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Klussmeier A, Putke K, Klasberg S, Kohler M, Sauter J, Schefzyk D, Schöfl G, Massalski C, Schäfer G, Schmidt AH, Roers A, Lange V. High population frequencies of MICA copy number variations originate from independent recombination events. Front Immunol 2023; 14:1297589. [PMID: 38035108 PMCID: PMC10684724 DOI: 10.3389/fimmu.2023.1297589] [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] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 10/24/2023] [Indexed: 12/02/2023] Open
Abstract
MICA is a stress-induced ligand of the NKG2D receptor that stimulates NK and T cell responses and was identified as a key determinant of anti-tumor immunity. The MICA gene is located inside the MHC complex and is in strong linkage disequilibrium with HLA-B. While an HLA-B*48-linked MICA deletion-haplotype was previously described in Asian populations, little is known about other MICA copy number variations. Here, we report the genotyping of more than two million individuals revealing high frequencies of MICA duplications (1%) and MICA deletions (0.4%). Their prevalence differs between ethnic groups and can rise to 2.8% (Croatia) and 9.2% (Mexico), respectively. Targeted sequencing of more than 70 samples indicates that these copy number variations originate from independent nonallelic homologous recombination events between segmental duplications upstream of MICA and MICB. Overall, our data warrant further investigation of disease associations and consideration of MICA copy number data in oncological study protocols.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Axel Roers
- Institute for Immunology, Medical Faculty Carl Gustav Carus, University of Technology (TU) Dresden, Dresden, Germany
- Institute for Immunology, University Hospital Heidelberg, Heidelberg, Germany
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Klasberg S, Schmidt AH, Lange V, Schöfl G. DR2S: an integrated algorithm providing reference-grade haplotype sequences from heterozygous samples. BMC Bioinformatics 2021; 22:236. [PMID: 33971817 PMCID: PMC8111713 DOI: 10.1186/s12859-021-04153-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 04/26/2021] [Indexed: 01/30/2023] Open
Abstract
Background High resolution HLA genotyping of donors and recipients is a crucially important prerequisite for haematopoetic stem-cell transplantation and relies heavily on the quality and completeness of immunogenetic reference sequence databases of allelic variation. Results Here, we report on DR2S, an R package that leverages the strengths of two sequencing technologies—the accuracy of next-generation sequencing with the read length of third-generation sequencing technologies like PacBio’s SMRT sequencing or ONT’s nanopore sequencing—to reconstruct fully-phased high-quality full-length haplotype sequences. Although optimised for HLA and KIR genes, DR2S is applicable to all loci with known reference sequences provided that full-length sequencing data is available for analysis. In addition, DR2S integrates supporting tools for easy visualisation and quality control of the reconstructed haplotype to ensure suitability for submission to public allele databases. Conclusions DR2S is a largely automated workflow designed to create high-quality fully-phased reference allele sequences for highly polymorphic gene regions such as HLA or KIR. It has been used by biologists to successfully characterise and submit more than 500 HLA alleles and more than 500 KIR alleles to the IPD-IMGT/HLA and IPD-KIR databases. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-021-04153-0.
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Paech C, Albrecht V, Putke K, Schöfl G, Schöne B, Schmidt AH, Lange V, Klussmeier A. HLA-E diversity unfolded: Identification and characterization of 170 novel HLA-E alleles. HLA 2021; 97:389-398. [PMID: 33527770 PMCID: PMC8247977 DOI: 10.1111/tan.14195] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [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: 12/12/2020] [Revised: 01/19/2021] [Accepted: 01/25/2021] [Indexed: 12/27/2022]
Abstract
HLA-E is a member of the nonclassical HLA class Ib genes. Even though it is structurally highly similar to the classical HLA class Ia genes, it is less diverse and only 45 alleles and 12 proteins were known in December 2019 (IPD-IMGT/HLA, release 3.38.0). Since 2017, we have genotyped over 3 million voluntary stem cell donors for HLA-E by sequencing the most relevant allele-determining bases of exons 2 and 3. As expected, most donors harbor the two predominant alleles HLA-E*01:01 and/or HLA-E*01:03. However, in 1666 (0.05%) of our samples we detected 345 distinct novel HLA-E sequences. The most frequent one was identified in 162 samples and has by now been named HLA-E*01:114. To characterize these novel alleles in full-length, we used both short-read Illumina and long-read PacBio sequencing to obtain fully phased and highly accurate sequences. This resulted in 234 submissions to IPD-IMGT/HLA comprising 170 novel HLA-E alleles, which encode for 93 novel HLA-E proteins, as well as 64 confirmations or sequence extensions. Consequently, the number of HLA-E alleles in the database (release 3.42.0) has now increased to 256 HLA-E alleles and 110 HLA-E proteins.
