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Wang S, Zhang Y, Yang W, Shen Y, Lin Z, Zhang S, Song G. Duplicate genes as sources for rapid adaptive evolution of sperm under environmental pollution in tree sparrow. Mol Ecol 2022; 32:1673-1684. [PMID: 36567644 DOI: 10.1111/mec.16833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Revised: 12/12/2022] [Accepted: 12/13/2022] [Indexed: 12/27/2022]
Abstract
Environmental pollution can result in poor sperm quality either directly or indirectly in birds. However, adaptive and compensatory sperm morphology changes and motility improvements have rapidly evolved in tree sparrows (Passer montanus) inhabiting polluted areas over the past 65 years. To identify the genetic underpinnings of the rapidly evolving sperm phenotype, we carried out population genomics and transcriptomics on tree sparrow populations in the two differently polluted places. We identified a gene encoding the serine/threonine protein kinase PIM1, which may drive rapid phenotypic evolution of sperm. An unprecedented and remarkable expansion of the PIM gene family, caused by tandem and segmental duplication of PIM1, was subsequently observed in the tree sparrow genome. Most PIM1 duplicates showed a testis-specific expression pattern, suggesting that their functions are related to male reproduction. Furthermore, the elevated expression level of PIM1 was consistent with our earlier findings of longer and faster swimming sperm in polluted sites, indicating an important role for duplicated PIM1 in facilitating the rapid evolution of sperm. Our results suggest that duplicated PIM1 provides sources of genetic variation that may enable the rapid evolution of sperm under environmental heavy metal pollution. The findings of this study indicated that duplicated genes can be targets of selection and predominant sources for rapid adaptation to environmental change and shed light on sperm evolution under pollution stress.
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Affiliation(s)
- Shengnan Wang
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environmental Pollution, School of Life Science, Lanzhou University, Lanzhou, China
| | - Yingmei Zhang
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environmental Pollution, School of Life Science, Lanzhou University, Lanzhou, China
| | - Wenzhi Yang
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environmental Pollution, School of Life Science, Lanzhou University, Lanzhou, China
| | - Yue Shen
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environmental Pollution, School of Life Science, Lanzhou University, Lanzhou, China
| | - Zhaocun Lin
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environmental Pollution, School of Life Science, Lanzhou University, Lanzhou, China
| | - Sheng Zhang
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environmental Pollution, School of Life Science, Lanzhou University, Lanzhou, China
| | - Gang Song
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Science, Beijing, China
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Friedrich SR, Nevue AA, Andrade ALP, Velho TAF, Mello CV. Emergence of sex-specific transcriptomes in a sexually dimorphic brain nucleus. Cell Rep 2022; 40:111152. [PMID: 35926465 PMCID: PMC9385264 DOI: 10.1016/j.celrep.2022.111152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 04/26/2022] [Accepted: 07/12/2022] [Indexed: 11/29/2022] Open
Abstract
We present the transcriptomic changes underlying the development of an extreme neuroanatomical sex difference. The robust nucleus of the arcopallium (RA) is a key component of the songbird vocal motor system. In zebra finch, the RA is initially monomorphic and then atrophies in females but grows up to 7-fold larger in males. Mirroring this divergence, we show here that sex-differential gene expression in the RA expands from hundreds of predominantly sex chromosome Z genes in early development to thousands of predominantly autosomal genes by the time sexual dimorphism asymptotes. Male-specific developmental processes include cell and axonal growth, synapse assembly and activity, and energy metabolism; female-specific processes include cell polarity and differentiation, transcriptional repression, and steroid hormone and immune signaling. Transcription factor binding site analyses support female-biased activation of pro-apoptotic regulatory networks. The extensive and sex-specific transcriptomic reorganization of RA provides insights into potential drivers of sexually dimorphic neurodevelopment. Friedrich et al. demonstrate extensive transcriptomic sex differences underlying the sexually dimorphic development of vocal nucleus RA in the songbird brain. They find sex-specific gene regulation linked to distinct biological processes, developmental shifts in the relative signal from sex chromosome to autosomal genes, and evidence of female-biased pro-apoptotic regulatory networks.
