51
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Lovell PV, Huizinga NA, Getachew A, Mees B, Friedrich SR, Wirthlin M, Mello CV. Curation of microarray oligonucleotides and corresponding ESTs/cDNAs used for gene expression analysis in zebra finches. BMC Res Notes 2018; 11:309. [PMID: 29776372 PMCID: PMC5960091 DOI: 10.1186/s13104-018-3402-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 05/07/2018] [Indexed: 12/24/2022] Open
Abstract
OBJECTIVES Zebra finches are a major model organism for investigating mechanisms of vocal learning, a trait that enables spoken language in humans. The development of cDNA collections with expressed sequence tags (ESTs) and microarrays has allowed for extensive molecular characterizations of circuitry underlying vocal learning and production. However, poor database curation can lead to errors in transcriptome and bioinformatics analyses, limiting the impact of these resources. Here we used genomic alignments and synteny analysis for orthology verification to curate and reannotate ~ 35% of the oligonucleotides and corresponding ESTs/cDNAs that make-up Agilent microarrays for gene expression analysis in finches. DATA DESCRIPTION We found that: (1) 5475 out of 43,084 oligos (a) failed to align to the zebra finch genome, (b) aligned to multiple loci, or (c) aligned to Chr_un only, and thus need to be flagged until a better genome assembly is available, or (d) reflect cloning artifacts; (2) Out of 9635 valid oligos examined further, 3120 were incorrectly named, including 1533 with no known orthologs; and (3) 2635 oligos required name update. The resulting curated dataset provides a reference for correcting gene identification errors in previous finch microarrays studies, and avoiding such errors in future studies.
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Affiliation(s)
- Peter V Lovell
- Department of Behavioral Neuroscience, OHSU, Portland, OR, 97221, USA
| | - Nicole A Huizinga
- Department of Behavioral Neuroscience, OHSU, Portland, OR, 97221, USA
| | - Abel Getachew
- Department of Behavioral Neuroscience, OHSU, Portland, OR, 97221, USA
| | - Brianna Mees
- Department of Behavioral Neuroscience, OHSU, Portland, OR, 97221, USA
| | | | - Morgan Wirthlin
- Department of Behavioral Neuroscience, OHSU, Portland, OR, 97221, USA.,Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Claudio V Mello
- Department of Behavioral Neuroscience, OHSU, Portland, OR, 97221, USA.
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52
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Rohde F, Schusser B, Hron T, Farkašová H, Plachý J, Härtle S, Hejnar J, Elleder D, Kaspers B. Characterization of Chicken Tumor Necrosis Factor-α, a Long Missed Cytokine in Birds. Front Immunol 2018; 9:605. [PMID: 29719531 PMCID: PMC5913325 DOI: 10.3389/fimmu.2018.00605] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 03/09/2018] [Indexed: 11/13/2022] Open
Abstract
Tumor necrosis factor-α (TNF-α) is a pleiotropic cytokine playing critical roles in host defense and acute and chronic inflammation. It has been described in fish, amphibians, and mammals but was considered to be absent in the avian genomes. Here, we report on the identification and functional characterization of the avian ortholog. The chicken TNF-α (chTNF-α) is encoded by a highly GC-rich gene, whose product shares with its mammalian counterpart 45% homology in the extracellular part displaying the characteristic TNF homology domain. Orthologs of chTNF-α were identified in the genomes of 12 additional avian species including Palaeognathae and Neognathae, and the synteny of the closely adjacent loci with mammalian TNF-α orthologs was demonstrated in the crow (Corvus cornix) genome. In addition to chTNF-α, we obtained full sequences for homologs of TNF-α receptors 1 and 2 (TNFR1, TNFR2). chTNF-α mRNA is strongly induced by lipopolysaccharide (LPS) stimulation of monocyte derived, splenic and bone marrow macrophages, and significantly upregulated in splenic tissue in response to i.v. LPS treatment. Activation of T-lymphocytes by TCR crosslinking induces chTNF-α expression in CD4+ but not in CD8+ cells. To gain insights into its biological activity, we generated recombinant chTNF-α in eukaryotic and prokaryotic expression systems. Both, the full-length cytokine and the extracellular domain rapidly induced an NFκB-luciferase reporter in stably transfected CEC-32 reporter cells. Collectively, these data provide strong evidence for the existence of a fully functional TNF-α/TNF-α receptor system in birds thus filling a gap in our understanding of the evolution of cytokine systems.
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Affiliation(s)
- Franziska Rohde
- Department of Veterinary Science, Ludwig-Maximilians-Universität, Munich, Germany
| | - Benjamin Schusser
- Reproductive Biotechnology, Department of Animal Sciences, Technical University Munich, Munich, Germany
| | - Tomáš Hron
- Laboratory of Viral and Cellular Genetics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czechia
| | - Helena Farkašová
- Laboratory of Viral and Cellular Genetics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czechia
| | - Jiří Plachý
- Laboratory of Viral and Cellular Genetics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czechia
| | - Sonja Härtle
- Department of Veterinary Science, Ludwig-Maximilians-Universität, Munich, Germany
| | - Jiří Hejnar
- Laboratory of Viral and Cellular Genetics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czechia
| | - Daniel Elleder
- Laboratory of Viral and Cellular Genetics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czechia
| | - Bernd Kaspers
- Department of Veterinary Science, Ludwig-Maximilians-Universität, Munich, Germany
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53
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Lovell PV, Huizinga NA, Friedrich SR, Wirthlin M, Mello CV. The constitutive differential transcriptome of a brain circuit for vocal learning. BMC Genomics 2018; 19:231. [PMID: 29614959 PMCID: PMC5883274 DOI: 10.1186/s12864-018-4578-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 03/02/2018] [Indexed: 01/25/2023] Open
Abstract
Background The ability to imitate the vocalizations of other organisms, a trait known as vocal learning, is shared by only a few organisms, including humans, where it subserves the acquisition of speech and language, and 3 groups of birds. In songbirds, vocal learning requires the coordinated activity of a set of specialized brain nuclei referred to as the song control system. Recent efforts have revealed some of the genes that are expressed in these vocal nuclei, however a thorough characterization of the transcriptional specializations of this system is still missing. We conducted a rigorous and comprehensive analysis of microarrays, and conducted a separate analysis of 380 genes by in situ hybridizations in order to identify molecular specializations of the major nuclei of the song system of zebra finches (Taeniopygia guttata), a songbird species. Results Our efforts identified more than 3300 genes that are differentially regulated in one or more vocal nuclei of adult male birds compared to the adjacent brain regions. Bioinformatics analyses provided insights into the possible involvement of these genes in molecular pathways such as cellular morphogenesis, intrinsic cellular excitability, neurotransmission and neuromodulation, axonal guidance and cela-to-cell interactions, and cell survival, which are known to strongly influence the functional properties of the song system. Moreover, an in-depth analysis of specific gene families with known involvement in regulating the development and physiological properties of neuronal circuits provides further insights into possible modulators of the song system. Conclusion Our study represents one of the most comprehensive molecular characterizations of a brain circuit that evolved to facilitate a learned behavior in a vertebrate. The data provide novel insights into possible molecular determinants of the functional properties of the song control circuitry. It also provides lists of compelling targets for pharmacological and genetic manipulations to elucidate the molecular regulation of song behavior and vocal learning. Electronic supplementary material The online version of this article (10.1186/s12864-018-4578-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Peter V Lovell
- Department of Behavioral Neuroscience, Oregon Health and Sciences University, 3181 Sam Jackson Park Rd L470, Portland, OR, USA
| | - Nicole A Huizinga
- Department of Behavioral Neuroscience, Oregon Health and Sciences University, 3181 Sam Jackson Park Rd L470, Portland, OR, USA
| | - Samantha R Friedrich
- Department of Behavioral Neuroscience, Oregon Health and Sciences University, 3181 Sam Jackson Park Rd L470, Portland, OR, USA
| | - Morgan Wirthlin
- Department of Behavioral Neuroscience, Oregon Health and Sciences University, 3181 Sam Jackson Park Rd L470, Portland, OR, USA.,Current affiliation: Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Claudio V Mello
- Department of Behavioral Neuroscience, Oregon Health and Sciences University, 3181 Sam Jackson Park Rd L470, Portland, OR, USA.
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54
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Pirson M, Clippe A, Knoops B. The curious case of peroxiredoxin-5: what its absence in aves can tell us and how it can be used. BMC Evol Biol 2018; 18:18. [PMID: 29422028 PMCID: PMC5806436 DOI: 10.1186/s12862-018-1135-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 01/31/2018] [Indexed: 12/02/2022] Open
Abstract
Background Peroxiredoxins are ubiquitous thiol-dependent peroxidases that represent a major antioxidant defense in both prokaryotic cells and eukaryotic organisms. Among the six vertebrate peroxiredoxin isoforms, peroxiredoxin-5 (PRDX5) appears to be a particular peroxiredoxin, displaying a different catalytic mechanism, as well as a wider substrate specificity and subcellular distribution. In addition, several evolutionary peculiarities, such as loss of subcellular targeting in certain species, have been reported for this enzyme. Results Western blotting analyses of 2-cys PRDXs (PRDX1–5) failed to identify the PRDX5 isoform in chicken tissue homogenates. Thereafter, via in silico analysis of PRDX5 orthologs, we went on to show that the PRDX5 gene is conserved in all branches of the amniotes clade, with the exception of aves. Further investigation of bird genomic sequences and expressed tag sequences confirmed the disappearance of the gene, though TRMT112, a gene located closely to the 5′ extremity of the PRDX5 gene, is conserved. Finally, using in ovo electroporation to overexpress the long and short forms of human PRDX5, we showed that, though the gene is lost in birds, subcellular targeting of human PRDX5 is conserved in the chick. Conclusions Further adding to the distinctiveness of this enzyme, this study reports converging evidence supporting loss of PRDX5 in aves. In-depth analysis revealed that this absence is proper to birds as PRDX5 appears to be conserved in non-avian amniotes. Finally, taking advantage of the in ovo electroporation technique, we validate the subcellular targeting of human PRDX5 in the chick embryo and bring forward this gain-of-function model as a potent way to study PRDX5 functions in vivo.
