avian HDPs has increased considerably. This review addresses our current knowledge on the evolution, regulation and biological functions of HDPs of birds.
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Affiliation(s)
- Tryntsje Cuperus
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, The Netherlands
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415
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Magor KE, Miranzo Navarro D, Barber MRW, Petkau K, Fleming-Canepa X, Blyth GAD, Blaine AH. Defense genes missing from the flight division. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2013; 41:377-88. [PMID: 23624185 PMCID: PMC7172724 DOI: 10.1016/j.dci.2013.04.010] [Citation(s) in RCA: 117] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2013] [Accepted: 04/16/2013] [Indexed: 05/12/2023]
Abstract
Birds have a smaller repertoire of immune genes than mammals. In our efforts to study antiviral responses to influenza in avian hosts, we have noted key genes that appear to be missing. As a result, we speculate that birds have impaired detection of viruses and intracellular pathogens. Birds are missing TLR8, a detector for single-stranded RNA. Chickens also lack RIG-I, the intracellular detector for single-stranded viral RNA. Riplet, an activator for RIG-I, is also missing in chickens. IRF3, the nuclear activator of interferon-beta in the RIG-I pathway is missing in birds. Downstream of interferon (IFN) signaling, some of the antiviral effectors are missing, including ISG15, and ISG54 and ISG56 (IFITs). Birds have only three antibody isotypes and IgD is missing. Ducks, but not chickens, make an unusual truncated IgY antibody that is missing the Fc fragment. Chickens have an expanded family of LILR leukocyte receptor genes, called CHIR genes, with hundreds of members, including several that encode IgY Fc receptors. Intriguingly, LILR homologues appear to be missing in ducks, including these IgY Fc receptors. The truncated IgY in ducks, and the duplicated IgY receptor genes in chickens may both have resulted from selective pressure by a pathogen on IgY FcR interactions. Birds have a minimal MHC, and the TAP transport and presentation of peptides on MHC class I is constrained, limiting function. Perhaps removing some constraint, ducks appear to lack tapasin, a chaperone involved in loading peptides on MHC class I. Finally, the absence of lymphotoxin-alpha and beta may account for the observed lack of lymph nodes in birds. As illustrated by these examples, the picture that emerges is some impairment of immune response to viruses in birds, either a cause or consequence of the host-pathogen arms race and long evolutionary relationship of birds and RNA viruses.
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Affiliation(s)
- Katharine E Magor
- Department of Biological Sciences, University of Alberta, Edmonton, Canada.
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416
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Medina CO, Lattin CR, McVey M, Romero LM. There is no correlation between glucocorticoid receptor mRNA expression and protein binding in the brains of house sparrows (Passer domesticus). Gen Comp Endocrinol 2013; 193:27-36. [PMID: 23892014 DOI: 10.1016/j.ygcen.2013.07.008] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/01/2012] [Revised: 06/30/2013] [Accepted: 07/08/2013] [Indexed: 12/27/2022]
Abstract
The stress response represents an animal's attempt to cope with a noxious stimulus through a rapid release of corticosterone or cortisol (CORT) into the bloodstream, resulting in a suite of physiological and behavioral changes. These changes are mediated in large part through CORT's binding to two different intracellular receptors, the high-affinity mineralocorticoid receptor (MR) and the lower-affinity glucocorticoid receptor (GR). We tested the hypothesis that GR and MR mRNA expression would correlate with functional protein expression in neuronal tissue of wild-caught house sparrows (Passer domesticus). To test this hypothesis, we performed a parallel procedure in which protein concentrations were quantified in one half of house sparrow brains (n=16) using radioligand binding assays, and mRNA levels were quantified in the other brain half using reverse-transcriptase quantitative PCR (RT-qPCR). Two reference genes, glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and TATA-box binding protein (TBP), were used for relative quantification of GR and MR mRNA. Quantifications showed that these two reference genes were not correlated with each other. Furthermore, there was no correlation between mRNA and protein levels for GR or MR using either reference gene, suggesting that regulation of mRNA and protein levels for MR and GR is not tightly linked. This study provides insight into the importance of regulatory steps between mRNA expression and the creation and stability of a functional protein. The overall conclusion is that mRNA expression cannot be used as a proxy for GR or MR binding in house sparrows.
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Affiliation(s)
- Carlos O Medina
- Department of Biology, Tufts University, Medford, MA 02155, USA
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417
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Brainard MS, Doupe AJ. Translating birdsong: songbirds as a model for basic and applied medical research. Annu Rev Neurosci 2013; 36:489-517. [PMID: 23750515 DOI: 10.1146/annurev-neuro-060909-152826] [Citation(s) in RCA: 157] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Songbirds, long of interest to basic neuroscience, have great potential as a model system for translational neuroscience. Songbirds learn their complex vocal behavior in a manner that exemplifies general processes of perceptual and motor skill learning and, more specifically, resembles human speech learning. Song is subserved by circuitry that is specialized for vocal learning and production but that has strong similarities to mammalian brain pathways. The combination of highly quantifiable behavior and discrete neural substrates facilitates understanding links between brain and behavior, both in normal states and in disease. Here we highlight (a) behavioral and mechanistic parallels between birdsong and aspects of speech and social communication, including insights into mirror neurons, the function of auditory feedback, and genes underlying social communication disorders, and (b) contributions of songbirds to understanding cortical-basal ganglia circuit function and dysfunction, including the possibility of harnessing adult neurogenesis for brain repair.
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Affiliation(s)
- Michael S Brainard
- Center for Integrative Neuroscience and Departments of Physiology and Psychiatry, University of California-San Francisco, CA 94143-0444, USA.
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418
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Murray JR, Varian-Ramos CW, Welch ZS, Saha MS. Embryological staging of the Zebra Finch, Taeniopygia guttata. J Morphol 2013; 274:1090-110. [PMID: 23813920 PMCID: PMC4239009 DOI: 10.1002/jmor.20165] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2012] [Revised: 04/22/2013] [Accepted: 04/25/2013] [Indexed: 01/02/2023]
Abstract
Zebra Finches (Taeniopygia guttata) are the most commonly used laboratory songbird species, yet their embryological development has been poorly characterized. Most studies to date apply Hamburger and Hamilton stages derived from chicken development; however, significant differences in development between precocial and altricial species suggest that they may not be directly comparable. We provide the first detailed description of embryological development in the Zebra Finch under standard artificial incubation. These descriptions confirm that some of the features used to classify chicken embryos into stages are not applicable in an altricial bird such as the Zebra Finch. This staging protocol will help to standardize future studies of embryological development in the Zebra Finch.
