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Kuhl H, Euclide PT, Klopp C, Cabau C, Zahm M, Roques C, Iampietro C, Kuchly C, Donnadieu C, Feron R, Parrinello H, Poncet C, Jaffrelo L, Confolent C, Wen M, Herpin A, Jouanno E, Bestin A, Haffray P, Morvezen R, de Almeida TR, Lecocq T, Schaerlinger B, Chardard D, Żarski D, Larson W, Postlethwait JH, Timirkhanov S, Kloas W, Wuertz S, Stöck M, Guiguen Y. Multi-genome comparisons reveal gain-and-loss evolution of the anti-Mullerian hormone receptor type 2 gene, an old master sex determining gene, in Percidae. bioRxiv 2023:2023.11.13.566804. [PMID: 38014084 PMCID: PMC10680665 DOI: 10.1101/2023.11.13.566804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
The Percidae family comprises many fish species of major importance for aquaculture and fisheries. Based on three new chromosome-scale assemblies in Perca fluviatilis , Perca schrenkii and Sander vitreus along with additional percid fish reference genomes, we provide an evolutionary and comparative genomic analysis of their sex-determination systems. We explored the fate of a duplicated anti-Mullerian hormone receptor type-2 gene ( amhr2bY ), previously suggested to be the master sex determining (MSD) gene in P. flavescens . Phylogenetically related and structurally similar a mhr2 duplications ( amhr2b ) were found in P. schrenkii and Sander lucioperca , potentially dating this duplication event to their last common ancestor around 19-27 Mya. In P. fluviatilis and S. vitreus , this amhr2b duplicate has been lost while it was subject to amplification in S. lucioperca . Analyses of the amhr2b locus in P. schrenkii suggest that this duplication could be also male-specific as it is in P. flavescens . In P. fluviatilis , a relatively small (100 kb) non-recombinant sex-determining region (SDR) was characterized on chromosome-18 using population-genomics approaches. This SDR is characterized by many male-specific single-nucleotide variants (SNVs) and no large duplication/insertion event, suggesting that P. fluviatilis has a male heterogametic sex determination system (XX/XY), generated by allelic diversification. This SDR contains six annotated genes, including three ( c18h1orf198 , hsdl1 , tbc1d32 ) with higher expression in testis than ovary. Together, our results provide a new example of the highly dynamic sex chromosome turnover in teleosts and provide new genomic resources for Percidae, including sex-genotyping tools for all three known Perca species.
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Li L, He S, Lin MH, Zhang YP, Kuhl H, Liang XF. Whole-genome resequencing and bisulfite sequencing provide new insights into the feeding habit domestication in mandarin fish ( Siniperca chuatsi). Front Genet 2023; 13:1088081. [PMID: 36712873 PMCID: PMC9878154 DOI: 10.3389/fgene.2022.1088081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 12/28/2022] [Indexed: 01/14/2023] Open
Abstract
Mandarin fish (Siniperca chuatsi) is one of the most economically important fish in China. However, it has the peculiar feeding habit that it feeds solely on live prey fish since first-feeding, while refuses dead prey fish or artificial diets. After the specific training procedure, partial individuals could accept dead prey fish and artificial diets. The genetic basis of individual difference in artificial diet feeding habit is still unknown. In the present study, the resequencing was performed between 10 individuals which could be domesticated to accept artificial diets and 10 individuals which could not. Through the selective sweep analysis based on heterozygosity (Hp) and population differentiation coefficient (Fst), 57 candidate windows were identified as the putative selected regions for feeding habit domestication of mandarin fish, involved in 149 genes. These genes were related to memory, vision and olfaction function, which could be potential targets of molecular marker assistant breeding of artificial diet feeding trait. Beside of the DNA sequence, we also explored the potential role of DNA methylation in feeding habit domestication in mandarin fish. Whole-genome bisulfite sequencing was performed between the individuals which could be domesticated to accept artificial diets and those could not. 5,976 differentially methylated regions were identified, referring to 3,522 genes, such as the genes involved in cAMP signaling pathway. The DNA methylation changes of these genes might contribute to the adaption of artificial diets in mandarin fish. In conclusion, the putative selected regions and the differentially methylated regions were identified in the whole genome, providing new insights into the feeding habit domestication from live prey fish to artificial diets in mandarin fish. And the involved genes were identified as the candidate genes for molecular breeding of artificial diet utilization in mandarin fish.
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Affiliation(s)
- Ling Li
- Chinese Perch Research Center, College of Fisheries, Huazhong Agricultural University, Wuhan, China,Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan, China
| | - Shan He
- Chinese Perch Research Center, College of Fisheries, Huazhong Agricultural University, Wuhan, China,Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan, China
| | - Ming-Hui Lin
- Chinese Perch Research Center, College of Fisheries, Huazhong Agricultural University, Wuhan, China,Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan, China
| | - Yan-Peng Zhang
- Chinese Perch Research Center, College of Fisheries, Huazhong Agricultural University, Wuhan, China,Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan, China
| | - Heiner Kuhl
- Department of Ecophysiology and Aquaculture, Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany,*Correspondence: Xu-Fang Liang, ; Heiner Kuhl,
| | - Xu-Fang Liang
- Chinese Perch Research Center, College of Fisheries, Huazhong Agricultural University, Wuhan, China,Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan, China,*Correspondence: Xu-Fang Liang, ; Heiner Kuhl,
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Stöck M, Kratochvíl L, Kuhl H, Rovatsos M, Evans BJ, Suh A, Valenzuela N, Veyrunes F, Zhou Q, Gamble T, Capel B, Schartl M, Guiguen Y. A brief review of vertebrate sex evolution with a pledge for integrative research: towards ' sexomics'. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200426. [PMID: 34247497 PMCID: PMC8293304 DOI: 10.1098/rstb.2020.0426] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/08/2021] [Indexed: 02/07/2023] Open
Abstract
Triggers and biological processes controlling male or female gonadal differentiation vary in vertebrates, with sex determination (SD) governed by environmental factors or simple to complex genetic mechanisms that evolved repeatedly and independently in various groups. Here, we review sex evolution across major clades of vertebrates with information on SD, sexual development and reproductive modes. We offer an up-to-date review of divergence times, species diversity, genomic resources, genome size, occurrence and nature of polyploids, SD systems, sex chromosomes, SD genes, dosage compensation and sex-biased gene expression. Advances in sequencing technologies now enable us to study the evolution of SD at broader evolutionary scales, and we now hope to pursue a sexomics integrative research initiative across vertebrates. The vertebrate sexome comprises interdisciplinary and integrated information on sexual differentiation, development and reproduction at all biological levels, from genomes, transcriptomes and proteomes, to the organs involved in sexual and sex-specific processes, including gonads, secondary sex organs and those with transcriptional sex-bias. The sexome also includes ontogenetic and behavioural aspects of sexual differentiation, including malfunction and impairment of SD, sexual differentiation and fertility. Starting from data generated by high-throughput approaches, we encourage others to contribute expertise to building understanding of the sexomes of many key vertebrate species. This article is part of the theme issue 'Challenging the paradigm in sex chromosome evolution: empirical and theoretical insights with a focus on vertebrates (Part I)'.
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Affiliation(s)
- Matthias Stöck
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries—IGB (Forschungsverbund Berlin), Müggelseedamm 301, 12587 Berlin, Germany
- Amphibian Research Center, Hiroshima University, Higashi-Hiroshima 739-8526, Japan
| | - Lukáš Kratochvíl
- Department of Ecology, Faculty of Science, Charles University, Viničná 7, 12844 Prague, Czech Republic
| | - Heiner Kuhl
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries—IGB (Forschungsverbund Berlin), Müggelseedamm 301, 12587 Berlin, Germany
| | - Michail Rovatsos
- Amphibian Research Center, Hiroshima University, Higashi-Hiroshima 739-8526, Japan
| | - Ben J. Evans
- Department of Biology, McMaster University, Life Sciences Building Room 328, 1280 Main Street West, Hamilton, Ontario, Canada L8S 4K1
| | - Alexander Suh
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TU, UK
- Department of Organismal Biology—Systematic Biology, Evolutionary Biology Centre, Science for Life Laboratory, Uppsala University, Norbyvägen 18D, 75236 Uppsala, Sweden
| | - Nicole Valenzuela
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
| | - Frédéric Veyrunes
- Institut des Sciences de l'Evolution de Montpellier, ISEM UMR 5554 (CNRS/Université de Montpellier/IRD/EPHE), Montpellier, France
| | - Qi Zhou
- MOE Laboratory of Biosystems Homeostasis and Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, People's Republic of China
- Department of Neuroscience and Developmental Biology, University of Vienna, A-1090 Vienna, Austria
| | - Tony Gamble
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53201, USA
| | - Blanche Capel
- Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA
| | - Manfred Schartl
- Developmental Biochemistry, Biocenter, University of Würzburg, 97074 Würzburg, Germany
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX 78666, USA
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Kuhl H, Guiguen Y, Höhne C, Kreuz E, Du K, Klopp C, Lopez-Roques C, Yebra-Pimentel ES, Ciorpac M, Gessner J, Holostenco D, Kleiner W, Kohlmann K, Lamatsch DK, Prokopov D, Bestin A, Bonpunt E, Debeuf B, Haffray P, Morvezen R, Patrice P, Suciu R, Dirks R, Wuertz S, Kloas W, Schartl M, Stöck M. A 180 Myr-old female-specific genome region in sturgeon reveals the oldest known vertebrate sex determining system with undifferentiated sex chromosomes. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200089. [PMID: 34247507 PMCID: PMC8273502 DOI: 10.1098/rstb.2020.0089] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Several hypotheses explain the prevalence of undifferentiated sex chromosomes in poikilothermic vertebrates. Turnovers change the master sex determination gene, the sex chromosome or the sex determination system (e.g. XY to WZ). Jumping master genes stay main triggers but translocate to other chromosomes. Occasional recombination (e.g. in sex-reversed females) prevents sex chromosome degeneration. Recent research has uncovered conserved heteromorphic or even homomorphic sex chromosomes in several clades of non-avian and non-mammalian vertebrates. Sex determination in sturgeons (Acipenseridae) has been a long-standing basic biological question, linked to economical demands by the caviar-producing aquaculture. Here, we report the discovery of a sex-specific sequence from sterlet (Acipenser ruthenus). Using chromosome-scale assemblies and pool-sequencing, we first identified an approximately 16 kb female-specific region. We developed a PCR-genotyping test, yielding female-specific products in six species, spanning the entire phylogeny with the most divergent extant lineages (A. sturio, A. oxyrinchus versus A. ruthenus, Huso huso), stemming from an ancient tetraploidization. Similar results were obtained in two octoploid species (A. gueldenstaedtii, A. baerii). Conservation of a female-specific sequence for a long period, representing 180 Myr of sturgeon evolution, and across at least one polyploidization event, raises many interesting biological questions. We discuss a conserved undifferentiated sex chromosome system with a ZZ/ZW-mode of sex determination and potential alternatives. This article is part of the theme issue ‘Challenging the paradigm in sex chromosome evolution: empirical and theoretical insights with a focus on vertebrates (Part I)’.
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Affiliation(s)
- Heiner Kuhl
- Department of Ecophysiology and Aquaculture, Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Müggelseedamm 301 and 310, 12587 Berlin, Germany
| | | | - Christin Höhne
- Department of Ecophysiology and Aquaculture, Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Müggelseedamm 301 and 310, 12587 Berlin, Germany
| | - Eva Kreuz
- Department of Ecophysiology and Aquaculture, Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Müggelseedamm 301 and 310, 12587 Berlin, Germany
| | - Kang Du
- Developmental Biochemistry, Biocenter, University of Würzburg, 97074 Würzburg, Germany.,The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX 78666, USA
| | - Christophe Klopp
- SIGENAE, Plate-forme Bio-informatique Genotoul, Mathématiques et Informatique Appliquées de Toulouse, INRAe, 31326 Castanet-Tolosan, France
| | | | | | - Mitica Ciorpac
- Danube Delta National Institute for Research and Development, Tulcea 820112, Romania.,Genetic Improvement Laboratory, Research Station for Cattle Breeding Dancu - Iasi (SCDCB Dancu), Academy of Agricultural and Forestry Sciences 'Gheorghe Ionescu-Sisesti', Iasi-Ungheni Street, No. 9, Holboca, Iași county 707252, Romania
| | - Jörn Gessner
- Department of Ecophysiology and Aquaculture, Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Müggelseedamm 301 and 310, 12587 Berlin, Germany
| | - Daniela Holostenco
- Danube Delta National Institute for Research and Development, Tulcea 820112, Romania
| | - Wibke Kleiner
- Department of Ecophysiology and Aquaculture, Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Müggelseedamm 301 and 310, 12587 Berlin, Germany
| | - Klaus Kohlmann
- Department of Ecophysiology and Aquaculture, Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Müggelseedamm 301 and 310, 12587 Berlin, Germany
| | - Dunja K Lamatsch
- Research Department for Limnology, University of Innsbruck, A-5310 Mondsee, Austria
| | - Dmitry Prokopov
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Anastasia Bestin
- SYSAAF, Station INRAE-LPGP, Campus de Beaulieu, 35042 Rennes cedex, France
| | | | - Bastien Debeuf
- SCEA Sturgeon, 29 rue du Carillon, 17240 Saint Fort sur Gironde, France
| | - Pierrick Haffray
- SYSAAF, Station INRAE-LPGP, Campus de Beaulieu, 35042 Rennes cedex, France
| | - Romain Morvezen
- SYSAAF, Station INRAE-LPGP, Campus de Beaulieu, 35042 Rennes cedex, France
| | - Pierre Patrice
- SYSAAF, Station INRAE-LPGP, Campus de Beaulieu, 35042 Rennes cedex, France
| | - Radu Suciu
- Danube Delta National Institute for Research and Development, Tulcea 820112, Romania
| | - Ron Dirks
- Future Genomics Technologies B.V., Sylviusweg 74, 2333 BD, Leiden, The Netherlands
| | - Sven Wuertz
- Department of Ecophysiology and Aquaculture, Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Müggelseedamm 301 and 310, 12587 Berlin, Germany
| | - Werner Kloas
- Department of Ecophysiology and Aquaculture, Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Müggelseedamm 301 and 310, 12587 Berlin, Germany
| | - Manfred Schartl
- Developmental Biochemistry, Biocenter, University of Würzburg, 97074 Würzburg, Germany.,The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX 78666, USA
| | - Matthias Stöck
- Department of Ecophysiology and Aquaculture, Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Müggelseedamm 301 and 310, 12587 Berlin, Germany
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Kuhl H, Frankl-Vilches C, Bakker A, Mayr G, Nikolaus G, Boerno ST, Klages S, Timmermann B, Gahr M. An Unbiased Molecular Approach Using 3'-UTRs Resolves the Avian Family-Level Tree of Life. Mol Biol Evol 2021; 38:108-127. [PMID: 32781465 PMCID: PMC7783168 DOI: 10.1093/molbev/msaa191] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Presumably, due to a rapid early diversification, major parts of the higher-level phylogeny of birds are still resolved controversially in different analyses or are considered unresolvable. To address this problem, we produced an avian tree of life, which includes molecular sequences of one or several species of ∼90% of the currently recognized family-level taxa (429 species, 379 genera) including all 106 family-level taxa of the nonpasserines and 115 of the passerines (Passeriformes). The unconstrained analyses of noncoding 3-prime untranslated region (3′-UTR) sequences and those of coding sequences yielded different trees. In contrast to the coding sequences, the 3′-UTR sequences resulted in a well-resolved and stable tree topology. The 3′-UTR contained, unexpectedly, transcription factor binding motifs that were specific for different higher-level taxa. In this tree, grebes and flamingos are the sister clade of all other Neoaves, which are subdivided into five major clades. All nonpasserine taxa were placed with robust statistical support including the long-time enigmatic hoatzin (Opisthocomiformes), which was found being the sister taxon of the Caprimulgiformes. The comparatively late radiation of family-level clades of the songbirds (oscine Passeriformes) contrasts with the attenuated diversification of nonpasseriform taxa since the early Miocene. This correlates with the evolution of vocal production learning, an important speciation factor, which is ancestral for songbirds and evolved convergent only in hummingbirds and parrots. As 3′-UTR-based phylotranscriptomics resolved the avian family-level tree of life, we suggest that this procedure will also resolve the all-species avian tree of life
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Affiliation(s)
- Heiner Kuhl
- Department of Behavioural Neurobiology, Max Planck Institute for Ornithology, Seewiesen, Germany.,Max Planck Institute for Molecular Genetics, Sequencing Core Facility, Berlin, Germany.,Department of Ecophysiology and Aquaculture, Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany
| | - Carolina Frankl-Vilches
- Department of Behavioural Neurobiology, Max Planck Institute for Ornithology, Seewiesen, Germany
| | - Antje Bakker
- Department of Behavioural Neurobiology, Max Planck Institute for Ornithology, Seewiesen, Germany
| | - Gerald Mayr
- Ornithological Section, Senckenberg Research Institute, Frankfurt am Main, Germany
| | - Gerhard Nikolaus
- Department of Behavioural Neurobiology, Max Planck Institute for Ornithology, Seewiesen, Germany
| | - Stefan T Boerno
- Max Planck Institute for Molecular Genetics, Sequencing Core Facility, Berlin, Germany
| | - Sven Klages
- Max Planck Institute for Molecular Genetics, Sequencing Core Facility, Berlin, Germany
| | - Bernd Timmermann
- Max Planck Institute for Molecular Genetics, Sequencing Core Facility, Berlin, Germany
| | - Manfred Gahr
- Department of Behavioural Neurobiology, Max Planck Institute for Ornithology, Seewiesen, Germany
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Tine M, Kuhl H, Teske PR, Reinhardt R. Genome-wide analysis of European sea bass provides insights into the evolution and functions of single-exon genes. Ecol Evol 2021; 11:6546-6557. [PMID: 34141239 PMCID: PMC8207432 DOI: 10.1002/ece3.7507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 01/24/2021] [Accepted: 03/12/2021] [Indexed: 11/17/2022] Open
Abstract
Several studies have attempted to understand the origin and evolution of single-exon genes (SEGs) in eukaryotic organisms, including fishes, but few have examined the functional and evolutionary relationships between SEGs and multiple-exon gene (MEG) paralogs, in particular the conservation of promoter regions. Given that SEGs originate via the reverse transcription of mRNA from a "parental" MEGs, such comparisons may enable identifying evolutionarily-related SEG/MEG paralogs, which might fulfill equivalent physiological functions. Here, the relationship of SEG proportion with MEG count, gene density, intron count, and chromosome size was assessed for the genome of the European sea bass, Dicentrarchus labrax. Then, SEGs with an MEG parent were identified, and promoter sequences of SEG/MEG paralogs were compared, to identify highly conserved functional motifs. The results revealed a total count of 1,585 (8.3% of total genes) SEGs in the European sea bass genome, which was correlated with MEG count but not with gene density. The significant correlation of SEG content with the number of MEGs suggests that SEGs were continuously and independently generated over evolutionary time following species divergence through retrotranscription events, followed by tandem duplications. Functional annotation showed that the majority of SEGs are functional, as is evident from their expression in RNA-seq data used to support homology-based genome annotation. Differences in 5'UTR and 3'UTR lengths between SEG/MEG paralogs observed in this study may contribute to gene expression divergence between them and therefore lead to the emergence of new SEG functions. The comparison of nonsynonymous to synonymous changes (Ka/Ks) between SEG/MEG parents showed that 74 of them are under positive selection (Ka/Ks > 1; p = .0447). An additional fifteen SEGs with an MEG parent have a common promoter, which implies that they are under the influence of common regulatory networks.