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Affiliation(s)
- Marc Pirson
- Group of Animal Molecular and Cellular Biology, Institut des Sciences de la Vie (ISV), Université catholique de Louvain, 4-5 Place Croix du Sud, 1348, Louvain-la-Neuve, Belgium
| | - André Clippe
- Group of Animal Molecular and Cellular Biology, Institut des Sciences de la Vie (ISV), Université catholique de Louvain, 4-5 Place Croix du Sud, 1348, Louvain-la-Neuve, Belgium
| | - Bernard Knoops
- Group of Animal Molecular and Cellular Biology, Institut des Sciences de la Vie (ISV), Université catholique de Louvain, 4-5 Place Croix du Sud, 1348, Louvain-la-Neuve, Belgium.
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55
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Liu D, Hunt M, Tsai IJ. Inferring synteny between genome assemblies: a systematic evaluation. BMC Bioinformatics 2018; 19:26. [PMID: 29382321 PMCID: PMC5791376 DOI: 10.1186/s12859-018-2026-4] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 01/15/2018] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Genome assemblies across all domains of life are being produced routinely. Initial analysis of a new genome usually includes annotation and comparative genomics. Synteny provides a framework in which conservation of homologous genes and gene order is identified between genomes of different species. The availability of human and mouse genomes paved the way for algorithm development in large-scale synteny mapping, which eventually became an integral part of comparative genomics. Synteny analysis is regularly performed on assembled sequences that are fragmented, neglecting the fact that most methods were developed using complete genomes. It is unknown to what extent draft assemblies lead to errors in such analysis. RESULTS We fragmented genome assemblies of model nematodes to various extents and conducted synteny identification and downstream analysis. We first show that synteny between species can be underestimated up to 40% and find disagreements between popular tools that infer synteny blocks. This inconsistency and further demonstration of erroneous gene ontology enrichment tests raise questions about the robustness of previous synteny analysis when gold standard genome sequences remain limited. In addition, assembly scaffolding using a reference guided approach with a closely related species may result in chimeric scaffolds with inflated assembly metrics if a true evolutionary relationship was overlooked. Annotation quality, however, has minimal effect on synteny if the assembled genome is highly contiguous. CONCLUSIONS Our results show that a minimum N50 of 1 Mb is required for robust downstream synteny analysis, which emphasizes the importance of gold standard genomes to the science community, and should be achieved given the current progress in sequencing technology.
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Affiliation(s)
- Dang Liu
- Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei, Taiwan
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Martin Hunt
- Nuffield Department of Clinical Medicine, Experimental Medicine Division, John Radcliffe Hospital, University of Oxford, Oxford, OX1 1NF UK
- European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD UK
| | - Isheng J Tsai
- Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei, Taiwan
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
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56
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Orgeur M, Martens M, Börno ST, Timmermann B, Duprez D, Stricker S. A dual transcript-discovery approach to improve the delimitation of gene features from RNA-seq data in the chicken model. Biol Open 2018; 7:bio.028498. [PMID: 29183907 PMCID: PMC5827264 DOI: 10.1242/bio.028498] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
The sequence of the chicken genome, like several other draft genome sequences, is presently not fully covered. Gaps, contigs assigned with low confidence and uncharacterized chromosomes result in gene fragmentation and imprecise gene annotation. Transcript abundance estimation from RNA sequencing (RNA-seq) data relies on read quality, library complexity and expression normalization. In addition, the quality of the genome sequence used to map sequencing reads, and the gene annotation that defines gene features, must also be taken into account. A partially covered genome sequence causes the loss of sequencing reads from the mapping step, while an inaccurate definition of gene features induces imprecise read counts from the assignment step. Both steps can significantly bias interpretation of RNA-seq data. Here, we describe a dual transcript-discovery approach combining a genome-guided gene prediction and a de novo transcriptome assembly. This dual approach enabled us to increase the assignment rate of RNA-seq data by nearly 20% as compared to when using only the chicken reference annotation, contributing therefore to a more accurate estimation of transcript abundance. More generally, this strategy could be applied to any organism with partial genome sequence and/or lacking a manually-curated reference annotation in order to improve the accuracy of gene expression studies.
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Affiliation(s)
- Mickael Orgeur
- Freie Universität Berlin, Institut für Chemie und Biochemie, Thielallee 63, 14195 Berlin, Germany.,Max Planck Institute for Molecular Genetics, Development and Disease Group, Ihnestrasse 63-73, 14195 Berlin, Germany.,Sorbonne Universités, UPMC Univ. Paris 06, CNRS UMR 7622, Inserm U1156, IBPS-Developmental Biology Laboratory, 9 Quai Saint-Bernard, 75252 Paris Cedex 05, France
| | - Marvin Martens
- Sorbonne Universités, UPMC Univ. Paris 06, CNRS UMR 7622, Inserm U1156, IBPS-Developmental Biology Laboratory, 9 Quai Saint-Bernard, 75252 Paris Cedex 05, France
| | - Stefan T Börno
- Max Planck Institute for Molecular Genetics, Development and Disease Group, Ihnestrasse 63-73, 14195 Berlin, Germany
| | - Bernd Timmermann
- Max Planck Institute for Molecular Genetics, Development and Disease Group, Ihnestrasse 63-73, 14195 Berlin, Germany
| | - Delphine Duprez
- Sorbonne Universités, UPMC Univ. Paris 06, CNRS UMR 7622, Inserm U1156, IBPS-Developmental Biology Laboratory, 9 Quai Saint-Bernard, 75252 Paris Cedex 05, France
| | - Sigmar Stricker
- Freie Universität Berlin, Institut für Chemie und Biochemie, Thielallee 63, 14195 Berlin, Germany .,Max Planck Institute for Molecular Genetics, Development and Disease Group, Ihnestrasse 63-73, 14195 Berlin, Germany
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57
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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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58
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Craig RJ, Suh A, Wang M, Ellegren H. Natural selection beyond genes: Identification and analyses of evolutionarily conserved elements in the genome of the collared flycatcher (Ficedula albicollis). Mol Ecol 2018; 27:476-492. [DOI: 10.1111/mec.14462] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 11/28/2017] [Accepted: 11/28/2017] [Indexed: 12/13/2022]
Affiliation(s)
- Rory J. Craig
- Department of Evolutionary Biology; Evolutionary Biology Centre; Uppsala University; Uppsala Sweden
- Institute of Evolutionary Biology; School of Biological Sciences; University of Edinburgh; Edinburgh UK
| | - Alexander Suh
- Department of Evolutionary Biology; Evolutionary Biology Centre; Uppsala University; Uppsala Sweden
| | - Mi Wang
- Department of Evolutionary Biology; Evolutionary Biology Centre; Uppsala University; Uppsala Sweden
| | - Hans Ellegren
- Department of Evolutionary Biology; Evolutionary Biology Centre; Uppsala University; Uppsala Sweden
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59
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Mellouk N, Ramé C, Barbe A, Grandhaye J, Froment P, Dupont J. Chicken Is a Useful Model to Investigate the Role of Adipokines in Metabolic and Reproductive Diseases. Int J Endocrinol 2018; 2018:4579734. [PMID: 30018639 PMCID: PMC6029501 DOI: 10.1155/2018/4579734] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 05/16/2018] [Indexed: 01/04/2023] Open
Abstract
Reproduction is a complex and essential physiological process required by all species to produce a new generation. This process involves strict hormonal regulation, depending on a connection between the hypothalamus-pituitary-gonadal axis and peripheral organs. Metabolic homeostasis influences the reproductive functions, and its alteration leads to disturbances in the reproductive functions of humans as well as animals. For a long time, adipose tissue has been recognised as an endocrine organ but its ability to secrete and release hormones called adipokines is now emerging. Adipokines have been found to play a major role in the regulation of metabolic and reproductive processes at both central and peripheral levels. Leptin was initially the first adipokine that has been described to be the most involved in the metabolism/reproduction interrelation in mammals. In avian species, the role of leptin is still under debate. Recently, three novel adipokines have been discovered: adiponectin (ADIPOQ, ACRP30), visfatin (NAMPT, PBEF), and chemerin (RARRES2, TIG2). However, their mode of action between mammalian and nonmammalian species is different due to the different reproductive and metabolic systems. Herein, we will provide an overview of the structure and function related to metabolic and reproductive mechanisms of the latter three adipokines with emphasis on avian species.
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Affiliation(s)
- Namya Mellouk
- INRA, UMR 85 Physiologie de la Reproduction et des Comportements, 37380 Nouzilly, France
| | - Christelle Ramé
- INRA, UMR 85 Physiologie de la Reproduction et des Comportements, 37380 Nouzilly, France
| | - Alix Barbe
- INRA, UMR 85 Physiologie de la Reproduction et des Comportements, 37380 Nouzilly, France
| | - Jérémy Grandhaye
- INRA, UMR 85 Physiologie de la Reproduction et des Comportements, 37380 Nouzilly, France
| | - Pascal Froment
- INRA, UMR 85 Physiologie de la Reproduction et des Comportements, 37380 Nouzilly, France
| | - Joëlle Dupont
- INRA, UMR 85 Physiologie de la Reproduction et des Comportements, 37380 Nouzilly, France
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60
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Frankl-Vilches C, Gahr M. Androgen and estrogen sensitivity of bird song: a comparative view on gene regulatory levels. J Comp Physiol A Neuroethol Sens Neural Behav Physiol 2018; 204:113-126. [PMID: 29209770 PMCID: PMC5790841 DOI: 10.1007/s00359-017-1236-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 11/02/2017] [Accepted: 11/09/2017] [Indexed: 12/16/2022]
Abstract
Singing of songbirds is sensitive to testosterone and its androgenic and estrogenic metabolites in a species-specific way. The hormonal effects on song pattern are likely mediated by androgen receptors (AR) and estrogen receptor alpha (ERα), ligand activated transcription factors that are expressed in neurons of various areas of the songbirds' vocal control circuit. The distribution of AR in this circuit is rather similar between species while that of ERα is species variant and concerns a key vocal control area, the HVC (proper name). We discuss the regulation of the expression of the cognate AR and ERα and putative splice variants. In particular, we suggest that transcription factor binding sites in the promoter of these receptors differ between bird species. Further, we suggest that AR- and ERα-dependent gene regulation in vocal areas differs between species due to species-specific DNA binding sites of putative target genes that are required for the transcriptional activity of the receptors. We suggest that species differences in the distribution of AR and ERα in vocal areas and in the genomic sensitivity to these receptors contribute to species-specific hormonal regulation of the song.