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Affiliation(s)
- Jessica R Murray
- Biology Department, College of William and MaryP.O. Box 8795, Williamsburg, Virginia, 23187
| | - Claire W Varian-Ramos
- Biology Department, College of William and MaryP.O. Box 8795, Williamsburg, Virginia, 23187
| | - Zoe S Welch
- Biology Department, College of William and MaryP.O. Box 8795, Williamsburg, Virginia, 23187
| | - Margaret S Saha
- Biology Department, College of William and MaryP.O. Box 8795, Williamsburg, Virginia, 23187
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419
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D'Angelo ME, Arjomand A, Trapani JA, Bird PI. Cloning and characterising an unusual perforin from chicken (Gallus gallus). DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2013; 41:105-109. [PMID: 23680640 DOI: 10.1016/j.dci.2013.05.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Revised: 05/01/2013] [Accepted: 05/03/2013] [Indexed: 06/02/2023]
Abstract
In mammals the 67 kDa pore-forming protein perforin is essential to the granule exocytosis pathway used by cytotoxic lymphocytes to eliminate virally infected and malignant cells. There is indirect evidence that this pathway exists in lower vertebrates such as teleost fish and birds, although in genome databases for the chicken and other bird species the perforin gene is incomplete and no full length expressed sequence tag has been reported. We present here the full gene and transcript sequence of chicken perforin. The inferred protein product contains an extended C-terminus that is at least 90 amino acids longer than any mammalian perforin, which is also evident in partial genomic sequences from other birds. To determine whether this extension is present in the translated protein, we raised two polyclonal antisera. The antisera identified a protein of just less than 80 kDa in both transfected COS-1 cells and concanavalin A stimulated chicken splenocytes, indicating that the extended C-terminus is present in the mature protein. Our findings confirm that perforin exists in birds, and show that it is considerably longer than perforin of non-avian vertebrates.
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Affiliation(s)
- Michael E D'Angelo
- Department of Biochemistry and Molecular Biology, Monash University, Wellington Road, Clayton, VIC 3800, Australia.
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420
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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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421
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Park TS, Kang KS, Han JY. Current genomic editing approaches in avian transgenesis. Gen Comp Endocrinol 2013; 190:144-8. [PMID: 23247275 DOI: 10.1016/j.ygcen.2012.11.020] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/06/2012] [Revised: 11/26/2012] [Accepted: 11/30/2012] [Indexed: 11/25/2022]
Abstract
The chicken was domesticated from Red Jungle Fowl over 8000years ago and became one of the major food sources worldwide. At present, the poultry industry is one of the largest industrial animal stocks in the world, and its economic scale is expanding significantly with increasing consumption. Additionally, since Aristotle used chicken eggs as a model to provide remarkable insights into how life begins, chickens have been used as invaluable and powerful experimental materials for studying embryo development, immune systems, biomedical processes, and hormonal regulation. Combined with advancements in efficient transgenic technology, avian models have become even more important than would have been expected.
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Affiliation(s)
- Tae Sub Park
- WCU Biomodulation Major, Department of Agricultural Biotechnology, Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Republic of Korea
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422
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Adkins-Regan E, Banerjee SB, Correa SM, Schweitzer C. Maternal effects in quail and zebra finches: Behavior and hormones. Gen Comp Endocrinol 2013; 190:34-41. [PMID: 23499787 DOI: 10.1016/j.ygcen.2013.03.002] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/30/2012] [Revised: 03/01/2013] [Accepted: 03/04/2013] [Indexed: 11/30/2022]
Abstract
Maternal effects are influences of parents on offspring phenotype occurring through pathways other than inherited DNA. In birds, two important routes for such transmission are parental behavior and non-DNA egg constituents such as yolk hormones. Offspring traits subject to parental effects include behavior and endocrine function. Research from the Adkins-Regan lab has used three avian species to investigate maternal effects related to hormones and behavior. Experiments with chickens and Japanese quail have shown that maternal sex steroids can influence sex determination to produce biased offspring sex ratios. Because all birds have a ZZ/ZW chromosomal sex determining system in which the female parent determines the sex of the offspring, these results raise the possibility that maternal steroids can influence the outcome of sex chromosome meiosis. Learning has been shown to influence egg investment by female quail in ways that are likely to alter offspring phenotype. In quail, embryonic and exogenous sex steroids have well established and long-lasting effects on sexual differentiation of behavior during a critical period in ovo, but elevated yolk testosterone has long-term effects on behavior that do not seem to be occurring through an alteration in sexual differentiation. In biparental zebra finches, removal of mothers alters not only later behavior, but also the adult response of the hypothalamic-pituitary-adrenal (HPA) axis to an environmental stressor, as indicated by plasma corticosterone. Birds raised only by fathers have lower levels of mRNA for both glucocorticoid receptors in several brain regions as adults. These studies add to the evidence that one generation influences the behavioral or endocrine phenotype of the next through routes other than transmission of DNA. Additional research will be required to understand the adaptive significance of these effects.
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423
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Stevenson TJ, Bernard DJ, McCarthy MM, Ball GF. Photoperiod-dependent regulation of gonadotropin-releasing hormone 1 messenger ribonucleic acid levels in the songbird brain. Gen Comp Endocrinol 2013; 190:81-7. [PMID: 23660447 PMCID: PMC3742601 DOI: 10.1016/j.ygcen.2013.04.011] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/08/2013] [Revised: 04/15/2013] [Accepted: 04/16/2013] [Indexed: 12/19/2022]
Abstract
Annual changes in day length induce marked changes in reproductive function in temperate zone vertebrates. In many avian species, in contrast to other seasonally breeding animals, plasticity in hypothalamic gonadotropin-releasing hormone - 1 (GnRH1) expression rather than (or in addition to) release governs changes in pituitary-gonadal activity. Investigations of the cellular and molecular mechanisms that govern GnRH1 plasticity were previously hindered by a collective inability of scientists in the field to characterize the gnrh1 cDNA in songbirds. We finally overcame this roadblock after data from the zebra finch (Taeniopygia guttata) genome project enabled us to rapidly clone the gnrh1 cDNA from hypothalamic RNA of zebra finches and European starlings (Sturnus vulgaris). Here, we review the original data that identified GnRH1 protein plasticity in the songbird brain and discuss earlier failed attempts to clone gnrh1 in these animals. Then, we present recent efforts, including our own, that successfully characterized gnrh1 in zebra finch and starling, and demonstrated dynamic regulation of gnrh1 mRNA expression, particularly in sub-populations of preoptic area neurons, in the latter. Overall, this paper highlights GnRH1 plasticity in the avian brain, and weaves into the narrative the previously untold story of the challenges to sequencing gnrh1 in songbirds.
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Affiliation(s)
- Tyler J Stevenson
- Institute for Mind and Biology, University of Chicago, Chicago, IL, USA.
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424
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London SE. Genome-brain-behavior interdependencies as a framework to understand hormone effects on learned behavior. Gen Comp Endocrinol 2013; 190:176-81. [PMID: 23684969 DOI: 10.1016/j.ygcen.2013.04.035] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/04/2012] [Revised: 04/28/2013] [Accepted: 04/30/2013] [Indexed: 12/16/2022]
Abstract
Hormones have profound effects on the maturation and function of the zebra finch song system. Hormones often signal through receptors that directly or indirectly regulate transcription. In this way, hormones and the genome are functionally connected. Genome-brain-behavior interdependencies are often studied on evolutionary timescales but we can now apply and test these relationships on short timescales, relevant to an individual. Here, we begin to place patterns of hormone-related gene expression into the timeframe of an individual's lifespan to consider how hormones contribute to organization of neural systems necessary for learned behavior, and how they might signal during experience in ways that affect future behavior. This framework illustrates both how much investigations into genome and hormone function are intertwined, and how much we still need to learn.