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Affiliation(s)
- Mbaye Tine
- UFR des Sciences Agronomiques, de l'Aquaculture et des Technologies Alimentaires (S2ATA)Université Gaston Berger (UGB)Saint‐LouisSenegal
- Genome Centre at the Max‐Planck Institute for Plant Breeding ResearchKölnGermany
| | - Heiner Kuhl
- Department of Ecophysiology and AquacultureLeibniz‐Institute of Freshwater Ecology and Inland Fisheries (IGB)BerlinGermany
| | - Peter R. Teske
- Department of ZoologyCentre for Ecological Genomics and Wildlife ConservationUniversity of JohannesburgJohannesburgSouth Africa
| | - Richard Reinhardt
- Genome Centre at the Max‐Planck Institute for Plant Breeding ResearchKölnGermany
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Fofanov MV, Prokopov DY, Kuhl H, Schartl M, Trifonov VA. Evolution of MicroRNA Biogenesis Genes in the Sterlet ( Acipenser ruthenus) and Other Polyploid Vertebrates. Int J Mol Sci 2020; 21:E9562. [PMID: 33334059 PMCID: PMC7765534 DOI: 10.3390/ijms21249562] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Revised: 12/09/2020] [Accepted: 12/14/2020] [Indexed: 01/14/2023] Open
Abstract
MicroRNAs play a crucial role in eukaryotic gene regulation. For a long time, only little was known about microRNA-based gene regulatory mechanisms in polyploid animal genomes due to difficulties of polyploid genome assembly. However, in recent years, several polyploid genomes of fish, amphibian, and even invertebrate species have been sequenced and assembled. Here we investigated several key microRNA-associated genes in the recently sequenced sterlet (Acipenser ruthenus) genome, whose lineage has undergone a whole genome duplication around 180 MYA. We show that two paralogs of drosha, dgcr8, xpo1, and xpo5 as well as most ago genes have been retained after the acipenserid-specific whole genome duplication, while ago1 and ago3 genes have lost one paralog. While most diploid vertebrates possess only a single copy of dicer1, we strikingly found four paralogs of this gene in the sterlet genome, derived from a tandem segmental duplication that occurred prior to the last whole genome duplication. ago1,3,4 and exportins1,5 look to be prone to additional segment duplications producing up to four-five paralog copies in ray-finned fishes. We demonstrate for the first time exon microsatellite amplification in the acipenserid drosha2 gene, resulting in a highly variable protein product, which may indicate sub- or neofunctionalization. Paralogous copies of most microRNA metabolism genes exhibit different expression profiles in various tissues and remain functional despite the rediploidization process. Subfunctionalization of microRNA processing gene paralogs may be beneficial for different pathways of microRNA metabolism. Genetic variability of microRNA processing genes may represent a substrate for natural selection, and, by increasing genetic plasticity, could facilitate adaptations to changing environments.
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Affiliation(s)
- Mikhail V. Fofanov
- Institute of Molecular and Cellular Biology SB RAS, Lavrentiev Ave. 8/2, 630090 Novosibirsk, Russia;
- Department of Natural Sciences, Novosibirsk State University, Pirogova 2, 630090 Novosibirsk, Russia
| | - Dmitry Yu. Prokopov
- Institute of Molecular and Cellular Biology SB RAS, Lavrentiev Ave. 8/2, 630090 Novosibirsk, Russia;
| | - Heiner Kuhl
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Müggelseedamm 301 and 310, 12587 Berlin, Germany;
| | - Manfred Schartl
- Developmental Biochemistry, Biocenter, University of Wuerzburg, Am Hubland, 97074 Wuerzburg, Germany;
- Xiphophorus Genetic Stock Center, Texas State University, 601 University Drive, 419 Centennial Hall, San Marcos, TX 78666-4616, USA
| | - Vladimir A. Trifonov
- Institute of Molecular and Cellular Biology SB RAS, Lavrentiev Ave. 8/2, 630090 Novosibirsk, Russia;
- Department of Natural Sciences, Novosibirsk State University, Pirogova 2, 630090 Novosibirsk, Russia
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8
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M Real F, Haas SA, Franchini P, Xiong P, Simakov O, Kuhl H, Schöpflin R, Heller D, Moeinzadeh MH, Heinrich V, Krannich T, Bressin A, Hartmann MF, Wudy SA, Dechmann DKN, Hurtado A, Barrionuevo FJ, Schindler M, Harabula I, Osterwalder M, Hiller M, Wittler L, Visel A, Timmermann B, Meyer A, Vingron M, Jiménez R, Mundlos S, Lupiáñez DG. The mole genome reveals regulatory rearrangements associated with adaptive intersexuality. Science 2020; 370:208-214. [PMID: 33033216 DOI: 10.1126/science.aaz2582] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 04/19/2020] [Accepted: 08/17/2020] [Indexed: 01/01/2023]
Abstract
Linking genomic variation to phenotypical traits remains a major challenge in evolutionary genetics. In this study, we use phylogenomic strategies to investigate a distinctive trait among mammals: the development of masculinizing ovotestes in female moles. By combining a chromosome-scale genome assembly of the Iberian mole, Talpa occidentalis, with transcriptomic, epigenetic, and chromatin interaction datasets, we identify rearrangements altering the regulatory landscape of genes with distinct gonadal expression patterns. These include a tandem triplication involving CYP17A1, a gene controlling androgen synthesis, and an intrachromosomal inversion involving the pro-testicular growth factor gene FGF9, which is heterochronically expressed in mole ovotestes. Transgenic mice with a knock-in mole CYP17A1 enhancer or overexpressing FGF9 showed phenotypes recapitulating mole sexual features. Our results highlight how integrative genomic approaches can reveal the phenotypic impact of noncoding sequence changes.
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Affiliation(s)
- Francisca M Real
- RG Development & Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany.,Institute for Medical and Human Genetics, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Stefan A Haas
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Paolo Franchini
- Chair in Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Peiwen Xiong
- Chair in Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Oleg Simakov
- Department of Molecular Evolution and Development, University of Vienna, 1090 Vienna, Austria
| | - Heiner Kuhl
- Department of Ecophysiology and Aquaculture, Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany
| | - Robert Schöpflin
- RG Development & Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany.,Institute for Medical and Human Genetics, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - David Heller
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - M-Hossein Moeinzadeh
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Verena Heinrich
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Thomas Krannich
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Annkatrin Bressin
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Michaela F Hartmann
- Steroid Research & Mass Spectrometry Unit, Laboratory for Translational Hormone Analytics in Paediatric Endocrinology, Division of Paediatric Endocrinology & Diabetology, Center of Child and Adolescent Medicine, Justus Liebig University, Giessen, Germany
| | - Stefan A Wudy
- Steroid Research & Mass Spectrometry Unit, Laboratory for Translational Hormone Analytics in Paediatric Endocrinology, Division of Paediatric Endocrinology & Diabetology, Center of Child and Adolescent Medicine, Justus Liebig University, Giessen, Germany
| | - Dina K N Dechmann
- Department of Migration and Immuno-Ecology, Max Planck Institute for Animal Behavior, Radolfzell, Germany.,Department of Biology, University of Konstanz, Konstanz, Germany
| | - Alicia Hurtado
- Departamento de Genética, Universidad de Granada, Granada, Spain.,Instituto de Biotecnología, Centro de Investigación Biomédica, Universidad de Granada, Armilla, Granada, Spain
| | - Francisco J Barrionuevo
- Departamento de Genética, Universidad de Granada, Granada, Spain.,Instituto de Biotecnología, Centro de Investigación Biomédica, Universidad de Granada, Armilla, Granada, Spain
| | - Magdalena Schindler
- RG Development & Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany.,Institute for Medical and Human Genetics, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Izabela Harabula
- RG Development & Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Marco Osterwalder
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.,Department for BioMedical Research (DBMR), University of Bern, 3008 Bern, Switzerland
| | - Michael Hiller
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany.,Max Planck Institute for the Physics of Complex Systems, 01187 Dresden, Germany.,Center for Systems Biology Dresden, 01307 Dresden, Germany
| | - Lars Wittler
- Department of Developmental Genetics, Transgenic Unit, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Axel Visel
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.,U.S. Department of Energy Joint Genome Institute, Berkeley, CA 94720, USA.,School of Natural Sciences, University of California, Merced, CA 95343, USA
| | - Bernd Timmermann
- RG Development & Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Axel Meyer
- Chair in Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Martin Vingron
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Rafael Jiménez
- Departamento de Genética, Universidad de Granada, Granada, Spain.,Instituto de Biotecnología, Centro de Investigación Biomédica, Universidad de Granada, Armilla, Granada, Spain
| | - Stefan Mundlos
- RG Development & Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany. .,Institute for Medical and Human Genetics, Charité - Universitätsmedizin Berlin, Berlin, Germany.,Berlin-Brandenburg Center for Regenerative Therapies (BCRT), Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Darío G Lupiáñez
- RG Development & Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany. .,Institute for Medical and Human Genetics, Charité - Universitätsmedizin Berlin, Berlin, Germany.,Berlin-Brandenburg Center for Regenerative Therapies (BCRT), Charité - Universitätsmedizin Berlin, Berlin, Germany.,Epigenetics and Sex Development Group, Berlin Institute for Medical Systems Biology, Max-Delbrück Center for Molecular Medicine, Berlin, Germany
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9
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Farrall AL, Lienhard M, Grimm C, Kuhl H, Sluka SHM, Caparros M, Forejt J, Timmermann B, Herwig R, Herrmann BG, Morkel M. PWD/Ph-Encoded Genetic Variants Modulate the Cellular Wnt/β-Catenin Response to Suppress Apc Min-Triggered Intestinal Tumor Formation. Cancer Res 2020; 81:38-49. [PMID: 33154092 DOI: 10.1158/0008-5472.can-20-1480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 08/26/2020] [Accepted: 10/15/2020] [Indexed: 11/16/2022]
Abstract
Genetic predisposition affects the penetrance of tumor-initiating mutations, such as APC mutations that stabilize β-catenin and cause intestinal tumors in mice and humans. However, the mechanisms involved in genetically predisposed penetrance are not well understood. Here, we analyzed tumor multiplicity and gene expression in tumor-prone Apc Min/+ mice on highly variant C57BL/6J (B6) and PWD/Ph (PWD) genetic backgrounds. (B6 × PWD) F1 APC Min offspring mice were largely free of intestinal adenoma, and several chromosome substitution (consomic) strains carrying single PWD chromosomes on the B6 genetic background displayed reduced adenoma numbers. Multiple dosage-dependent modifier loci on PWD chromosome 5 each contributed to tumor suppression. Activation of β-catenin-driven and stem cell-specific gene expression in the presence of Apc Min or following APC loss remained moderate in intestines carrying PWD chromosome 5, suggesting that PWD variants restrict adenoma initiation by controlling stem cell homeostasis. Gene expression of modifier candidates and DNA methylation on chromosome 5 were predominantly cis controlled and largely reflected parental patterns, providing a genetic basis for inheritance of tumor susceptibility. Human SNP variants of several modifier candidates were depleted in colorectal cancer genomes, suggesting that similar mechanisms may also affect the penetrance of cancer driver mutations in humans. Overall, our analysis highlights the strong impact that multiple genetic variants acting in networks can exert on tumor development. SIGNIFICANCE: These findings in mice show that, in addition to accidental mutations, cancer risk is determined by networks of individual gene variants.
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Affiliation(s)
- Alexandra L Farrall
- Max Planck Institute for Molecular Genetics, Berlin, Germany.,College of Medicine and Public Health, Flinders University, Adelaide, South Australia, Australia
| | | | - Christina Grimm
- Max Planck Institute for Molecular Genetics, Berlin, Germany.,Department of Translational Epigenetics and Tumor Genetics, University Hospital Cologne, Cologne, Germany
| | - Heiner Kuhl
- Max Planck Institute for Molecular Genetics, Berlin, Germany.,Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Department of Ecophysiology and Aquaculture, Berlin, Germany
| | | | - Marta Caparros
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Jiri Forejt
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Vestec, Prague, Czech Republic
| | | | - Ralf Herwig
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Bernhard G Herrmann
- Max Planck Institute for Molecular Genetics, Berlin, Germany. .,Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute for Medical Genetics, Berlin, Germany
| | - Markus Morkel
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Pathology, Berlin, Germany.
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10
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Aparicio‐Soto M, Riedel F, Leddermann M, Bacher P, Scheffold A, Kuhl H, Timmermann B, Chudakov DM, Molin S, Worm M, Heine G, Thierse H, Luch A, Siewert K. TCRs with segment TRAV9-2 or a CDR3 histidine are overrepresented among nickel-specific CD4+ T cells. Allergy 2020; 75:2574-2586. [PMID: 32298488 DOI: 10.1111/all.14322] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 03/24/2020] [Accepted: 03/31/2020] [Indexed: 12/23/2022]
Abstract
BACKGROUND Nickel is the most frequent cause of T cell-mediated allergic contact dermatitis worldwide. In vitro, CD4+ T cells from all donors respond to nickel but the involved αβ T cell receptor (TCR) repertoire has not been comprehensively analyzed. METHODS We introduce CD154 (CD40L) upregulation as a fast, unbiased, and quantitative method to detect nickel-specific CD4+ T cells ex vivo in blood of clinically characterized allergic and non allergic donors. Naïve (CCR7+ CD45RA+) and memory (not naïve) CD154+ CD4+ T cells were analyzed by flow cytometry after 5 hours of stimulation with 200 µmol/L NiSO4 ., TCR α- and β-chains of sorted nickel-specific and control cells were studied by high-throughput sequencing. RESULTS Stimulation of PBMCs with NiSO4 induced CD154 expression on ~0.1% (mean) of naïve and memory CD4+ T cells. In allergic donors with recent positive patch test, memory frequencies further increased ~13-fold and were associated with markers of in vivo activation. CD154 expression was TCR-mediated since single clones could be specifically restimulated. Among nickel-specific CD4+ T cells of allergic and non allergic donors, TCRs expressing the α-chain segment TRAV9-2 or a histidine in their α- or β-chain complementarity determining region 3 (CDR3) were highly overrepresented. CONCLUSIONS Induced CD154 expression represents a reliable method to study nickel-specific CD4+ T cells. TCRs with particular features respond in all donors, while strongly increased blood frequencies indicate nickel allergy for some donors. Our approach may be extended to other contact allergens for the further development of diagnostic and predictive in vitro tests.
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Affiliation(s)
- Marina Aparicio‐Soto
- Department of Chemical and Product Safety German Federal Institute for Risk Assessment Berlin Germany
| | - Franziska Riedel
- Department of Chemical and Product Safety German Federal Institute for Risk Assessment Berlin Germany
| | - Melanie Leddermann
- Department of Chemical and Product Safety German Federal Institute for Risk Assessment Berlin Germany
| | - Petra Bacher
- Institute of Immunology Christian‐Albrechts Universität zu Kiel and Universitätsklinik Schleswig‐Holstein Kiel Germany
- Institute of Clinical Molecular Biology Christian‐Albrechts Universität zu Kiel Kiel Germany
| | - Alexander Scheffold
- Institute of Immunology Christian‐Albrechts Universität zu Kiel and Universitätsklinik Schleswig‐Holstein Kiel Germany
| | - Heiner Kuhl
- Sequencing Core Facility Max‐Planck‐Institute of Molecular Genetics Berlin Germany
| | - Bernd Timmermann
- Sequencing Core Facility Max‐Planck‐Institute of Molecular Genetics Berlin Germany
| | - Dmitriy M. Chudakov
- Genomics of Adaptive Immunity Department Shemyakin‐Ovchinnikov Institute of Bioorganic Chemistry Russian Academy of Science Moscow Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine Pirogov Russian National Research Medical University Moscow Russia
- Center of Molecular Medicine CEITEC Masaryk University Brno Czech Republic
| | - Sonja Molin
- Division of Dermatology Queen's University Kingston ON Canada
- Department of Dermatology and Allergy Ludwig Maximilian University Munich Germany
| | - Margitta Worm
- Division of Allergy and Immunology Department of Dermatology, Venerology, and Allergy Charité – Universitätsmedizin Berlin Berlin Germany
| | - Guido Heine
- Division of Allergy and Immunology Department of Dermatology, Venerology, and Allergy Charité – Universitätsmedizin Berlin Berlin Germany
- Department of Dermatology and Allergy University Hospital Schleswig‐Holstein Kiel Germany
| | - Hermann‐Josef Thierse
- Department of Chemical and Product Safety German Federal Institute for Risk Assessment Berlin Germany
| | - Andreas Luch
- Department of Chemical and Product Safety German Federal Institute for Risk Assessment Berlin Germany
| | - Katherina Siewert
- Department of Chemical and Product Safety German Federal Institute for Risk Assessment Berlin Germany
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11
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Mueller JC, Carrete M, Boerno S, Kuhl H, Tella JL, Kempenaers B. Genes acting in synapses and neuron projections are early targets of selection during urban colonization. Mol Ecol 2020; 29:3403-3412. [DOI: 10.1111/mec.15451] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 04/08/2020] [Indexed: 02/06/2023]
Affiliation(s)
- Jakob C. Mueller
- Department of Behavioural Ecology & Evolutionary Genetics Max Planck Institute for Ornithology Seewiesen Germany
| | - Martina Carrete
- Department of Conservation Biology Estación Biológica de Doñana – CSIC Sevilla Spain
- Department of Physical, Chemical and Natural Systems University Pablo de Olavide Sevilla Spain
| | - Stefan Boerno
- Sequencing Core Facility Max Planck Institute for Molecular Genetics Berlin Germany
| | - Heiner Kuhl
- Sequencing Core Facility Max Planck Institute for Molecular Genetics Berlin Germany
- Department of Ecophysiology and Aquaculture Leibniz‐Institute of Freshwater Ecology and Inland Fisheries Berlin Germany
| | - José L. Tella
- Department of Conservation Biology Estación Biológica de Doñana – CSIC Sevilla Spain
| | - Bart Kempenaers
- Department of Behavioural Ecology & Evolutionary Genetics Max Planck Institute for Ornithology Seewiesen Germany
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12
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Kuhl H, Li L, Wuertz S, Stöck M, Liang XF, Klopp C. CSA: A high-throughput chromosome-scale assembly pipeline for vertebrate genomes. Gigascience 2020; 9:giaa034. [PMID: 32449778 PMCID: PMC7247394 DOI: 10.1093/gigascience/giaa034] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 01/29/2020] [Accepted: 03/24/2020] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND Easy-to-use and fast bioinformatics pipelines for long-read assembly that go beyond the contig level to generate highly continuous chromosome-scale genomes from raw data remain scarce. RESULT Chromosome-Scale Assembler (CSA) is a novel computationally highly efficient bioinformatics pipeline that fills this gap. CSA integrates information from scaffolded assemblies (e.g., Hi-C or 10X Genomics) or even from diverged reference genomes into the assembly process. As CSA performs automated assembly of chromosome-sized scaffolds, we benchmark its performance against state-of-the-art reference genomes, i.e., conventionally built in a laborious fashion using multiple separate assembly tools and manual curation. CSA increases the contig lengths using scaffolding, local re-assembly, and gap closing. On certain datasets, initial contig N50 may be increased up to 4.5-fold. For smaller vertebrate genomes, chromosome-scale assemblies can be achieved within 12 h using low-cost, high-end desktop computers. Mammalian genomes can be processed within 16 h on compute-servers. Using diverged reference genomes for fish, birds, and mammals, we demonstrate that CSA calculates chromosome-scale assemblies from long-read data and genome comparisons alone. Even contig-level draft assemblies of diverged genomes are helpful for reconstructing chromosome-scale sequences. CSA is also capable of assembling ultra-long reads. CONCLUSIONS CSA can speed up and simplify chromosome-level assembly and significantly lower costs of large-scale family-level vertebrate genome projects.