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Affiliation(s)
- Carolina Frankl-Vilches
- Department of Behavioural Neurobiology, Max Planck Institute for Ornithology, 82319, Seewiesen, Germany
| | - Manfred Gahr
- Department of Behavioural Neurobiology, Max Planck Institute for Ornithology, 82319, Seewiesen, Germany.
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61
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Teeling EC, Vernes SC, Dávalos LM, Ray DA, Gilbert MTP, Myers E. Bat Biology, Genomes, and the Bat1K Project: To Generate Chromosome-Level Genomes for All Living Bat Species. Annu Rev Anim Biosci 2017; 6:23-46. [PMID: 29166127 DOI: 10.1146/annurev-animal-022516-022811] [Citation(s) in RCA: 121] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Bats are unique among mammals, possessing some of the rarest mammalian adaptations, including true self-powered flight, laryngeal echolocation, exceptional longevity, unique immunity, contracted genomes, and vocal learning. They provide key ecosystem services, pollinating tropical plants, dispersing seeds, and controlling insect pest populations, thus driving healthy ecosystems. They account for more than 20% of all living mammalian diversity, and their crown-group evolutionary history dates back to the Eocene. Despite their great numbers and diversity, many species are threatened and endangered. Here we announce Bat1K, an initiative to sequence the genomes of all living bat species (n∼1,300) to chromosome-level assembly. The Bat1K genome consortium unites bat biologists (>148 members as of writing), computational scientists, conservation organizations, genome technologists, and any interested individuals committed to a better understanding of the genetic and evolutionary mechanisms that underlie the unique adaptations of bats. Our aim is to catalog the unique genetic diversity present in all living bats to better understand the molecular basis of their unique adaptations; uncover their evolutionary history; link genotype with phenotype; and ultimately better understand, promote, and conserve bats. Here we review the unique adaptations of bats and highlight how chromosome-level genome assemblies can uncover the molecular basis of these traits. We present a novel sequencing and assembly strategy and review the striking societal and scientific benefits that will result from the Bat1K initiative.
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Affiliation(s)
- Emma C Teeling
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland;
| | - Sonja C Vernes
- Neurogenetics of Vocal Communication Group, Max Planck Institute for Psycholinguistics, Nijmegen, 6500 AH, The Netherlands.,Donders Centre for Cognitive Neuroimaging, Nijmegen, 6525 EN, The Netherlands
| | - Liliana M Dávalos
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York 11794-5245, USA
| | - David A Ray
- Department of Biological Sciences, Texas Tech University, Lubbock, Texas 79409, USA
| | - M Thomas P Gilbert
- Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark.,University Museum, Norwegian University of Science and Technology, 7491 Trondheim, Norway
| | - Eugene Myers
- Max Planck Institute for Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | -
- *Full list of Bat1K Consortium members in Supplemental Appendix
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62
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Fonseca E, Ruivo R, Lopes-Marques M, Zhang H, Santos MM, Venkatesh B, Castro LFC. LXRα and LXRβ Nuclear Receptors Evolved in the Common Ancestor of Gnathostomes. Genome Biol Evol 2017; 9:222-230. [PMID: 28057729 PMCID: PMC5381633 DOI: 10.1093/gbe/evw305] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/29/2016] [Indexed: 12/25/2022] Open
Abstract
Nuclear receptors (NRs) regulate numerous aspects of the endocrine system. They mediate endogenous and exogenous cues, ensuring a homeostatic control of development and metabolism. Gene duplication, loss and mutation have shaped the repertoire and function of NRs in metazoans. Here, we examine the evolution of a pivotal orchestrator of cholesterol metabolism in vertebrates, the liver X receptors (LXRs). Previous studies suggested that LXRα and LXRβ genes emerged in the mammalian ancestor. However, we show through genome analysis and functional assay that bona fide LXRα and LXRβ orthologues are present in reptiles, coelacanth and chondrichthyans but not in cyclostomes. These findings show that LXR duplicated before gnathostome radiation, followed by asymmetric paralogue loss in some lineages. We suggest that a tighter control of cholesterol levels in vertebrates was achieved through the exploitation of a wider range of oxysterols, an ability contingent on ligand-binding pocket remodeling.
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Affiliation(s)
- Elza Fonseca
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, U. Porto, Portugal.,Department of Biology, FCUP - Faculty of Sciences, U. Porto, Portugal
| | - Raquel Ruivo
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, U. Porto, Portugal
| | - Mónica Lopes-Marques
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, U. Porto, Portugal.,ICBAS - Institute of Biomedical Sciences Abel Salazar - U. Porto, Portugal
| | - Huixian Zhang
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Biopolis, Singapore
| | - Miguel M Santos
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, U. Porto, Portugal.,Department of Biology, FCUP - Faculty of Sciences, U. Porto, Portugal
| | - Byrappa Venkatesh
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Biopolis, Singapore.,Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - L Filipe C Castro
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, U. Porto, Portugal.,Department of Biology, FCUP - Faculty of Sciences, U. Porto, Portugal
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63
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Wang YC, Wang CW, Lin WC, Tsai YJ, Chang CP, Lee YJ, Lin MJ, Li C. Identification, chromosomal arrangements and expression analyses of the evolutionarily conserved prmt1 gene in chicken in comparison with its vertebrate paralogue prmt8. PLoS One 2017; 12:e0185042. [PMID: 28934323 PMCID: PMC5608299 DOI: 10.1371/journal.pone.0185042] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 09/04/2017] [Indexed: 01/22/2023] Open
Abstract
Nine protein arginine methyltransferases (PRMTs) are conserved in mammals and fish. Among these, PRMT1 is the major type I PRMT for asymmetric dimethylarginine (ADMA) formation and is the most conserved and widely distributed one. Two chicken prmt1 splicing variants were assembled and confirmed by RT-PCR experiments. However, only two scaffolds containing single separate prmt1 exon with high GC contents are present in the current chicken genome assembly. Besides, prmt1 exons are scattered in separate small scaffolds in most avian species. Complete prmt1 gene has only been predicted from two falcon species with few neighboring genes. Crocodilians are considered close to the common ancestor shared by crocodilians and birds. The gene arrangements around prmt1 in American alligator are different from that in birds but are largely conserved in human. Orthologues of genes in a large segment of human chromosomal 19 around PRMT1 are missing or not assigned to the current chicken chromosomes. In comparison, prmt8, the prmt1 paralogue, is on chicken chromosome 1 with the gene arrangements downstream of prmt8 highly conserved in birds, crocodilians, and human. However, the ones upstream vary greatly in birds. Biochemically, we found that though prmt1 transcripts were detected, limited or none PRMT1 protein was present in chicken tissues. Moreover, a much higher level of PRMT8 protein was detected in chicken brain than in mouse brain. While PRMT8 is brain specific in other vertebrate species studied, low level of PRMT8 was present in chicken but not mouse liver and muscle. We also showed that the ADMA level in chicken was similar to that in mouse. This study provides the critical information of chicken PRMT1 and PRMT8 for future analyses of the function of protein arginine methyltransferases in birds.
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Affiliation(s)
- Yi-Chun Wang
- Department of Biomedical Sciences, Chung Shan Medical University, Taichung, Taiwan
- Department of Medical Research, Chung Shan Medical University Hospital, Taichung, Taiwan, ROC
| | - Chien-Wen Wang
- Department of Biomedical Sciences, Chung Shan Medical University, Taichung, Taiwan
| | - Wen-Chang Lin
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan, ROC
| | - Yun-Jung Tsai
- Department of Biomedical Sciences, Chung Shan Medical University, Taichung, Taiwan
| | - Chien-Ping Chang
- Department of Biomedical Sciences, Chung Shan Medical University, Taichung, Taiwan
| | - Yu-Jen Lee
- Department of Biomedical Sciences, Chung Shan Medical University, Taichung, Taiwan
| | - Min-Jon Lin
- Department of Biomedical Sciences, Chung Shan Medical University, Taichung, Taiwan
- Department of Medical Research, Chung Shan Medical University Hospital, Taichung, Taiwan, ROC
| | - Chuan Li
- Department of Biomedical Sciences, Chung Shan Medical University, Taichung, Taiwan
- Department of Medical Research, Chung Shan Medical University Hospital, Taichung, Taiwan, ROC
- * E-mail:
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64
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Botero-Castro F, Figuet E, Tilak MK, Nabholz B, Galtier N. Avian Genomes Revisited: Hidden Genes Uncovered and the Rates versus Traits Paradox in Birds. Mol Biol Evol 2017; 34:3123-3131. [DOI: 10.1093/molbev/msx236] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
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65
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Seroussi E, Pitel F, Leroux S, Morisson M, Bornelöv S, Miyara S, Yosefi S, Cogburn LA, Burt DW, Anderson L, Friedman-Einat M. Mapping of leptin and its syntenic genes to chicken chromosome 1p. BMC Genet 2017; 18:77. [PMID: 28793857 PMCID: PMC5550943 DOI: 10.1186/s12863-017-0543-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2017] [Accepted: 08/02/2017] [Indexed: 01/22/2023] Open
Abstract
Background Misidentification of the chicken leptin gene has hampered research of leptin signaling in this species for almost two decades. Recently, the genuine leptin gene with a GC-rich (~70%) repetitive-sequence content was identified in the chicken genome but without indicating its genomic position. This suggests that such GC-rich sequences are difficult to sequence and therefore substantial regions are missing from the current chicken genome assembly. Results A radiation hybrid panel of chicken-hamster Wg3hCl2 cells was used to map the genome location of the chicken leptin gene. Contrary to our expectations, based on comparative genome mapping and sequence characteristics, the chicken leptin was not located on a microchromosome, which are known to contain GC-rich and repetitive regions, but at the distal tip of the largest chromosome (1p). Following conserved synteny with other vertebrates, we also mapped five additional genes to this genomic region (ARF5, SND1, LRRC4, RBM28, and FLNC), bridging the genomic gap in the current Galgal5 build for this chromosome region. All of the short scaffolds containing these genes were found to consist of GC-rich (54 to 65%) sequences comparing to the average GC-content of 40% on chromosome 1. In this syntenic group, the RNA-binding protein 28 (RBM28) was in closest proximity to leptin. We deduced the full-length of the RBM28 cDNA sequence and profiled its expression patterns detecting a negative correlation (R = − 0.7) between the expression of leptin and of RBM28 across tissues that expressed at least one of the genes above the average level. This observation suggested a local regulatory interaction between these genes. In adipose tissues, we observed a significant increase in RBM28 mRNA expression in breeds with lean phenotypes. Conclusion Mapping chicken leptin together with a cluster of five syntenic genes provided the final proof for its identification as the true chicken ortholog. The high GC-content observed for the chicken leptin syntenic group suggests that other similar clusters of genes in GC-rich genomic regions are missing from the current genome assembly (Galgal5), which should be resolved in future assemblies of the chicken genome. Electronic supplementary material The online version of this article (doi:10.1186/s12863-017-0543-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Eyal Seroussi
- Department of Animal Science, Agricultural Research Organization, Volcani Center, P.O. Box 15159, 7528809, Rishon LeTsiyon, Israel.
