601
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Songbird genome provides clues about speech. Lab Anim (NY) 2010; 39:126. [DOI: 10.1038/laban0510-126a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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602
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Abstract
An international collaborative effort has recently uncovered the genome of the zebra finch, a songbird model that has provided unique insights into an array of biological phenomena. See research articles http://www.biomedcentral.com/1471-2164/9/131, http://www.biomedcentral.com/1471-2164/11/220/, http://www.biomedcentral.com/1471-2202/11/46/ and http://www.biomedcentral.com/1741-7007/8/28/
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Affiliation(s)
- Raphael Pinaud
- Department of Brain and Cognitive Sciences, 117 Meliora Hall, River Campus, University of Rochester, Rochester, NY 14627, USA.
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603
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Balakrishnan CN, Ekblom R, Völker M, Westerdahl H, Godinez R, Kotkiewicz H, Burt DW, Graves T, Griffin DK, Warren WC, Edwards SV. Gene duplication and fragmentation in the zebra finch major histocompatibility complex. BMC Biol 2010; 8:29. [PMID: 20359332 PMCID: PMC2907588 DOI: 10.1186/1741-7007-8-29] [Citation(s) in RCA: 105] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2009] [Accepted: 04/01/2010] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Due to its high polymorphism and importance for disease resistance, the major histocompatibility complex (MHC) has been an important focus of many vertebrate genome projects. Avian MHC organization is of particular interest because the chicken Gallus gallus, the avian species with the best characterized MHC, possesses a highly streamlined minimal essential MHC, which is linked to resistance against specific pathogens. It remains unclear the extent to which this organization describes the situation in other birds and whether it represents a derived or ancestral condition. The sequencing of the zebra finch Taeniopygia guttata genome, in combination with targeted bacterial artificial chromosome (BAC) sequencing, has allowed us to characterize an MHC from a highly divergent and diverse avian lineage, the passerines. RESULTS The zebra finch MHC exhibits a complex structure and history involving gene duplication and fragmentation. The zebra finch MHC includes multiple Class I and Class II genes, some of which appear to be pseudogenes, and spans a much more extensive genomic region than the chicken MHC, as evidenced by the presence of MHC genes on each of seven BACs spanning 739 kb. Cytogenetic (FISH) evidence and the genome assembly itself place core MHC genes on as many as four chromosomes with TAP and Class I genes mapping to different chromosomes. MHC Class II regions are further characterized by high endogenous retroviral content. Lastly, we find strong evidence of selection acting on sites within passerine MHC Class I and Class II genes. CONCLUSION The zebra finch MHC differs markedly from that of the chicken, the only other bird species with a complete genome sequence. The apparent lack of synteny between TAP and the expressed MHC Class I locus is in fact reminiscent of a pattern seen in some mammalian lineages and may represent convergent evolution. Our analyses of the zebra finch MHC suggest a complex history involving chromosomal fission, gene duplication and translocation in the history of the MHC in birds, and highlight striking differences in MHC structure and organization among avian lineages.