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Affiliation(s)
- Heiner Kuhl
- Department of Ecophysiology and Aquaculture, Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Müggelseedamm 310, 12587 Berlin, Germany
| | - Ling Li
- Department of Ecophysiology and Aquaculture, Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Müggelseedamm 310, 12587 Berlin, Germany
- College of Fisheries, Chinese Perch Research Center, Huazhong Agricultural University; Innovation Base for Chinese Perch Breeding, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, No.1 Shizishan Street, Hongshan District, 430070 Wuhan, Hubei Province, P.R. China
| | - Sven Wuertz
- Department of Ecophysiology and Aquaculture, Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Müggelseedamm 310, 12587 Berlin, Germany
| | - Matthias Stöck
- Department of Ecophysiology and Aquaculture, Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Müggelseedamm 310, 12587 Berlin, Germany
| | - Xu-Fang Liang
- College of Fisheries, Chinese Perch Research Center, Huazhong Agricultural University; Innovation Base for Chinese Perch Breeding, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, No.1 Shizishan Street, Hongshan District, 430070 Wuhan, Hubei Province, P.R. China
| | - Christophe Klopp
- Sigenae, Bioinfo Genotoul, Mathématiques et Informatique Appliquées de Toulouse, INRAe, 24 Chemin de Borde Rouge, 31320 Auzeville-Tolosane, Castanet Tolosan, France
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13
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Ribas L, Crespo B, Sánchez-Baizán N, Xavier D, Kuhl H, Rodríguez JM, Díaz N, Boltañá S, MacKenzie S, Morán F, Zanuy S, Gómez A, Piferrer F. Characterization of the European Sea Bass (Dicentrarchus labrax) Gonadal Transcriptome During Sexual Development. Mar Biotechnol (NY) 2019; 21:359-373. [PMID: 30919121 DOI: 10.1007/s10126-019-09886-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 02/18/2019] [Indexed: 06/09/2023]
Abstract
The European sea bass is one of the most important cultured fish in Europe and has a marked sexual growth dimorphism in favor of females. It is a gonochoristic species with polygenic sex determination, where a combination between still undifferentiated genetic factors and environmental temperature determines sex ratios. The molecular mechanisms responsible for gonadal sex differentiation are still unknown. Here, we sampled fish during the gonadal developmental period (110 to 350 days post fertilization, dpf), and performed a comprehensive transcriptomic study by using a species-specific microarray. This analysis uncovered sex-specific gonadal transcriptomic profiles at each stage of development, identifying larger number of differentially expressed genes in ovaries when compared to testis. The expression patterns of 54 reproduction-related genes were analyzed. We found that hsd17β10 is a reliable marker of early ovarian differentiation. Further, three genes, pdgfb, snx1, and nfy, not previously related to fish sex differentiation, were tightly associated with testis development in the sea bass. Regarding signaling pathways, lysine degradation, bladder cancer, and NOD-like receptor signaling were enriched for ovarian development while eight pathways including basal transcription factors and steroid biosynthesis were enriched for testis development. Analysis of the transcription factor abundance showed an earlier increase in females than in males. Our results show that, although many players in the sex differentiation pathways are conserved among species, there are peculiarities in gene expression worth exploring. The genes identified in this study illustrate the diversity of players involved in fish sex differentiation and can become potential biomarkers for the management of sex ratios in the European sea bass and perhaps other cultured species.
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Affiliation(s)
- L Ribas
- Institute of Marine Sciences (ICM), Spanish National Research Council (CSIC), Barcelona, Catalonia, Spain
| | - B Crespo
- Institute of Aquaculture of Torre de la Sal (IATS-CSIC), Ribera de Cabanes s/n. Torre la Sal, 12595, Castellón, Spain
- UCL GOS Institute of Child Health, University College London, London, UK
| | - N Sánchez-Baizán
- Institute of Marine Sciences (ICM), Spanish National Research Council (CSIC), Barcelona, Catalonia, Spain
| | - D Xavier
- Department of Biochemistry and Molecular Biology I, Complutense University, Madrid, Spain
| | - H Kuhl
- Max Planck Institute for Molecular Genetics, Berlin, Germany
- Department of Ecophysiology and Aquaculture, Leibniz Institute for Freshwater Ecology and Inland Fisheries, Berlin, Germany
| | - J M Rodríguez
- Spanish National Bioinformatics Institute, Madrid, Spain
- Cardiovascular Proteomics Laboratory, Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Madrid, Spain
| | - N Díaz
- Institute of Marine Sciences (ICM), Spanish National Research Council (CSIC), Barcelona, Catalonia, Spain
- Max Planck Institute for Molecular Biomedicine, Muenster, Germany
| | - S Boltañá
- Autonomous University of Barcelona, Barcelona, Spain
- Interdisciplinary Center for Aquaculture Research (INCAR), Department of Oceanography, Biotechnology Center, University of Concepción, Concepción, Chile
| | - S MacKenzie
- Autonomous University of Barcelona, Barcelona, Spain
- Institute of Aquaculture, University of Stirling, Stirling, Scotland, UK
| | - F Morán
- Department of Biochemistry and Molecular Biology I, Complutense University, Madrid, Spain
| | - S Zanuy
- Institute of Aquaculture of Torre de la Sal (IATS-CSIC), Ribera de Cabanes s/n. Torre la Sal, 12595, Castellón, Spain
| | - A Gómez
- Institute of Aquaculture of Torre de la Sal (IATS-CSIC), Ribera de Cabanes s/n. Torre la Sal, 12595, Castellón, Spain.
| | - F Piferrer
- Institute of Marine Sciences (ICM), Spanish National Research Council (CSIC), Barcelona, Catalonia, Spain.
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14
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Gossmann TI, Shanmugasundram A, Börno S, Duvaux L, Lemaire C, Kuhl H, Klages S, Roberts LD, Schade S, Gostner JM, Hildebrand F, Vowinckel J, Bichet C, Mülleder M, Calvani E, Zelezniak A, Griffin JL, Bork P, Allaine D, Cohas A, Welch JJ, Timmermann B, Ralser M. Ice-Age Climate Adaptations Trap the Alpine Marmot in a State of Low Genetic Diversity. Curr Biol 2019; 29:1712-1720.e7. [PMID: 31080084 PMCID: PMC6538971 DOI: 10.1016/j.cub.2019.04.020] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Revised: 02/16/2019] [Accepted: 04/09/2019] [Indexed: 12/30/2022]
Abstract
Some species responded successfully to prehistoric changes in climate [1, 2], while others failed to adapt and became extinct [3]. The factors that determine successful climate adaptation remain poorly understood. We constructed a reference genome and studied physiological adaptations in the Alpine marmot (Marmota marmota), a large ground-dwelling squirrel exquisitely adapted to the "ice-age" climate of the Pleistocene steppe [4, 5]. Since the disappearance of this habitat, the rodent persists in large numbers in the high-altitude Alpine meadow [6, 7]. Genome and metabolome showed evidence of adaptation consistent with cold climate, affecting white adipose tissue. Conversely, however, we found that the Alpine marmot has levels of genetic variation that are among the lowest for mammals, such that deleterious mutations are less effectively purged. Our data rule out typical explanations for low diversity, such as high levels of consanguineous mating, or a very recent bottleneck. Instead, ancient demographic reconstruction revealed that genetic diversity was lost during the climate shifts of the Pleistocene and has not recovered, despite the current high population size. We attribute this slow recovery to the marmot's adaptive life history. The case of the Alpine marmot reveals a complicated relationship between climatic changes, genetic diversity, and conservation status. It shows that species of extremely low genetic diversity can be very successful and persist over thousands of years, but also that climate-adapted life history can trap a species in a persistent state of low genetic diversity.
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Affiliation(s)
- Toni I Gossmann
- University of Sheffield, Department of Animal and Plant Sciences, Sheffield S10 2TN, UK; Bielefeld University, Department of Animal Behaviour, 33501 Bielefeld, Germany
| | - Achchuthan Shanmugasundram
- Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Centre for Genomic Research, Institute of Integrative Biology, University of Liverpool, Biosciences Building, Crown Street, Liverpool L69 7ZB, UK
| | - Stefan Börno
- Max Planck Institute for Molecular Genetics, Sequencing Core Facility, Ihnestrasse 73, 14195 Berlin, Germany
| | - Ludovic Duvaux
- IRHS, Université d'Angers, INRA, Agrocampus-Ouest, SFR 4207 QuaSaV, 49071 Beaucouzé, France; BIOGECO, INRA, Université de Bordeaux, 69 Route d'Arcachon, 33612 Cestas, France
| | - Christophe Lemaire
- IRHS, Université d'Angers, INRA, Agrocampus-Ouest, SFR 4207 QuaSaV, 49071 Beaucouzé, France
| | - Heiner Kuhl
- Max Planck Institute for Molecular Genetics, Sequencing Core Facility, Ihnestrasse 73, 14195 Berlin, Germany; Department of Ecophysiology and Aquaculture, Leibniz-Institute of Freshwater Ecology and Inland Fisheries, 12587 Berlin, Germany
| | - Sven Klages
- Max Planck Institute for Molecular Genetics, Sequencing Core Facility, Ihnestrasse 73, 14195 Berlin, Germany
| | - Lee D Roberts
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK; Leeds Institute of Cardiovascular and Metabolic Medicine, University of Leeds, Leeds LS2 9JT, UK
| | - Sophia Schade
- Max Planck Institute for Molecular Genetics, Sequencing Core Facility, Ihnestrasse 73, 14195 Berlin, Germany
| | - Johanna M Gostner
- Division of Medical Biochemistry, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Falk Hildebrand
- European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany; Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK; Gut Health and Microbes Programme, Quadram Institute, Norwich Research Park, Norwich NR4 7UQ, UK
| | - Jakob Vowinckel
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | | | - Michael Mülleder
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK; Department of Biochemistry, Charitè, Am Chariteplatz 1, 10117 Berlin, Germany
| | - Enrica Calvani
- Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Aleksej Zelezniak
- Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Göteborg, Sweden; Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm 171 65, Sweden
| | - Julian L Griffin
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Peer Bork
- European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany; Max-Delbrück-Centre for Molecular Medicine, 13092 Berlin, Germany; Molecular Medicine Partnership Unit, 69120 Heidelberg, Germany
| | - Dominique Allaine
- Université de Lyon, F-69000, Lyon; Université Lyon 1; CNRS, UMR 5558, Laboratoire de Biométrie et Biologie Evolutive, 69622 Villeurbanne, France
| | - Aurélie Cohas
- Université de Lyon, F-69000, Lyon; Université Lyon 1; CNRS, UMR 5558, Laboratoire de Biométrie et Biologie Evolutive, 69622 Villeurbanne, France
| | - John J Welch
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK
| | - Bernd Timmermann
- Max Planck Institute for Molecular Genetics, Sequencing Core Facility, Ihnestrasse 73, 14195 Berlin, Germany
| | - Markus Ralser
- Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK; Department of Biochemistry, Charitè, Am Chariteplatz 1, 10117 Berlin, Germany.
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15
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Stöck M, Fakharzadeh F, Kuhl H, Rozenblut-Kościsty B, Leinweber S, Patel R, Ebrahimi M, Voitel S, Schmidtler JF, Kami HG, Ogielska M, Förster DW. Shedding Light on a Secretive Tertiary urodelean Relict: Hynobiid salamanders ( Paradactylodon persicus s.l.) from Iran, Illuminated by Phylogeographic, Developmental and Transcriptomic Data. Genes (Basel) 2019; 10:genes10040306. [PMID: 31003559 PMCID: PMC6523714 DOI: 10.3390/genes10040306] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2019] [Revised: 04/10/2019] [Accepted: 04/11/2019] [Indexed: 12/21/2022] Open
Abstract
The Hyrcanian Forests present a unique Tertiary relict ecosystem, covering the northern Elburz and Talysh Ranges (Iran, Azerbaijan), a poorly investigated, unique biodiversity hotspot with many cryptic species. Since the 1970s, two nominal species of Urodela, Hynobiidae, Batrachuperus (later: Paradactylodon) have been described: Paradactylodon persicus from northwestern and P. gorganensis from northeastern Iran. Although P. gorganensis has been involved in studies on phylogeny and development, there is little data on the phylogeography, systematics, and development of the genus throughout the Hyrcanian Forests; genome-wide resources have been entirely missing. Given the huge genome size of hynobiids, making whole genome sequencing hardly affordable, we aimed to publish the first transcriptomic resources for Paradactylodon from an embryo and a larva (9.17 Gb RNA sequences; assembled to 78,918 unigenes). We also listed 32 genes involved in vertebrate sexual development and sex determination. Photographic documentation of the development from egg sacs across several embryonal and larval stages until metamorphosis enabled, for the first time, comparison of the ontogeny with that of other hynobiids and new histological and transcriptomic insights into early gonads and timing of their differentiation. Transcriptomes from central Elburz, next-generation sequencing (NGS) libraries of archival DNA of topotypic P. persicus, and GenBank-sequences of eastern P. gorganensis allowed phylogenetic analysis with three mitochondrial genomes, supplemented by PCR-amplified mtDNA-fragments from 17 museum specimens, documenting <2% uncorrected intraspecific genetic distance. Our data suggest that these rare salamanders belong to a single species P. persicus s.l. Humankind has a great responsibility to protect this species and the unique biodiversity of the Hyrcanian Forest ecosystems.
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Affiliation(s)
- Matthias Stöck
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Müggelseedamm 301, D-12587 Berlin, Germany.
| | - Fatemeh Fakharzadeh
- Department of Biology, Faculty of Sciences, Shahid Chamran University of Ahvaz, Ahvaz 61357-43135, Iran.
| | - Heiner Kuhl
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Müggelseedamm 301, D-12587 Berlin, Germany.
| | - Beata Rozenblut-Kościsty
- Department of Evolutionary Biology and Conservation of Vertebrates, Wroclaw University, Sienkiewicza 21,50-335 Wroclaw, Poland.
| | - Sophie Leinweber
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Müggelseedamm 301, D-12587 Berlin, Germany.
| | - Rhiddi Patel
- Evolutionary Genetics Department, Leibniz-Institute for Zoo and Wildlife Research, Alfred-Kowalke-Str. 17, 10315 Berlin, Germany.
| | - Mehregan Ebrahimi
- Department of Biology, College of Sciences, Shiraz University, Shiraz 71467-13565, Iran.
- School of Biological Sciences, Flinders University, Adelaide, South Australia 5001, Australia.
| | - Sebastian Voitel
- Independent Researcher, Spangenbergstraße 81, D-06295 Eisleben, Germany.
| | | | - Haji Gholi Kami
- Department of Biology, Faculty of Sciences, Golestan University, Gorgan 49136-15759, Iran.
| | - Maria Ogielska
- Department of Evolutionary Biology and Conservation of Vertebrates, Wroclaw University, Sienkiewicza 21,50-335 Wroclaw, Poland.
| | - Daniel W Förster
- Evolutionary Genetics Department, Leibniz-Institute for Zoo and Wildlife Research, Alfred-Kowalke-Str. 17, 10315 Berlin, Germany.
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16
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Mueller JC, Kuhl H, Boerno S, Tella JL, Carrete M, Kempenaers B. Evolution of genomic variation in the burrowing owl in response to recent colonization of urban areas. Proc Biol Sci 2019; 285:rspb.2018.0206. [PMID: 29769357 PMCID: PMC5966595 DOI: 10.1098/rspb.2018.0206] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 04/16/2018] [Indexed: 11/12/2022] Open
Abstract
When a species successfully colonizes an urban habitat it can be expected that its population rapidly adapts to the new environment but also experiences demographic perturbations. It is, therefore, essential to gain an understanding of the population structure and the demographic history of the urban and neighbouring rural populations before studying adaptation at the genome level. Here, we investigate populations of the burrowing owl (Athene cunicularia), a species that colonized South American cities just a few decades ago. We assembled a high-quality genome of the burrowing owl and re-sequenced 137 owls from three urban-rural population pairs at 17-fold median sequencing coverage per individual. Our data indicate that each city was independently colonized by a limited number of founders and that restricted gene flow occurred between neighbouring urban and rural populations, but not between urban populations of different cities. Using long-range linkage disequilibrium statistics in an approximate Bayesian computation approach, we estimated consistently lower population sizes in the recent past for the urban populations in comparison to the rural ones. The current urban populations all show reduced standing variation in rare single nucleotide polymorphisms (SNPs), but with different subsets of rare SNPs in different cities. This lowers the potential for local adaptation based on rare variants and makes it harder to detect consistent signals of selection in the genome.
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Affiliation(s)
- Jakob C Mueller
- Department of Behavioural Ecology & Evolutionary Genetics, Max Planck Institute for Ornithology, Seewiesen, Germany
| | - Heiner Kuhl
- Sequencing Core Facility, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Stefan Boerno
- Sequencing Core Facility, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Jose L Tella
- Department of Conservation Biology, Estación Biológica de Doñana - CSIC, Sevilla, Spain
| | - Martina Carrete
- Department of Conservation Biology, Estación Biológica de Doñana - CSIC, Sevilla, Spain.,Department of Physical, Chemical and Natural Systems, University Pablo de Olavide, Sevilla, Spain
| | - Bart Kempenaers
- Department of Behavioural Ecology & Evolutionary Genetics, Max Planck Institute for Ornithology, Seewiesen, Germany
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17
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Bousquet J, Price D, Meltzer E, Nguyen D, Kuhl H, Kopietz F, Koltun A, Munzel U. P502 Onset of action for intranasal azelastine-fluticasone propionate versus oral loratadine with intranasal fluticasone propionate. Ann Allergy Asthma Immunol 2017. [DOI: 10.1016/j.anai.2017.09.068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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18
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Yang J, Moeinzadeh MH, Kuhl H, Helmuth J, Xiao P, Haas S, Liu G, Zheng J, Sun Z, Fan W, Deng G, Wang H, Hu F, Zhao S, Fernie AR, Boerno S, Timmermann B, Zhang P, Vingron M. Haplotype-resolved sweet potato genome traces back its hexaploidization history. Nat Plants 2017; 3:696-703. [PMID: 28827752 DOI: 10.1038/s41477-017-0002-z] [Citation(s) in RCA: 158] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 07/11/2017] [Indexed: 05/20/2023]
Abstract
Here we present the 15 pseudochromosomes of sweet potato, Ipomoea batatas, the seventh most important crop in the world and the fourth most significant in China. By using a novel haplotyping method based on genome assembly, we have produced a half haplotype-resolved genome from ~296 Gb of paired-end sequence reads amounting to roughly 67-fold coverage. By phylogenetic tree analysis of homologous chromosomes, it was possible to estimate the time of two recent whole-genome duplication events as occurring about 0.8 and 0.5 million years ago. This half haplotype-resolved hexaploid genome represents the first successful attempt to investigate the complexity of chromosome sequence composition directly in a polyploid genome, using sequencing of the polyploid organism itself rather than any of its simplified proxy relatives. Adaptation and application of our approach should provide higher resolution in future genomic structure investigations, especially for similarly complex genomes.
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Affiliation(s)
- Jun Yang
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai Chenshan Botanical Garden, 3888 Chenhua Road, Shanghai, 201602, China
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195, Berlin, Germany
- Department of Molecular Physiology, Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam, Germany
| | - M-Hossein Moeinzadeh
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195, Berlin, Germany
| | - Heiner Kuhl
- Max Planck Institute for Molecular Genetics, Sequencing Core Facility, Ihnestraße 63-73, 14195, Berlin, Germany
| | - Johannes Helmuth
- Max Planck Institute for Molecular Genetics, Otto-Warburg-Laboratory: Computational Epigenomics Group, Ihnestraße 63-73, 14195, Berlin, Germany
| | - Peng Xiao
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195, Berlin, Germany
| | - Stefan Haas
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195, Berlin, Germany
| | - Guiling Liu
- Tai'an Academy of Agricultural Sciences, 16 Tailai Road, Tai'an, 271000, Shandong, China
| | - Jianli Zheng
- Tai'an Academy of Agricultural Sciences, 16 Tailai Road, Tai'an, 271000, Shandong, China
| | - Zhe Sun
- Tai'an Academy of Agricultural Sciences, 16 Tailai Road, Tai'an, 271000, Shandong, China
| | - Weijuan Fan
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Gaifang Deng
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Hongxia Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Fenhong Hu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Shanshan Zhao
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai Chenshan Botanical Garden, 3888 Chenhua Road, Shanghai, 201602, China
| | - Alisdair R Fernie
- Department of Molecular Physiology, Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam, Germany
| | - Stefan Boerno
- Max Planck Institute for Molecular Genetics, Sequencing Core Facility, Ihnestraße 63-73, 14195, Berlin, Germany
| | - Bernd Timmermann
- Max Planck Institute for Molecular Genetics, Sequencing Core Facility, Ihnestraße 63-73, 14195, Berlin, Germany
| | - Peng Zhang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China.
| | - Martin Vingron
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195, Berlin, Germany.