| | - Frédérique Pitel
- GenPhySE, Université de Toulouse, INRA, INPT, ENVT, 31326, Castanet Tolosan, France
| | - Sophie Leroux
- GenPhySE, Université de Toulouse, INRA, INPT, ENVT, 31326, Castanet Tolosan, France
| | - Mireille Morisson
- GenPhySE, Université de Toulouse, INRA, INPT, ENVT, 31326, Castanet Tolosan, France
| | - Susanne Bornelöv
- Department of Medical Biochemistry and Microbiology, Uppsala University, SE-75123, Uppsala, Sweden
| | - Shoval Miyara
- Department of Animal Science, Agricultural Research Organization, Volcani Center, P.O. Box 15159, 7528809, Rishon LeTsiyon, Israel
| | - Sara Yosefi
- Department of Animal Science, Agricultural Research Organization, Volcani Center, P.O. Box 15159, 7528809, Rishon LeTsiyon, Israel
| | - Larry A Cogburn
- Department of Animal and Food Sciences, University of Delaware, Newark, DE 19716, USA
| | - David W Burt
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, EH25 9RG, UK
| | - Leif Anderson
- Department of Medical Biochemistry and Microbiology, Uppsala University, SE-75123, Uppsala, Sweden.,Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, 77843-4458, USA.,Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, SE-75007, Uppsala, Sweden
| | - Miriam Friedman-Einat
- Department of Animal Science, Agricultural Research Organization, Volcani Center, P.O. Box 15159, 7528809, Rishon LeTsiyon, Israel.
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66
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Lovell PV, Mello CV. Correspondence on Lovell et al.: response to Bornelöv et al. Genome Biol 2017; 18:113. [PMID: 28615074 PMCID: PMC5470261 DOI: 10.1186/s13059-017-1234-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 05/08/2017] [Indexed: 11/15/2022] Open
Abstract
While the analysis of Bornelöv et al. is informative, they provide evidence for the existence of only 3% of the reported avian missing genes set, and thus do not significantly challenge our main findings that specific groups of syntenic protein-coding genes are missing in birds. This is a response to the Correspondence article: https://www.dx.doi.org/10.1186/s13059-017-1231-1
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Affiliation(s)
- Peter V Lovell
- Department of Behavioral Neuroscience, Oregon Health and Science University, Portland, OR, 97017, USA
| | - Claudio V Mello
- Department of Behavioral Neuroscience, Oregon Health and Science University, Portland, OR, 97017, USA.
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Bornelöv S, Seroussi E, Yosefi S, Pendavis K, Burgess SC, Grabherr M, Friedman-Einat M, Andersson L. Correspondence on Lovell et al.: identification of chicken genes previously assumed to be evolutionarily lost. Genome Biol 2017; 18:112. [PMID: 28615067 PMCID: PMC5470226 DOI: 10.1186/s13059-017-1231-1] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Through RNA-Seq analyses, we identified 137 genes that are missing in chicken, including the long-sought-after nephrin and tumor necrosis factor genes. These genes tended to cluster in GC-rich regions that have poor coverage in genome sequence databases. Hence, the occurrence of syntenic groups of vertebrate genes that have not been observed in Aves does not prove the evolutionary loss of such genes.Please see related Research article: http://dx.doi.org/10.1186/s13059-014-0565-1 and Please see response from Lovell et al: https://www.dx.doi.org/10.1186/s13059-017-1234-y.
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Affiliation(s)
- Susanne Bornelöv
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, SE-751 23, Sweden.,Present Address: Wellcome Trust Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, CB2 1QR, UK
| | - Eyal Seroussi
- Agricultural Research Organization, Volcani Center, Rishon LeZion, Israel
| | - Sara Yosefi
- Agricultural Research Organization, Volcani Center, Rishon LeZion, Israel
| | - Ken Pendavis
- College of Agriculture and Life Sciences, University of Arizona, Tucson, AZ, 85721-0036, USA
| | - Shane C Burgess
- College of Agriculture and Life Sciences, University of Arizona, Tucson, AZ, 85721-0036, USA
| | - Manfred Grabherr
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, SE-751 23, Sweden.,Bioinformatics Infrastructure for Life Sciences, Uppsala University, Uppsala, Sweden
| | | | - Leif Andersson
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, SE-751 23, Sweden. .,Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, SE-750 07, Sweden. .,Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, 77843-4458, USA.
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68
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Patthey C, Tong YG, Tait CM, Wilson SI. Evolution of the functionally conserved DCC gene in birds. Sci Rep 2017; 7:42029. [PMID: 28240293 PMCID: PMC5327406 DOI: 10.1038/srep42029] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Accepted: 01/03/2017] [Indexed: 11/09/2022] Open
Abstract
Understanding the loss of conserved genes is critical for determining how phenotypic diversity is generated. Here we focus on the evolution of DCC, a gene that encodes a highly conserved neural guidance receptor. Disruption of DCC in animal models and humans results in major neurodevelopmental defects including commissural axon defects. Here we examine DCC evolution in birds, which is of particular interest as a major model system in neurodevelopmental research. We found the DCC containing locus was disrupted several times during evolution, resulting in both gene losses and faster evolution rate of salvaged genes. These data suggest that DCC had been lost independently twice during bird evolution, including in chicken and zebra finch, whereas it was preserved in many other closely related bird species, including ducks. Strikingly, we observed that commissural axon trajectory appeared similar regardless of whether DCC could be detected or not. We conclude that the DCC locus is susceptible to genomic instability leading to independent disruptions in different branches of birds and a significant influence on evolution rate. Overall, the phenomenon of loss or molecular evolution of a highly conserved gene without apparent phenotype change is of conceptual importance for understanding molecular evolution of key biological processes.
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Affiliation(s)
- Cedric Patthey
- Umeå Center for Molecular Medicine, Umeå University, 901-87 Umeå, Sweden
| | - Yong Guang Tong
- Umeå Center for Molecular Medicine, Umeå University, 901-87 Umeå, Sweden
| | | | - Sara Ivy Wilson
- Umeå Center for Molecular Medicine, Umeå University, 901-87 Umeå, Sweden
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69
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Abstract
Genome size in mammals and birds shows remarkably little interspecific variation compared with other taxa. However, genome sequencing has revealed that many mammal and bird lineages have experienced differential rates of transposable element (TE) accumulation, which would be predicted to cause substantial variation in genome size between species. Thus, we hypothesize that there has been covariation between the amount of DNA gained by transposition and lost by deletion during mammal and avian evolution, resulting in genome size equilibrium. To test this model, we develop computational methods to quantify the amount of DNA gained by TE expansion and lost by deletion over the last 100 My in the lineages of 10 species of eutherian mammals and 24 species of birds. The results reveal extensive variation in the amount of DNA gained via lineage-specific transposition, but that DNA loss counteracted this expansion to various extents across lineages. Our analysis of the rate and size spectrum of deletion events implies that DNA removal in both mammals and birds has proceeded mostly through large segmental deletions (>10 kb). These findings support a unified "accordion" model of genome size evolution in eukaryotes whereby DNA loss counteracting TE expansion is a major determinant of genome size. Furthermore, we propose that extensive DNA loss, and not necessarily a dearth of TE activity, has been the primary force maintaining the greater genomic compaction of flying birds and bats relative to their flightless relatives.
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70
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Warren WC, Hillier LW, Tomlinson C, Minx P, Kremitzki M, Graves T, Markovic C, Bouk N, Pruitt KD, Thibaud-Nissen F, Schneider V, Mansour TA, Brown CT, Zimin A, Hawken R, Abrahamsen M, Pyrkosz AB, Morisson M, Fillon V, Vignal A, Chow W, Howe K, Fulton JE, Miller MM, Lovell P, Mello CV, Wirthlin M, Mason AS, Kuo R, Burt DW, Dodgson JB, Cheng HH. A New Chicken Genome Assembly Provides Insight into Avian Genome Structure. G3 (BETHESDA, MD.) 2017; 7:109-117. [PMID: 27852011 PMCID: PMC5217101 DOI: 10.1534/g3.116.035923] [Citation(s) in RCA: 157] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 10/27/2016] [Indexed: 12/18/2022]
Abstract
The importance of the Gallus gallus (chicken) as a model organism and agricultural animal merits a continuation of sequence assembly improvement efforts. We present a new version of the chicken genome assembly (Gallus_gallus-5.0; GCA_000002315.3), built from combined long single molecule sequencing technology, finished BACs, and improved physical maps. In overall assembled bases, we see a gain of 183 Mb, including 16.4 Mb in placed chromosomes with a corresponding gain in the percentage of intact repeat elements characterized. Of the 1.21 Gb genome, we include three previously missing autosomes, GGA30, 31, and 33, and improve sequence contig length 10-fold over the previous Gallus_gallus-4.0. Despite the significant base representation improvements made, 138 Mb of sequence is not yet located to chromosomes. When annotated for gene content, Gallus_gallus-5.0 shows an increase of 4679 annotated genes (2768 noncoding and 1911 protein-coding) over those in Gallus_gallus-4.0. We also revisited the question of what genes are missing in the avian lineage, as assessed by the highest quality avian genome assembly to date, and found that a large fraction of the original set of missing genes are still absent in sequenced bird species. Finally, our new data support a detailed map of MHC-B, encompassing two segments: one with a highly stable gene copy number and another in which the gene copy number is highly variable. The chicken model has been a critical resource for many other fields of study, and this new reference assembly will substantially further these efforts.