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Schöne B, Fuhrmann M, Surendranath V, Schmidt AH, Lange V, Schöfl G. TypeLoader2: Automated submission of novel HLA and killer-cell immunoglobulin-like receptor alleles in full length. HLA 2020; 93:195-202. [PMID: 30821128 PMCID: PMC6594033 DOI: 10.1111/tan.13508] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [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: 12/03/2018] [Revised: 02/25/2019] [Accepted: 02/27/2019] [Indexed: 11/29/2022]
Abstract
The Immuno Polymorphism Database (IPD) databases provide global, curated repositories for information regarding polymorphisms of genes of the immune system, thereby generating immense value for the research and clinical communities. The advent of high‐throughput genotyping in immunogenetics has led to dramatically growing numbers of heretofore unknown HLA and lately also killer‐cell immunoglobulin‐like receptor (KIR) alleles, which are to be curated and deposited in the IPD‐IMGT/HLA and IPD‐KIR databases, respectively. It is highly desirable that these novel alleles are characterised and submitted in full length, and that known alleles are extended to cover the complete gene sequence. However, the manual annotation and submission of sequences to European Molecular Biology Laboratory's European Nucleotide Archive and the IPD‐IMGT/HLA and IPD‐KIR databases is time‐consuming and error‐prone. Here, we report the substantial extension of the HLA allele submission tool TypeLoader, which now also supports the annotation and submission of KIR alleles. To enable a more widespread use of this tool, we have made it available as a stand‐alone application that can easily be installed on standard Windows or Linux computers. Furthermore, an internal SQLite database was added to store a wide range of metadata about each allele. This allows TypeLoader2 to be used as a lab's central information platform for the annotation, curation and submission of full‐length HLA and KIR allele sequences. The software is freely available from GitHub (https://github.com/DKMS-LSL/typeloader). We hope that the increased convenience and scope of TypeLoader2 will foster the submission of more full‐length sequences to the IPD‐IMGT/HLA and IPD‐KIR databases, ultimately promoting the use of full‐length sequencing for genotyping both HLA and KIR.
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Schmidt AH, Sauter J, Baier DM, Daiss J, Keller A, Klussmeier A, Mengling T, Rall G, Riethmüller T, Schöfl G, Solloch UV, Torosian T, Means D, Kelly H, Jagannathan L, Paul P, Giani AS, Hildebrand S, Schumacher S, Markert J, Füssel M, Hofmann JA, Schäfer T, Pingel J, Lange V, Schetelig J. Immunogenetics in stem cell donor registry work: The DKMS example (Part 2). Int J Immunogenet 2020; 47:139-148. [PMID: 32034894 PMCID: PMC7079094 DOI: 10.1111/iji.12479] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [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: 12/02/2019] [Revised: 01/08/2020] [Accepted: 01/20/2020] [Indexed: 12/12/2022]
Abstract
DKMS is a leading stem cell donor registry with more than 9 million donors. Donor registry activities share many touch points with topics from immunogenetics or population genetics. In this two-part review article, we deal with these aspects of donor registry work by using the example of DKMS. In the second part of the review, we focus on donor typing of non-HLA genes, the impact of donor age, gender and CMV serostatus on donation probabilities, the identification of novel HLA, KIR and MIC alleles by high-throughput donor typing, the activities of the Collaborative Biobank and pharmacogenetics in the donor registry context.