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19
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Oral M, Colléter J, Bekaert M, Taggart JB, Palaiokostas C, McAndrew BJ, Vandeputte M, Chatain B, Kuhl H, Reinhardt R, Peruzzi S, Penman DJ. Gene-centromere mapping in meiotic gynogenetic European seabass. BMC Genomics 2017; 18:449. [PMID: 28592235 PMCID: PMC5463376 DOI: 10.1186/s12864-017-3826-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 05/28/2017] [Indexed: 12/14/2022] Open
Abstract
Background Fully isogenic lines in fish can be developed using “mitotic” gynogenesis (suppression of first zygotic mitosis following inactivation of the sperm genome). However, genome-wide verification of the steps in this process has seldom been applied. We used ddRADseq to generate SNP markers in a meiotic gynogenetic family of European seabass (Dicentrarchus labrax): (i) to verify the lack of paternal contribution in a meiotic gynogenetic family; (ii) to generate a gene-centromere map from this family; (iii) to identify telomeric markers that could distinguish mitotic gynogenetics from meiotic gynogenetics, which sometimes arise spontaneously in mitotic gynogenetic families. Results From a single meiotic gynogenetic family consisting of 79 progeny, 42 million sequencing reads (Illumina, trimmed to 148 bases) resolved 6866 unique RAD-tags. The 340 male-informative SNP markers that were identified confirmed the lack of paternal contribution. A gene-centromere map was constructed based on 804 female-informative SNPs in 24 linkage groups (2n = 48) with a total length of 1251.02 cM (initial LG assignment was based on the seabass genome assembly, dicLab v1). Chromosome arm structure could be clearly discerned from the pattern of heterozygosity in each linkage group in 18 out of 24 LGs: the other six showed anomalies that appeared to be related to issues in the genome assembly. Conclusion Genome-wide screening enabled substantive verification of the production of the gynogenetic family used in this study. The large number of telomeric and subtelomeric markers with high heterozygosity values in the meiotic gynogenetic family indicate that such markers could be used to clearly distinguish between meiotic and mitotic gynogenetics. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3826-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Münevver Oral
- Institute of Aquaculture, School of Natural Sciences, University of Stirling, FK9 4LA, Stirling, Scotland, UK
| | - Julie Colléter
- Cirad, Persyst, UMR Intrepid, Campus International de Baillarguet, 34398, Montpellier, France.,Ifremer, 34250, Palavas-Les-Flots, France
| | - Michaël Bekaert
- Institute of Aquaculture, School of Natural Sciences, University of Stirling, FK9 4LA, Stirling, Scotland, UK
| | - John B Taggart
- Institute of Aquaculture, School of Natural Sciences, University of Stirling, FK9 4LA, Stirling, Scotland, UK
| | - Christos Palaiokostas
- Institute of Aquaculture, School of Natural Sciences, University of Stirling, FK9 4LA, Stirling, Scotland, UK
| | - Brendan J McAndrew
- Institute of Aquaculture, School of Natural Sciences, University of Stirling, FK9 4LA, Stirling, Scotland, UK
| | - Marc Vandeputte
- Ifremer, 34250, Palavas-Les-Flots, France.,INRA, GABI, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | | | - Heiner Kuhl
- Leibniz-Institute of Freshwater Biology and Inland Fisheries, Müggelseedamm 310, 12587, Berlin, Germany
| | - Richard Reinhardt
- Max-Planck-Institute for Plant Breeding, Max-Planck Genome Centre Cologne, Carl-von-Linné-Weg 10, D-50829, Cologne, Germany
| | - Stefano Peruzzi
- Department of Arctic and Marine Biology, Faculty of Biosciences, Fisheries and Economics, University of Tromsø, 9037, Breivika, Tromsø, Norway
| | - David J Penman
- Institute of Aquaculture, School of Natural Sciences, University of Stirling, FK9 4LA, Stirling, Scotland, UK.
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20
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Xu S, Brockmöller T, Navarro-Quezada A, Kuhl H, Gase K, Ling Z, Zhou W, Kreitzer C, Stanke M, Tang H, Lyons E, Pandey P, Pandey SP, Timmermann B, Gaquerel E, Baldwin IT. Wild tobacco genomes reveal the evolution of nicotine biosynthesis. Proc Natl Acad Sci U S A 2017; 114:6133-6138. [PMID: 28536194 PMCID: PMC5468653 DOI: 10.1073/pnas.1700073114] [Citation(s) in RCA: 108] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Nicotine, the signature alkaloid of Nicotiana species responsible for the addictive properties of human tobacco smoking, functions as a defensive neurotoxin against attacking herbivores. However, the evolution of the genetic features that contributed to the assembly of the nicotine biosynthetic pathway remains unknown. We sequenced and assembled genomes of two wild tobaccos, Nicotiana attenuata (2.5 Gb) and Nicotiana obtusifolia (1.5 Gb), two ecological models for investigating adaptive traits in nature. We show that after the Solanaceae whole-genome triplication event, a repertoire of rapidly expanding transposable elements (TEs) bloated these Nicotiana genomes, promoted expression divergences among duplicated genes, and contributed to the evolution of herbivory-induced signaling and defenses, including nicotine biosynthesis. The biosynthetic machinery that allows for nicotine synthesis in the roots evolved from the stepwise duplications of two ancient primary metabolic pathways: the polyamine and nicotinamide adenine dinucleotide (NAD) pathways. In contrast to the duplication of the polyamine pathway that is shared among several solanaceous genera producing polyamine-derived tropane alkaloids, we found that lineage-specific duplications within the NAD pathway and the evolution of root-specific expression of the duplicated Solanaceae-specific ethylene response factor that activates the expression of all nicotine biosynthetic genes resulted in the innovative and efficient production of nicotine in the genus Nicotiana Transcription factor binding motifs derived from TEs may have contributed to the coexpression of nicotine biosynthetic pathway genes and coordinated the metabolic flux. Together, these results provide evidence that TEs and gene duplications facilitated the emergence of a key metabolic innovation relevant to plant fitness.
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Affiliation(s)
- Shuqing Xu
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, 07745 Jena, Germany;
| | - Thomas Brockmöller
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, 07745 Jena, Germany
| | - Aura Navarro-Quezada
- Centre for Organismal Studies, University of Heidelberg, 69120 Heidelberg, Germany
| | - Heiner Kuhl
- Sequencing Core Facility, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Klaus Gase
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, 07745 Jena, Germany
| | - Zhihao Ling
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, 07745 Jena, Germany
| | - Wenwu Zhou
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, 07745 Jena, Germany
| | - Christoph Kreitzer
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, 07745 Jena, Germany
- Institute of Animal Nutrition and Functional Plant Compounds, University of Veterinary Medicine, 1210 Vienna, Austria
| | - Mario Stanke
- Institute for Mathematics and Computer Science, Universität Greifswald, 17489 Greifswald, Germany
| | - Haibao Tang
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, 350002 Fuzhou, Fujian, China
| | - Eric Lyons
- School of Plant Sciences, BIO5 Institute, CyVerse, University of Arizona, Tucson, AZ 85721
| | - Priyanka Pandey
- National Institute of Biomedical Genomics, Kalyani, 741251 West Bengal, India
| | - Shree P Pandey
- Department of Biological Sciences, Indian Institute of Science Education and Research-Kolkata, Mohanpur, 700064 West Bengal, India
| | - Bernd Timmermann
- Sequencing Core Facility, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Emmanuel Gaquerel
- Centre for Organismal Studies, University of Heidelberg, 69120 Heidelberg, Germany;
| | - Ian T Baldwin
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, 07745 Jena, Germany;
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21
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Vij S, Kuhl H, Kuznetsova IS, Komissarov A, Yurchenko AA, Van Heusden P, Singh S, Thevasagayam NM, Prakki SRS, Purushothaman K, Saju JM, Jiang J, Mbandi SK, Jonas M, Hin Yan Tong A, Mwangi S, Lau D, Ngoh SY, Liew WC, Shen X, Hon LS, Drake JP, Boitano M, Hall R, Chin CS, Lachumanan R, Korlach J, Trifonov V, Kabilov M, Tupikin A, Green D, Moxon S, Garvin T, Sedlazeck FJ, Vurture GW, Gopalapillai G, Kumar Katneni V, Noble TH, Scaria V, Sivasubbu S, Jerry DR, O'Brien SJ, Schatz MC, Dalmay T, Turner SW, Lok S, Christoffels A, Orbán L. Chromosomal-Level Assembly of the Asian Seabass Genome Using Long Sequence Reads and Multi-layered Scaffolding. PLoS Genet 2016; 12:e1005954. [PMID: 27082250 PMCID: PMC4833346 DOI: 10.1371/journal.pgen.1005954] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2015] [Accepted: 03/03/2016] [Indexed: 11/18/2022] Open
Abstract
We report here the ~670 Mb genome assembly of the Asian seabass (Lates calcarifer), a tropical marine teleost. We used long-read sequencing augmented by transcriptomics, optical and genetic mapping along with shared synteny from closely related fish species to derive a chromosome-level assembly with a contig N50 size over 1 Mb and scaffold N50 size over 25 Mb that span ~90% of the genome. The population structure of L. calcarifer species complex was analyzed by re-sequencing 61 individuals representing various regions across the species' native range. SNP analyses identified high levels of genetic diversity and confirmed earlier indications of a population stratification comprising three clades with signs of admixture apparent in the South-East Asian population. The quality of the Asian seabass genome assembly far exceeds that of any other fish species, and will serve as a new standard for fish genomics.
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Affiliation(s)
- Shubha Vij
- Reproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore
| | - Heiner Kuhl
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Inna S. Kuznetsova
- Reproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore
- Laboratory of Chromosome Structure and Function, Department of Cytology and Histology, Biological Faculty, Saint Petersburg State University, St. Petersburg, Russia
| | - Aleksey Komissarov
- Theodosius Dobzhansky Center for Genome Bioinformatics, Saint Petersburg State University, St. Petersburg, Russia
| | - Andrey A. Yurchenko
- Theodosius Dobzhansky Center for Genome Bioinformatics, Saint Petersburg State University, St. Petersburg, Russia
| | - Peter Van Heusden
- South African MRC Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Bellville, South Africa
| | - Siddharth Singh
- Pacific Biosciences, Menlo Park, California, United States of America
| | | | | | | | - Jolly M. Saju
- Reproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore
| | - Junhui Jiang
- Reproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore
| | - Stanley Kimbung Mbandi
- South African MRC Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Bellville, South Africa
| | - Mario Jonas
- South African MRC Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Bellville, South Africa
| | - Amy Hin Yan Tong
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Canada
| | - Sarah Mwangi
- South African MRC Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Bellville, South Africa
| | - Doreen Lau
- Reproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore
| | - Si Yan Ngoh
- Reproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore
| | - Woei Chang Liew
- Reproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore
| | - Xueyan Shen
- Reproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore
| | - Lawrence S. Hon
- Pacific Biosciences, Menlo Park, California, United States of America
| | - James P. Drake
- Pacific Biosciences, Menlo Park, California, United States of America
| | - Matthew Boitano
- Pacific Biosciences, Menlo Park, California, United States of America
| | - Richard Hall
- Pacific Biosciences, Menlo Park, California, United States of America
| | - Chen-Shan Chin
- Pacific Biosciences, Menlo Park, California, United States of America
| | | | - Jonas Korlach
- Pacific Biosciences, Menlo Park, California, United States of America
| | - Vladimir Trifonov
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation
| | - Marsel Kabilov
- Genomics Core Facility, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Alexey Tupikin
- Genomics Core Facility, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Darrell Green
- Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Simon Moxon
- The Genome Analysis Centre, Norwich, United Kingdom
| | - Tyler Garvin
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, New York, United States of America
| | - Fritz J. Sedlazeck
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, New York, United States of America
- Department of Computer Science, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Gregory W. Vurture
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, New York, United States of America
| | - Gopikrishna Gopalapillai
- Nutrition, Genetics & Biotechnology Division, ICAR-Central Institute of Brackishwater Aquaculture, Tamil Nadu, India
| | - Vinaya Kumar Katneni
- Nutrition, Genetics & Biotechnology Division, ICAR-Central Institute of Brackishwater Aquaculture, Tamil Nadu, India
| | - Tansyn H. Noble
- College of Marine and Environmental Sciences and Center for Sustainable Tropical Fisheries and Aquaculture, James Cook University, Townsville, Queensland, Australia
| | - Vinod Scaria
- CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India
| | - Sridhar Sivasubbu
- CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India
| | - Dean R. Jerry
- College of Marine and Environmental Sciences and Center for Sustainable Tropical Fisheries and Aquaculture, James Cook University, Townsville, Queensland, Australia
| | - Stephen J. O'Brien
- Theodosius Dobzhansky Center for Genome Bioinformatics, Saint Petersburg State University, St. Petersburg, Russia
- Oceanographic Center, Nova Southeastern University Ft. Lauderdale, Ft. Lauderdale, Florida, United States of America
| | - Michael C. Schatz
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, New York, United States of America
- Department of Computer Science, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Tamás Dalmay
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Stephen W. Turner
- Pacific Biosciences, Menlo Park, California, United States of America
| | - Si Lok
- The Centre for Applied Genomics, The Hospital for Sick Children, Peter Gilgan Centre for Research and Learning, Toronto, Ontario, Canada
| | - Alan Christoffels
- South African MRC Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Bellville, South Africa
| | - László Orbán
- Reproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore
- Department of Animal Sciences and Animal Husbandry, Georgikon Faculty, University of Pannonia, Keszthely, Hungary
- Centre for Comparative Genomics, Murdoch University, Murdoch, Australia
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22
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Tine M, Kuhl H, Teske PR, Tschöp MH, Jastroch M. Diversification and coevolution of the ghrelin/growth hormone secretagogue receptor system in vertebrates. Ecol Evol 2016; 6:2516-35. [PMID: 27066235 PMCID: PMC4797157 DOI: 10.1002/ece3.2057] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2015] [Revised: 02/08/2016] [Accepted: 02/09/2016] [Indexed: 12/13/2022] Open
Abstract
The gut hormone ghrelin is involved in numerous metabolic functions, such as the stimulation of growth hormone secretion, gastric motility, and food intake. Ghrelin is modified by ghrelin O-acyltransferase (GOAT) or membrane-bound O-acyltransferase domain-containing 4 (MBOAT4) enabling action through the growth hormone secretagogue receptors (GHS-R). During the course of evolution, initially strong ligand/receptor specificities can be disrupted by genomic changes, potentially modifying physiological roles of the ligand/receptor system. Here, we investigated the coevolution of ghrelin, GOAT, and GHS-R in vertebrates. We combined similarity search, conserved synteny analyses, phylogenetic reconstructions, and protein structure comparisons to reconstruct the evolutionary history of the ghrelin system. Ghrelin remained a single-gene locus in all vertebrate species, and accordingly, a single GHS-R isoform was identified in all tetrapods. Similar patterns of the nonsynonymous (dN) and synonymous (dS) ratio (dN/dS) in the vertebrate lineage strongly suggest coevolution of the ghrelin and GHS-R genes, supporting specific functional interactions and common physiological pathways. The selection profiles do not allow confirmation as to whether ghrelin binds specifically to GOAT, but the ghrelin dN/dS patterns are more similar to those of GOAT compared to MBOAT1 and MBOAT2 isoforms. Four GHS-R isoforms were identified in teleost genomes. This diversification of GHS-R resulted from successive rounds of duplications, some of which remained specific to the teleost lineage. Coevolution signals are lost in teleosts, presumably due to the diversification of GHS-R but not the ghrelin gene. The identification of the GHS-R diversity in teleosts provides a molecular basis for comparative studies on ghrelin's physiological roles and regulation, while the comparative sequence and structure analyses will assist translational medicine to determine structure-function relationships of the ghrelin/GHS-R system.
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Affiliation(s)
- Mbaye Tine
- Genome Centre at Max Planck Institute for Plant Breeding Research Carl-von-Linné-Weg 10D-50829 Köln Germany; Molecular Zoology Laboratory Department of Zoology University of Johannesburg Kingsway Campus Auckland Park 2006 South Africa
| | - Heiner Kuhl
- Max Planck Institute for Molecular Genetics Ihnestrasse 63-73 14195 Berlin Germany
| | - Peter R Teske
- Molecular Zoology Laboratory Department of Zoology University of Johannesburg Kingsway Campus Auckland Park 2006 South Africa
| | - Matthias H Tschöp
- Helmholtz Diabetes Center & German Diabetes Center (DZD) Helmholtz Zentrum München, 85764 Neuherberg, Germany; Division of Metabolic Diseases Technische Universität München 80333 Munich Germany
| | - Martin Jastroch
- Helmholtz Diabetes Center & German Diabetes Center (DZD) Helmholtz Zentrum München, 85764 Neuherberg, Germany; Division of Metabolic Diseases Technische Universität München 80333 Munich Germany
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23
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Mertes F, Lichtner B, Kuhl H, Blattner M, Otte J, Wruck W, Timmermann B, Lehrach H, Adjaye J. Combined ultra-low input mRNA and whole-genome sequencing of human embryonic stem cells. BMC Genomics 2015; 16:925. [PMID: 26564201 PMCID: PMC4643517 DOI: 10.1186/s12864-015-2025-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Accepted: 10/07/2015] [Indexed: 12/21/2022] Open
Abstract
Background Next Generation Sequencing has proven to be an exceptionally powerful tool in the field of genomics and transcriptomics. With recent development it is nowadays possible to analyze ultra-low input sample material down to single cells. Nevertheless, investigating such sample material often limits the analysis to either the genome or transcriptome. We describe here a combined analysis of both types of nucleic acids from the same sample material. Methods The method described enables the combined preparation of amplified cDNA as well as amplified whole-genome DNA from an ultra-low input sample material derived from a sub-colony of in-vitro cultivated human embryonic stem cells. cDNA is prepared by the application of oligo-dT coupled magnetic beads for mRNA capture, first strand synthesis and 3’-tailing followed by PCR. Whole-genome amplified DNA is prepared by Phi29 mediated amplification. Illumina sequencing is applied to short fragment libraries prepared from the amplified samples. Results We developed a protocol which enables the combined analysis of the genome as well as the transcriptome by Next Generation Sequencing from ultra-low input samples. The protocol was evaluated by sequencing sub-colony structures from human embryonic stem cells containing 150 to 200 cells. The method can be adapted to any available sequencing system. Conclusions To our knowledge, this is the first report where sub-colonies of human embryonic stem cells have been analyzed both at the genomic as well as transcriptome level. The method of this proof of concept study may find useful practical applications for cases where only a limited number of cells are available, e.g. for tissues samples from biopsies, tumor spheres, circulating tumor cells and cells from early embryonic development. The results we present demonstrate that a combined analysis of genomic DNA and messenger RNA from ultra-low input samples is feasible and can readily be applied to other cellular systems with limited material available.
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Affiliation(s)
- Florian Mertes
- Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Ihnestr. 63-73, 14195, Berlin, Germany. .,Molecular Exposomics, Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany.
| | - Björn Lichtner
- Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Ihnestr. 63-73, 14195, Berlin, Germany.
| | - Heiner Kuhl
- Next Generation Sequencing Group, Max Planck Institute for Molecular Genetics, Ihnestr. 63-73, 14195, Berlin, Germany.
| | - Mirjam Blattner
- Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Ihnestr. 63-73, 14195, Berlin, Germany.
| | - Jörg Otte
- Institute for stem cell research and regenerative medicine, Medical Faculty, Heinrich Heine University, Moorenstr. 5, 40225, Düsseldorf, Germany.
| | - Wasco Wruck
- Institute for stem cell research and regenerative medicine, Medical Faculty, Heinrich Heine University, Moorenstr. 5, 40225, Düsseldorf, Germany.
| | - Bernd Timmermann
- Next Generation Sequencing Group, Max Planck Institute for Molecular Genetics, Ihnestr. 63-73, 14195, Berlin, Germany.
| | - Hans Lehrach
- Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Ihnestr. 63-73, 14195, Berlin, Germany.
| | - James Adjaye
- Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Ihnestr. 63-73, 14195, Berlin, Germany. .,Institute for stem cell research and regenerative medicine, Medical Faculty, Heinrich Heine University, Moorenstr. 5, 40225, Düsseldorf, Germany.