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Affiliation(s)
- Sarah E London
- Department of Psychology, Institute for Mind and Biology, Committee on Neurobiology, University of Chicago, 129A BPSB, 940 E 57th Street, Chicago, IL 60637, USA.
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425
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Huang CH, Tanaka Y, Fujito NT, Nonaka M. Dimorphisms of the proteasome subunit beta type 8 gene (PSMB8) of ectothermic tetrapods originated in multiple independent evolutionary events. Immunogenetics 2013; 65:811-21. [PMID: 23982299 DOI: 10.1007/s00251-013-0729-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2013] [Accepted: 08/07/2013] [Indexed: 01/23/2023]
Abstract
The proteasome subunit beta type 8 gene (PSMB8) encodes one of the beta subunits of the immunoproteasome responsible for the generation of peptides presented by major histocompatibility complex class I molecules. Dimorphic alleles of the PSMB8 gene, termed A and F types, based on the deduced 31st amino acid residue of the mature protein have been reported from various vertebrates. Phylogenetic analysis revealed the presence of dichotomous ancient lineages, one comprising the F-type PSMB8 of basal ray-finned fishes, and the other comprising the A-type PSMB8 of these animals and both the F- and A-type PSMB8 of Xenopus and acanthopterygians, indicating that evolutionary history of the PSMB8 dimorphism was not straightforward. We analyzed the PSMB8 gene of five reptile and one amphibian species and found both the A and F types from all six. Phylogenetic analysis indicated that the PSMB8 F type was apparently regenerated from the PSMB8 A type at least five times independently during tetrapod evolution. Genomic typing of wild individuals of geckos and newts indicated that the frequencies of the A- and F-type alleles are not highly biased in these species. Phylogenetic analysis of each exon of the reptile PSMB8 gene suggested interallelic sequence homogenization as a possible evolutionary mechanism for the apparent recurrent regeneration of PSMB8 dimorphism in tetrapods. An extremely strong balancing selection acting on PSMB8 dimorphism was implicated in an unprecedented pattern of allele evolution.
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Affiliation(s)
- Ching-Huei Huang
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
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426
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Mann K, Mann M. The proteome of the calcified layer organic matrix of turkey (Meleagris gallopavo) eggshell. Proteome Sci 2013; 11:40. [PMID: 23981693 PMCID: PMC3766105 DOI: 10.1186/1477-5956-11-40] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2013] [Accepted: 08/23/2013] [Indexed: 12/30/2022] Open
Abstract
Background Chicken eggshell mineralization is a prominent model for biomineralization not only because of its importance for avian reproduction but also because of the commercial interest associated with eggshell quality. An analysis and comparison of the protein constituents of eggshells of several species would contribute to a better understanding of the shell mineralization process. The recent publication of the turkey genome sequence now provides a basis for the in-depth analysis of the turkey eggshell proteome. Results Proteomic analysis of turkey acid-soluble and acid-insoluble organic eggshell matrix yielded 697 identified proteins/protein groups. However, intensity-based absolute quantification (iBAQ) results indicated that the 47 most abundant identified proteins already constituted 95% of the total turkey eggshell matrix proteome. Forty-four of these proteins were also identified in chicken eggshell matrix previously. Despite these similarities there were important and unexpected differences. While ovocleidin-116 and ovocalyxin-36 were major proteins constituting approximately 37% of the identified proteome, other members of the group of so-called eggshell-specific proteins were not identified. Thus ovocalyxin-21 and ovocalyxin-32 were missing among matrix proteins. Conversely, major turkey eggshell proteins were not detected in chicken, such as the bone protein periostin, the mammalian counterpart of which is involved in many aspects of bone metabolism and which represented 10-11% of the total identified proteome. Conclusions Even members of the same avian family show important differences in eggshell matrix composition and more studies on the proteome and the transcriptome level will be necessary to identify a common toolkit of eggshell mineralization and to work out species differences among functional eggshell protein sets and their role in eggshell production.
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Affiliation(s)
- Karlheinz Mann
- Max-Planck-Institut für Biochemie, Abteilung Proteomics und Signaltransduktion, D-82152, Martinsried, Am Klopferspitz 18, Germany.
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427
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McCarthy FM, Lyons E. From data to function: functional modeling of poultry genomics data. Poult Sci 2013; 92:2519-29. [PMID: 23960137 DOI: 10.3382/ps.2012-02808] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
One of the challenges of functional genomics is to create a better understanding of the biological system being studied so that the data produced are leveraged to provide gains for agriculture, human health, and the environment. Functional modeling enables researchers to make sense of these data as it reframes a long list of genes or gene products (mRNA, ncRNA, and proteins) by grouping based upon function, be it individual molecular functions or interactions between these molecules or broader biological processes, including metabolic and signaling pathways. However, poultry researchers have been hampered by a lack of functional annotation data, tools, and training to use these data and tools. Moreover, this lack is becoming more critical as new sequencing technologies enable us to generate data not only for an increasingly diverse range of species but also individual genomes and populations of individuals. We discuss the impact of these new sequencing technologies on poultry research, with a specific focus on what functional modeling resources are available for poultry researchers. We also describe key strategies for researchers who wish to functionally model their own data, providing background information about functional modeling approaches, the data and tools to support these approaches, and the strengths and limitations of each. Specifically, we describe methods for functional analysis using Gene Ontology (GO) functional summaries, functional enrichment analysis, and pathways and network modeling. As annotation efforts begin to provide the fundamental data that underpin poultry functional modeling (such as improved gene identification, standardized gene nomenclature, temporal and spatial expression data and gene product function), tool developers are incorporating these data into new and existing tools that are used for functional modeling, and cyberinfrastructure is being developed to provide the necessary extendibility and scalability for storing and analyzing these data. This process will support the efforts of poultry researchers to make sense of their functional genomics data sets, and we provide here a starting point for researchers who wish to take advantage of these tools.
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Affiliation(s)
- F M McCarthy
- Department of Veterinary Science and Microbiology, University of Arizona, Tucson, AZ 85721, USA.
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428
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High-throughput sequencing of a single chromosome: a moth W chromosome. Chromosome Res 2013; 21:491-505. [PMID: 23949445 DOI: 10.1007/s10577-013-9376-6] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Revised: 07/23/2013] [Accepted: 07/23/2013] [Indexed: 10/26/2022]
Abstract
Y and W chromosomes have mostly been excluded from whole genome sequencing projects. Due to the high amount of repetitive sequences they are 'difficult' to assemble and therefore need special treatment in the form of, e.g. adapted assembly programs, a range of different libraries, and accurate maps, if possible. A minimum requirement for these approaches is pure template DNA. We therefore microdissected the W chromatin of highly polyploid cells from the flour moth, Ephestia kuehniella, and used Roche/454 and Sanger sequencing to generate 72.6 Mbp of DNA sequence. Nominal coverage was 4.3× of the 16.7 Mbp of W chromosomal DNA. We used these data to assess the genetic content of the W chromosome. This approach allowed us to determine constituent families of transposable elements, microsatellites, and recent insertion sites of mitochondrial DNA. However, no conventional protein-coding gene has yet been found. The sequence collection is a rich source for the definition of W-specific PCR markers and the reconstruction of W chromosome loci, as a step towards full reconstruction of the chromosome.