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Affiliation(s)
- Alexander H. Schmidt
- DKMSTübingenGermany
- DKMS Life Science LabDresdenGermany
- Clinical Trials UnitDKMSDresdenGermany
| | | | | | | | | | | | | | | | | | | | | | | | | | | | - Latha Jagannathan
- DKMS‐BMST Foundation IndiaBangaloreIndia
- Bangalore Medical Services TrustBangaloreIndia
| | | | | | | | | | | | | | | | | | | | | | - Johannes Schetelig
- Clinical Trials UnitDKMSDresdenGermany
- Medizinische Klinik IUniversity Hospital Carl Gustav CarusDresdenGermany
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Schmidt AH, Sauter J, Baier DM, Daiss J, Keller A, Klussmeier A, Mengling T, Rall G, Riethmüller T, Schöfl G, Solloch UV, Torosian T, Means D, Kelly H, Jagannathan L, Paul P, Giani AS, Hildebrand S, Schumacher S, Markert J, Füssel M, Hofmann JA, Schäfer T, Pingel J, Lange V, Schetelig J. Immunogenetics in stem cell donor registry work: The DKMS example (Part 1). Int J Immunogenet 2020; 47:13-23. [PMID: 31903698 PMCID: PMC7003907 DOI: 10.1111/iji.12471] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [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: 11/18/2019] [Revised: 12/06/2019] [Accepted: 12/06/2019] [Indexed: 01/27/2023]
Abstract
Currently, stem cell donor registries include more than 35 million potential donors worldwide to provide HLA-matched stem cell products for patients in need of an unrelated donor transplant. DKMS is a leading stem cell donor registry with more than 9 million donors from Germany, Poland, the United States, the United Kingdom, India and Chile. DKMS donors have donated hematopoietic stem cells more than 80,000 times. Many aspects of donor registry work are closely related to topics from immunogenetics or population genetics. In this two-part review article, we describe, analyse and discuss these areas of donor registry work by using the example of DKMS. Part 1 of the review gives a general overview on DKMS and includes typical donor registry activities with special focus on the HLA system: high-throughput HLA typing of potential stem cell donors, HLA haplotype frequencies and resulting matching probabilities, and donor file optimization with regard to HLA diversity.
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Affiliation(s)
- Alexander H. Schmidt
- DKMSTübingenGermany
- DKMS Life Science LabDresdenGermany
- DKMSClinical Trials UnitDresdenGermany
| | | | | | | | | | | | | | | | | | | | | | | | | | | | - Latha Jagannathan
- DKMS BMST Foundation IndiaBangaloreIndia
- Bangalore Medical Services TrustBangaloreIndia
| | | | | | | | | | | | | | | | | | | | | | - Johannes Schetelig
- DKMSClinical Trials UnitDresdenGermany
- University Hospital Carl Gustav CarusMedizinische Klinik IDresdenGermany
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Klasberg S, Surendranath V, Lange V, Schöfl G. Bioinformatics Strategies, Challenges, and Opportunities for Next Generation Sequencing-Based HLA Genotyping. Transfus Med Hemother 2019; 46:312-325. [PMID: 31832057 PMCID: PMC6876610 DOI: 10.1159/000502487] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2019] [Accepted: 07/30/2019] [Indexed: 12/16/2022] Open
Abstract
The advent of next generation sequencing (NGS) has altered the face of genotyping the human leukocyte antigen (HLA) system in clinical, stem cell donor registry, and research contexts. NGS has led to a dramatically increased sequencing throughput at high accuracy, while being more time and cost efficient than precursor technologies. This has led to a broader and deeper profiling of the key genes in the human immunogenetic make-up. The rapid evolution of sequencing technologies is evidenced by the development of varied short-read sequencing platforms with differing read lengths and sequencing capacities to long-read sequencing platforms capable of profiling full genes without fragmentation. Concomitantly, there has been development of a diverse set of computational analyses and software tools developed to deal with the various strengths and limitations of the sequencing data generated by the different sequencing platforms. This review surveys the different modalities involved in generating NGS HLA profiling sequence data. It systematically describes various computational approaches that have been developed to achieve HLA genotyping to different degrees of resolution. At each stage, this review enumerates the drawbacks and advantages of each of the platforms and analysis approaches, thus providing a comprehensive picture of the current state of HLA genotyping technologies.
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Behrens GA, Brehm M, Groß R, Heider J, Wehde T, Castriciano S, Schöfl G, Schmidt A, Lange V. P105 High-throughput CMV-status determination from buccal swab samples at donor registration. Hum Immunol 2019. [DOI: 10.1016/j.humimm.2019.07.158] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Albrecht V, Paech C, Putke K, Klasberg S, Massalski C, Schöne B, Fuhrmann M, Schöfl G, Schmidt A, Lange V, Klußmeier A. P061 Full-length characterisation of 150 novel MICA and MICB alleles. Hum Immunol 2019. [DOI: 10.1016/j.humimm.2019.07.113] [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: 10/26/2022]
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Groot AT, van Wijk M, Villacis-Perez E, Kuperus P, Schöfl G, van Veldhuizen D, Heckel DG. Within-population variability in a moth sex pheromone blend, part 2: selection towards fixation. R Soc Open Sci 2019; 6:182050. [PMID: 31032049 PMCID: PMC6458377 DOI: 10.1098/rsos.182050] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 02/18/2019] [Indexed: 06/09/2023]
Abstract
To understand how variation in sexual communication systems evolves, the genetic architecture underlying sexual signals and responses needs to be identified. Especially in animals where mating signals are important for mate recognition, and signals and responses are governed by independently assorting genes, it is difficult to envision how signals and preferences can (co)evolve. Moths are a prime example of such animals. In the noctuid moth Heliothis virescens, we found within-population variation in the female pheromone. In previous selection experiments followed by quantitative trait locus (QTL) analysis and expression analysis of candidate desaturase genes, we developed a model involving a trans-acting repressor of the delta-11-desaturase. In our current study with new selection lines, we fixed the most extreme phenotype and found a single underlying mutation: a premature stop codon in the first coding exon of delta-11-desaturase, which we could trace back to its origin in the laboratory. Interestingly, we found no pleiotropic effects of this knock-out mutation on the male physiological or behavioural response, or on growth or fertility. This finding is in contrast to Drosophila melanogaster, where a single desaturase gene affects both female pheromone production and male behavioural response, but similar to other Lepidoptera where these traits are under independent genetic control. To our knowledge, this is the first time that a single point mutation has been identified that underlies the phenotypic variation in the pheromone signal of a moth.