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Affiliation(s)
- Samantha R Friedrich
- Department of Behavioral Neuroscience, Oregon Health & Science University (OHSU), Portland, OR 97239, USA
| | - Alexander A Nevue
- Department of Behavioral Neuroscience, Oregon Health & Science University (OHSU), Portland, OR 97239, USA
| | - Abraão L P Andrade
- Brain Institute, Federal University of Rio Grande do Norte, Natal, RN 59078-970, Brazil
| | - Tarciso A F Velho
- Brain Institute, Federal University of Rio Grande do Norte, Natal, RN 59078-970, Brazil
| | - Claudio V Mello
- Department of Behavioral Neuroscience, Oregon Health & Science University (OHSU), Portland, OR 97239, USA.
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Choe HN, Jarvis ED. The role of sex chromosomes and sex hormones in vocal learning systems. Horm Behav 2021; 132:104978. [PMID: 33895570 DOI: 10.1016/j.yhbeh.2021.104978] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 03/22/2021] [Accepted: 03/23/2021] [Indexed: 12/12/2022]
Abstract
Vocal learning is the ability to imitate and modify sounds through auditory experience, a rare trait found in only a few lineages of mammals and birds. It is a critical component of human spoken language, allowing us to verbally transmit speech repertoires and knowledge across generations. In many vocal learning species, the vocal learning trait is sexually dimorphic, where it is either limited to males or present in both sexes to different degrees. In humans, recent findings have revealed subtle sexual dimorphism in vocal learning/spoken language brain regions and some associated disorders. For songbirds, where the neural mechanisms of vocal learning have been well studied, vocal learning appears to have been present in both sexes at the origin of the lineage and was then independently lost in females of some subsequent lineages. This loss is associated with an interplay between sex chromosomes and sex steroid hormones. Even in species with little dimorphism, like humans, sex chromosomes and hormones still have some influence on learned vocalizations. Here we present a brief synthesis of these studies, in the context of sex determination broadly, and identify areas of needed investigation to further understand how sex chromosomes and sex steroid hormones help establish sexually dimorphic neural structures for vocal learning.
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Affiliation(s)
- Ha Na Choe
- Duke University Medical Center, The Rockefeller University, Howard Hughes Medical Institute, United States of America.
| | - Erich D Jarvis
- Duke University Medical Center, The Rockefeller University, Howard Hughes Medical Institute, United States of America.
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Mello CV, Lovell PV. Avian genomics lends insights into endocrine function in birds. Gen Comp Endocrinol 2018; 256:123-129. [PMID: 28596079 PMCID: PMC5749246 DOI: 10.1016/j.ygcen.2017.05.023] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Revised: 05/23/2017] [Accepted: 05/30/2017] [Indexed: 01/12/2023]
Abstract
The genomics era has brought along the completed sequencing of a large number of bird genomes that cover a broad range of the avian phylogenetic tree (>30 orders), leading to major novel insights into avian biology and evolution. Among recent findings, the discovery that birds lack a large number of protein coding genes that are organized in highly conserved syntenic clusters in other vertebrates is very intriguing, given the physiological importance of many of these genes. A considerable number of them play prominent endocrine roles, suggesting that birds evolved compensatory genetic or physiological mechanisms that allowed them to survive and thrive in spite of these losses. While further studies are needed to establish the exact extent of avian gene losses, these findings point to birds as potentially highly relevant model organisms for exploring the genetic basis and possible therapeutic approaches for a wide range of endocrine functions and disorders.
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Affiliation(s)
- C V Mello
- Dept. Behavioral Neuroscience, Oregon Health & Science University, L470, 3181 SW Sam Jackson Park Rd., Portland, OR 97239, United States.
| | - P V Lovell
- Dept. Behavioral Neuroscience, Oregon Health & Science University, L470, 3181 SW Sam Jackson Park Rd., Portland, OR 97239, United States.