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429
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Wan QH, Pan SK, Hu L, Zhu Y, Xu PW, Xia JQ, Chen H, He GY, He J, Ni XW, Hou HL, Liao SG, Yang HQ, Chen Y, Gao SK, Ge YF, Cao CC, Li PF, Fang LM, Liao L, Zhang S, Wang MZ, Dong W, Fang SG. Genome analysis and signature discovery for diving and sensory properties of the endangered Chinese alligator. Cell Res 2013; 23:1091-105. [PMID: 23917531 PMCID: PMC3760627 DOI: 10.1038/cr.2013.104] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2013] [Revised: 06/20/2013] [Accepted: 07/08/2013] [Indexed: 12/27/2022] Open
Abstract
Crocodilians are diving reptiles that can hold their breath under water for long periods of time and are crepuscular animals with excellent sensory abilities. They comprise a sister lineage of birds and have no sex chromosome. Here we report the genome sequence of the endangered Chinese alligator (Alligator sinensis) and describe its unique features. The next-generation sequencing generated 314 Gb of raw sequence, yielding a genome size of 2.3 Gb. A total of 22 200 genes were predicted in Alligator sinensis using a de novo, homology- and RNA-based combined model. The genetic basis of long-diving behavior includes duplication of the bicarbonate-binding hemoglobin gene, co-functioning of routine phosphate-binding and special bicarbonate-binding oxygen transport, and positively selected energy metabolism, ammonium bicarbonate excretion and cardiac muscle contraction. Further, we elucidated the robust Alligator sinensis sensory system, including a significantly expanded olfactory receptor repertoire, rapidly evolving nerve-related cellular components and visual perception, and positive selection of the night vision-related opsin and sound detection-associated otopetrin. We also discovered a well-developed immune system with a considerable number of lineage-specific antigen-presentation genes for adaptive immunity as well as expansion of the tripartite motif-containing C-type lectin and butyrophilin genes for innate immunity and expression of antibacterial peptides. Multifluorescence in situ hybridization showed that alligator chromosome 3, which encodes DMRT1, exhibits significant synteny with chicken chromosome Z. Finally, population history analysis indicated population admixture 0.60-1.05 million years ago, when the Qinghai-Tibetan Plateau was uplifted.
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Affiliation(s)
- Qiu-Hong Wan
- The Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, State Conservation Center for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
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430
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Abstract
Songbirds have unique value as a model for memory and learning. In their natural social life, they communicate through vocalizations that they must learn to produce and recognize. Song communication elicits abrupt changes in gene expression in regions of the forebrain responsible for song perception and production--what is the functional significance of this genomic response? For 20 years, the focus of research was on just a few genes [primarily ZENK, now known as egr1 (early gene response 1)]. Recently, however, DNA microarrays have been developed and applied to songbird behavioral research, and in 2010 the initial draft assembly of the zebra finch genome was published. Together, these new data reveal that the genomic involvement in song processing is far more complex than anticipated. The concepts of neurogenomic computation and biological embedding are introduced as frameworks for future research.
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Affiliation(s)
- David F Clayton
- Biological and Experimental Psychology Division, School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, United Kingdom;
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431
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Bourgeois YXC, Lhuillier E, Cézard T, Bertrand JAM, Delahaie B, Cornuault J, Duval T, Bouchez O, Milá B, Thébaud C. Mass production of
SNP
markers in a nonmodel passerine bird through
RAD
sequencing and contig mapping to the zebra finch genome. Mol Ecol Resour 2013; 13:899-907. [DOI: 10.1111/1755-0998.12137] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Revised: 05/24/2013] [Accepted: 06/04/2013] [Indexed: 01/01/2023]
Affiliation(s)
- Yann X. C. Bourgeois
- Laboratoire Évolution et Diversité Biologique UMR 5174 CNRS ‐ Université Paul Sabatier – ENFA 118 route de Narbonne, Bâtiment 4R1 F‐31062 Toulouse Cedex 9 France
| | - Emeline Lhuillier
- INRA UAR 1209 Département de Génétique Animale INRA Auzeville F‐31326 Castanet‐Tolosan France
- GeT‐PlaGe Genotoul INRA Auzeville F‐31326 Castanet‐Tolosan France
| | - Timothée Cézard
- The GenePool Ashworth Laboratories The University of Edinburgh The King's Building Edinburgh EH9 3JT UK
| | - Joris A. M. Bertrand
- Laboratoire Évolution et Diversité Biologique UMR 5174 CNRS ‐ Université Paul Sabatier – ENFA 118 route de Narbonne, Bâtiment 4R1 F‐31062 Toulouse Cedex 9 France
| | - Boris Delahaie
- Laboratoire Évolution et Diversité Biologique UMR 5174 CNRS ‐ Université Paul Sabatier – ENFA 118 route de Narbonne, Bâtiment 4R1 F‐31062 Toulouse Cedex 9 France
| | - Josselin Cornuault
- Laboratoire Évolution et Diversité Biologique UMR 5174 CNRS ‐ Université Paul Sabatier – ENFA 118 route de Narbonne, Bâtiment 4R1 F‐31062 Toulouse Cedex 9 France
| | - Thomas Duval
- Société Calédonienne d'Ornithologie Nord BP 236 F‐98822 Poindimié Nouvelle Calédonie France
| | - Olivier Bouchez
- GeT‐PlaGe Genotoul INRA Auzeville F‐31326 Castanet‐Tolosan France
- INRA UMR 444 Laboratoire de Génétique Cellulaire INRA Auzeville F‐31326 Castanet‐Tolosan France
| | - Borja Milá
- Museo Nacional de Ciencias Naturales CSIC José Gutiérrez Abascal 2 Madrid 28006 Spain
| | - Christophe Thébaud
- Laboratoire Évolution et Diversité Biologique UMR 5174 CNRS ‐ Université Paul Sabatier – ENFA 118 route de Narbonne, Bâtiment 4R1 F‐31062 Toulouse Cedex 9 France
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432
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Lovell PV, Carleton JB, Mello CV. Genomics analysis of potassium channel genes in songbirds reveals molecular specializations of brain circuits for the maintenance and production of learned vocalizations. BMC Genomics 2013; 14:470. [PMID: 23845108 PMCID: PMC3711925 DOI: 10.1186/1471-2164-14-470] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2012] [Accepted: 06/19/2013] [Indexed: 02/08/2023] Open
Abstract
Background A fundamental question in molecular neurobiology is how genes that determine basic neuronal properties shape the functional organization of brain circuits underlying complex learned behaviors. Given the growing availability of complete vertebrate genomes, comparative genomics represents a promising approach to address this question. Here we used genomics and molecular approaches to study how ion channel genes influence the properties of the brain circuitry that regulates birdsong, a learned vocal behavior with important similarities to human speech acquisition. We focused on potassium (K-)Channels, which are major determinants of neuronal cell excitability. Starting with the human gene set of K-Channels, we used cross-species mRNA/protein alignments, and syntenic analysis to define the full complement of orthologs, paralogs, allelic variants, as well as novel loci not previously predicted in the genome of zebra finch (Taeniopygia guttata). We also compared protein coding domains in chicken and zebra finch orthologs to identify genes under positive selective pressure, and those that contained lineage-specific insertions/deletions in functional domains. Finally, we conducted comprehensive in situ hybridizations to determine the extent of brain expression, and identify K-Channel gene enrichments in nuclei of the avian song system. Results We identified 107 K-Channel finch genes, including 6 novel genes common to non-mammalian vertebrate lineages. Twenty human genes are absent in songbirds, birds, or sauropsids, or unique to mammals, suggesting K-Channel properties may be lineage-specific. We also identified specific family members with insertions/deletions and/or high dN/dS ratios compared to chicken, a non-vocal learner. In situ hybridization revealed that while most K-Channel genes are broadly expressed in the brain, a subset is selectively expressed in song nuclei, representing molecular specializations of the vocal circuitry. Conclusions Together, these findings shed new light on genes that may regulate biophysical and excitable properties of the song circuitry, identify potential targets for the manipulation of the song system, and reveal genomic specializations that may relate to the emergence of vocal learning and associated brain areas in birds.