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Affiliation(s)
- Astrid T. Groot
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
- Department Entomology, Max Planck Institute for Chemical Ecology, Hans Knoell Strasse 8, 07745 Jena, Germany
| | - Michiel van Wijk
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Ernesto Villacis-Perez
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Peter Kuperus
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Gerhard Schöfl
- Department Entomology, Max Planck Institute for Chemical Ecology, Hans Knoell Strasse 8, 07745 Jena, Germany
| | - Dennis van Veldhuizen
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - David G. Heckel
- Department Entomology, Max Planck Institute for Chemical Ecology, Hans Knoell Strasse 8, 07745 Jena, Germany
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Klasberg S, Lang K, Günther M, Schober G, Massalski C, Schmidt AH, Lange V, Schöfl G. Patterns of non-ARD variation in more than 300 full-length HLA-DPB1 alleles. Hum Immunol 2019; 80:44-52. [DOI: 10.1016/j.humimm.2018.05.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 05/13/2018] [Accepted: 05/29/2018] [Indexed: 12/26/2022]
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12
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Wagner I, Schefzyk D, Pruschke J, Schöfl G, Schöne B, Gruber N, Lang K, Hofmann J, Gnahm C, Heyn B, Marin WM, Dandekar R, Hollenbach JA, Schetelig J, Pingel J, Norman PJ, Sauter J, Schmidt AH, Lange V. Allele-Level KIR Genotyping of More Than a Million Samples: Workflow, Algorithm, and Observations. Front Immunol 2018; 9:2843. [PMID: 30564239 PMCID: PMC6288436 DOI: 10.3389/fimmu.2018.02843] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [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: 10/23/2018] [Accepted: 11/19/2018] [Indexed: 11/13/2022] Open
Abstract
The killer-cell immunoglobulin-like receptor (KIR) genes regulate natural killer cell activity, influencing predisposition to immune mediated disease, and affecting hematopoietic stem cell transplantation (HSCT) outcome. Owing to the complexity of the KIR locus, with extensive gene copy number variation (CNV) and allelic diversity, high-resolution characterization of KIR has so far been applied only to relatively small cohorts. Here, we present a comprehensive high-throughput KIR genotyping approach based on next generation sequencing. Through PCR amplification of specific exons, our approach delivers both copy numbers of the individual genes and allelic information for every KIR gene. Ten-fold replicate analysis of a set of 190 samples revealed a precision of 99.9%. Genotyping of an independent set of 360 samples resulted in an accuracy of more than 99% taking into account consistent copy number prediction. We applied the workflow to genotype 1.8 million stem cell donor registry samples. We report on the observed KIR allele diversity and relative abundance of alleles based on a subset of more than 300,000 samples. Furthermore, we identified more than 2,000 previously unreported KIR variants repeatedly in independent samples, underscoring the large diversity of the KIR region that awaits discovery. This cost-efficient high-resolution KIR genotyping approach is now applied to samples of volunteers registering as potential donors for HSCT. This will facilitate the utilization of KIR as additional selection criterion to improve unrelated donor stem cell transplantation outcome. In addition, the approach may serve studies requiring high-resolution KIR genotyping, like population genetics and disease association studies.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Wesley M. Marin
- San Francisco School of Medicine, University of California, San Francisco, San Francisco, CA, United States
| | - Ravi Dandekar
- San Francisco School of Medicine, University of California, San Francisco, San Francisco, CA, United States
| | - Jill A. Hollenbach
- San Francisco School of Medicine, University of California, San Francisco, San Francisco, CA, United States
| | - Johannes Schetelig
- DKMS, Tübingen, Germany
- Department of Internal Medicine I, University Hospital Carl Gustav Carus at the Technische Universität Dresden, Dresden, Germany
| | | | - Paul J. Norman
- Division of Biomedical Informatics and Personalized Medicine, and Department of Immunology, University of Colorado Anschutz Medical, Aurora, CO, United States