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Affiliation(s)
- Christopher N Balakrishnan
- Department of Organismic & Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, USA
- Current address: Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, IL, USA
| | - Robert Ekblom
- Department of Animal & Plant Sciences, University of Sheffield, Sheffield, UK
- Department of Population Biology and Conservation Biology, Uppsala University, Uppsala, Sweden
| | - Martin Völker
- Department of Biosciences, University of Kent, Kent, UK
| | | | - Ricardo Godinez
- Department of Organismic & Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, USA
| | - Holly Kotkiewicz
- School of Medicine, Genome Sequencing Center, Washington University, St Louis, MO, USA
| | - David W Burt
- Roslin Institute, Division of Genetics & Genomics, University of Edinburgh, Edinburgh, UK
| | - Tina Graves
- School of Medicine, Genome Sequencing Center, Washington University, St Louis, MO, USA
| | | | - Wesley C Warren
- School of Medicine, Genome Sequencing Center, Washington University, St Louis, MO, USA
| | - Scott V Edwards
- Department of Organismic & Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, USA
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604
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Backström N, Forstmeier W, Schielzeth H, Mellenius H, Nam K, Bolund E, Webster MT, Öst T, Schneider M, Kempenaers B, Ellegren H. The recombination landscape of the zebra finch Taeniopygia guttata genome. Genome Res 2010; 20:485-95. [PMID: 20357052 PMCID: PMC2847751 DOI: 10.1101/gr.101410.109] [Citation(s) in RCA: 168] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2009] [Accepted: 12/02/2009] [Indexed: 12/18/2022]
Abstract
Understanding the causes and consequences of variation in the rate of recombination is essential since this parameter is considered to affect levels of genetic variability, the efficacy of selection, and the design of association and linkage mapping studies. However, there is limited knowledge about the factors governing recombination rate variation. We genotyped 1920 single nucleotide polymorphisms in a multigeneration pedigree of more than 1000 zebra finches (Taeniopygia guttata) to develop a genetic linkage map, and then we used these map data together with the recently available draft genome sequence of the zebra finch to estimate recombination rates in 1 Mb intervals across the genome. The average zebra finch recombination rate (1.5 cM/Mb) is higher than in humans, but significantly lower than in chicken. The local rates of recombination in chicken and zebra finch were only weakly correlated, demonstrating evolutionary turnover of the recombination landscape in birds. The distribution of recombination events was heavily biased toward ends of chromosomes, with a stronger telomere effect than so far seen in any organism. In fact, the recombination rate was as low as 0.1 cM/Mb in intervals up to 100 Mb long in the middle of the larger chromosomes. We found a positive correlation between recombination rate and GC content, as well as GC-rich sequence motifs. Levels of linkage disequilibrium (LD) were significantly higher in regions of low recombination, showing that heterogeneity in recombination rates have left a footprint on the genomic landscape of LD in zebra finch populations.
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Affiliation(s)
- Niclas Backström
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, SE-752 36 Uppsala, Sweden
| | - Wolfgang Forstmeier
- Max Planck Institute for Ornithology, Department of Behavioural Ecology and Evolutionary Genetics, 82319 Seewiesen, Germany
| | - Holger Schielzeth
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, SE-752 36 Uppsala, Sweden
- Max Planck Institute for Ornithology, Department of Behavioural Ecology and Evolutionary Genetics, 82319 Seewiesen, Germany
| | - Harriet Mellenius
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, SE-752 36 Uppsala, Sweden
| | - Kiwoong Nam
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, SE-752 36 Uppsala, Sweden
| | - Elisabeth Bolund
- Max Planck Institute for Ornithology, Department of Behavioural Ecology and Evolutionary Genetics, 82319 Seewiesen, Germany
| | - Matthew T. Webster
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, SE-752 36 Uppsala, Sweden
| | - Torbjörn Öst
- Molecular Medicine, Department of Medical Sciences, University Hospital, SE-751 85 Uppsala, Sweden
| | - Melanie Schneider
- Max Planck Institute for Ornithology, Department of Behavioural Ecology and Evolutionary Genetics, 82319 Seewiesen, Germany
| | - Bart Kempenaers
- Max Planck Institute for Ornithology, Department of Behavioural Ecology and Evolutionary Genetics, 82319 Seewiesen, Germany
| | - Hans Ellegren
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, SE-752 36 Uppsala, Sweden
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605
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Itoh Y, Replogle K, Kim YH, Wade J, Clayton DF, Arnold AP. Sex bias and dosage compensation in the zebra finch versus chicken genomes: general and specialized patterns among birds. Genome Res 2010; 20:512-8. [PMID: 20357053 PMCID: PMC2847754 DOI: 10.1101/gr.102343.109] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2009] [Accepted: 02/11/2010] [Indexed: 11/25/2022]
Abstract
We compared global patterns of gene expression between two bird species, the chicken and zebra finch, with regard to sex bias of autosomal versus Z chromosome genes, dosage compensation, and evolution of sex bias. Both species appear to lack a Z chromosome-wide mechanism of dosage compensation, because both have a similar pattern of significantly higher expression of Z genes in males relative to females. Unlike the chicken Z chromosome, which has female-specific expression of the noncoding RNA MHM (male hypermethylated) and acetylation of histone 4 lysine 16 (H4K16) near MHM, the zebra finch Z chromosome appears to lack the MHM sequence and acetylation of H4K16. The zebra finch also does not show the reduced male-to-female (M:F) ratio of gene expression near MHM similar to that found in the chicken. Although the M:F ratios of Z chromosome gene expression are similar across tissues and ages within each species, they differ between the two species. Z genes showing the greatest species difference in M:F ratio were concentrated near the MHM region of the chicken Z chromosome. This study shows that the zebra finch differs from the chicken because it lacks a specialized region of greater dosage compensation along the Z chromosome, and shows other differences in sex bias. These patterns suggest that different avian taxa may have evolved specific compensatory mechanisms.