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433
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The avian XPR1 gammaretrovirus receptor is under positive selection and is disabled in bird species in contact with virus-infected wild mice. J Virol 2013; 87:10094-104. [PMID: 23843647 DOI: 10.1128/jvi.01327-13] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Xenotropic mouse leukemia viruses (X-MLVs) are broadly infectious for mammals except most of the classical strains of laboratory mice. These gammaretroviruses rely on the XPR1 receptor for entry, and the unique resistance of laboratory mice is due to two mutations in different putative XPR1 extracellular loops. Cells from avian species differ in susceptibility to X-MLVs, and 2 replacement mutations in the virus-resistant chicken XPR1 (K496Q and Q579E) distinguish it from the more permissive duck and quail receptors. These substitutions align with the two mutations that disable the laboratory mouse XPR1. Mutagenesis of the chicken and duck genes confirms that residues at both sites are critical for virus entry. Among 32 avian species, the 2 disabling XPR1 mutations are found together only in the chicken, an omnivorous, ground-dwelling fowl that was domesticated in India and/or Southeast Asia, which is also where X-MLV-infected house mice evolved. The receptor-disabling mutations are also present separately in 5 additional fowl and raptor species, all of which are native to areas of Asia populated by the virus-infected subspecies Mus musculus castaneus. Phylogenetic analysis showed that the avian XPR1 gene is under positive selection at sites implicated in receptor function, suggesting a defensive role for XPR1 in the avian lineage. Contact between bird species and virus-infected mice may thus have favored selection of mouse virus-resistant receptor orthologs in the birds, and our data suggest that similar receptor-disabling mutations were fixed in mammalian and avian species exposed to similar virus challenges.
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434
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Abstract
In most people, language is processed predominantly by the left hemisphere of the brain, but we do not know how or why. A popular view is that developmental language disorders result from a poorly lateralized brain, but until recently, evidence has been weak and indirect. Modern neuroimaging methods have made it possible to study normal and abnormal development of lateralized function in the developing brain and have confirmed links with language and literacy impairments. However, there is little evidence that weak cerebral lateralization has common genetic origins with language and literacy impairments. Our understanding of the association between atypical language lateralization and developmental disorders may benefit if we reconceptualize the nature of cerebral asymmetry to recognize its multidimensionality and consider variation in lateralization over developmental time. Contrary to popular belief, cerebral lateralization may not be a highly heritable, stable characteristic of individuals; rather, weak lateralization may be a consequence of impaired language learning.
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Affiliation(s)
- Dorothy V M Bishop
- Department of Experimental Psychology, University of Oxford, 9 South Parks Road, Oxford OX1 3UD, UK.
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435
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Ten unanswered questions in multimodal communication. Behav Ecol Sociobiol 2013; 67:1523-1539. [PMID: 23956487 PMCID: PMC3742419 DOI: 10.1007/s00265-013-1565-y] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2012] [Revised: 04/04/2013] [Accepted: 04/16/2013] [Indexed: 11/19/2022]
Abstract
The study of multimodal communication has become an active and vibrant field. This special issue of Behavioral Ecology and Sociobiology brings together new developments in this rapidly expanding area. In this final contribution to the special issue, I look to the future and discuss ten questions in need of further work, touching on issues ranging from theoretical modeling and the evolution of behavior to molecular mechanisms and the development of behavior. In particular, I emphasize that the use of multimodal communication allows animals to switch between sensory channels when one channel becomes too noisy, and suggest that a better understanding of this process may help us both to understand the evolution of multisensory signaling and to predict the success of species facing environmental changes that affect signaling channels, such as urbanization and climate change. An expanded section is included on the effects of climate change on animal communication across sensory channels, urging researchers to pursue this topic due to the rapidity with which the environment is currently transforming.
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436
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Kimball RT, Wang N, Heimer-McGinn V, Ferguson C, Braun EL. Identifying localized biases in large datasets: a case study using the avian tree of life. Mol Phylogenet Evol 2013; 69:1021-32. [PMID: 23791948 DOI: 10.1016/j.ympev.2013.05.029] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2012] [Revised: 05/12/2013] [Accepted: 05/29/2013] [Indexed: 01/27/2023]
Abstract
Large-scale multi-locus studies have become common in molecular phylogenetics, with new studies continually adding to previous datasets in an effort to fully resolve the tree of life. Total evidence analyses that combine existing data with newly collected data are expected to increase the power of phylogenetic analyses to resolve difficult relationships. However, they might be subject to localized biases, with one or a few loci having a strong and potentially misleading influence upon the results. To examine this possibility we combined a newly collected 31-locus dataset that includes representatives of all major avian lineages with a published dataset of 19 loci that has a comparable number of sites (Hackett et al., 2008. Science 320, 1763-1768). This allowed us to explore the advantages of conducting total evidence analyses, and to determine whether it was also important to analyze new datasets independent of published ones. The total evidence analysis yielded results very similar to the published results, with only slightly increased support at a few nodes. However, analyzing the 31- and 19-locus datasets separately highlighted several differences. Two clades received strong support in the published dataset and total evidence analysis, but the support appeared to reflect bias at a single locus (β-fibrinogen [FGB]). The signal in FGB that supported these relationships was sufficient to result in their recovery with bootstrap support, even when combined with 49 loci lacking that signal. FGB did not appear to have a substantial impact upon the results of species tree methods, but another locus (brain-derived neurotrophic factor [BDNF]) did have an impact upon those analyses. These results demonstrated that localized biases can influence large-scale phylogenetic analyses but they also indicated that considering independent evidence and exploring multiple analytical approaches could reveal them.
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Affiliation(s)
- Rebecca T Kimball
- Department of Biology, University of Florida, Gainesville, FL 32611, United States.