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5
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Frankl-Vilches C, Kuhl H, Werber M, Klages S, Kerick M, Bakker A, de Oliveira EH, Reusch C, Capuano F, Vowinckel J, Leitner S, Ralser M, Timmermann B, Gahr M. Using the canary genome to decipher the evolution of hormone-sensitive gene regulation in seasonal singing birds. Genome Biol 2015; 16:19. [PMID: 25631560 PMCID: PMC4373106 DOI: 10.1186/s13059-014-0578-9] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Accepted: 12/23/2014] [Indexed: 11/15/2022] Open
Abstract
BACKGROUND While the song of all songbirds is controlled by the same neural circuit, the hormone dependence of singing behavior varies greatly between species. For this reason, songbirds are ideal organisms to study ultimate and proximate mechanisms of hormone-dependent behavior and neuronal plasticity. RESULTS We present the high quality assembly and annotation of a female 1.2-Gbp canary genome. Whole genome alignments between the canary and 13 genomes throughout the bird taxa show a much-conserved synteny, whereas at the single-base resolution there are considerable species differences. These differences impact small sequence motifs like transcription factor binding sites such as estrogen response elements and androgen response elements. To relate these species-specific response elements to the hormone-sensitivity of the canary singing behavior, we identify seasonal testosterone-sensitive transcriptomes of major song-related brain regions, HVC and RA, and find the seasonal gene networks related to neuronal differentiation only in the HVC. Testosterone-sensitive up-regulated gene networks of HVC of singing males concerned neuronal differentiation. Among the testosterone-regulated genes of canary HVC, 20% lack estrogen response elements and 4 to 8% lack androgen response elements in orthologous promoters in the zebra finch. CONCLUSIONS The canary genome sequence and complementary expression analysis reveal intra-regional evolutionary changes in a multi-regional neural circuit controlling seasonal singing behavior and identify gene evolution related to the hormone-sensitivity of this seasonal singing behavior. Such genes that are testosterone- and estrogen-sensitive specifically in the canary and that are involved in rewiring of neurons might be crucial for seasonal re-differentiation of HVC underlying seasonal song patterning.
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Affiliation(s)
- Carolina Frankl-Vilches
- Department of Behavioral Neurobiology, Max Planck Institute for Ornithology, 82319, Seewiesen, Germany.
| | - Heiner Kuhl
- Department of Behavioral Neurobiology, Max Planck Institute for Ornithology, 82319, Seewiesen, Germany.
- Max Planck Institute for Molecular Genetics, Sequencing Core Facility, 14195, Berlin, Germany.
| | - Martin Werber
- Max Planck Institute for Molecular Genetics, Sequencing Core Facility, 14195, Berlin, Germany.
| | - Sven Klages
- Max Planck Institute for Molecular Genetics, Sequencing Core Facility, 14195, Berlin, Germany.
| | - Martin Kerick
- Max Planck Institute for Molecular Genetics, Sequencing Core Facility, 14195, Berlin, Germany.
| | - Antje Bakker
- Department of Behavioral Neurobiology, Max Planck Institute for Ornithology, 82319, Seewiesen, Germany.
| | - Edivaldo Hc de Oliveira
- Laboratório de Cultura de Tecidos e Citogenética, SAMAM, Instituto Evandro Chagas, Ananindeua, Pará, and Faculdade de Ciências Naturais (ICEN), Universidade Federal do Pará, Belém, 66075-110, Brazil.
| | - Christina Reusch
- Department of Behavioral Neurobiology, Max Planck Institute for Ornithology, 82319, Seewiesen, Germany.
| | - Floriana Capuano
- Department of Biochemistry and Cambridge Systems Biology Centre, 80 Tennis Court Road, Cambridge, CB2 1GA, UK.
| | - Jakob Vowinckel
- Department of Biochemistry and Cambridge Systems Biology Centre, 80 Tennis Court Road, Cambridge, CB2 1GA, UK.
| | - Stefan Leitner
- Department of Behavioral Neurobiology, Max Planck Institute for Ornithology, 82319, Seewiesen, Germany.
| | - Markus Ralser
- Department of Biochemistry and Cambridge Systems Biology Centre, 80 Tennis Court Road, Cambridge, CB2 1GA, UK.