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Affiliation(s)
- Wesley C Warren
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108
| | - LaDeana W Hillier
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108
| | - Chad Tomlinson
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108
| | - Patrick Minx
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108
| | - Milinn Kremitzki
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108
| | - Tina Graves
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108
| | - Chris Markovic
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108
| | - Nathan Bouk
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894
| | - Kim D Pruitt
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894
| | - Francoise Thibaud-Nissen
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894
| | - Valerie Schneider
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894
| | | | | | - Aleksey Zimin
- Institute for Physical Sciences and Technology, University of Maryland, College Park, Maryland 20742
| | - Rachel Hawken
- Cobb-Vantress Inc., Siloam Springs, Arkansas 72761-1030
| | | | - Alexis B Pyrkosz
- United States Department of Agriculture-Agricultural Research Service, Avian Disease and Oncology, East Lansing, Michigan 48823
| | - Mireille Morisson
- Génétique Physiologie et Systèmes d'Elevage, Université de Toulouse, Institut National de la Recherche Agronomique, Auzeville Castanet Tolosan, France
| | - Valerie Fillon
- Génétique Physiologie et Systèmes d'Elevage, Université de Toulouse, Institut National de la Recherche Agronomique, Auzeville Castanet Tolosan, France
| | - Alain Vignal
- Génétique Physiologie et Systèmes d'Elevage, Université de Toulouse, Institut National de la Recherche Agronomique, Auzeville Castanet Tolosan, France
| | - William Chow
- Wellcome Trust Sanger Institute, Cambridgeshire CB10 1SA, United Kingdom
| | - Kerstin Howe
- Wellcome Trust Sanger Institute, Cambridgeshire CB10 1SA, United Kingdom
| | | | | | - Peter Lovell
- Department of Behavioral Neuroscience, Oregon Health and Science University, Portland, Oregon 97239-3098
| | - Claudio V Mello
- Department of Behavioral Neuroscience, Oregon Health and Science University, Portland, Oregon 97239-3098
| | - Morgan Wirthlin
- Department of Behavioral Neuroscience, Oregon Health and Science University, Portland, Oregon 97239-3098
| | - Andrew S Mason
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian EH25 9RG, United Kingdom
| | - Richard Kuo
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian EH25 9RG, United Kingdom
| | - David W Burt
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian EH25 9RG, United Kingdom
| | - Jerry B Dodgson
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan 48824
| | - Hans H Cheng
- United States Department of Agriculture-Agricultural Research Service, Avian Disease and Oncology, East Lansing, Michigan 48823
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71
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Farré M, Narayan J, Slavov GT, Damas J, Auvil L, Li C, Jarvis ED, Burt DW, Griffin DK, Larkin DM. Novel Insights into Chromosome Evolution in Birds, Archosaurs, and Reptiles. Genome Biol Evol 2016; 8:2442-51. [PMID: 27401172 PMCID: PMC5010900 DOI: 10.1093/gbe/evw166] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Homologous synteny blocks (HSBs) and evolutionary breakpoint regions (EBRs) in mammalian chromosomes are enriched for distinct DNA features, contributing to distinct phenotypes. To reveal HSB and EBR roles in avian evolution, we performed a sequence-based comparison of 21 avian and 5 outgroup species using recently sequenced genomes across the avian family tree and a newly-developed algorithm. We identified EBRs and HSBs in ancestral bird, archosaurian (bird, crocodile, and dinosaur), and reptile chromosomes. Genes involved in the regulation of gene expression and biosynthetic processes were preferably located in HSBs, including for example, avian-specific HSBs enriched for genes involved in limb development. Within birds, some lineage-specific EBRs rearranged genes were related to distinct phenotypes, such as forebrain development in parrots. Our findings provide novel evolutionary insights into genome evolution in birds, particularly on how chromosome rearrangements likely contributed to the formation of novel phenotypes.
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Affiliation(s)
- Marta Farré
- Department of Comparative Biomedical Sciences, Royal Veterinary College, Royal College Street, University of London, NW1 0TU, UK
| | - Jitendra Narayan
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, SY23 3DA, UK
| | - Gancho T Slavov
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, SY23 3DA, UK
| | - Joana Damas
- Department of Comparative Biomedical Sciences, Royal Veterinary College, Royal College Street, University of London, NW1 0TU, UK
| | - Loretta Auvil
- Illinois Informatics Institute, University of Illinois, Urbana, IL 61801, USA
| | - Cai Li
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, 1350, Denmark
| | - Erich D Jarvis
- Department of Neurobiology, Duke University Medical Center, Durham, NC, 27710, USA Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA
| | - David W Burt
- Department of Genomics and Genetics, the Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian EH25 9RG, UK
| | - Darren K Griffin
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK
| | - Denis M Larkin
- Department of Comparative Biomedical Sciences, Royal Veterinary College, Royal College Street, University of London, NW1 0TU, UK
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72
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Guizard S, Piégu B, Arensburger P, Guillou F, Bigot Y. Deep landscape update of dispersed and tandem repeats in the genome model of the red jungle fowl, Gallus gallus, using a series of de novo investigating tools. BMC Genomics 2016; 17:659. [PMID: 27542599 PMCID: PMC4992247 DOI: 10.1186/s12864-016-3015-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2016] [Accepted: 08/12/2016] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND The program RepeatMasker and the database Repbase-ISB are part of the most widely used strategy for annotating repeats in animal genomes. They have been used to show that avian genomes have a lower repeat content (8-12 %) than the sequenced genomes of many vertebrate species (30-55 %). However, the efficiency of such a library-based strategies is dependent on the quality and completeness of the sequences in the database that is used. An alternative to these library based methods are methods that identify repeats de novo. These alternative methods have existed for a least a decade and may be more powerful than the library based methods. We have used an annotation strategy involving several complementary de novo tools to determine the repeat content of the model genome galGal4 (1.04 Gbp), including identifying simple sequence repeats (SSRs), tandem repeats and transposable elements (TEs). RESULTS We annotated over one Gbp. of the galGal4 genome and showed that it is composed of approximately 19 % SSRs and TEs repeats. Furthermore, we estimate that the actual genome of the red jungle fowl contains about 31-35 % repeats. We find that library-based methods tend to overestimate TE diversity. These results have a major impact on the current understanding of repeats distributions throughout chromosomes in the red jungle fowl. CONCLUSIONS Our results are a proof of concept of the reliability of using de novo tools to annotate repeats in large animal genomes. They have also revealed issues that will need to be resolved in order to develop gold-standard methodologies for annotating repeats in eukaryote genomes.
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Affiliation(s)
- Sébastien Guizard
- Physiologie de la Reproduction et des Comportements, UMR INRA-CNRS 7247, PRC, 37380 Nouzilly, France
| | - Benoît Piégu
- Physiologie de la Reproduction et des Comportements, UMR INRA-CNRS 7247, PRC, 37380 Nouzilly, France
| | - Peter Arensburger
- Physiologie de la Reproduction et des Comportements, UMR INRA-CNRS 7247, PRC, 37380 Nouzilly, France
- Biological Sciences Department, California State Polytechnic University, Pomona, CA 91768 USA
| | - Florian Guillou
- Physiologie de la Reproduction et des Comportements, UMR INRA-CNRS 7247, PRC, 37380 Nouzilly, France
| | - Yves Bigot
- Physiologie de la Reproduction et des Comportements, UMR INRA-CNRS 7247, PRC, 37380 Nouzilly, France
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73
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Farkašová H, Hron T, Pačes J, Pajer P, Elleder D. Identification of a GC-rich leptin gene in chicken. ACTA ACUST UNITED AC 2016. [DOI: 10.1016/j.aggene.2016.04.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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74
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Cardoso JCR, Bergqvist CA, Félix RC, Larhammar D. Corticotropin-releasing hormone family evolution: five ancestral genes remain in some lineages. J Mol Endocrinol 2016; 57:73-86. [PMID: 27220618 DOI: 10.1530/jme-16-0051] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 05/24/2016] [Indexed: 12/25/2022]
Abstract
The evolution of the peptide family consisting of corticotropin-releasing hormone (CRH) and the three urocortins (UCN1-3) has been puzzling due to uneven evolutionary rates. Distinct gene duplication scenarios have been proposed in relation to the two basal rounds of vertebrate genome doubling (2R) and the teleost fish-specific genome doubling (3R). By analyses of sequences and chromosomal regions, including many neighboring gene families, we show here that the vertebrate progenitor had two peptide genes that served as the founders of separate subfamilies. Then, 2R resulted in a total of five members: one subfamily consists of CRH1, CRH2, and UCN1. The other subfamily contains UCN2 and UCN3. All five peptide genes are present in the slowly evolving genomes of the coelacanth Latimeria chalumnae (a lobe-finned fish), the spotted gar Lepisosteus oculatus (a basal ray-finned fish), and the elephant shark Callorhinchus milii (a cartilaginous fish). The CRH2 gene has been lost independently in placental mammals and in teleost fish, but is present in birds (except chicken), anole lizard, and the nonplacental mammals platypus and opossum. Teleost 3R resulted in an additional surviving duplicate only for crh1 in some teleosts including zebrafish (crh1a and crh1b). We have previously reported that the two vertebrate CRH/UCN receptors arose in 2R and that CRHR1 was duplicated in 3R. Thus, we can now conclude that this peptide-receptor system was quite complex in the ancestor of the jawed vertebrates with five CRH/UCN peptides and two receptors, and that crh and crhr1 were duplicated in the teleost fish tetraploidization.