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Affiliation(s)
- Yuichiro Itoh
- Department of Integrative Biology and Physiology and Laboratory of Neuroendocrinology of the Brain Research Institute, University of California, Los Angeles, California 90095-1606, USA
| | - Kirstin Replogle
- Institute for Genomic Biology, University of Illinois, Urbana–Champaign, Urbana, Illinois 61801, USA
| | - Yong-Hwan Kim
- Department of Integrative Biology and Physiology and Laboratory of Neuroendocrinology of the Brain Research Institute, University of California, Los Angeles, California 90095-1606, USA
| | - Juli Wade
- Departments of Psychology and Zoology, Neuroscience Program, Michigan State University, East Lansing, Michigan 48824, USA
| | - David F. Clayton
- Institute for Genomic Biology, University of Illinois, Urbana–Champaign, Urbana, Illinois 61801, USA
| | - Arthur P. Arnold
- Department of Integrative Biology and Physiology and Laboratory of Neuroendocrinology of the Brain Research Institute, University of California, Los Angeles, California 90095-1606, USA
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606
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Völker M, Backström N, Skinner BM, Langley EJ, Bunzey SK, Ellegren H, Griffin DK. Copy number variation, chromosome rearrangement, and their association with recombination during avian evolution. Genome Res 2010; 20:503-11. [PMID: 20357050 PMCID: PMC2847753 DOI: 10.1101/gr.103663.109] [Citation(s) in RCA: 111] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2009] [Accepted: 02/08/2010] [Indexed: 11/25/2022]
Abstract
Chromosomal rearrangements and copy number variants (CNVs) play key roles in genome evolution and genetic disease; however, the molecular mechanisms underlying these types of structural genomic variation are not fully understood. The availability of complete genome sequences for two bird species, the chicken and the zebra finch, provides, for the first time, an ideal opportunity to analyze the relationship between structural genomic variation (chromosomal and CNV) and recombination on a genome-wide level. The aims of this study were therefore threefold: (1) to combine bioinformatics, physical mapping to produce comprehensive comparative maps of the genomes of chicken and zebra finch. In so doing, this allowed the identification of evolutionary chromosomal rearrangements distinguishing them. The previously reported interchromosomal conservation of synteny was confirmed, but a larger than expected number of intrachromosomal rearrangements were reported; (2) to hybridize zebra finch genomic DNA to a chicken tiling path microarray and identify CNVs in the zebra finch genome relative to chicken; 32 interspecific CNVs were identified; and (3) to test the hypothesis that there is an association between CNV, chromosomal rearrangements, and recombination by correlating data from (1) and (2) with recombination rate data from a high-resolution genetic linkage map of the zebra finch. We found a highly significant association of both chromosomal rearrangements and CNVs with elevated recombination rates. The results thus provide support for the notion of recombination-based processes playing a major role in avian genome evolution.