- Division of Physiology and Metabolism, MRC National Institute for Medical Research, the Ridgeway, Mill Hill, London, NW7 1AA, UK.
| | - Bernd Timmermann
- Max Planck Institute for Molecular Genetics, Sequencing Core Facility, 14195, Berlin, Germany.
| | - Manfred Gahr
- Department of Behavioral Neurobiology, Max Planck Institute for Ornithology, 82319, Seewiesen, Germany.
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6
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Cheng Y, Wang X, Yao J, Voegele RT, Zhang Y, Wang W, Huang L, Kang Z. Characterization of protein kinase PsSRPKL, a novel pathogenicity factor in the wheat stripe rust fungus. Environ Microbiol 2015; 17:2601-17. [PMID: 25407954 DOI: 10.1111/1462-2920.12719] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Revised: 11/09/2014] [Accepted: 11/10/2014] [Indexed: 12/31/2022]
Abstract
As in other eukaryotes, protein kinases (PKs) are generally evolutionarily conserved and play major regulatory roles in plant pathogenic fungi. Many PKs have been proven to be important for pathogenesis in model fungal plant pathogens, but little is currently known about their roles in the pathogenesis of cereal rust fungi, devastating pathogens in agriculture worldwide. Here, we report on an in planta highly induced PK gene PsSRPKL from the wheat stripe rust fungus Puccinia striiformis f. sp. tritici (Pst), one of the most important cereal rust fungi. PsSRPKL belongs to a group of PKs that are evolutionarily specific to cereal rust fungi. It shows a high level of intraspecies polymorphism in the kinase domains and directed green fluorescent protein chimers to plant nuclei. Overexpression of PsSRPKL in fission yeast induces aberrant cell morphology and a decreased resistance to environmental stresses. Most importantly, PsSRPKL is proven to be an important pathogenicity factor responsible for fungal growth and responses to environmental stresses, therefore contributing significantly to Pst virulence in wheat. We hypothesize that cereal rust fungi have developed specific PKs as pathogenicity factors for adaptation to their host species during evolution. Thus, our findings provide significant insights into pathogenicity and virulence evolution in cereal rust fungi.
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Affiliation(s)
- Yulin Cheng
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Xiaojie Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Juanni Yao
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Ralf T Voegele
- Fachgebiet Phytopathologie, Fakultät Agrarwissenschaften, Institut für Phytomedizin, Universität Hohenheim, Stuttgart, Germany
| | - Yanru Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Wumei Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Lili Huang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Zhensheng Kang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
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7
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Wirthlin M, Lovell PV, Jarvis ED, Mello CV. Comparative genomics reveals molecular features unique to the songbird lineage. BMC Genomics 2014; 15:1082. [PMID: 25494627 PMCID: PMC4377847 DOI: 10.1186/1471-2164-15-1082] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Accepted: 12/09/2014] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND Songbirds (oscine Passeriformes) are among the most diverse and successful vertebrate groups, comprising almost half of all known bird species. Identifying the genomic innovations that might be associated with this success, as well as with characteristic songbird traits such as vocal learning and the brain circuits that underlie this behavior, has proven difficult, in part due to the small number of avian genomes available until recently. Here we performed a comparative analysis of 48 avian genomes to identify genomic features that are unique to songbirds, as well as an initial assessment of function by investigating their tissue distribution and predicted protein domain structure. RESULTS Using BLAT alignments and gene synteny analysis, we curated a large set of Ensembl gene models that were annotated as novel or duplicated in the most commonly studied songbird, the Zebra finch (Taeniopygia guttata), and then extended this analysis to 47 additional avian and 4 non-avian genomes. We identified 10 novel genes uniquely present in songbird genomes. A refined map of chromosomal synteny disruptions in the Zebra finch genome revealed that the majority of these novel genes localized to regions of genomic instability associated with apparent chromosomal breakpoints. Analyses of in situ hybridization and RNA-seq data revealed that a subset of songbird-unique genes is expressed in the brain and/or other tissues, and that 2 of these (YTHDC2L1 and TMRA) are highly differentially expressed in vocal learning-associated nuclei relative to the rest of the brain. CONCLUSIONS Our study reveals novel genes unique to songbirds, including some that may subserve their unique vocal control system, substantially improves the quality of Zebra finch genome annotations, and contributes to a better understanding of how genomic features may have evolved in conjunction with the emergence of the songbird lineage.