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Affiliation(s)
- João C R Cardoso
- Comparative Endocrinology and Integrative BiologyCentre of Marine Sciences, Universidade do Algarve, Campus de Gambelas, Faro, Portugal
| | - Christina A Bergqvist
- Department of NeuroscienceScience for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Rute C Félix
- Comparative Endocrinology and Integrative BiologyCentre of Marine Sciences, Universidade do Algarve, Campus de Gambelas, Faro, Portugal
| | - Dan Larhammar
- Department of NeuroscienceScience for Life Laboratory, Uppsala University, Uppsala, Sweden
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75
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Bourgeois NMA, Van Herck SLJ, Vancamp P, Delbaere J, Zevenbergen C, Kersseboom S, Darras VM, Visser TJ. Characterization of Chicken Thyroid Hormone Transporters. Endocrinology 2016; 157:2560-74. [PMID: 27070099 DOI: 10.1210/en.2015-2025] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Thyroid hormone (TH) transmembrane transporters are key regulators of TH availability in target cells where correct TH signaling is essential for normal development. Although the chicken embryo is a valuable model for developmental studies, the only functionally characterized chicken TH transporter so far is the organic anion transporting polypeptide 1C1 (OATP1C1). We therefore cloned the chicken L-type amino acid transporter 1 (LAT1) and the monocarboxylate transporters 8 (MCT8) and 10 (MCT10), and functionally characterized them, together with OATP1C1, in JEG3, COS1, and DF-1 cells. In addition, we used in situ hybridization to study their mRNA expression pattern during development. MCT8 and OATP1C1 are both high affinity transporters for the prohormone T4, whereas receptor-active T3 is preferably transported by MCT8 and MCT10. The latter one shows lower affinity but has a high Vmax and seems to be especially good at T3 export. Also, LAT1 has a lower affinity for its preferred substrate 3,3'-diiodothyronine. Reverse T3 is transported by all 4 TH transporters and is a good export product for OATP1C1. TH transporters are strongly expressed in eye (LAT1, MCT8, MCT10), pancreas (LAT1, MCT10), kidney, and testis (MCT8). Their extensive expression in the central nervous system, especially at the brain barriers, indicates an important role in brain development. In conclusion, we show TH transport by chicken MCT8, MCT10, and LAT1. Together with OATP1C1, these transporters have functional characteristics similar to their mammalian orthologs and are interesting target genes to further elucidate the role of THs during embryonic development.
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Affiliation(s)
- Nele M A Bourgeois
- Laboratory of Comparative Endocrinology (N.M.A.B., S.L.J.V.H., P.V., J.D., V.M.D.), Department of Biology, Katholieke Universiteit Leuven, 3000 Leuven, Belgium; and Department of Internal Medicine (C.Z., S.K., T.J.V.), Erasmus University Medical Center, 3015 GE Rotterdam, The Netherlands
| | - Stijn L J Van Herck
- Laboratory of Comparative Endocrinology (N.M.A.B., S.L.J.V.H., P.V., J.D., V.M.D.), Department of Biology, Katholieke Universiteit Leuven, 3000 Leuven, Belgium; and Department of Internal Medicine (C.Z., S.K., T.J.V.), Erasmus University Medical Center, 3015 GE Rotterdam, The Netherlands
| | - Pieter Vancamp
- Laboratory of Comparative Endocrinology (N.M.A.B., S.L.J.V.H., P.V., J.D., V.M.D.), Department of Biology, Katholieke Universiteit Leuven, 3000 Leuven, Belgium; and Department of Internal Medicine (C.Z., S.K., T.J.V.), Erasmus University Medical Center, 3015 GE Rotterdam, The Netherlands
| | - Joke Delbaere
- Laboratory of Comparative Endocrinology (N.M.A.B., S.L.J.V.H., P.V., J.D., V.M.D.), Department of Biology, Katholieke Universiteit Leuven, 3000 Leuven, Belgium; and Department of Internal Medicine (C.Z., S.K., T.J.V.), Erasmus University Medical Center, 3015 GE Rotterdam, The Netherlands
| | - Chantal Zevenbergen
- Laboratory of Comparative Endocrinology (N.M.A.B., S.L.J.V.H., P.V., J.D., V.M.D.), Department of Biology, Katholieke Universiteit Leuven, 3000 Leuven, Belgium; and Department of Internal Medicine (C.Z., S.K., T.J.V.), Erasmus University Medical Center, 3015 GE Rotterdam, The Netherlands
| | - Simone Kersseboom
- Laboratory of Comparative Endocrinology (N.M.A.B., S.L.J.V.H., P.V., J.D., V.M.D.), Department of Biology, Katholieke Universiteit Leuven, 3000 Leuven, Belgium; and Department of Internal Medicine (C.Z., S.K., T.J.V.), Erasmus University Medical Center, 3015 GE Rotterdam, The Netherlands
| | - Veerle M Darras
- Laboratory of Comparative Endocrinology (N.M.A.B., S.L.J.V.H., P.V., J.D., V.M.D.), Department of Biology, Katholieke Universiteit Leuven, 3000 Leuven, Belgium; and Department of Internal Medicine (C.Z., S.K., T.J.V.), Erasmus University Medical Center, 3015 GE Rotterdam, The Netherlands
| | - Theo J Visser
- Laboratory of Comparative Endocrinology (N.M.A.B., S.L.J.V.H., P.V., J.D., V.M.D.), Department of Biology, Katholieke Universiteit Leuven, 3000 Leuven, Belgium; and Department of Internal Medicine (C.Z., S.K., T.J.V.), Erasmus University Medical Center, 3015 GE Rotterdam, The Netherlands
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76
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Abstract
The recent availability of multiple avian genomes has laid the foundation for a huge variety of comparative genomics analyses including scans for changes and signatures of selection that arose from adaptions to new ecological niches. Nocturnal adaptation in birds, unlike in mammals, is comparatively recent, a fact that makes birds good candidates for identifying early genetic changes that support adaptation to dim-light environments. In this review, we give examples of comparative genomics analyses that could shed light on mechanisms of adaptation to nocturnality. We present advantages and disadvantages of both "data-driven" and "hypothesis-driven" approaches that lead to the discovery of candidate genes and genetic changes promoting nocturnality. We anticipate that the accessibility of multiple genomes from the Genome 10K Project will allow a better understanding of evolutionary mechanisms and adaptation in general.
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Affiliation(s)
- Diana Le Duc
- Medical Faculty, Rudolf Schönheimer Institute of Biochemistry, University of Leipzig, Leipzig, Germany.,Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Torsten Schöneberg
- Medical Faculty, Rudolf Schönheimer Institute of Biochemistry, University of Leipzig, Leipzig, Germany
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77
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Contraction of the type I IFN locus and unusual constitutive expression of IFN-α in bats. Proc Natl Acad Sci U S A 2016; 113:2696-701. [PMID: 26903655 DOI: 10.1073/pnas.1518240113] [Citation(s) in RCA: 210] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Bats harbor many emerging and reemerging viruses, several of which are highly pathogenic in other mammals but cause no clinical signs of disease in bats. To determine the role of interferons (IFNs) in the ability of bats to coexist with viruses, we sequenced the type I IFN locus of the Australian black flying fox, Pteropus alecto, providing what is, to our knowledge, the first gene map of the IFN region of any bat species. Our results reveal a highly contracted type I IFN family consisting of only 10 IFNs, including three functional IFN-α loci. Furthermore, the three IFN-α genes are constitutively expressed in unstimulated bat tissues and cells and their expression is unaffected by viral infection. Constitutively expressed IFN-α results in the induction of a subset of IFN-stimulated genes associated with antiviral activity and resistance to DNA damage, providing evidence for a unique IFN system that may be linked to the ability of bats to coexist with viruses.
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78
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Seroussi E, Cinnamon Y, Yosefi S, Genin O, Smith JG, Rafati N, Bornelöv S, Andersson L, Friedman-Einat M. Identification of the Long-Sought Leptin in Chicken and Duck: Expression Pattern of the Highly GC-Rich Avian leptin Fits an Autocrine/Paracrine Rather Than Endocrine Function. Endocrinology 2016; 157:737-51. [PMID: 26587783 DOI: 10.1210/en.2015-1634] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
More than 20 years after characterization of the key regulator of mammalian energy balance, leptin, we identified the leptin (LEP) genes of chicken (Gallus gallus) and duck (Anas platyrhynchos). The extreme guanine-cytosine content (∼70%), the location in a genomic region with low-complexity repetitive and palindromic sequence elements, the relatively low sequence conservation, and low level of expression have hampered the identification of these genes until now. In vitro-expressed chicken and duck leptins specifically activated signaling through the chicken leptin receptor in cell culture. In situ hybridization demonstrated expression of LEP mRNA in granular and Purkinje cells of the cerebellum, anterior pituitary, and in embryonic limb buds, somites, and branchial arches, suggesting roles in adult brain control of energy balance and during embryonic development. The expression patterns of LEP and the leptin receptor (LEPR) were explored in chicken, duck, and quail (Coturnix japonica) using RNA-sequencing experiments available in the Short Read Archive and by quantitative RT-PCR. In adipose tissue, LEP and LEPR were scarcely transcribed, and the expression level was not correlated to adiposity. Our identification of the leptin genes in chicken and duck genomes resolves a long lasting controversy regarding the existence of leptin genes in these species. This identification was confirmed by sequence and structural similarity, conserved exon-intron boundaries, detection in numerous genomic, and transcriptomic datasets and characterization by PCR, quantitative RT-PCR, in situ hybridization, and bioassays. Our results point to an autocrine/paracrine mode of action for bird leptin instead of being a circulating hormone as in mammals.