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437
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Huang Y, Li Y, Burt DW, Chen H, Zhang Y, Qian W, Kim H, Gan S, Zhao Y, Li J, Yi K, Feng H, Zhu P, Li B, Liu Q, Fairley S, Magor KE, Du Z, Hu X, Goodman L, Tafer H, Vignal A, Lee T, Kim KW, Sheng Z, An Y, Searle S, Herrero J, Groenen MAM, Crooijmans RPMA, Faraut T, Cai Q, Webster RG, Aldridge JR, Warren WC, Bartschat S, Kehr S, Marz M, Stadler PF, Smith J, Kraus RHS, Zhao Y, Ren L, Fei J, Morisson M, Kaiser P, Griffin DK, Rao M, Pitel F, Wang J, Li N. The duck genome and transcriptome provide insight into an avian influenza virus reservoir species. Nat Genet 2013; 45:776-783. [PMID: 23749191 PMCID: PMC4003391 DOI: 10.1038/ng.2657] [Citation(s) in RCA: 243] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2012] [Accepted: 05/08/2013] [Indexed: 12/19/2022]
Abstract
The duck (Anas platyrhynchos) is one of the principal natural hosts of influenza A viruses. We present the duck genome sequence and perform deep transcriptome analyses to investigate immune-related genes. Our data indicate that the duck possesses a contractive immune gene repertoire, as in chicken and zebra finch, and this repertoire has been shaped through lineage-specific duplications. We identify genes that are responsive to influenza A viruses using the lung transcriptomes of control ducks and ones that were infected with either a highly pathogenic (A/duck/Hubei/49/05) or a weakly pathogenic (A/goose/Hubei/65/05) H5N1 virus. Further, we show how the duck's defense mechanisms against influenza infection have been optimized through the diversification of its β-defensin and butyrophilin-like repertoires. These analyses, in combination with the genomic and transcriptomic data, provide a resource for characterizing the interaction between host and influenza viruses.
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Affiliation(s)
- Yinhua Huang
- State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing, China.,The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK
| | | | - David W Burt
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK
| | - Hualan Chen
- National Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Harbin, China
| | | | | | - Heebal Kim
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Korea
| | - Shangquan Gan
- State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing, China
| | - Yiqiang Zhao
- State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing, China
| | | | - Kang Yi
- BGI-Shenzhen, Shenzhen, China
| | - Huapeng Feng
- National Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Harbin, China
| | - Pengyang Zhu
- National Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Harbin, China
| | - Bo Li
- BGI-Shenzhen, Shenzhen, China
| | - Qiuyue Liu
- State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing, China
| | - Suan Fairley
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Katharine E Magor
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Zhenlin Du
- State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing, China
| | - Xiaoxiang Hu
- State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing, China
| | | | - Hakim Tafer
- Department of Computer Science, University of Leipzig, Leipzig, Germany.,Department of Theoretical Chemistry, University of Vienna, Vienna, Austria
| | - Alain Vignal
- Laboratoire de Génétique Cellulaire, Institut National de la Recherche Agronomique (INRA), Castanet-Tolosan, France
| | - Taeheon Lee
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Korea
| | - Kyu-Won Kim
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Korea
| | - Zheya Sheng
- State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing, China
| | - Yang An
- State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing, China
| | - Steve Searle
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Javier Herrero
- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Martien A M Groenen
- Animal Breeding and Genomics Centre, Wageningen University, Wageningen, The Netherlands
| | | | - Thomas Faraut
- Laboratoire de Génétique Cellulaire, Institut National de la Recherche Agronomique (INRA), Castanet-Tolosan, France
| | | | - Robert G Webster
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Jerry R Aldridge
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Wesley C Warren
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri, USA
| | | | - Stephanie Kehr
- Department of Computer Science, University of Leipzig, Leipzig, Germany
| | - Manja Marz
- Department of Computer Science, University of Leipzig, Leipzig, Germany
| | - Peter F Stadler
- Department of Computer Science, University of Leipzig, Leipzig, Germany.,Department of Theoretical Chemistry, University of Vienna, Vienna, Austria
| | - Jacqueline Smith
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK
| | - Robert H S Kraus
- Resource Ecology Group, Wageningen University, Wageningen, The Netherlands.,Conservation Genetics Group, Senckenberg Research Institute and Natural History Museum, Gelnhausen, Germany
| | - Yaofeng Zhao
- State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing, China
| | - Liming Ren
- State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing, China
| | - Jing Fei
- State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing, China
| | - Mireille Morisson
- Laboratoire de Génétique Cellulaire, Institut National de la Recherche Agronomique (INRA), Castanet-Tolosan, France
| | - Pete Kaiser
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK
| | | | - Man Rao
- State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing, China
| | - Frederique Pitel
- Laboratoire de Génétique Cellulaire, Institut National de la Recherche Agronomique (INRA), Castanet-Tolosan, France
| | - Jun Wang
- BGI-Shenzhen, Shenzhen, China.,Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Ning Li
- State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing, China
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438
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Greenwold MJ, Sawyer RH. Molecular evolution and expression of archosaurian β-keratins: Diversification and expansion of archosaurian β-keratins and the origin of feather β-keratins. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2013; 320:393-405. [DOI: 10.1002/jez.b.22514] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Revised: 04/25/2013] [Accepted: 05/04/2013] [Indexed: 12/20/2022]
Affiliation(s)
- Matthew J. Greenwold
- Department of Biological Sciences; University of South Carolina; Columbia; South Carolina
| | - Roger H. Sawyer
- Department of Biological Sciences; University of South Carolina; Columbia; South Carolina
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439
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Liu G, Mattick JS, Taft RJ. A meta-analysis of the genomic and transcriptomic composition of complex life. Cell Cycle 2013; 12:2061-72. [PMID: 23759593 DOI: 10.4161/cc.25134] [Citation(s) in RCA: 107] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
It is now clear that animal genomes are predominantly non-protein-coding, and that these sequences encode a wide array of RNA transcripts and other regulatory elements that are fundamental to the development of complex life. We have previously argued that the proportion of an animal genome that is non-protein-coding DNA (ncDNA) correlates well with its apparent biological complexity. Here we extend on that work and, using data from a total of 1,627 prokaryotic and 153 eukaryotic complete and annotated genomes, show that the proportion of ncDNA per haploid genome is significantly positively correlated with a previously published proxy of biological complexity, the number of distinct cell types. This is in contrast to the amount of the genome that encodes proteins, which we show is essentially unchanged across Metazoa. Furthermore, using a total of 179 RNA-seq data sets from nematode (47), fruit fly (72), zebrafish (20) and human (42), we show, consistent with other recent reports, that the vast majority of ncDNA in animals is transcribed. This includes more than 60 human loci previously considered "gene deserts," many of which are expressed tissue-specifically and associated with previously reported GWAS SNPs. These results suggest that ncDNA, and the ncRNAs encoded within it, may be intimately involved in the evolution, maintenance and development of complex life.
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Affiliation(s)
- Ganqiang Liu
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD Australia
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440
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Abstract
Complete genomes of hybridizing bird species demonstrate the importance of the sex chromosomes, telomeres and centromeres to the initial stages of speciation.