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Affiliation(s)
| | | | | | - Claudio V Mello
- Department of Behavioral Neuroscience, Oregon Health & Science University, Portland, OR 97214, USA.
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8
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Field J, Manser E. The PAKs come of age: Celebrating 18 years of discovery. CELLULAR LOGISTICS 2014; 2:54-58. [PMID: 23125949 PMCID: PMC3485743 DOI: 10.4161/cl.22084] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Protein kinases are versatile signaling molecules that are involved in the regulation most physiological responses. The p21-activated kinases (PAKs) can be activated directly by the small GTPases Rac and Cdc42 and are among the best characterized downstream effectors of these Rho proteins. The structure, substrate specificity and functional role of PAKS are evolutionarily conserved from protozoa to mammals. Vertebrate PAKs are particularly important for cytoskeletal remodeling and focal adhesion assembly, thereby contributing to dynamic processes such as cell migration and synaptic plasticity. This issue of Cellular Logistics focuses on the PAK family of kinases, with ten reviews written by researchers currently working in the field. Here in this introductory overview we highlight some of the most interesting recent discoveries regarding PAK biochemistry and biology. The reviews in this issue cover a range of topics including the atomic structures of PAK1 and PAK4, their role in animals as assessed by knockout studies, and how PAKs are likely to contribute to cancer and neurodegenerative diseases. The promise remains that PAK inhibitors will emerge that validate current pre-clinical studies suggesting that blocking PAK activity will positively contribute to human health.
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Affiliation(s)
- Jeffrey Field
- Department of Pharmacology; Perelman School of Medicine; University of Pennsylvania; Philadelphia, PA USA
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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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Itoh Y, Kampf K, Balakrishnan CN, Arnold AP. Karyotypic polymorphism of the zebra finch Z chromosome. Chromosoma 2011; 120:255-64. [PMID: 21369954 PMCID: PMC3099001 DOI: 10.1007/s00412-010-0308-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2010] [Revised: 12/02/2010] [Accepted: 12/16/2010] [Indexed: 01/28/2023]
Abstract
We describe a karyotypic polymorphism on the zebra finch Z chromosome. This polymorphism was discovered because of a difference in the position of the centromere and because it occurs at varying frequencies in domesticated colonies in the USA and Germany and among two zebra finch subspecies. Using DNA fluorescent in situ hybridization to map specific Z genes and measurements of DNA replication, we show that this polymorphism is the result of a large pericentric inversion involving the majority of the chromosome. We sequenced a likely breakpoint for the inversion and found many repetitive sequences. Around the breakpoint, there are numerous repetitive sequences and several copies of PAK3 (p21-activated kinase 3)-related sequences (PAK3Z) which showed testes-specific expression by RT-PCR. Our findings further suggest that the sequenced genome of the zebra finch may be derived from a male heterozygote for the Z chromosome polymorphism. This finding, in combination with regional differences in the frequency of the polymorphism, has important consequences for future studies using zebra finches.
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Affiliation(s)
- Yuichiro Itoh
- Department of Integrative Biology and Physiology, University of California, Los Angeles, CA 90095-1606, USA.
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