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24
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Mueller JC, Kuhl H, Timmermann B, Kempenaers B. Characterization of the genome and transcriptome of the blue tit Cyanistes caeruleus: polymorphisms, sex-biased expression and selection signals. Mol Ecol Resour 2015. [PMID: 26220359 DOI: 10.1111/1755-0998.12450] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Decoding genomic sequences and determining their variation within populations has potential to reveal adaptive processes and unravel the genetic basis of ecologically relevant trait variation within a species. The blue tit Cyanistes caeruleus--a long-time ecological model species--has been used to investigate fitness consequences of variation in mating and reproductive behaviour. However, very little is known about the underlying genetic changes due to natural and sexual selection in the genome of this songbird. As a step to bridge this gap, we assembled the first draft genome of a single blue tit, mapped the transcriptome of five females and five males to this reference, identified genomewide variants and performed sex-differential expression analysis in the gonads, brain and other tissues. In the gonads, we found a high number of sex-biased genes, and of those, a similar proportion were sex-limited (genes only expressed in one sex) in males and females. However, in the brain, the proportion of female-limited genes within the female-biased gene category (82%) was substantially higher than the proportion of male-limited genes within the male-biased category (6%). This suggests a predominant on-off switching mechanism for the female-limited genes. In addition, most male-biased genes were located on the Z-chromosome, indicating incomplete dosage compensation for the male-biased genes. We called more than 500,000 SNPs from the RNA-seq data. Heterozygote detection in the single reference individual was highly congruent between DNA-seq and RNA-seq calling. Using information from these polymorphisms, we identified potential selection signals in the genome. We list candidate genes which can be used for further sequencing and detailed selection studies, including genes potentially related to meiotic drive evolution. A public genome browser of the blue tit with the described information is available at http://public-genomes-ngs.molgen.mpg.de.
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Affiliation(s)
- Jakob C Mueller
- Department of Behavioural Ecology & Evolutionary Genetics, Max Planck Institute for Ornithology, 82319 Seewiesen, Germany
| | - Heiner Kuhl
- Sequencing Core Facility, Max Planck Institute for Molecular Genetics, Ihnestrasse 73, 14195 Berlin, Germany
| | - Bernd Timmermann
- Sequencing Core Facility, Max Planck Institute for Molecular Genetics, Ihnestrasse 73, 14195 Berlin, Germany
| | - Bart Kempenaers
- Department of Behavioural Ecology & Evolutionary Genetics, Max Planck Institute for Ornithology, 82319 Seewiesen, Germany
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25
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Frankl-Vilches C, Kuhl H, Werber M, Klages S, Kerick M, Bakker A, de Oliveira EH, Reusch C, Capuano F, Vowinckel J, Leitner S, Ralser M, Timmermann B, Gahr M. Using the canary genome to decipher the evolution of hormone-sensitive gene regulation in seasonal singing birds. Genome Biol 2015; 16:19. [PMID: 25631560 PMCID: PMC4373106 DOI: 10.1186/s13059-014-0578-9] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Accepted: 12/23/2014] [Indexed: 11/15/2022] Open
Abstract
BACKGROUND While the song of all songbirds is controlled by the same neural circuit, the hormone dependence of singing behavior varies greatly between species. For this reason, songbirds are ideal organisms to study ultimate and proximate mechanisms of hormone-dependent behavior and neuronal plasticity. RESULTS We present the high quality assembly and annotation of a female 1.2-Gbp canary genome. Whole genome alignments between the canary and 13 genomes throughout the bird taxa show a much-conserved synteny, whereas at the single-base resolution there are considerable species differences. These differences impact small sequence motifs like transcription factor binding sites such as estrogen response elements and androgen response elements. To relate these species-specific response elements to the hormone-sensitivity of the canary singing behavior, we identify seasonal testosterone-sensitive transcriptomes of major song-related brain regions, HVC and RA, and find the seasonal gene networks related to neuronal differentiation only in the HVC. Testosterone-sensitive up-regulated gene networks of HVC of singing males concerned neuronal differentiation. Among the testosterone-regulated genes of canary HVC, 20% lack estrogen response elements and 4 to 8% lack androgen response elements in orthologous promoters in the zebra finch. CONCLUSIONS The canary genome sequence and complementary expression analysis reveal intra-regional evolutionary changes in a multi-regional neural circuit controlling seasonal singing behavior and identify gene evolution related to the hormone-sensitivity of this seasonal singing behavior. Such genes that are testosterone- and estrogen-sensitive specifically in the canary and that are involved in rewiring of neurons might be crucial for seasonal re-differentiation of HVC underlying seasonal song patterning.
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Affiliation(s)
- Carolina Frankl-Vilches
- Department of Behavioral Neurobiology, Max Planck Institute for Ornithology, 82319, Seewiesen, Germany.
| | - Heiner Kuhl
- Department of Behavioral Neurobiology, Max Planck Institute for Ornithology, 82319, Seewiesen, Germany.
- Max Planck Institute for Molecular Genetics, Sequencing Core Facility, 14195, Berlin, Germany.
| | - Martin Werber
- Max Planck Institute for Molecular Genetics, Sequencing Core Facility, 14195, Berlin, Germany.
| | - Sven Klages
- Max Planck Institute for Molecular Genetics, Sequencing Core Facility, 14195, Berlin, Germany.
| | - Martin Kerick
- Max Planck Institute for Molecular Genetics, Sequencing Core Facility, 14195, Berlin, Germany.
| | - Antje Bakker
- Department of Behavioral Neurobiology, Max Planck Institute for Ornithology, 82319, Seewiesen, Germany.
| | - Edivaldo Hc de Oliveira
- Laboratório de Cultura de Tecidos e Citogenética, SAMAM, Instituto Evandro Chagas, Ananindeua, Pará, and Faculdade de Ciências Naturais (ICEN), Universidade Federal do Pará, Belém, 66075-110, Brazil.
| | - Christina Reusch
- Department of Behavioral Neurobiology, Max Planck Institute for Ornithology, 82319, Seewiesen, Germany.
| | - Floriana Capuano
- Department of Biochemistry and Cambridge Systems Biology Centre, 80 Tennis Court Road, Cambridge, CB2 1GA, UK.
| | - Jakob Vowinckel
- Department of Biochemistry and Cambridge Systems Biology Centre, 80 Tennis Court Road, Cambridge, CB2 1GA, UK.
| | - Stefan Leitner
- Department of Behavioral Neurobiology, Max Planck Institute for Ornithology, 82319, Seewiesen, Germany.
| | - Markus Ralser
- Department of Biochemistry and Cambridge Systems Biology Centre, 80 Tennis Court Road, Cambridge, CB2 1GA, UK.
- Division of Physiology and Metabolism, MRC National Institute for Medical Research, the Ridgeway, Mill Hill, London, NW7 1AA, UK.
| | - Bernd Timmermann
- Max Planck Institute for Molecular Genetics, Sequencing Core Facility, 14195, Berlin, Germany.
| | - Manfred Gahr
- Department of Behavioral Neurobiology, Max Planck Institute for Ornithology, 82319, Seewiesen, Germany.
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26
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Tine M, Kuhl H, Gagnaire PA, Louro B, Desmarais E, Martins RST, Hecht J, Knaust F, Belkhir K, Klages S, Dieterich R, Stueber K, Piferrer F, Guinand B, Bierne N, Volckaert FAM, Bargelloni L, Power DM, Bonhomme F, Canario AVM, Reinhardt R. European sea bass genome and its variation provide insights into adaptation to euryhalinity and speciation. Nat Commun 2014; 5:5770. [PMID: 25534655 PMCID: PMC4284805 DOI: 10.1038/ncomms6770] [Citation(s) in RCA: 262] [Impact Index Per Article: 26.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2014] [Accepted: 11/05/2014] [Indexed: 01/30/2023] Open
Abstract
The European sea bass (Dicentrarchus labrax) is a temperate-zone euryhaline teleost of prime importance for aquaculture and fisheries. This species is subdivided into two naturally hybridizing lineages, one inhabiting the north-eastern Atlantic Ocean and the other the Mediterranean and Black seas. Here we provide a high-quality chromosome-scale assembly of its genome that shows a high degree of synteny with the more highly derived teleosts. We find expansions of gene families specifically associated with ion and water regulation, highlighting adaptation to variation in salinity. We further generate a genome-wide variation map through RAD-sequencing of Atlantic and Mediterranean populations. We show that variation in local recombination rates strongly influences the genomic landscape of diversity within and differentiation between lineages. Comparing predictions of alternative demographic models to the joint allele-frequency spectrum indicates that genomic islands of differentiation between sea bass lineages were generated by varying rates of introgression across the genome following a period of geographical isolation. The European sea bass is an economically important fish species, which is subject to intense selective breeding. Here, the authors sequence the genome of the European sea bass and highlight gene family expansions underlying adaptation to salinity change, as well as the genomic architecture of speciation between two divergent sea bass lineages.
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Affiliation(s)
- Mbaye Tine
- 1] Max Planck Genome-centre Cologne, Carl-von-Linné-Weg 10, D-50829 Köln, Germany [2] Max Planck Institute for Molecular Genetics, Ihnestrasse 63, D-14195 Berlin, Germany [3]
| | - Heiner Kuhl
- 1] Max Planck Institute for Molecular Genetics, Ihnestrasse 63, D-14195 Berlin, Germany [2]
| | - Pierre-Alexandre Gagnaire
- 1] Institut des Sciences de l'Evolution (UMR 5554), CNRS-UM2-IRD, Place Eugène Bataillon, F-34095 Montpellier, France [2] Station Méditerranéenne de l'Environnement Littoral, Université Montpellier 2, 2 Rue des Chantiers, F-34200 Sète, France [3]
| | - Bruno Louro
- CCMAR-Centre of Marine Sciences, University of Algarve, Building 7, Campus de Gambelas, 8005-139 Faro, Portugal
| | - Erick Desmarais
- Institut des Sciences de l'Evolution (UMR 5554), CNRS-UM2-IRD, Place Eugène Bataillon, F-34095 Montpellier, France
| | - Rute S T Martins
- CCMAR-Centre of Marine Sciences, University of Algarve, Building 7, Campus de Gambelas, 8005-139 Faro, Portugal
| | - Jochen Hecht
- 1] Max Planck Institute for Molecular Genetics, Ihnestrasse 63, D-14195 Berlin, Germany [2] BCRT, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, D-13353 Berlin, Germany
| | - Florian Knaust
- Max Planck Institute for Molecular Genetics, Ihnestrasse 63, D-14195 Berlin, Germany
| | - Khalid Belkhir
- Institut des Sciences de l'Evolution (UMR 5554), CNRS-UM2-IRD, Place Eugène Bataillon, F-34095 Montpellier, France
| | - Sven Klages
- Max Planck Institute for Molecular Genetics, Ihnestrasse 63, D-14195 Berlin, Germany
| | - Roland Dieterich
- Max Planck Genome-centre Cologne, Carl-von-Linné-Weg 10, D-50829 Köln, Germany
| | - Kurt Stueber
- Max Planck Genome-centre Cologne, Carl-von-Linné-Weg 10, D-50829 Köln, Germany
| | - Francesc Piferrer
- Institut de Ciències del Mar, Consejo Superior de Investigaciones Científicas (CSIC), Passeig Marítim, 37-49, 08003 Barcelona, Spain
| | - Bruno Guinand
- Institut des Sciences de l'Evolution (UMR 5554), CNRS-UM2-IRD, Place Eugène Bataillon, F-34095 Montpellier, France
| | - Nicolas Bierne
- 1] Institut des Sciences de l'Evolution (UMR 5554), CNRS-UM2-IRD, Place Eugène Bataillon, F-34095 Montpellier, France [2] Station Méditerranéenne de l'Environnement Littoral, Université Montpellier 2, 2 Rue des Chantiers, F-34200 Sète, France
| | - Filip A M Volckaert
- Laboratory of Biodiversity and Evolutionary Genomics, University of Leuven, Charles Deberiotstraat 32, B-3000 Leuven, Belgium
| | - Luca Bargelloni
- Dipartimento di Biomedicina Comparata e Alimentazione, Università di Padova, I-35124 Padova, Italy
| | - Deborah M Power
- CCMAR-Centre of Marine Sciences, University of Algarve, Building 7, Campus de Gambelas, 8005-139 Faro, Portugal
| | - François Bonhomme
- 1] Institut des Sciences de l'Evolution (UMR 5554), CNRS-UM2-IRD, Place Eugène Bataillon, F-34095 Montpellier, France [2] Station Méditerranéenne de l'Environnement Littoral, Université Montpellier 2, 2 Rue des Chantiers, F-34200 Sète, France
| | - Adelino V M Canario
- CCMAR-Centre of Marine Sciences, University of Algarve, Building 7, Campus de Gambelas, 8005-139 Faro, Portugal
| | - Richard Reinhardt
- 1] Max Planck Genome-centre Cologne, Carl-von-Linné-Weg 10, D-50829 Köln, Germany [2] Max Planck Institute for Molecular Genetics, Ihnestrasse 63, D-14195 Berlin, Germany
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27
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Seifert R, Flick M, Bönigk W, Alvarez L, Trötschel C, Poetsch A, Müller A, Goodwin N, Pelzer P, Kashikar ND, Kremmer E, Jikeli J, Timmermann B, Kuhl H, Fridman D, Windler F, Kaupp UB, Strünker T. The CatSper channel controls chemosensation in sea urchin sperm. EMBO J 2014; 34:379-92. [PMID: 25535245 DOI: 10.15252/embj.201489376] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Sperm guidance is controlled by chemical and physical cues. In many species, Ca(2+) bursts in the flagellum govern navigation to the egg. In Arbacia punctulata, a model system of sperm chemotaxis, a cGMP signaling pathway controls these Ca(2+) bursts. The underlying Ca(2+) channel and its mechanisms of activation are unknown. Here, we identify CatSper Ca(2+) channels in the flagellum of A. punctulata sperm. We show that CatSper mediates the chemoattractant-evoked Ca(2+) influx and controls chemotactic steering; a concomitant alkalization serves as a highly cooperative mechanism that enables CatSper to transduce periodic voltage changes into Ca(2+) bursts. Our results reveal intriguing phylogenetic commonalities but also variations between marine invertebrates and mammals regarding the function and control of CatSper. The variations probably reflect functional and mechanistic adaptations that evolved during the transition from external to internal fertilization.
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Affiliation(s)
- Reinhard Seifert
- Center of Advanced European Studies and Research (Caesar), Abteilung Molekulare Neurosensorik, Bonn, Germany Marine Biological Laboratory, Woods Hole, MA, USA
| | - Melanie Flick
- Center of Advanced European Studies and Research (Caesar), Abteilung Molekulare Neurosensorik, Bonn, Germany
| | - Wolfgang Bönigk
- Center of Advanced European Studies and Research (Caesar), Abteilung Molekulare Neurosensorik, Bonn, Germany
| | - Luis Alvarez
- Center of Advanced European Studies and Research (Caesar), Abteilung Molekulare Neurosensorik, Bonn, Germany
| | | | - Ansgar Poetsch
- Ruhr-Universität Bochum Lehrstuhl Biochemie der Pflanzen, Bochum, Germany
| | - Astrid Müller
- Center of Advanced European Studies and Research (Caesar), Abteilung Molekulare Neurosensorik, Bonn, Germany
| | - Normann Goodwin
- Marine Biological Laboratory, Woods Hole, MA, USA Laboratory of Molecular Signalling, Babraham Institute, Cambridge, UK
| | - Patric Pelzer
- Marine Biological Laboratory, Woods Hole, MA, USA Institut für Anatomie und Zellbiologie, Abteilung für Funktionelle Neuroanatomie, Universität Heidelberg, Heidelberg, Germany
| | - Nachiket D Kashikar
- Marine Biological Laboratory, Woods Hole, MA, USA Sussex Neuroscience, School of Life Sciences, University of Sussex, Falmer, Brighton, UK
| | - Elisabeth Kremmer
- Helmholtz-Zentrum München, Institut für Molekulare Immunologie, München, Germany
| | - Jan Jikeli
- Center of Advanced European Studies and Research (Caesar), Abteilung Molekulare Neurosensorik, Bonn, Germany
| | | | - Heiner Kuhl
- Max-Planck-Institut für Molekulare Genetik, Berlin, Germany
| | - Dmitry Fridman
- Center of Advanced European Studies and Research (Caesar), Abteilung Molekulare Neurosensorik, Bonn, Germany Marine Biological Laboratory, Woods Hole, MA, USA
| | - Florian Windler
- Center of Advanced European Studies and Research (Caesar), Abteilung Molekulare Neurosensorik, Bonn, Germany Marine Biological Laboratory, Woods Hole, MA, USA
| | - U Benjamin Kaupp
- Center of Advanced European Studies and Research (Caesar), Abteilung Molekulare Neurosensorik, Bonn, Germany Marine Biological Laboratory, Woods Hole, MA, USA
| | - Timo Strünker
- Center of Advanced European Studies and Research (Caesar), Abteilung Molekulare Neurosensorik, Bonn, Germany Marine Biological Laboratory, Woods Hole, MA, USA
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28
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Dohle DS, Tsagakis K, Janosi A, Benedik J, Kuhl H, Penkova L, Wendt D, Jakob HG. 001 * AORTIC REMODELLING IN AORTIC DISSECTION AFTER FROZEN ELEPHANT TRUNK. Interact Cardiovasc Thorac Surg 2014. [DOI: 10.1093/icvts/ivu276.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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29
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Draaken M, Baudisch F, Timmermann B, Kuhl H, Kerick M, Proske J, Wittler L, Pennimpede T, Ebert AK, Rösch W, Stein R, Bartels E, von Lowtzow C, Boemers TM, Herms S, Gearhart JP, Lakshmanan Y, Kockum CC, Holmdahl G, Läckgren G, Nordenskjöld A, Boyadjiev SA, Herrmann BG, Nöthen MM, Ludwig M, Reutter H. Classic bladder exstrophy: Frequent 22q11.21 duplications and definition of a 414 kb phenocritical region. ACTA ACUST UNITED AC 2014; 100:512-7. [DOI: 10.1002/bdra.23249] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Revised: 03/18/2014] [Accepted: 03/27/2014] [Indexed: 01/06/2023]
Affiliation(s)
- Markus Draaken
- Institute of Human Genetics; University of Bonn; Bonn Germany
- Department of Genomics; Life & Brain Center; University of Bonn; Bonn Germany
| | - Friederike Baudisch
- Institute of Human Genetics; University of Bonn; Bonn Germany
- Department of Clinical Chemistry and Clinical Pharmacology; University of Bonn; Bonn Germany
| | - Bernd Timmermann
- Next Generation Sequencing Group; Max Planck Institute for Molecular Genetics; Berlin Germany
| | - Heiner Kuhl
- Next Generation Sequencing Group; Max Planck Institute for Molecular Genetics; Berlin Germany
| | - Martin Kerick
- Next Generation Sequencing Group; Max Planck Institute for Molecular Genetics; Berlin Germany
| | - Judith Proske
- Department of Developmental Genetics; Max Planck Institute for Molecular Genetics; Berlin Germany
| | - Lars Wittler
- Department of Developmental Genetics; Max Planck Institute for Molecular Genetics; Berlin Germany
| | - Tracie Pennimpede
- Department of Developmental Genetics; Max Planck Institute for Molecular Genetics; Berlin Germany
| | | | - Wolfgang Rösch
- Department of Pediatric Urology; St. Hedwig Hospital Barmherzige Brμder; Regensburg Germany
| | - Raimund Stein
- Department of Urology; University of Mainz; Mainz Germany
| | - Enrika Bartels
- Institute of Human Genetics; University of Bonn; Bonn Germany
| | - Catharina von Lowtzow
- Institute of Human Genetics; University of Bonn; Bonn Germany
- Department of Genomics; Life & Brain Center; University of Bonn; Bonn Germany
| | - Thomas M. Boemers
- Department of Pediatric Surgery and Pediatric Urology; Children's Hospital Cologne; Cologne Germany
| | - Stefan Herms
- Institute of Human Genetics; University of Bonn; Bonn Germany
- Department of Genomics; Life & Brain Center; University of Bonn; Bonn Germany
- Division of Medical Genetics and Department of Biomedicine; University of Basel; Basel Switzerland
| | - John P. Gearhart
- Division of Urology; The James Buchanan Brady Urological Institute; Johns Hopkins University School of Medicine; Baltimore
| | - Yegappan Lakshmanan
- Children's Hospital of Michigan; Department of Pediatric Urology; Detroit Michigan
| | | | - Gundela Holmdahl
- Department of Pediatric Surgery; Queen Silvia Children's Hospital; Gothenburg Sweden
| | - Göran Läckgren
- Section of Urology; Uppsala Academic Children Hospital; Uppsala Sweden
| | - Agnetha Nordenskjöld
- Department of Women's and Children's Health; Center for Molecular Medicine; Karolinska Institute; Stockholm Sweden
- Department of Pediatric Surgery; Astrid Lindgren Children's Hospital; Karolinska University Hospital; Stockholm Sweden
| | - Simeon A. Boyadjiev
- Section of Genetics; Department of Pediatrics; University of California Davis; Sacramento California
| | - Bernhard G. Herrmann
- Department of Developmental Genetics; Max Planck Institute for Molecular Genetics; Berlin Germany
| | - Markus M. Nöthen
- Institute of Human Genetics; University of Bonn; Bonn Germany
- Department of Genomics; Life & Brain Center; University of Bonn; Bonn Germany
| | - Michael Ludwig
- Department of Clinical Chemistry and Clinical Pharmacology; University of Bonn; Bonn Germany
| | - Heiko Reutter
- Institute of Human Genetics; University of Bonn; Bonn Germany
- Department of Neonatology; Children's Hospital; University of Bonn; Bonn Germany
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Prigione A, Lichtner B, Kuhl H, Struys EA, Wamelink M, Lehrach H, Ralser M, Timmermann B, Adjaye J. HIF1α modulates cell fate reprogramming through early glycolytic shift and upregulation of PDK1-3 and PKM2. Stem Cells 2014; 32:364-76. [PMID: 24123565 PMCID: PMC5730046 DOI: 10.1002/stem.1552] [Citation(s) in RCA: 202] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2013] [Revised: 08/15/2013] [Accepted: 08/27/2013] [Indexed: 12/13/2022]
Abstract
Reprogramming somatic cells to a pluripotent state drastically reconfigures the cellular anabolic requirements, thus potentially inducing cancer-like metabolic transformation. Accordingly, we and others previously showed that somatic mitochondria and bioenergetics are extensively remodeled upon derivation of induced pluripotent stem cells (iPSCs), as the cells transit from oxidative to glycolytic metabolism. In the attempt to identify possible regulatory mechanisms underlying this metabolic restructuring, we investigated the contributing role of hypoxia-inducible factor one alpha (HIF1α), a master regulator of energy metabolism, in the induction and maintenance of pluripotency. We discovered that the ablation of HIF1α function in dermal fibroblasts dramatically hampers reprogramming efficiency, while small molecule-based activation of HIF1α significantly improves cell fate conversion. Transcriptional and bioenergetic analysis during reprogramming initiation indicated that the transduction of the four factors is sufficient to upregulate the HIF1α target pyruvate dehydrogenase kinase (PDK) one and set in motion the glycolytic shift. However, additional HIF1α activation appears critical in the early upregulation of other HIF1α-associated metabolic regulators, including PDK3 and pyruvate kinase (PK) isoform M2 (PKM2), resulting in increased glycolysis and enhanced reprogramming. Accordingly, elevated levels of PDK1, PDK3, and PKM2 and reduced PK activity could be observed in iPSCs and human embryonic stem cells in the undifferentiated state. Overall, the findings suggest that the early induction of HIF1α targets may be instrumental in iPSC derivation via the activation of a glycolytic program. These findings implicate the HIF1α pathway as an enabling regulator of cellular reprogramming.