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Affiliation(s)
- Eyal Seroussi
- Agricultural Research Organization (E.S., Y.C., S.Y., O.G., J.G.-S., M.F.-E.), Volcani Center, 50250 Bet-Dagan, Israel; Department of Medical Biochemistry and Microbiology (N.R., S.B., L.A.), Uppsala University, SE-75123 Uppsala, Sweden; Department of Animal Breeding and Genetics (L.A.), Swedish University of Agricultural Sciences, SE-75007 Uppsala, Sweden; and Department of Veterinary Integrative Biosciences (L.A.), College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas 77843-4458
| | - Yuval Cinnamon
- Agricultural Research Organization (E.S., Y.C., S.Y., O.G., J.G.-S., M.F.-E.), Volcani Center, 50250 Bet-Dagan, Israel; Department of Medical Biochemistry and Microbiology (N.R., S.B., L.A.), Uppsala University, SE-75123 Uppsala, Sweden; Department of Animal Breeding and Genetics (L.A.), Swedish University of Agricultural Sciences, SE-75007 Uppsala, Sweden; and Department of Veterinary Integrative Biosciences (L.A.), College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas 77843-4458
| | - Sara Yosefi
- Agricultural Research Organization (E.S., Y.C., S.Y., O.G., J.G.-S., M.F.-E.), Volcani Center, 50250 Bet-Dagan, Israel; Department of Medical Biochemistry and Microbiology (N.R., S.B., L.A.), Uppsala University, SE-75123 Uppsala, Sweden; Department of Animal Breeding and Genetics (L.A.), Swedish University of Agricultural Sciences, SE-75007 Uppsala, Sweden; and Department of Veterinary Integrative Biosciences (L.A.), College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas 77843-4458
| | - Olga Genin
- Agricultural Research Organization (E.S., Y.C., S.Y., O.G., J.G.-S., M.F.-E.), Volcani Center, 50250 Bet-Dagan, Israel; Department of Medical Biochemistry and Microbiology (N.R., S.B., L.A.), Uppsala University, SE-75123 Uppsala, Sweden; Department of Animal Breeding and Genetics (L.A.), Swedish University of Agricultural Sciences, SE-75007 Uppsala, Sweden; and Department of Veterinary Integrative Biosciences (L.A.), College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas 77843-4458
| | - Julia Gage Smith
- Agricultural Research Organization (E.S., Y.C., S.Y., O.G., J.G.-S., M.F.-E.), Volcani Center, 50250 Bet-Dagan, Israel; Department of Medical Biochemistry and Microbiology (N.R., S.B., L.A.), Uppsala University, SE-75123 Uppsala, Sweden; Department of Animal Breeding and Genetics (L.A.), Swedish University of Agricultural Sciences, SE-75007 Uppsala, Sweden; and Department of Veterinary Integrative Biosciences (L.A.), College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas 77843-4458
| | - Nima Rafati
- Agricultural Research Organization (E.S., Y.C., S.Y., O.G., J.G.-S., M.F.-E.), Volcani Center, 50250 Bet-Dagan, Israel; Department of Medical Biochemistry and Microbiology (N.R., S.B., L.A.), Uppsala University, SE-75123 Uppsala, Sweden; Department of Animal Breeding and Genetics (L.A.), Swedish University of Agricultural Sciences, SE-75007 Uppsala, Sweden; and Department of Veterinary Integrative Biosciences (L.A.), College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas 77843-4458
| | - Susanne Bornelöv
- Agricultural Research Organization (E.S., Y.C., S.Y., O.G., J.G.-S., M.F.-E.), Volcani Center, 50250 Bet-Dagan, Israel; Department of Medical Biochemistry and Microbiology (N.R., S.B., L.A.), Uppsala University, SE-75123 Uppsala, Sweden; Department of Animal Breeding and Genetics (L.A.), Swedish University of Agricultural Sciences, SE-75007 Uppsala, Sweden; and Department of Veterinary Integrative Biosciences (L.A.), College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas 77843-4458
| | - Leif Andersson
- Agricultural Research Organization (E.S., Y.C., S.Y., O.G., J.G.-S., M.F.-E.), Volcani Center, 50250 Bet-Dagan, Israel; Department of Medical Biochemistry and Microbiology (N.R., S.B., L.A.), Uppsala University, SE-75123 Uppsala, Sweden; Department of Animal Breeding and Genetics (L.A.), Swedish University of Agricultural Sciences, SE-75007 Uppsala, Sweden; and Department of Veterinary Integrative Biosciences (L.A.), College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas 77843-4458
| | - Miriam Friedman-Einat
- Agricultural Research Organization (E.S., Y.C., S.Y., O.G., J.G.-S., M.F.-E.), Volcani Center, 50250 Bet-Dagan, Israel; Department of Medical Biochemistry and Microbiology (N.R., S.B., L.A.), Uppsala University, SE-75123 Uppsala, Sweden; Department of Animal Breeding and Genetics (L.A.), Swedish University of Agricultural Sciences, SE-75007 Uppsala, Sweden; and Department of Veterinary Integrative Biosciences (L.A.), College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas 77843-4458
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79
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Kuraku S, Feiner N, Keeley SD, Hara Y. Incorporating tree-thinking and evolutionary time scale into developmental biology. Dev Growth Differ 2016; 58:131-42. [PMID: 26818824 DOI: 10.1111/dgd.12258] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Revised: 11/04/2015] [Accepted: 11/04/2015] [Indexed: 01/11/2023]
Abstract
Phylogenetic approaches are indispensable in any comparative molecular study involving multiple species. These approaches are in increasing demand as the amount and availability of DNA sequence information continues to increase exponentially, even for organisms that were previously not extensively studied. Without the sound application of phylogenetic concepts and knowledge, one can be misled when attempting to infer ancestral character states as well as the timing and order of evolutionary events, both of which are frequently exerted in evolutionary developmental biology. The ignorance of phylogenetic approaches can also impact non-evolutionary studies and cause misidentification of the target gene or protein to be examined in functional characterization. This review aims to promote tree-thinking in evolutionary conjecture and stress the importance of a sense of time scale in cross-species comparisons, in order to enhance the understanding of phylogenetics in all biological fields including developmental biology. To this end, molecular phylogenies of several developmental regulatory genes, including those denoted as "cryptic pan-vertebrate genes", are introduced as examples.
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Affiliation(s)
- Shigehiro Kuraku
- Phyloinformatics Unit, RIKEN Center for Life Science Technologies, 2-2-3 Minatojima-minami, Chuo-ku, Kobe, 650-0047, Japan
| | | | - Sean D Keeley
- Phyloinformatics Unit, RIKEN Center for Life Science Technologies, 2-2-3 Minatojima-minami, Chuo-ku, Kobe, 650-0047, Japan
| | - Yuichiro Hara
- Phyloinformatics Unit, RIKEN Center for Life Science Technologies, 2-2-3 Minatojima-minami, Chuo-ku, Kobe, 650-0047, Japan
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80
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Rapid genome reshaping by multiple-gene loss after whole-genome duplication in teleost fish suggested by mathematical modeling. Proc Natl Acad Sci U S A 2015; 112:14918-23. [PMID: 26578810 DOI: 10.1073/pnas.1507669112] [Citation(s) in RCA: 107] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Whole-genome duplication (WGD) is believed to be a significant source of major evolutionary innovation. Redundant genes resulting from WGD are thought to be lost or acquire new functions. However, the rates of gene loss and thus temporal process of genome reshaping after WGD remain unclear. The WGD shared by all teleost fish, one-half of all jawed vertebrates, was more recent than the two ancient WGDs that occurred before the origin of jawed vertebrates, and thus lends itself to analysis of gene loss and genome reshaping. Using a newly developed orthology identification pipeline, we inferred the post-teleost-specific WGD evolutionary histories of 6,892 protein-coding genes from nine phylogenetically representative teleost genomes on a time-calibrated tree. We found that rapid gene loss did occur in the first 60 My, with a loss of more than 70-80% of duplicated genes, and produced similar genomic gene arrangements within teleosts in that relatively short time. Mathematical modeling suggests that rapid gene loss occurred mainly by events involving simultaneous loss of multiple genes. We found that the subsequent 250 My were characterized by slow and steady loss of individual genes. Our pipeline also identified about 1,100 shared single-copy genes that are inferred to have become singletons before the divergence of clupeocephalan teleosts. Therefore, our comparative genome analysis suggests that rapid gene loss just after the WGD reshaped teleost genomes before the major divergence, and provides a useful set of marker genes for future phylogenetic analysis.
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81
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Lopes-Marques M, Delgado ILS, Ruivo R, Torres Y, Sainath SB, Rocha E, Cunha I, Santos MM, Castro LFC. The Origin and Diversity of Cpt1 Genes in Vertebrate Species. PLoS One 2015; 10:e0138447. [PMID: 26421611 PMCID: PMC4589379 DOI: 10.1371/journal.pone.0138447] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Accepted: 08/31/2015] [Indexed: 01/09/2023] Open
Abstract
The Carnitine palmitoyltransferase I (Cpt1) gene family plays a crucial role in energy homeostasis since it is required for the occurrence of fatty acid β-oxidation in the mitochondria. The exact gene repertoire in different vertebrate lineages is variable. Presently, four genes are documented: Cpt1a, also known as Cpt1a1, Cpt1a2; Cpt1b and Cpt1c. The later is considered a mammalian innovation resulting from a gene duplication event in the ancestor of mammals, after the divergence of sauropsids. In contrast, Cpt1a2 has been found exclusively in teleosts. Here, we reassess the overall evolutionary relationships of Cpt1 genes using a combination of approaches, including the survey of the gene repertoire in basal gnathostome lineages. Through molecular phylogenetics and synteny studies, we find that Cpt1c is most likely a rapidly evolving orthologue of Cpt1a2. Thus, Cpt1c is present in other lineages such as cartilaginous fish, reptiles, amphibians and the coelacanth. We show that genome duplications (2R) and variable rates of sequence evolution contribute to the history of Cpt1 genes in vertebrates. Finally, we propose that loss of Cpt1b is the likely cause for the unusual energy metabolism of elasmobranch.