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Affiliation(s)
- Martin Völker
- School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, United Kingdom
| | - Niclas Backström
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden
| | - Benjamin M. Skinner
- School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, United Kingdom
| | - Elizabeth J. Langley
- School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, United Kingdom
| | - Sydney K. Bunzey
- School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, United Kingdom
| | - Hans Ellegren
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden
| | - Darren K. Griffin
- School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, United Kingdom
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607
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London SE, Itoh Y, Lance VA, Wise PM, Ekanayake PS, Oyama RK, Arnold AP, Schlinger BA. Neural expression and post-transcriptional dosage compensation of the steroid metabolic enzyme 17beta-HSD type 4. BMC Neurosci 2010; 11:47. [PMID: 20359329 PMCID: PMC2858028 DOI: 10.1186/1471-2202-11-47] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2009] [Accepted: 04/01/2010] [Indexed: 11/10/2022] Open
Abstract
Background Steroids affect many tissues, including the brain. In the zebra finch, the estrogenic steroid estradiol (E2) is especially effective at promoting growth of the neural circuit specialized for song. In this species, only the males sing and they have a much larger and more interconnected song circuit than females. Thus, it was surprising that the gene for 17β-hydroxysteroid dehydrogenase type 4 (HSD17B4), an enzyme that converts E2 to a less potent estrogen, had been mapped to the Z sex chromosome. As a consequence, it was likely that HSD17B4 was differentially expressed in males (ZZ) and females (ZW) because dosage compensation of Z chromosome genes is incomplete in birds. If a higher abundance of HSD17B4 mRNA in males than females was translated into functional enzyme in the brain, then contrary to expectation, males could produce less E2 in their brains than females. Results Here, we used molecular and biochemical techniques to confirm the HSD17B4 Z chromosome location in the zebra finch and to determine that HSD17B4 mRNA and activity were detectable in the early developing and adult brain. As expected, HSD17B4 mRNA expression levels were higher in males compared to females. This provides further evidence of the incomplete Z chromosome inactivation mechanisms in birds. We detected HSD17B4 mRNA in regions that suggested a role for this enzyme in the early organization and adult function of song nuclei. We did not, however, detect significant sex differences in HSD17B4 activity levels in the adult brain. Conclusions Our results demonstrate that the HSD17B4 gene is expressed and active in the zebra finch brain as an E2 metabolizing enzyme, but that dosage compensation of this Z-linked gene may occur via post-transcriptional mechanisms.
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Affiliation(s)
- Sarah E London
- Interdepartmental Program in Neuroscience, University of California at Los Angeles, Los Angeles, CA, USA.
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608
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Kong L, Lovell PV, Heger A, Mello CV, Ponting CP. Accelerated evolution of PAK3- and PIM1-like kinase gene families in the zebra finch, Taeniopygia guttata. Mol Biol Evol 2010; 27:1923-34. [PMID: 20237222 DOI: 10.1093/molbev/msq080] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Genes encoding protein kinases tend to evolve slowly over evolutionary time, and only rarely do they appear as recent duplications in sequenced vertebrate genomes. Consequently, it was a surprise to find two families of kinase genes that have greatly and recently expanded in the zebra finch (Taeniopygia guttata) lineage. In contrast to other amniotic genomes (including chicken) that harbor only single copies of p21-activated serine/threonine kinase 3 (PAK3) and proviral integration site 1 (PIM1) genes, the zebra finch genome appeared at first to additionally contain 67 PAK3-like (PAK3L) and 51 PIM1-like (PIM1L) protein kinase genes. An exhaustive analysis of these gene models, however, revealed most to be incomplete, owing to the absence of terminal exons. After reprediction, 31 PAK3L genes and 10 PIM1L genes remain, and all but three are predicted, from the retention of functional sites and open reading frames, to be enzymatically active. PAK3L, but not PIM1L, gene sequences show evidence of recurrent episodes of positive selection, concentrated within structures spatially adjacent to N- and C-terminal protein regions that have been discarded from zebra finch PAK3L genes. At least seven zebra finch PAK3L genes were observed to be expressed in testis, whereas two sequences were found transcribed in the brain, one broadly including the song nuclei and the other in the ventricular zone and in cells resembling Bergmann's glia in the cerebellar Purkinje cell layer. Two PIM1L sequences were also observed to be expressed with broad distributions in the zebra finch brain, one in both the ventricular zone and the cerebellum and apparently associated with glial cells and the other showing neuronal cell expression and marked enrichment in midbrain/thalamic nuclei. These expression patterns do not correlate with zebra finch-specific features such as vocal learning. Nevertheless, our results show how ancient and conserved intracellular signaling molecules can be co-opted, following duplication, thereby resulting in lineage-specific functions, presumably affecting the zebra finch testis and brain.
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Affiliation(s)
- Lesheng Kong
- Medical Research Council Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
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