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Affiliation(s)
- Alessandro Prigione
- Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Björn Lichtner
- Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Heiner Kuhl
- Next Generation Sequencing Group, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Eduard A. Struys
- Department of Clinical Chemistry, Metabolic Unit, VU Medical Center, de Boelelaan 1117, 1081 HV Amsterdam, The Netherlands
| | - Mirjam Wamelink
- Department of Clinical Chemistry, Metabolic Unit, VU Medical Center, de Boelelaan 1117, 1081 HV Amsterdam, The Netherlands
| | - Hans Lehrach
- Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Markus Ralser
- Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Bernd Timmermann
- Next Generation Sequencing Group, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - James Adjaye
- Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
- The Stem Cell Unit, Department of Anatomy, College of Medicine, King Saud University, Riyadh, 11461, Saudi Arabia
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Ralser M, Kuhl H, Ralser M, Werber M, Lehrach H, Breitenbach M, Timmermann B. The Saccharomyces cerevisiae W303-K6001 cross-platform genome sequence: insights into ancestry and physiology of a laboratory mutt. Open Biol 2013; 2:120093. [PMID: 22977733 PMCID: PMC3438534 DOI: 10.1098/rsob.120093] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2012] [Accepted: 07/06/2012] [Indexed: 01/09/2023] Open
Abstract
Saccharomyces cerevisiae strain W303 is a widely used model organism. However, little is known about its genetic origins, as it was created in the 1970s from crossing yeast strains of uncertain genealogy. To obtain insights into its ancestry and physiology, we sequenced the genome of its variant W303-K6001, a yeast model of ageing research. The combination of two next-generation sequencing (NGS) technologies (Illumina and Roche/454 sequencing) yielded an 11.8 Mb genome assembly at an N50 contig length of 262 kb. Although sequencing was substantially more precise and sensitive than whole-genome tiling arrays, both NGS platforms produced a number of false positives. At a 378× average coverage, only 74 per cent of called differences to the S288c reference genome were confirmed by both techniques. The consensus W303-K6001 genome differs in 8133 positions from S288c, predicting altered amino acid sequence in 799 proteins, including factors of ageing and stress resistance. The W303-K6001 (85.4%) genome is virtually identical (less than equal to 0.5 variations per kb) to S288c, and thus originates in the same ancestor. Non-S288c regions distribute unequally over the genome, with chromosome XVI the most (99.6%) and chromosome XI the least (54.5%) S288c-like. Several of these clusters are shared with Σ1278B, another widely used S288c-related model, indicating that these strains share a second ancestor. Thus, the W303-K6001 genome pictures details of complex genetic relationships between the model strains that date back to the early days of experimental yeast genetics. Moreover, this study underlines the necessity of combining multiple NGS and genome-assembling techniques for achieving accurate variant calling in genomic studies.
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Affiliation(s)
- Markus Ralser
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK.
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Abstract
Based on the results of a French cohort of postmenopausal women, it has been claimed that micronized progesterone does not enhance breast cancer risk. The impact of reproductive factors on breast cancer risk and a high prevalence of occult breast carcinomas at the time of menopause suggest an involvement of endogenous progesterone in the development of breast cancer. High mammographic density in the luteal phase and during treatment with estrogen/progestogen combinations reflect a change in the composition of mammary stroma and an increased water accumulation in the extracellular matrix which is caused by hygroscopic hyaluronan-proteoglycan aggregates. Proteoglycans are also involved in the regulation of proliferation, migration, and differentiation of epithelial cells and angiogenesis, and may influence malignant transformation of breast cells and progression of tumors. Reports on a lack of effect of estrogen/progesterone therapy on breast cancer risk may be rooted in a selective prescription to overweight women and/or to the very low progesterone serum levels after oral administration owing to a strong inactivation rate. The contradictory results concerning the proliferative effect of progesterone may be associated with a different local metabolism in normal compared to malignant breast tissue. Similar to other progestogens, hormone replacement therapy with progesterone seems to promote the development of breast cancer, provided that the progesterone serum levels have reached the threshold for endometrial protection.
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Affiliation(s)
- H Kuhl
- Department of Obstetrics and Gynecology, J. W. Goethe University of Frankfurt, Germany
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Buonocore F, Castro R, Randelli E, Lefranc MP, Six A, Kuhl H, Reinhardt R, Facchiano A, Boudinot P, Scapigliati G. Diversity, molecular characterization and expression of T cell receptor γ in a teleost fish, the sea bass (Dicentrarchus labrax, L). PLoS One 2012; 7:e47957. [PMID: 23133531 PMCID: PMC3485050 DOI: 10.1371/journal.pone.0047957] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2012] [Accepted: 09/18/2012] [Indexed: 11/19/2022] Open
Abstract
Two lineages of T cells, expressing either the αβ T cell receptor (TR) or the γδ TR, exist in Gnathostomes. The latter type of T cells account for 1–10 % of T cells in blood and up to 30 % in the small intestine. They may recognize unconventional antigens (phosphorylated microbial metabolites, lipid antigens) without the need of major histocompatibility class I (MH1) or class II (MH2) presentation. In this work we have described cloning and structural characterization of TR -chain (TRG) from the teleost Dicentrarchus labrax. Further, by means of quantitative PCR analysis, we analyzed TRG expression levels both in poly I:C stimulated leukocytes in vitro, and following infection with betanodavirus in vivo. Two full length cDNAs relative to TRG, with the highest peptide and nucleotide identity with Japanese flounder, were identified. A multiple alignment analysis showed the conservation of peptides fundamental for TRG biological functions, and of the FGXG motif in the FR4 region, typical of most TR and immunoglobulin light chains. A 3D structure consisting of two domains mainly folded as beta strands with a sandwich architecture for each domain was also reported. TRG CDR3 of 8–18 AA in length and diversity in the TRG rearrangements expressed in thymus and intestine for a given V/C combination were evidenced by junction length spectratyping. TRG mRNA expression levels were high in basal conditions both in thymus and intestine, while in kidney and gut leukocytes they were up-regulated after in vitro stimulation by poly I:C. Finally, in juveniles the TRG expression levels were up-regulated in the head kidney and down-regulated in intestine after in vivo infection with betanodavirus. Overall, in this study the involvement of TRG-bearing T cells during viral stimulation was described for the first time, leading to new insights for the identification of T cell subsets in fish.
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Affiliation(s)
- Francesco Buonocore
- Department for Innovation in Biological, Agro-Food and Forest Systems, University of Tuscia, Largo dell’Università, Viterbo, Italy
| | - Rosario Castro
- Institut National de la Recherche Agronomique, Unité de Virologie et Immunologie Moléculaires, Jouy-en-Josas, Paris, France
| | - Elisa Randelli
- Department for Innovation in Biological, Agro-Food and Forest Systems, University of Tuscia, Largo dell’Università, Viterbo, Italy
| | - Marie-Paule Lefranc
- The International ImMunoGeneTics Information System®, Laboratoire d’ImmunoGénétique Moléculaire, Institut de Génétique Humaine, Centre National de la Recherche Scientifique and Université Montpellier 2, Montpellier, France
| | - Adrien Six
- Université Pierre et Marie Curie (Université Paris-06), Unité Mixte de Recherches 7211, “Integrative Immunology” Team, Paris, France
- Centre National Recherche Scientifique, Unité Mixte de Recherches, “Immunology, Immunopathology, Immunotherapy”, Paris, France
| | - Heiner Kuhl
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Richard Reinhardt
- Genome Centre at Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Angelo Facchiano
- Laboratory of Bioinformatics and Computational Biology – National Research Council, Istitute of Sciences of Alimentation, Avellino, Italy
| | - Pierre Boudinot
- Institut National de la Recherche Agronomique, Unité de Virologie et Immunologie Moléculaires, Jouy-en-Josas, Paris, France
| | - Giuseppe Scapigliati
- Department for Innovation in Biological, Agro-Food and Forest Systems, University of Tuscia, Largo dell’Università, Viterbo, Italy
- * E-mail:
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Kleppe L, Edvardsen RB, Kuhl H, Malde K, Furmanek T, Drivenes Ø, Reinhardt R, Taranger GL, Wargelius A. Maternal 3'UTRs: from egg to onset of zygotic transcription in Atlantic cod. BMC Genomics 2012; 13:443. [PMID: 22937762 PMCID: PMC3462720 DOI: 10.1186/1471-2164-13-443] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2012] [Accepted: 08/29/2012] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Zygotic transcription in fish embryos initiates around the time of gastrulation, and all prior development is initiated and controlled by maternally derived messenger RNAs. Atlantic cod egg and embryo viability is variable, and it is hypothesized that the early development depends upon the feature of these maternal RNAs. Both the length and the presence of specific motifs in the 3'UTR of maternal RNAs are believed to regulate expression and stability of the maternal transcripts. Therefore, the aim of this study was to characterize the overall composition and 3'UTR structure of the most common maternal RNAs found in cod eggs and pre-zygotic embryos. RESULTS 22229 Sanger-sequences were obtained from 3'-end sequenced cDNA libraries prepared from oocyte, 1-2 cell, blastula and gastrula stages. Quantitative PCR revealed that EST copy number below 9 did not reflect the gene expression profile. Consequently genes represented by less than 9 ESTs were excluded from downstream analyses, in addition to sequences with low-quality gene hits. This provided 12764 EST sequences, encoding 257 unique genes, for further analysis. Mitochondrial transcripts accounted for 45.9-50.6% of the transcripts isolated from the maternal stages, but only 12.2% of those present at the onset of zygotic transcription. 3'UTR length was predicted in nuclear sequences with poly-A tail, which identified 191 3'UTRs. Their characteristics indicated a more complex regulation of transcripts that are abundant prior to the onset of zygotic transcription. Maternal and stable transcripts had longer 3'UTR (mean 187.1 and 208.8 bp) and more 3'UTR isoforms (45.7 and 34.6%) compared to zygotic transcripts, where 15.4% had 3'UTR isoforms and the mean 3'UTR length was 76 bp. Also, diversity and the amount of putative polyadenylation motifs were higher in both maternal and stable transcripts. CONCLUSIONS We report on the most pronounced processes in the maternally transferred cod transcriptome. Maternal stages are characterized by a rich abundance of mitochondrial transcripts. Maternal and stable transcripts display longer 3'UTRs with more variation of both polyadenylation motifs and 3'UTR isoforms. These data suggest that cod eggs possess a complex array of maternal RNAs which likely act to tightly regulate early developmental processes in the newly fertilized egg.
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Affiliation(s)
- Lene Kleppe
- Institute of Marine Research, P. O. Box 1870, Nordnesgaten 50, 5817, Bergen, Norway
| | - Rolf B Edvardsen
- Institute of Marine Research, P. O. Box 1870, Nordnesgaten 50, 5817, Bergen, Norway
| | - Heiner Kuhl
- Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, D-14195, Berlin-Dahlem, Germany
| | - Ketil Malde
- Institute of Marine Research, P. O. Box 1870, Nordnesgaten 50, 5817, Bergen, Norway
| | - Tomasz Furmanek
- Institute of Marine Research, P. O. Box 1870, Nordnesgaten 50, 5817, Bergen, Norway
| | - Øyvind Drivenes
- Institute of Marine Research, P. O. Box 1870, Nordnesgaten 50, 5817, Bergen, Norway
| | - Richard Reinhardt
- Max-Planck Genome centre, MPI fuer Pflanzenzüchtungsforschung, Carl-von-Linné-Weg 10, D-80829, Koeln, Germany
| | - Geir L Taranger
- Institute of Marine Research, P. O. Box 1870, Nordnesgaten 50, 5817, Bergen, Norway
| | - Anna Wargelius
- Institute of Marine Research, P. O. Box 1870, Nordnesgaten 50, 5817, Bergen, Norway
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Tine M, Kuhl H, Jastroch M, Reinhardt R. Genomic characterization of the European sea bass Dicentrarchus labrax reveals the presence of a novel uncoupling protein (UCP) gene family member in the teleost fish lineage. BMC Evol Biol 2012; 12:62. [PMID: 22577775 PMCID: PMC3428666 DOI: 10.1186/1471-2148-12-62] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2011] [Accepted: 05/11/2012] [Indexed: 01/12/2023] Open
Abstract
Background Uncoupling proteins (UCP) are evolutionary conserved mitochondrial carriers that control energy metabolism and therefore play important roles in several physiological processes such as thermogenesis, regulation of reactive oxygen species (ROS), growth control, lipid metabolism and regulation of insulin secretion. Despite their importance in various physiological processes, their molecular function remains controversial. The evolution and phylogenetic distribution may assist to identify their general biological function and structure-function relationships. The exact number of uncoupling protein genes in the fish genome and their evolution is unresolved. Results Here we report the first characterisation of UCP gene family members in sea bass, Dicentrarchus labrax, and then retrace the evolution of the protein family in vertebrates. Four UCP genes that are shared by five other fish species were identified in sea bass genome. Phylogenetic reconstitution among vertebrate species and synteny analysis revealed that UCP1, UCP2 and UCP3 evolved from duplication events that occurred in the common ancestor of vertebrates, whereas the novel fourth UCP originated specifically in the teleost lineage. Functional divergence analysis among teleost species revealed specific amino acid positions that have been subjected to altered functional constraints after duplications. Conclusions This work provides the first unambiguous evidence for the presence of a fourth UCP gene in teleost fish genome and brings new insights into the evolutionary history of the gene family. Our results suggest functional divergence among paralogues which might result from long-term and differential selective pressures, and therefore, provide the indication that UCP genes may have diverse physiological functions in teleost fishes. Further experimental analysis of the critical amino acids identified here may provide valuable information on the physiological functions of UCP genes.
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Affiliation(s)
- Mbaye Tine
- Max Planck Institute for Molecular Genetics, Ihnestresse 63-73, 14195, Berlin, Germany.
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Geay F, Zambonino-Infante J, Reinhardt R, Kuhl H, Santigosa E, Cahu C, Mazurais D. Characteristics of fads2 gene expression and putative promoter in European sea bass (Dicentrarchus labrax): Comparison with salmonid species and analysis of CpG methylation. Mar Genomics 2012; 5:7-13. [DOI: 10.1016/j.margen.2011.08.003] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2011] [Revised: 08/11/2011] [Accepted: 08/13/2011] [Indexed: 11/28/2022]
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Prigione A, Lichtner B, Kuhl H, Struys EA, Wamelink M, Lehrach H, Ralser M, Timmermann B, Adjaye J. Human induced pluripotent stem cells harbor homoplasmic and heteroplasmic mitochondrial DNA mutations while maintaining human embryonic stem cell-like metabolic reprogramming. Stem Cells 2012; 29:1338-48. [PMID: 21732474 DOI: 10.1002/stem.683] [Citation(s) in RCA: 113] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Human induced pluripotent stem cells (iPSCs) have been recently found to harbor genomic alterations. However, the integrity of mitochondrial DNA (mtDNA) within reprogrammed cells has yet to be investigated. mtDNA mutations occur at a high rate and contribute to the pathology of a number of human disorders. Furthermore, the lack of mtDNA integrity may alter cellular bioenergetics and limit efficient differentiation. We demonstrated previously that the derivation of iPSCs is associated with mitochondrial remodeling and a metabolic switch towards glycolysis. Here, we have discovered that alterations of mtDNA can occur upon the induction of pluripotency. Massively parallel pyrosequencing of mtDNA revealed that human iPSCs derived from young healthy donors harbored single base mtDNA mutations (substitutions, insertions, and deletions), both homoplasmic (in all mtDNA molecules) and heteroplasmic (in a fraction of mtDNAs), not present in the parental cells. mtDNA modifications were mostly common variants and not disease related. Moreover, iPSC lines bearing different mtDNA mutational loads maintained a consistent human embryonic stem cell-like reprogramming of energy metabolism. This involved the upregulation of glycolytic enzymes, increased glucose-6-phosphate levels, and the over-expression of pyruvate dehydrogenase kinase 1 protein, which reroutes the bioenergetic flux toward glycolysis. Hence, mtDNA mutations within iPSCs may not necessarily impair the correct establishment of pluripotency and the associated metabolic reprogramming. Nonetheless, the occurrence of pathogenic mtDNA modifications might be an important aspect to monitor when characterizing iPSC lines. Finally, we speculate that this random rearrangement of mtDNA molecules might prove beneficial for the derivation of mutation-free iPSCs from patients with mtDNA disorders.