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Affiliation(s)
- Mónica Lopes-Marques
- CIIMAR, Interdisciplinary Centre of Marine and Environmental Research, CIMAR Associate Laboratory, UPorto–University of Porto, Porto, Portugal
- ICBAS, Abel Salazar Biomedical Sciences Institute, University of Porto, Porto, Portugal
| | - Inês L. S. Delgado
- CIIMAR, Interdisciplinary Centre of Marine and Environmental Research, CIMAR Associate Laboratory, UPorto–University of Porto, Porto, Portugal
| | - Raquel Ruivo
- CIIMAR, Interdisciplinary Centre of Marine and Environmental Research, CIMAR Associate Laboratory, UPorto–University of Porto, Porto, Portugal
| | - Yan Torres
- CIIMAR, Interdisciplinary Centre of Marine and Environmental Research, CIMAR Associate Laboratory, UPorto–University of Porto, Porto, Portugal
- ICBAS, Abel Salazar Biomedical Sciences Institute, University of Porto, Porto, Portugal
| | - Sri Bhashyam Sainath
- CIIMAR, Interdisciplinary Centre of Marine and Environmental Research, CIMAR Associate Laboratory, UPorto–University of Porto, Porto, Portugal
| | - Eduardo Rocha
- CIIMAR, Interdisciplinary Centre of Marine and Environmental Research, CIMAR Associate Laboratory, UPorto–University of Porto, Porto, Portugal
- ICBAS, Abel Salazar Biomedical Sciences Institute, University of Porto, Porto, Portugal
| | - Isabel Cunha
- CIIMAR, Interdisciplinary Centre of Marine and Environmental Research, CIMAR Associate Laboratory, UPorto–University of Porto, Porto, Portugal
| | - Miguel M. Santos
- CIIMAR, Interdisciplinary Centre of Marine and Environmental Research, CIMAR Associate Laboratory, UPorto–University of Porto, Porto, Portugal
- Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
| | - L. Filipe C. Castro
- CIIMAR, Interdisciplinary Centre of Marine and Environmental Research, CIMAR Associate Laboratory, UPorto–University of Porto, Porto, Portugal
- Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
- * E-mail:
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82
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Early Vertebrate Evolution of the Host Restriction Factor Tetherin. J Virol 2015; 89:12154-65. [PMID: 26401043 DOI: 10.1128/jvi.02149-15] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Accepted: 09/17/2015] [Indexed: 01/07/2023] Open
Abstract
UNLABELLED Tetherin is an interferon-inducible restriction factor targeting a broad range of enveloped viruses. Its antiviral activity depends on an unusual topology comprising an N-terminal transmembrane domain (TMD) followed by an extracellular coiled-coil region and a C-terminal glycosylphosphatidylinositol (GPI) anchor. One of the two membrane anchors is inserted into assembling virions, while the other remains in the plasma membrane of the infected cell. Thus, tetherin entraps budding viruses by physically bridging viral and cellular membranes. Although tetherin restricts the release of a large variety of diverse human and animal viruses, only mammalian orthologs have been described to date. Here, we examined the evolutionary origin of this protein and demonstrate that tetherin orthologs are also found in fish, reptiles, and birds. Notably, alligator tetherin efficiently blocks the release of retroviral particles. Thus, tetherin emerged early during vertebrate evolution and acquired its antiviral activity before the mammal/reptile divergence. Although there is only limited sequence homology, all orthologs share the typical topology. Two unrelated proteins of the slime mold Dictyostelium discoideum also adopt a tetherin-like configuration with an N-terminal TMD and a C-terminal GPI anchor. However, these proteins showed no evidence for convergent evolution and failed to inhibit virion release. In summary, our findings demonstrate that tetherin emerged at least 450 million years ago and is more widespread than previously anticipated. The early evolution of antiviral activity together with the high topology conservation but low sequence homology suggests that restriction of virus release is the primary function of tetherin. IMPORTANCE The continuous arms race with viruses has driven the evolution of a variety of cell-intrinsic immunity factors that inhibit different steps of the viral replication cycle. One of these restriction factors, tetherin, inhibits the release of newly formed progeny virions from infected cells. Although tetherin targets a broad range of enveloped viruses, including retro-, filo-, herpes-, and arenaviruses, the evolutionary origin of this restriction factor and its antiviral activity remained obscure. Here, we examined diverse vertebrate genomes for genes encoding cellular proteins that share with tetherin the highly unusual combination of an N-terminal transmembrane domain and a C-terminal glycosylphosphatidylinositol anchor. We show that tetherin orthologs are found in fish, reptiles, and birds and demonstrate that alligator tetherin efficiently inhibits the release of retroviral particles. Our findings identify tetherin as an evolutionarily ancient restriction factor and provide new important insights into the continuous arms race between viruses and their hosts.
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83
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Living without DAT: Loss and compensation of the dopamine transporter gene in sauropsids (birds and reptiles). Sci Rep 2015; 5:14093. [PMID: 26364979 PMCID: PMC4894405 DOI: 10.1038/srep14093] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Accepted: 08/18/2015] [Indexed: 11/17/2022] Open
Abstract
The dopamine transporter (DAT) is a major regulator of synaptic dopamine (DA) availability. It plays key roles in motor control and motor learning, memory formation, and reward-seeking behavior, is a major target of cocaine and methamphetamines, and has been assumed to be conserved among vertebrates. We have found, however, that birds, crocodiles, and lizards lack the DAT gene. We also found that the unprecedented loss of this important gene is compensated for by the expression of the noradrenaline transporter (NAT) gene, and not the serotonin transporter genes, in dopaminergic cells, which explains the peculiar pharmacology of the DA reuptake activity previously noted in bird striatum. This unexpected pattern contrasts with that of ancestral vertebrates (e.g. fish) and mammals, where the NAT gene is selectively expressed in noradrenergic cells. DA circuits in birds/reptiles and mammals thus operate with an analogous reuptake mechanism exerted by different genes, bringing new insights into gene expression regulation in dopaminergic cells and the evolution of a key molecular player in reward and addiction pathways.
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84
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Abstract
Hron et al. provide transcriptome evidence that three (1.1 %) of the 274 genes reported by Lovell et al. as missing in birds may actually be 'hidden' as a result of high GC content. Although this factor may explain some gene absences from genomic assemblies, we believe it is insufficient to account for the extensive syntenic losses described in Lovell et al. Please see related article: www.dx.doi.org/10.1186/s13059-015-0724-z.
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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
| | - 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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85
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Abstract
We report that a subset of avian genes is characterized by very high GC content and long G/C stretches. These sequence characteristics correlate with the frequent absence of these genes from genomic databases. We provide several examples where genes in this subset are mistakenly reported as missing in birds. www.dx.doi.org/10.1186/s13059-015-0725-y
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Affiliation(s)
- Tomáš Hron
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Vídeňská 1083, 14220, Prague, Czech Republic.
| | - Petr Pajer
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Vídeňská 1083, 14220, Prague, Czech Republic.
| | - Jan Pačes
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Vídeňská 1083, 14220, Prague, Czech Republic.
| | - Petr Bartůněk
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Vídeňská 1083, 14220, Prague, Czech Republic.
| | - Daniel Elleder
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Vídeňská 1083, 14220, Prague, Czech Republic.
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86
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Lautwein T, Lerch S, Schäfer D, Schmidt ER. The serine/threonine kinase 33 is present and expressed in palaeognath birds but has become a unitary pseudogene in neognaths about 100 million years ago. BMC Genomics 2015. [PMID: 26199010 PMCID: PMC4509753 DOI: 10.1186/s12864-015-1769-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Background Serine/threonine kinase 33 (STK33) has been shown to be conserved across all major vertebrate classes including reptiles, mammals, amphibians and fish, suggesting its importance within vertebrates. It has been shown to phosphorylate vimentin and might play a role in spermatogenesis and organ ontogenesis. In this study we analyzed the genomic locus and expression of stk33 in the class Aves, using a combination of large scale next generation sequencing data analysis and traditional PCR. Results Within the subclass Palaeognathae we analyzed the white-throated tinamou (Tinamus guttatus), the African ostrich (Struthio camelus) and the emu (Dromaius novaehollandiae). For the African ostrich we were able to generate a 62,778 bp long genomic contig and an mRNA sequence that encodes a protein showing highly significant similarity to STK33 proteins from other vertebrates. The emu has been shown to encode and transcribe a functional STK33 as well. For the white-throated tinamou we were able to identify 13 exons by sequence comparison encoding a protein similar to STK33 as well. In contrast, in all 28 neognath birds analyzed, we could not find evidence for the existence of a functional copy of stk33 or its expression. In the genomes of these 28 bird species, we found only remnants of the stk33 locus carrying several large genomic deletions, leading to the loss of multiple exons. The remaining exons have acquired various indels and premature stop codons. Conclusions We were able to elucidate and describe the genomic structure and the transcription of a functional stk33 gene within the subclass Palaeognathae, but we could only find degenerate remnants of stk33 in all neognath birds analyzed. This led us to the conclusion that stk33 became a unitary pseudogene in the evolutionary history of the class Aves at the paleognath-neognath branch point during the late cretaceous period about 100 million years ago. We hypothesize that the pseudogenization of stk33 might have become fixed in neognaths due to either genetic redundancy or a non-orthologous gene displacement and present potential candidate genes for such an incident. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1769-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Tobias Lautwein
- Institute for Molecular Genetics, Johannes Gutenberg University Mainz, Johann-Joachim-Becherweg 32, 55128, Mainz, Germany.
| | - Steffen Lerch
- Institute for Molecular Genetics, Johannes Gutenberg University Mainz, Johann-Joachim-Becherweg 32, 55128, Mainz, Germany. .,Departement of Neurology, University Medical Center, Johannes Gutenberg-University Mainz, Langenbeckstr.1, 55131, Mainz, Germany.
| | - Daniel Schäfer
- Institute for Molecular Genetics, Johannes Gutenberg University Mainz, Johann-Joachim-Becherweg 32, 55128, Mainz, Germany. .,Departement of Pediatric Oncology, Hematology and Clinical Immunology, University Children's Hospital, Medical Faculty, Heinrich Heine University, Moorenstr. 5, 40225, Düsseldorf, Germany.
| | - Erwin R Schmidt
- Institute for Molecular Genetics, Johannes Gutenberg University Mainz, Johann-Joachim-Becherweg 32, 55128, Mainz, Germany.
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87
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Schmid M, Smith J, Burt DW, Aken BL, Antin PB, Archibald AL, Ashwell C, Blackshear PJ, Boschiero C, Brown CT, Burgess SC, Cheng HH, Chow W, Coble DJ, Cooksey A, Crooijmans RPMA, Damas J, Davis RVN, de Koning DJ, Delany ME, Derrien T, Desta TT, Dunn IC, Dunn M, Ellegren H, Eöry L, Erb I, Farré M, Fasold M, Fleming D, Flicek P, Fowler KE, Frésard L, Froman DP, Garceau V, Gardner PP, Gheyas AA, Griffin DK, Groenen MAM, Haaf T, Hanotte O, Hart A, Häsler J, Hedges SB, Hertel J, Howe K, Hubbard A, Hume DA, Kaiser P, Kedra D, Kemp SJ, Klopp C, Kniel KE, Kuo R, Lagarrigue S, Lamont SJ, Larkin DM, Lawal RA, Markland SM, McCarthy F, McCormack HA, McPherson MC, Motegi A, Muljo SA, Münsterberg A, Nag R, Nanda I, Neuberger M, Nitsche A, Notredame C, Noyes H, O'Connor R, O'Hare EA, Oler AJ, Ommeh SC, Pais H, Persia M, Pitel F, Preeyanon L, Prieto Barja P, Pritchett EM, Rhoads DD, Robinson CM, Romanov MN, Rothschild M, Roux PF, Schmidt CJ, Schneider AS, Schwartz MG, Searle SM, Skinner MA, Smith CA, Stadler PF, Steeves TE, Steinlein C, Sun L, Takata M, Ulitsky I, Wang Q, Wang Y, Warren WC, Wood JMD, Wragg D, Zhou H. Third Report on Chicken Genes and Chromosomes 2015. Cytogenet Genome Res 2015; 145:78-179. [PMID: 26282327 PMCID: PMC5120589 DOI: 10.1159/000430927] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Affiliation(s)
- Michael Schmid
- Department of Human Genetics, University of Würzburg, Würzburg, Germany
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