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441
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Molecular cytogenetic map of the central bearded dragon, Pogona vitticeps (Squamata: Agamidae). Chromosome Res 2013; 21:361-74. [PMID: 23703235 DOI: 10.1007/s10577-013-9362-z] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2013] [Revised: 04/12/2013] [Accepted: 04/27/2013] [Indexed: 12/20/2022]
Abstract
Reptiles, as the sister group to birds and mammals, are particularly valuable for comparative genomic studies among amniotes. The Australian central bearded dragon (Pogona vitticeps) is being developed as a reptilian model for such comparisons, with whole-genome sequencing near completion. The karyotype consists of 6 pairs of macrochromosomes and 10 pairs microchromosomes (2n = 32), including a female heterogametic ZW sex microchromosome pair. Here, we present a molecular cytogenetic map for P. vitticeps comprising 87 anchor bacterial artificial chromosome clones that together span each macro- and microchromosome. It is the first comprehensive cytogenetic map for any non-avian reptile. We identified an active nucleolus organizer region (NOR) on the sub-telomeric region of 2q by mapping 18S rDNA and Ag-NOR staining. We identified interstitial telomeric sequences in two microchromosome pairs and the W chromosome, indicating that microchromosome fusion has been a mechanism of karyotypic evolution in Australian agamids within the last 21 to 19 million years. Orthology searches against the chicken genome revealed an intrachromosomal rearrangement of P. vitticeps 1q, identified regions orthologous to chicken Z on P. vitticeps 2q, snake Z on P. vitticeps 6q and the autosomal microchromosome pair in P. vitticeps orthologous to turtle Pelodiscus sinensis ZW and lizard Anolis carolinensis XY. This cytogenetic map will be a valuable reference tool for future gene mapping studies and will provide the framework for the work currently underway to physically anchor genome sequences to chromosomes for this model Australian squamate.
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442
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Acharya KD, Veney SL. Sexually dimorphic expression and estradiol mediated up-regulation of a sex-linked ribosomal gene, RPS6, in the zebra finch brain. Dev Neurobiol 2013; 73:599-608. [PMID: 23554148 DOI: 10.1002/dneu.22085] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2013] [Revised: 03/12/2013] [Accepted: 03/26/2013] [Indexed: 12/24/2022]
Abstract
Sex-linked genes are considered to be a major contributor to neural sex differences in zebra finches. While several candidates have been identified, additional ones are continuously being discovered. Here we report on a novel Z-linked ribosomal gene (rpS6) that is enhanced in the male brain as compared to the female's throughout life. In both sexes, expression of rpS6 is highest at P3 and P8 (just before the onset of morphologically detectable sex differences), decreases around P15, and then remains decreased through adulthood. Analysis of rpS6 mRNA revealed widespread distribution throughout the brain. However, within song regions HVC and RA, mRNA containing cells were greater in males as compared to females. Hormones are also involved in the development of neural dimorphisms, so we additionally investigated whether rpS6 might interact with estradiol (E2 ). An up-regulation of rpS6 gene was observed in both sexes following treatment with E2 and the effect was approximately twice as large in males as compared with females. These data suggest that rpS6 may be involved in sexual differentiation of the zebra finch brain, and that the effect is facilitated by E2 .
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Affiliation(s)
- Kalpana D Acharya
- School of Biomedical Sciences, Kent State University, Kent, OH 44242, USA
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443
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A multi-platform draft de novo genome assembly and comparative analysis for the Scarlet Macaw (Ara macao). PLoS One 2013; 8:e62415. [PMID: 23667475 PMCID: PMC3648530 DOI: 10.1371/journal.pone.0062415] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2013] [Accepted: 03/21/2013] [Indexed: 12/31/2022] Open
Abstract
Data deposition to NCBI Genomes: This Whole Genome Shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession AMXX00000000 (SMACv1.0, unscaffolded genome assembly). The version described in this paper is the first version (AMXX01000000). The scaffolded assembly (SMACv1.1) has been deposited at DDBJ/EMBL/GenBank under the accession AOUJ00000000, and is also the first version (AOUJ01000000). Strong biological interest in traits such as the acquisition and utilization of speech, cognitive abilities, and longevity catalyzed the utilization of two next-generation sequencing platforms to provide the first-draft de novo genome assembly for the large, new world parrot Ara macao (Scarlet Macaw). Despite the challenges associated with genome assembly for an outbred avian species, including 951,507 high-quality putative single nucleotide polymorphisms, the final genome assembly (>1.035 Gb) includes more than 997 Mb of unambiguous sequence data (excluding N's). Cytogenetic analyses including ZooFISH revealed complex rearrangements associated with two scarlet macaw macrochromosomes (AMA6, AMA7), which supports the hypothesis that translocations, fusions, and intragenomic rearrangements are key factors associated with karyotype evolution among parrots. In silico annotation of the scarlet macaw genome provided robust evidence for 14,405 nuclear gene annotation models, their predicted transcripts and proteins, and a complete mitochondrial genome. Comparative analyses involving the scarlet macaw, chicken, and zebra finch genomes revealed high levels of nucleotide-based conservation as well as evidence for overall genome stability among the three highly divergent species. Application of a new whole-genome analysis of divergence involving all three species yielded prioritized candidate genes and noncoding regions for parrot traits of interest (i.e., speech, intelligence, longevity) which were independently supported by the results of previous human GWAS studies. We also observed evidence for genes and noncoding loci that displayed extreme conservation across the three avian lineages, thereby reflecting their likely biological and developmental importance among birds.
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444
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Renn SC, Schumer ME. Genetic accommodation and behavioural evolution: insights from genomic studies. Anim Behav 2013. [DOI: 10.1016/j.anbehav.2013.02.012] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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445
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Smith JJ, Kuraku S, Holt C, Sauka-Spengler T, Jiang N, Campbell MS, Yandell MD, Manousaki T, Meyer A, Bloom OE, Morgan JR, Buxbaum JD, Sachidanandam R, Sims C, Garruss AS, Cook M, Krumlauf R, Wiedemann LM, Sower SA, Decatur WA, Hall JA, Amemiya CT, Saha NR, Buckley KM, Rast JP, Das S, Hirano M, McCurley N, Guo P, Rohner N, Tabin CJ, Piccinelli P, Elgar G, Ruffier M, Aken BL, Searle SMJ, Muffato M, Pignatelli M, Herrero J, Jones M, Brown CT, Chung-Davidson YW, Nanlohy KG, Libants SV, Yeh CY, McCauley DW, Langeland JA, Pancer Z, Fritzsch B, de Jong PJ, Zhu B, Fulton LL, Theising B, Flicek P, Bronner ME, Warren WC, Clifton SW, Wilson RK, Li W. Sequencing of the sea lamprey (Petromyzon marinus) genome provides insights into vertebrate evolution. Nat Genet 2013; 45:415-21, 421e1-2. [PMID: 23435085 PMCID: PMC3709584 DOI: 10.1038/ng.2568] [Citation(s) in RCA: 437] [Impact Index Per Article: 39.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2012] [Accepted: 01/31/2013] [Indexed: 12/19/2022]
Abstract
Lampreys are representatives of an ancient vertebrate lineage that diverged from our own ∼500 million years ago. By virtue of this deeply shared ancestry, the sea lamprey (P. marinus) genome is uniquely poised to provide insight into the ancestry of vertebrate genomes and the underlying principles of vertebrate biology. Here, we present the first lamprey whole-genome sequence and assembly. We note challenges faced owing to its high content of repetitive elements and GC bases, as well as the absence of broad-scale sequence information from closely related species. Analyses of the assembly indicate that two whole-genome duplications likely occurred before the divergence of ancestral lamprey and gnathostome lineages. Moreover, the results help define key evolutionary events within vertebrate lineages, including the origin of myelin-associated proteins and the development of appendages. The lamprey genome provides an important resource for reconstructing vertebrate origins and the evolutionary events that have shaped the genomes of extant organisms.