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Affiliation(s)
- Alessandro Prigione
- Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Berlin, Germany.
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Wang M, Yan G, Yue W, Siu C, Tse H, Perperidis A, Cusack D, White A, Macgillivray T, Mcdicken W, Anderson T, Ryabov V, Shurupov V, Suslova T, Markov V, Elmstedt N, Ferm Widlund K, Lind B, Brodin LA, Westgren M, Mantovani F, Barbieri A, Bursi F, Valenti C, Quaglia M, Modena M, Peluso D, Muraru D, Dal Bianco L, Beraldo M, Solda' E, Tuveri M, Cucchini U, Al Mamary A, Badano L, Iliceto S, Goncalves A, Almeria C, Marcos-Alberca P, Feltes G, Hernandez-Antolin R, Rodriguez H, Maroto L, Silva Cardoso J, Macaya C, Zamorano J, Squarciotta S, Innocenti F, Guzzo A, Bianchi S, Lazzeretti D, De Villa E, Vicidomini S, Del Taglia B, Donnini C, Pini R, Mennie C, Salmasi AM, Kutyifa V, Nagy V, Edes E, Apor A, Merkely B, Nyrnes S, Lovstakken L, Torp H, Haugen B, Said K, Shehata A, Ashour Z, El-Tobgy S, Cameli M, Bigio E, Lisi M, Righini F, Franchi F, Scolletta S, Mondillo S, Gayat E, Weinert L, Yodwut C, Mor-Avi V, Lang R, Hrynchyshyn N, Kachenoura N, Diebold B, Khedim R, Senesi M, Redheuil A, Mousseaux E, Perdrix L, Yurdakul S, Erdemir V, Tayyareci Y, Memic K, Yildirimturk O, Aytekin V, Gurel M, Aytekin S, Gargani L, Fernandez Cimadevilla C, La Falce S, Landi P, Picano E, Sicari R, Smedsrud MK, Gravning J, Eek C, Morkrid L, Skulstad H, Aaberge L, Bendz B, Kjekshus J, Edvardsen T, Bajraktari G, Hyseni V, Morina B, Batalli A, Tafarshiku R, Olloni R, Henein M, Mjolstad O, Snare S, Folkvord L, Helland F, Torp H, Haraldseth O, Grimsmo A, Haugen B, Berry M, Zaghden O, Nahum J, Macron L, Lairez O, Damy T, Bensaid A, Dubois Rande J, Gueret P, Lim P, Nciri N, Issaoui Z, Tlili C, Wanes I, Foudhil H, Dachraoui F, Grapsa J, Dawson D, Nihoyannopoulos P, Gianturco L, Turiel M, Atzeni F, Sarzi-Puttini P, Stella D, Donato L, Tomasoni L, Jung P, Mueller M, Huber T, Sevilmis G, Kroetz F, Sohn H, Panoulas V, Bratsas A, Dawson D, Nihoyannopoulos P, Raso R, Tartarisco G, Gargani L, La Falce S, Pioggia G, Picano E, Gargiulo P, Petretta M, Cuocolo A, Prastaro M, D'amore C, Vassallo E, Savarese G, Marciano C, Paolillo S, Perrone Filardi P, Aggeli C, Felekos I, Roussakis G, Poulidakis E, Pietri P, Toutouzas K, Stefanadis C, Kaladaridis A, Skaltsiotis I, Kottis G, Bramos D, Takos D, Matthaios I, Agrios I, Papadopoulou E, Moulopoulos S, Toumanidis S, Carrilho-Ferreira P, Cortez-Dias N, Jorge C, Silva D, Silva Marques J, Placido R, Santos L, Ribeiro S, Fiuza M, Pinto F, Stoickov V, Ilic S, Deljanin Ilic M, Kim W, Woo J, Bae J, Kim K, Descalzo M, Rodriguez J, Moral S, Otaegui I, Mahia P, Garcia Del Blanco L, Gonzalez Alujas T, Figueras J, Evangelista A, Garcia-Dorado D, Takeuchi M, Kaku K, Otani K, Iwataki M, Kuwaki H, Haruki N, Yoshitani H, Otsuji Y, Kukucka M, Pasic M, Unbehaun A, Dreysse S, Mladenow A, Kuppe H, Hetzer R, Rajamannan N, Yurdakul S, Tayyareci Y, Tanrikulu A, Yildirimturk O, Aytekin V, Aytekin S, Kristiansson L, Gustafsson S, Lindmark K, Henein MY, Evdoridis C, Stougiannos P, Thomopoulos M, Fosteris M, Spanos P, Sionis G, Giatsios D, Paschalis A, Sakellaris C, Trikas A, Yong ZY, Boerlage-Van Dijk K, Koch K, Vis M, Bouma B, Piek J, Baan J, Abid L, Frikha Z, Makni K, Maazoun N, Abid D, Hentati M, Kammoun S, Barbier P, Staron A, Cefalu' C, Berna G, Gripari P, Andreini D, Pontone G, Pepi M, Ring L, Rana B, Ho S, Wells F, Yurdakul S, Tayyareci Y, Yildirimturk O, Dogan A, Aytekin V, Aytekin S, Karaca O, Guler G, Guler E, Gunes H, Alizade E, Agus H, Gol G, Esen O, Esen A, Turkmen M, Agricola E, Ingallina G, Ancona M, Maggio S, Slavich M, Tufaro V, Oppizzi M, Margonato A, Orsborne C, Irwin B, Pearce K, Ray S, Garcia Alonso C, Vallejo N, Labata C, Lopez Ayerbe J, Teis A, Ferrer E, Nunez Aragon R, Gual F, Pedro Botet M, Bayes Genis A, Santos CM, Carvalho M, Andrade M, Dores H, Madeira S, Cardoso G, Ventosa A, Aguiar C, Ribeiras R, Mendes M, Petrovic M, Petrovic M, Milasinovic G, Vujisic-Tesic B, Nedeljkovic I, Zamaklar-Trifunovic D, Petrovic I, Draganic G, Banovic M, Boricic M, Villarraga H, Molini-Griggs Bs C, Silen-Rivera Bs P, Payne Mph Ms B, Koshino Md Phd Y, Hsiao Md J, Monivas Palomero V, Mingo Santos S, Mitroi C, Garcia Lunar I, Garcia Pavia P, Castro Urda V, Toquero J, Gonzalez Mirelis J, Cavero Gibanel M, Fernandez Lozano I, Oko-Sarnowska Z, Wachowiak-Baszynska H, Katarzynska-Szymanska A, Trojnarska O, Grajek S, Bellavia D, Pellikka P, Dispenzieri A, Oh JK, Polizzi V, Pitrolo F, Musumeci F, Miller F, Ancona R, Comenale Pinto S, Caso P, Severino S, Cavallaro C, Vecchione F, D'onofrio A, Calabro' R, Maceira Gonzalez AM, Ripoll C, Cosin-Sales J, Igual B, Salazar J, Belloch V, Cosin-Aguilar J, Pinamonti B, Iorio A, Bobbo M, Merlo M, Barbati G, Massa L, Faganello G, Di Lenarda A, Sinagra GF, Ishizu T, Seo Y, Enomoto M, Kameda Y, Ishibashi N, Inoue M, Aonuma K, Saleh A, Matsumori A, Negm H, Fouad H, Onsy A, Hamodraka E, Paraskevaidis I, Kallistratos M, Lezos V, Zamfir T, Manetos C, Mavropoulos D, Poulimenos L, Kremastinos D, Manolis A, Citro R, Rigo F, Ciampi Q, Patella M, Provenza G, Zito C, Tagliamonte E, Rotondi F, Silvestri F, Bossone E, Monivas Palomero V, Mingo Santos S, Beltran Correas P, Gutierrez Landaluce C, Mitroi C, Garcia Lunar I, Gonzalez Mirelis J, Cavero Gibanel M, Gomez Bueno M, Segovia Cubero J, Beladan C, Matei F, Popescu B, Calin A, Rosca M, Boanta A, Enache R, Savu O, Usurelu C, Ginghina C, Ciobanu AO, Dulgheru R, Magda S, Dragoi R, Florescu M, Vinereanu D, Silva Marques J, Robalo Martins S, Jorge C, Calisto C, Goncalves S, Ribeiro S, Barrigoto I, Carvalho De Sousa J, Almeida A, Nunes Diogo A, Sargento L, Satendra M, Sousa C, Lousada N, Palma Reis R, Schiano Lomoriello V, Esposito R, Santoro A, Raia R, Schiattarella P, Dores E, Galderisi M, Mansencal N, Caille V, Dupland A, Perrot S, Bouferrache K, Vieillard-Baron A, Jouffroy R, Moceri P, Liodakis E, Gatzoulis M, Li W, Dimopoulos K, Sadron M, Seguela PE, Arnaudis B, Dulac Y, Cognet T, Acar P, Shiina Y, Gatzoulis M, Uemura H, Li W, Kupczynska K, Kasprzak J, Michalski B, Lipiec P, Carvalho V, Almeida AMG, David C, Marques J, Silva D, Cortez-Dias N, Ferreira P, Amaro M, Costa P, Diogo A, Tritakis V, Ikonomidis I, Paraskevaidis I, Lekakis J, Tzortzis S, Kadoglou N, Papadakis I, Trivilou P, Koukoulis C, Anastasiou-Nana M, Bombardini T, Picano E, Gherardi S, Arpesella G, Maccherini M, Serra W, Magnani G, Del Bene R, Pasanisi E, Sicari R, Startari U, Panchetti L, Rossi A, Piacenti M, Morales M, Mansencal N, El Hajjaji I, El Mahmoud R, Digne F, Dubourg O, Gargani L, Agoston G, Moreo A, Pratali L, Moggi Pignone A, Pavellini A, Doveri M, Musca F, Varga A, Picano E, Pratali L, Faita F, Rimoldi S, Sartori C, Alleman Y, Salinas Salmon C, Villena M, Scherrer U, Picano E, Sicari R, Baptista R, Serra S, Castro G, Martins R, Salvador M, Monteiro P, Silva J, Szudi L, Temesvary A, Fekete B, Kassai I, Szekely L, Abdel Moneim SS, Martinez M, Mankad S, Bernier M, Dhoble A, Pellikka P, Chandrasekaran K, Oh J, Mulvagh S, Hong GR, Kim JY, Lee SC, Choi SH, Sohn IS, Seo HS, Choi JH, Cho KI, Yoon SJ, Lim SJ, Lipiec P, Wejner-Mik P, Kusmierek J, Plachcinska A, Szuminski R, Kasprzak J, Stoebe S, Tarr A, Trache T, Hagendorff A, Mor-Avi V, Yodwut C, Jenkins C, Kuhl H, Nesser H, Marwick T, Franke A, Niel J, Sugeng L, Lang R, Gustafsson S, Henein M, Soderberg S, Lindmark K, Lindqvist P, Necas J, Kovalova S, Saha SK, Kiotsekoglou A, Toole R, Govind S, Gopal A, Amzulescu MS, Florian A, Bogaert J, Janssens S, Voigt J, Parisi V, Losi M, Parrella L, Contaldi C, Chiacchio E, Caputi A, Scatteia A, Buonauro A, Betocchi S, Rimbas R, Dulgheru R, Mihaila S, Vinereanu D, Caputo M, Navarri R, Innelli P, Urselli R, Capati E, Ballo P, Furiozzi F, Favilli R, Mondillo S, Lindquist R, Miller A, Reece C, O'leary P, Cetta F, Eidem BW, Cikes M, Gasparovic H, Bijnens B, Velagic V, Kopjar T, Biocina B, Milicic D, Ta-Shma A, Nir A, Perles Z, Gavri S, Golender J, Rein A, Pinnacchio G, Barone L, Battipaglia I, Cosenza A, Marinaccio L, Coviello I, Scalone G, Sestito A, Lanza G, Crea F, Cakal S, Eroglu E, Ozkan B, Kulahcioglu S, Bulut M, Koyuncu A, Acar G, Alici G, Dundar C, Esen A, Labombarda F, Zangl E, Pellissier A, Bougle D, Maragnes P, Milliez P, Saloux E, Aggeli C, Lagoudakou S, Felekos I, Gialafos E, Poulidakis E, Tsokanis A, Roussakis G, Stefanadis C, Nagy A, Kovats T, Apor A, Vago H, Toth A, Sax B, Kovacs A, Merkely B, Elnoamany MF, Badran H, Abdelfattah I, Khalil T, Salama M, Butz T, Taubenberger C, Thangarajah F, Meissner A, Van Bracht M, Prull M, Yeni H, Plehn G, Trappe H, Rydman R, Bone D, Alam M, Caidahl K, Larsen F, Staron A, Gasior Z, Tabor Z, Sengupta P, Liu D, Niemann M, Hu K, Herrmann S, Stoerk S, Morbach C, Knop S, Voelker W, Ertl G, Weidemann F, Cawley P, Hamilton-Craig C, Mitsumori L, Maki J, Otto C, Astrom Aneq M, Nylander E, Ebbers T, Engvall J, Arvanitis P, Flachskampf F, Duvernoy O, De Torres Alba F, Valbuena Lopez S, Guzman Martinez G, Gomez De Diego J, Rey Blas J, Armada Romero E, Lopez De Sa E, Moreno Yanguela M, Lopez Sendon J, Aggeli C, Felekos I, Poulidakis E, Trikalinos N, Siasos G, Aggeli A, Roussakis G, Stefanadis C, Tomaszewski A, Kutarski A, Tomaszewski M, Ikonomidis I, Lekakis J, Tritakis V, Tzortzis S, Kadoglou N, Papadakis I, Trivilou P, Anastasiou-Nana M, Koukoulis C, Paraskevaidis I, Vriz O, Driussi C, Bettio M, Pavan D, Bossone E, Antonini Canterin F, Doltra Magarolas A, Fernandez-Armenta J, Silva E, Solanes N, Rigol M, Barcelo A, Mont L, Berruezo A, Brugada J, Sitges M, Ciciarello FL, Mandolesi S, Fedele F, Agati L, Marceca A, Rhee S, Shin S, Kim S, Yun K, Yoo N, Kim N, Oh S, Jeong J, Alabdulkarim N. Poster Session 4: Friday 9 December 2011, 14:00-18:00 * Location: Poster Area. European Journal of Echocardiography 2011. [DOI: 10.1093/ejechocard/jer216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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Star B, Nederbragt AJ, Jentoft S, Grimholt U, Malmstrøm M, Gregers TF, Rounge TB, Paulsen J, Solbakken MH, Sharma A, Wetten OF, Lanzén A, Winer R, Knight J, Vogel JH, Aken B, Andersen O, Lagesen K, Tooming-Klunderud A, Edvardsen RB, Tina KG, Espelund M, Nepal C, Previti C, Karlsen BO, Moum T, Skage M, Berg PR, Gjøen T, Kuhl H, Thorsen J, Malde K, Reinhardt R, Du L, Johansen SD, Searle S, Lien S, Nilsen F, Jonassen I, Omholt SW, Stenseth NC, Jakobsen KS. The genome sequence of Atlantic cod reveals a unique immune system. Nature 2011; 477:207-10. [PMID: 21832995 DOI: 10.1038/nature10342] [Citation(s) in RCA: 532] [Impact Index Per Article: 40.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2011] [Accepted: 06/28/2011] [Indexed: 01/24/2023]
Abstract
Atlantic cod (Gadus morhua) is a large, cold-adapted teleost that sustains long-standing commercial fisheries and incipient aquaculture. Here we present the genome sequence of Atlantic cod, showing evidence for complex thermal adaptations in its haemoglobin gene cluster and an unusual immune architecture compared to other sequenced vertebrates. The genome assembly was obtained exclusively by 454 sequencing of shotgun and paired-end libraries, and automated annotation identified 22,154 genes. The major histocompatibility complex (MHC) II is a conserved feature of the adaptive immune system of jawed vertebrates, but we show that Atlantic cod has lost the genes for MHC II, CD4 and invariant chain (Ii) that are essential for the function of this pathway. Nevertheless, Atlantic cod is not exceptionally susceptible to disease under natural conditions. We find a highly expanded number of MHC I genes and a unique composition of its Toll-like receptor (TLR) families. This indicates how the Atlantic cod immune system has evolved compensatory mechanisms in both adaptive and innate immunity in the absence of MHC II. These observations affect fundamental assumptions about the evolution of the adaptive immune system and its components in vertebrates.
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Affiliation(s)
- Bastiaan Star
- Centre for Ecological and Evolutionary Synthesis, Department of Biology, University of Oslo, PO Box 1066, Blindern, N-0316 Oslo, Norway
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Kuhl H, Tine M, Beck A, Timmermann B, Kodira C, Reinhardt R. Directed sequencing and annotation of three Dicentrarchus labrax L. chromosomes by applying Sanger- and pyrosequencing technologies on pooled DNA of comparatively mapped BAC clones. Genomics 2011; 98:202-12. [PMID: 21693181 DOI: 10.1016/j.ygeno.2011.06.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2010] [Revised: 05/31/2011] [Accepted: 06/03/2011] [Indexed: 02/02/2023]
Abstract
Dicentrarchus labrax is one of the major marine aquaculture species in the European Union. In this study, we have developed a directed-sequencing strategy to sequence three sea bass chromosomes and compared results with other teleosts. Three BAC DNA pools were created from sea bass BAC clones that mapped to stickleback chromosomes/groups V, XVII and XXI. The pools were sequenced to 17-39x coverage by pyrosequencing. Data assembly was supported by Sanger reads and mate pair data and resulted in superscaffolds of 13.2 Mb, 17.5 Mb and 13.7 Mb respectively. Annotation features of the superscaffolds include 1477 genes. We analyzed size change of exon, intron and intergenic sequence between teleost species and deduced a simple model for the evolution of genome composition in teleost lineage. Combination of second generation sequencing technologies, Sanger sequencing and genome partitioning strategies allows "high-quality draft assemblies" of chromosome-sized superscaffolds, which are crucial for the prediction and annotation of complete genes.
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Affiliation(s)
- Heiner Kuhl
- Max Planck Institute for Molecular Genetics, Ihnestrasse 63, D-14195 Berlin, Germany.
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Neves JV, Wilson JM, Kuhl H, Reinhardt R, Castro LFC, Rodrigues PNS. Natural history of SLC11 genes in vertebrates: tales from the fish world. BMC Evol Biol 2011; 11:106. [PMID: 21501491 PMCID: PMC3103463 DOI: 10.1186/1471-2148-11-106] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2010] [Accepted: 04/18/2011] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND The SLC11A1/Nramp1 and SLC11A2/Nramp2 genes belong to the SLC11/Nramp family of transmembrane divalent metal transporters, with SLC11A1 being associated with resistance to pathogens and SLC11A2 involved in intestinal iron uptake and transferrin-bound iron transport. Both members of the SLC11 gene family have been clearly identified in tetrapods; however SLC11A1 has never been documented in teleost fish and is believed to have been lost in this lineage during early vertebrate evolution. In the present work we characterized the SLC11 genes in teleosts and evaluated if the roles attributed to mammalian SLC11 genes are assured by other fish specific SLC11 gene members. RESULTS Two different SLC11 genes were isolated in the European sea bass (Dicentrarchus. labrax), and named slc11a2-α and slc11a2-β, since both were found to be evolutionary closer to tetrapods SLC11A2, through phylogenetic analysis and comparative genomics. Induction of slc11a2-α and slc11a2-β in sea bass, upon iron modulation or exposure to Photobacterium damselae spp. piscicida, was evaluated in in vivo or in vitro experimental models. Overall, slc11a2-α was found to respond only to iron deficiency in the intestine, whereas slc11a2-β was found to respond to iron overload and bacterial infection in several tissues and also in the leukocytes. CONCLUSIONS Our data suggests that despite the absence of slc11a1, its functions have been undertaken by one of the slc11a2 duplicated paralogs in teleost fish in a case of synfunctionalization, being involved in both iron metabolism and response to bacterial infection. This study provides, to our knowledge, the first example of this type of sub-functionalization in iron metabolism genes, illustrating how conserving the various functions of the SLC11 gene family is of crucial evolutionary importance.