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Affiliation(s)
- Jeramiah J Smith
- Department of Biology, University of Kentucky, Lexington, Kentucky, USA.
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446
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Moghadam HK, Harrison PW, Zachar G, Székely T, Mank JE. The plover neurotranscriptome assembly: transcriptomic analysis in an ecological model species without a reference genome. Mol Ecol Resour 2013; 13:696-705. [DOI: 10.1111/1755-0998.12096] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2012] [Revised: 02/24/2013] [Accepted: 02/25/2013] [Indexed: 10/27/2022]
Affiliation(s)
- Hooman K. Moghadam
- Institute of Marine Biology Biotechnology & Aquaculture (IMBBC) Hellenic Centre for Marine Research (HCMR) PO Box 2214 71500 Heraklion Crete Greece
| | - Peter W. Harrison
- Department of Genetics Evolution and Environment University College London The Darwin Building Gower Street London WC1E 6BT UK
| | - Gergely Zachar
- Department of Anatomy Histology and Embryology Semmelweis University Budapest H‐1094 Hungary
| | - Tamás Székely
- Department of Biology and Biochemistry University of Bath Claverton Down Bath BA2 7AY UK
| | - Judith E. Mank
- Department of Genetics Evolution and Environment University College London The Darwin Building Gower Street London WC1E 6BT UK
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447
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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: 229] [Impact Index Per Article: 20.8] [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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448
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Cai Q, Qian X, Lang Y, Luo Y, Xu J, Pan S, Hui Y, Gou C, Cai Y, Hao M, Zhao J, Wang S, Wang Z, Zhang X, He R, Liu J, Luo L, Li Y, Wang J. Genome sequence of ground tit Pseudopodoces humilis and its adaptation to high altitude. Genome Biol 2013; 14:R29. [PMID: 23537097 PMCID: PMC4053790 DOI: 10.1186/gb-2013-14-3-r29] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2012] [Accepted: 03/28/2013] [Indexed: 12/04/2022] Open
Abstract
Background The mechanism of high-altitude adaptation has been studied in certain mammals. However, in avian species like the ground tit Pseudopodoces humilis, the adaptation mechanism remains unclear. The phylogeny of the ground tit is also controversial. Results Using next generation sequencing technology, we generated and assembled a draft genome sequence of the ground tit. The assembly contained 1.04 Gb of sequence that covered 95.4% of the whole genome and had higher N50 values, at the level of both scaffolds and contigs, than other sequenced avian genomes. About 1.7 million SNPs were detected, 16,998 protein-coding genes were predicted and 7% of the genome was identified as repeat sequences. Comparisons between the ground tit genome and other avian genomes revealed a conserved genome structure and confirmed the phylogeny of ground tit as not belonging to the Corvidae family. Gene family expansion and positively selected gene analysis revealed genes that were related to cardiac function. Our findings contribute to our understanding of the adaptation of this species to extreme environmental living conditions. Conclusions Our data and analysis contribute to the study of avian evolutionary history and provide new insights into the adaptation mechanisms to extreme conditions in animals.
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449
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Miksys S, Cappendijk SLT, Perry WM, Zhao B, Tyndale RF. Nicotine kinetics in zebra finches in vivo and in vitro. Drug Metab Dispos 2013; 41:1240-6. [PMID: 23530019 DOI: 10.1124/dmd.112.050765] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Nicotine enhances cognitive performance, and in the zebra finch (Taeniopygia guttata), which is a well-established model of cognition, the effects of nicotine on song production have been reported. Nicotine and cotinine plasma levels were assessed in vivo after subcutaneous injection of 0.18 mg/kg nicotine, a dose that elicits changes in song production. The half-life of nicotine elimination was 33 minutes, and levels were undetectable by 4 hours. Average plasma nicotine over 2 hours was 32 ng/ml, similar to levels seen in human smokers and rat models of nicotine behavior. Nicotine brain levels were 30 and 14 ng/g 1 and 2 hours after treatment. To understand the potential for drug interactions and the regulation of nicotine metabolism in zebra finches, we characterized in vitro nicotine metabolism and the hepatic enzyme involved. In humans, cytochrome P450 2A6 metabolizes nicotine to cotinine, and CYP2A-like activity and protein have been reported in some birds. Zebra finch liver microsomes metabolized nicotine and bupropion (a CYP2B substrate) but not coumarin (a CYP2A substrate). Nicotine was metabolized to cotinine with a Michaelis-Menten constant (K(m)) of 96 µM and a V(max) of 56 pmol/min per milligram. Nicotine and bupropion metabolism was inhibited by C-8-xanthate (a specific CYP2B inhibitor) but not by CYP2A-specific inhibitors, and hepatic levels of CYP2B-like but not CYP2A-like proteins correlated with nicotine (r = 0.52; P = 0.04) and bupropion metabolism (r = 0.81; P < 0.001), suggesting CYP2B-mediation of nicotine metabolism as seen in rats. These results will facilitate further investigation of nicotine's effects in zebra finches.
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Affiliation(s)
- Sharon Miksys
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Departments of Pharmacology and Toxicology and Psychiatry, University of Toronto, Toronto, Canada
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Zhan X, Pan S, Wang J, Dixon A, He J, Muller MG, Ni P, Hu L, Liu Y, Hou H, Chen Y, Xia J, Luo Q, Xu P, Chen Y, Liao S, Cao C, Gao S, Wang Z, Yue Z, Li G, Yin Y, Fox NC, Wang J, Bruford MW. Peregrine and saker falcon genome sequences provide insights into evolution of a predatory lifestyle. Nat Genet 2013; 45:563-6. [PMID: 23525076 DOI: 10.1038/ng.2588] [Citation(s) in RCA: 112] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2012] [Accepted: 02/28/2013] [Indexed: 01/03/2023]
Abstract
As top predators, falcons possess unique morphological, physiological and behavioral adaptations that allow them to be successful hunters: for example, the peregrine is renowned as the world's fastest animal. To examine the evolutionary basis of predatory adaptations, we sequenced the genomes of both the peregrine (Falco peregrinus) and saker falcon (Falco cherrug), and we present parallel, genome-wide evidence for evolutionary innovation and selection for a predatory lifestyle. The genomes, assembled using Illumina deep sequencing with greater than 100-fold coverage, are both approximately 1.2 Gb in length, with transcriptome-assisted prediction of approximately 16,200 genes for both species. Analysis of 8,424 orthologs in both falcons, chicken, zebra finch and turkey identified consistent evidence for genome-wide rapid evolution in these raptors. SNP-based inference showed contrasting recent demographic trajectories for the two falcons, and gene-based analysis highlighted falcon-specific evolutionary novelties for beak development and olfaction and specifically for homeostasis-related genes in the arid environment-adapted saker.
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Affiliation(s)
- Xiangjiang Zhan
- Organisms and Environment Division, Cardiff School of Bioscience, Cardiff University, Cardiff, UK
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