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Affiliation(s)
- João V Neves
- Iron and Innate Immunity, Instituto de Biologia Molecular e Celular (IBMC), Rua do Campo Alegre 823, 4150-180 Porto, Portugal
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Tine M, Kuhl H, Beck A, Bargelloni L, Reinhardt R. Comparative analysis of intronless genes in teleost fish genomes: insights into their evolution and molecular function. Mar Genomics 2011; 4:109-19. [PMID: 21620332 DOI: 10.1016/j.margen.2011.03.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2011] [Revised: 02/28/2011] [Accepted: 03/09/2011] [Indexed: 10/18/2022]
Abstract
This study assessed the relationship between the occurrence and function of intronless or single exon genes (SEG) in the genome of five teleost species and their phylogenetic distance. The results revealed that Takifugu rubripes, Tetraodon nigroviridis, Oryzias latipes, Gasterosteus aculeatus and Danio rerio genomes are respectively comprised of 2.83%, 3.42%, 4.49%, 4.35% and 4.02% SEGs. These SEGs encode for a variety of family proteins including claudins, olfactory receptors and histones that are essential for various biological functions. Subsequently, we predicted and annotated SEGs in three European sea bass, Dicentrarchus labrax chromosomes that we have sequenced, and compared results with those of stickleback (G. aculeatus) homologous chromosomes. While the annotation features of three D. labrax chromosomes revealed 78 (5.30%) intronless genes, comparisons with G. aculeatus showed that SEG composition and their order varied significantly among corresponding chromosomes, even for those with nearly complete synteny. More than half of SEGs identified in most of the species have at least one ortholog multiple exon gene in the same genome, which provides insight to their possible origin by retrotransposition. In spite of the fact that they belong to the same lineage, the fraction of predicted SEGs varied significantly between the genomes analyzed, and only a low fraction of proteins (4.1%) is conserved between all five species. Furthermore, the inter-specific distribution of SEGs as well as the functional categories shared by species did not reflect their phylogenetic relationships. These results indicate that new SEGs are continuously and independently generated after species divergence over evolutionary time as evidenced by the phylogenetic results of single exon claudins genes. Although the origin of SEGs cannot be inferred directly from the phylogeny, our results provide strong support for the idea that retrotransposition followed by tandem duplications is the most probable event that can explain the expansion of SEGs in eukaryotic organisms.
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Affiliation(s)
- Mbaye Tine
- Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, D-14195 Berlin, Germany.
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Santigosa E, Geay F, Tonon T, Le Delliou H, Kuhl H, Reinhardt R, Corcos L, Cahu C, Zambonino-Infante JL, Mazurais D. Cloning, tissue expression analysis, and functional characterization of two Δ6-desaturase variants of sea bass (Dicentrarchus labrax L.). Mar Biotechnol (NY) 2011; 13:22-31. [PMID: 20333428 DOI: 10.1007/s10126-010-9264-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2009] [Accepted: 12/16/2009] [Indexed: 05/29/2023]
Abstract
Fish are the main source of the n-3 highly unsaturated fatty acids, which are crucial for human health. Their synthesis from C(18) precursors is mediated by desaturases and elongases, but the activity of these enzymes has not been conclusively established in marine fish species. This study reports the cloning, tissue expression, and functional characterization of a sea bass (Dicentrarchus labrax L.) Δ6-desaturase and one of its splicing variants. Two cDNAs with open reading frames of 1,346 and 1,354 bp were cloned and named D6D and D6D-V, respectively. Both deduced protein sequences (445 and 387 amino acids, respectively) contained two transmembrane regions and the N-terminal cytochrome b(5) domain with the HPGG motif characteristic of microsomal desaturases. D6D presents three histidine-rich regions, whereas in D6D-V, an insertion of eight nucleotides in the boundaries of exons 10 and 11 modified the third histidine-rich domain and led to insertion of a premature STOP codon, resulting in a shorter predicted protein. Quantitative real-time polymerase chain reaction assay of gene expression showed that D6D was highly expressed in the brain and intestine, and to a lesser extent, in muscle and liver; meanwhile, D6D-V was expressed in all tissues tested, but at level at least 200-fold lower than D6D. Functional analysis in yeast showed that sea bass D6D encodes a fully functional Δ6-desaturase with no residual Δ5-desaturase activity. This desaturase does not exhibit a clear preference for n-3 versus n-6 C(18) substrates. Interestingly, D6D-V is a nonfunctional protein, suggesting that the C-terminal end is indispensable for protein activity.
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Affiliation(s)
- Ester Santigosa
- Ifremer Marine Fish Nutrition Team, Nutrition Aquaculture and Genomics Research Unit, UMR 1067, Ifremer, Technopole Brest-Iroise, BP 70, 29280, Plouzané, France
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Negrisolo E, Kuhl H, Forcato C, Vitulo N, Reinhardt R, Patarnello T, Bargelloni L. Different phylogenomic approaches to resolve the evolutionary relationships among model fish species. Mol Biol Evol 2010; 27:2757-74. [PMID: 20591844 DOI: 10.1093/molbev/msq165] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Comparative genomics holds the promise to magnify the information obtained from individual genome sequencing projects, revealing common features conserved across genomes and identifying lineage-specific characteristics. To implement such a comparative approach, a robust phylogenetic framework is required to accurately reconstruct evolution at the genome level. Among vertebrate taxa, teleosts represent the second best characterized group, with high-quality draft genome sequences for five model species (Danio rerio, Gasterosteus aculeatus, Oryzias latipes, Takifugu rubripes, and Tetraodon nigroviridis), and several others are in the finishing lane. However, the relationships among the acanthomorph teleost model fishes remain an unresolved taxonomic issue. Here, a genomic region spanning over 1.2 million base pairs was sequenced in the teleost fish Dicentrarchus labrax. Together with genomic data available for the above fish models, the new sequence was used to identify unique orthologous genomic regions shared across all target taxa. Different strategies were applied to produce robust multiple gene and genomic alignments spanning from 11,802 to 186,474 amino acid/nucleotide positions. Ten data sets were analyzed according to Bayesian inference, maximum likelihood, maximum parsimony, and neighbor joining methods. Extensive analyses were performed to explore the influence of several factors (e.g., alignment methodology, substitution model, data set partitions, and long-branch attraction) on the tree topology. Although a general consensus was observed for a closer relationship between G. aculeatus (Gasterosteidae) and Di. labrax (Moronidae) with the atherinomorph O. latipes (Beloniformes) sister taxon of this clade, with the tetraodontiform group Ta. rubripes and Te. nigroviridis (Tetraodontiformes) representing a more distantly related taxon among acanthomorph model fish species, conflicting results were obtained between data sets and methods, especially with respect to the choice of alignment methodology applied to noncoding parts of the genomic region under study. This may limit the use of intergenic/noncoding sequences in phylogenomics until more robust alignment algorithms are developed.
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Affiliation(s)
- Enrico Negrisolo
- Department of Public Health, Comparative Pathology and Veterinary Hygiene, University of Padova, Agripolis, Legnaro, Italy.
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Kube M, Migdoll AM, Gehring I, Heitmann K, Mayer Y, Kuhl H, Knaust F, Geider K, Reinhardt R. Genome comparison of the epiphytic bacteria Erwinia billingiae and E. tasmaniensis with the pear pathogen E. pyrifoliae. BMC Genomics 2010; 11:393. [PMID: 20565991 PMCID: PMC2897811 DOI: 10.1186/1471-2164-11-393] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2009] [Accepted: 06/22/2010] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND The genus Erwinia includes plant-associated pathogenic and non-pathogenic Enterobacteria. Important pathogens such as Erwinia amylovora, the causative agent of fire blight and E. pyrifoliae causing bacterial shoot blight of pear in Asia belong to this genus. The species E. tasmaniensis and E. billingiae are epiphytic bacteria and may represent antagonists for biocontrol of fire blight. The presence of genes that are putatively involved in virulence in E. amylovora and E. pyrifoliae is of special interest for these species in consequence. RESULTS Here we provide the complete genome sequences of the pathogenic E. pyrifoliae strain Ep1/96 with a size of 4.1 Mb and of the non-pathogenic species E. billingiae strain Eb661 with a size of 5.4 Mb, de novo determined by conventional Sanger sequencing and next generation sequencing techniques. Genome comparison reveals large inversions resulting from homologous recombination events. Furthermore, comparison of deduced proteins highlights a relation of E. billingiae strain Eb661 to E. tasmaniensis strain Et1/99 and a distance to E. pyrifoliae for the overall gene content as well as for the presence of encoded proteins representing virulence factors for the pathogenic species. Pathogenicity of E. pyrifoliae is supposed to have evolved by accumulation of potential virulence factors. E. pyrifoliae carries factors for type III secretion and cell invasion. Other genes described as virulence factors for E. amylovora are involved in the production of exopolysaccharides, the utilization of plant metabolites such as sorbitol and sucrose. Some virulence-associated genes of the pathogenic species are present in E. tasmaniensis but mostly absent in E. billingiae. CONCLUSION The data of the genome analyses correspond to the pathogenic lifestyle of E. pyrifoliae and underlines the epiphytic localization of E. tasmaniensis and E. billingiae as a saprophyte.
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Affiliation(s)
- Michael Kube
- Max Planck Institute for Molecular Genetics, htpt group, Ihnestr. 63, D-14195 Berlin, Germany
| | - Alexander M Migdoll
- Max Planck Institute for Molecular Genetics, htpt group, Ihnestr. 63, D-14195 Berlin, Germany
| | - Isabel Gehring
- Julius Kuehn Institute, Institute for Plant Protection in Fruit Crops and Viticulture, Schwabenheimer Str. 101, D-69221 Dossenheim, Germany
- Heidelberg Institute for Plant Science, Neuenheimer Feld 360, D-69120 Heidelberg, Germany
| | - Katja Heitmann
- Max Planck Institute for Molecular Genetics, htpt group, Ihnestr. 63, D-14195 Berlin, Germany
| | - Yvonne Mayer
- Max Planck Institute for Molecular Genetics, htpt group, Ihnestr. 63, D-14195 Berlin, Germany
| | - Heiner Kuhl
- Max Planck Institute for Molecular Genetics, htpt group, Ihnestr. 63, D-14195 Berlin, Germany
| | - Florian Knaust
- Max Planck Institute for Molecular Genetics, htpt group, Ihnestr. 63, D-14195 Berlin, Germany
| | - Klaus Geider
- Julius Kuehn Institute, Institute for Plant Protection in Fruit Crops and Viticulture, Schwabenheimer Str. 101, D-69221 Dossenheim, Germany
| | - Richard Reinhardt
- Max Planck Institute for Molecular Genetics, htpt group, Ihnestr. 63, D-14195 Berlin, Germany
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Wiegratz I, Stahlberg S, Manthey T, Sänger N, Mittmann K, Palombo-Kinne E, Mellinger U, Lange E, Kuhl H. Effects of combined oral contraceptive ethinylestradiol (30 microg) and dienogest (2 mg) on carbohydrate metabolism during 1 year of conventional or extended-cycle use. Horm Metab Res 2010; 42:358-63. [PMID: 20213585 DOI: 10.1055/s-0030-1248263] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
The effects of extended regimens of combined oral contraceptives (COCs) on carbohydrate metabolism are largely unknown. The present study compared the effects of a COC containing 30 microg ethinylestradiol and 2 mg dienogest (EE/DNG) in conventional and extended-cycle regimen over 1 year. Parameters of carbohydrate metabolism were measured in 59 women treated with EE/DNG either conventionally (13 cycles of 21+7 days) or in extended-cycle regimen (4 cycles of 84+7 days). Blood samples were taken in a control cycle, and at 3 and 12 months of treatment. The mean levels of HbA1c and fasting glucose levels remained stable in both conventional and extended-regimen of EE/DNG. The mean levels of fasting insulin and C-peptide underwent comparable increases in both regimens, suggesting a similar readjustment of glucose metabolism via slightly increased insulin secretion. For both regimens, the response to the oral glucose tolerance test (OGTT) showed a slightly impaired glucose tolerance and insulin resistance at 3 months. These changes improved or returned to baseline at 12 months. Accordingly, the mean index for insulin resistance (homeostasis model assessment of insulin resistance, HOMA-IR) increased and the mean insulin sensitivity index [ISI (composite)] decreased modestly in both groups. The present study demonstrates that there are no statistically significant differences between the effects of conventional and extended-cycle treatment on carbohydrate metabolism over 1 year of treatment. In general, the effects of both regimens were moderate and mostly transient.
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Affiliation(s)
- I Wiegratz
- Center of Obstetrics and Gynecology, University Hospital of Frankfurt, Frankfurt am Main, Germany.
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Kuhl H, Tine M, Hecht J, Knaust F, Reinhardt R. Analysis of single nucleotide polymorphisms in three chromosomes of European sea bass Dicentrarchus labrax. Comp Biochem Physiol Part D Genomics Proteomics 2010; 6:70-5. [PMID: 20452842 DOI: 10.1016/j.cbd.2010.04.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2010] [Revised: 04/09/2010] [Accepted: 04/10/2010] [Indexed: 12/16/2022]
Abstract
Single nucleotide polymorphisms (SNPs) are believed to contain relevant information and have been therefore extensively used as genetic markers in population and conservation genetics, and molecular ecology studies. This study reports on the identification of potential SNPs in a diploid European sea bass Dicentrarchus labrax genome by using reference sequences from three assembled chromosomes and mapping all WGS datasets onto them (3× Sanger, 3× 454 and 20× SOLEXA). A total of 20,779 SNPs were identified over the 1469 gene loci and intergenic space analysed. Within chromosomes the occurrence of SNPs was the lowest in exons and higher in introns and intergenic regions, which may be explained by the fact, that coding regions are under strong selective pressure to maintain their biological function. The ratio of nonsynonymous to synonymous mutations was smaller than one for all the chromosomes, suggesting that most of deleterious nonsynonymous mutations were eliminated by negative selection. SNPs were not uniformly distributed over the chromosomes. Two chromosomes exhibited large regions with extremely low SNP density, which might represent homozygous regions in the diploid genome. The results of this study show how SNP detection can take profit from sequencing a single diploid individual, but also uncover the limits of such an approach. SNPs that have been identified will support marker development for genetic linkage mapping, population genetics and aquaculture related questions in general.
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Affiliation(s)
- Heiner Kuhl
- Max Planck Institute for Molecular Genetics, Berlin, Germany.
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Kuhl H, Beck A, Wozniak G, Canario AVM, Volckaert FAM, Reinhardt R. The European sea bass Dicentrarchus labrax genome puzzle: comparative BAC-mapping and low coverage shotgun sequencing. BMC Genomics 2010; 11:68. [PMID: 20105308 PMCID: PMC2837037 DOI: 10.1186/1471-2164-11-68] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2009] [Accepted: 01/27/2010] [Indexed: 11/20/2022] Open
Abstract
Background Food supply from the ocean is constrained by the shortage of domesticated and selected fish. Development of genomic models of economically important fishes should assist with the removal of this bottleneck. European sea bass Dicentrarchus labrax L. (Moronidae, Perciformes, Teleostei) is one of the most important fishes in European marine aquaculture; growing genomic resources put it on its way to serve as an economic model. Results End sequencing of a sea bass genomic BAC-library enabled the comparative mapping of the sea bass genome using the three-spined stickleback Gasterosteus aculeatus genome as a reference. BAC-end sequences (102,690) were aligned to the stickleback genome. The number of mappable BACs was improved using a two-fold coverage WGS dataset of sea bass resulting in a comparative BAC-map covering 87% of stickleback chromosomes with 588 BAC-contigs. The minimum size of 83 contigs covering 50% of the reference was 1.2 Mbp; the largest BAC-contig comprised 8.86 Mbp. More than 22,000 BAC-clones aligned with both ends to the reference genome. Intra-chromosomal rearrangements between sea bass and stickleback were identified. Size distributions of mapped BACs were used to calculate that the genome of sea bass may be only 1.3 fold larger than the 460 Mbp stickleback genome. Conclusions The BAC map is used for sequencing single BACs or BAC-pools covering defined genomic entities by second generation sequencing technologies. Together with the WGS dataset it initiates a sea bass genome sequencing project. This will allow the quantification of polymorphisms through resequencing, which is important for selecting highly performing domesticated fish.
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Affiliation(s)
- Heiner Kuhl
- Max Planck Institute for Molecular Genetics, D-14195 Berlin, Germany.
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Abi-Rached L, Kuhl H, Roos C, ten Hallers B, Zhu B, Carbone L, de Jong PJ, Mootnick AR, Knaust F, Reinhardt R, Parham P, Walter L. A small, variable, and irregular killer cell Ig-like receptor locus accompanies the absence of MHC-C and MHC-G in gibbons. J Immunol 2009; 184:1379-91. [PMID: 20026738 DOI: 10.4049/jimmunol.0903016] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The killer cell Ig-like receptors (KIRs) of NK cells recognize MHC class I ligands and function in placental reproduction and immune defense against pathogens. During the evolution of monkeys, great apes, and humans, an ancestral KIR3DL gene expanded to become a diverse and rapidly evolving gene family of four KIR lineages. Characterizing the KIR locus are three framework regions, defining two intervals of variable gene content. By analysis of four KIR haplotypes from two species of gibbon, we find that the smaller apes do not conform to these rules. Although diverse and irregular in structure, the gibbon haplotypes are unusually small, containing only two to five functional genes. Comparison with the predicted ancestral hominoid KIR haplotype indicates that modern gibbon KIR haplotypes were formed by a series of deletion events, which created new hybrid genes as well as eliminating ancestral genes. Of the three framework regions, only KIR3DL3 (lineage V), defining the 5' end of the KIR locus, is present and intact on all gibbon KIR haplotypes. KIR2DL4 (lineage I) defining the central framework region has been a major target for elimination or inactivation, correlating with the absence of its putative ligand, MHC-G, in gibbons. Similarly, the MHC-C-driven expansion of lineage III KIR genes in great apes has not occurred in gibbons because they lack MHC-C. Our results indicate that the selective forces shaping the size and organization of the gibbon KIR locus differed from those acting upon the KIR of other hominoid species.
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Affiliation(s)
- Laurent Abi-Rached
- Department of Structural Biology, Stanford University, Stanford, CA 94305, USA
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Ferraresso S, Kuhl H, Milan M, Ritchie DW, Secombes CJ, Reinhardt R, Bargelloni L. Identification and characterisation of a novel immune-type receptor (NITR) gene cluster in the European sea bass, Dicentrarchus labrax, reveals recurrent gene expansion and diversification by positive selection. Immunogenetics 2009; 61:773-88. [PMID: 19851764 PMCID: PMC2921055 DOI: 10.1007/s00251-009-0398-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2009] [Accepted: 09/18/2009] [Indexed: 01/17/2023]
Abstract
In the last decade, a new gene family encoding non-rearranging receptors, called novel immune-type receptors (NITRs), has been discovered in teleost fish. NITRs belong to the immunoglobulin superfamily and represent an extraordinarily divergent and rapidly evolving gene complex. Genomic analysis of a region spanning 270 kb led to the discovery of a NITR gene cluster in the European sea bass (Dicentrarchus labrax). In total, 27 NITR genes and three putative pseudogenes, organised in a tandemly arrayed cluster, were identified. Sea bass NITR genes maintain the three major genomic organisations that appear to be essentially conserved among fish species along with new features presumably involving processes of intron loss, exon deletion and acquisition of new exons. Comparative and evolutionary analyses suggest that these receptors have evolved following a “birth-and-death” model of gene evolution in which duplication events together with lineage-specific gain and loss of individual members contributed to the rapid diversification of individual gene families. In this study, we demonstrate that species-specific gene expansions provide the raw material for diversifying, positive Darwinian selection favouring the evolution of a highly diverse array of molecules.
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Affiliation(s)
- Serena Ferraresso
- Department of Public Health, Comparative Pathology and Veterinary Hygiene, Faculty of Veterinary Medicine, University of Padova, Viale dell'Università 16, 35020 Legnaro, Italy.
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