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Schöfl G, Sauter J, Klasberg S, Schmidt AH, Lange V. P061Allele-level genotyping of KIR2DL4 in large european population samples reveals highly significant heterozygote excess for 9A/10A allelic variants. Hum Immunol 2018. [DOI: 10.1016/j.humimm.2018.07.120] [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: 10/28/2022]
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Klasberg S, Lang K, Günther M, Schmidt AH, Lange V, Schöfl G. P062Coding and non-coding variation in 60 novel full-length sequences of KIR2DL1. Hum Immunol 2018. [DOI: 10.1016/j.humimm.2018.07.121] [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: 11/29/2022]
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Surendranath V, Lang K, Schmidt AH, Schöfl G, Lange V. P103 The promise of cost-efficient full-length HLA class I genotyping: Advances using nanopore sequencing. Hum Immunol 2018. [DOI: 10.1016/j.humimm.2018.07.162] [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: 10/28/2022]
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Abstract
Nanopore sequencing, a paradigm change in sequencing technologies, offers a new cost-effective and scalable platform for HLA genotyping. Among the new generation of high-throughput sequencing technologies, the MinION nanopore sequencer is the first to offer a non-template-based direct DNA sensing sequencing technology. Oxford Nanopore Technologies (ONT) introduced the first version of the MinION in 2014; since then, the platform has gone through multiple iterations resulting in higher throughput and sequencing accuracy. The "what you put in is what you get" nature of the platform enables molecules to be sequenced without fragmentation. This results in ultra-long read lengths in the order of tens of kilobases enabling entire genes to be characterized with fully phased sequence information. With release R9.5, the MinION platform has reached a quality that enables HLA genotyping with minor shortcomings in long homopolymer regions. Within this chapter, we describe a protocol for sequencing and genotyping HLA Class I alleles using the MinION.
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Schöfl G, Lang K, Günther M, Schober G, Massalski C, Schmidt AH, Lange V. P016 Extending the IMGT/HLA database: Whole GENE sequencing of 247 distinct HLA-DPB1 alleles. Hum Immunol 2017. [DOI: 10.1016/j.humimm.2017.06.076] [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: 10/18/2022]
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Bentink S, Schöfl G, Lang K, Ahci M, Toffalori C, Gnahm C, Sauter J, Schmidt AH, Vago L, Fleischhauer K, Lange V. P130 An algorithm to detect and quantify low frequency HLA-genotypes in NGS data. Hum Immunol 2017. [DOI: 10.1016/j.humimm.2017.06.190] [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: 10/18/2022]
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Albrecht V, Zweiniger C, Surendranath V, Lang K, Schöfl G, Dahl A, Winkler S, Lange V, Böhme I, Schmidt AH. Dual redundant sequencing strategy: Full-length gene characterisation of 1056 novel and confirmatory HLA alleles. HLA 2017; 90:79-87. [PMID: 28547825 PMCID: PMC6084308 DOI: 10.1111/tan.13057] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [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: 09/05/2016] [Revised: 04/19/2017] [Accepted: 05/01/2017] [Indexed: 01/26/2023]
Abstract
The high‐throughput department of DKMS Life Science Lab encounters novel human leukocyte antigen (HLA) alleles on a daily basis. To characterise these alleles, we have developed a system to sequence the whole gene from 5′‐ to 3′‐UTR for the HLA loci A, B, C, DQB1 and DPB1 for submission to the European Molecular Biology Laboratory – European Nucleotide Archive (EMBL‐ENA) and the IPD‐IMGT/HLA Database. Our workflow is based on a dual redundant sequencing strategy. Using shotgun sequencing on an Illumina MiSeq instrument and single molecule real‐time (SMRT) sequencing on a PacBio RS II instrument, we are able to achieve highly accurate HLA full‐length consensus sequences. Remaining conflicts are resolved using the R package DR2S (Dual Redundant Reference Sequencing). Given the relatively high throughput of this strategy, we have developed the semi‐automated web service TypeLoader, to aid in the submission of sequences to the EMBL‐ENA and the IPD‐IMGT/HLA Database. In the IPD‐IMGT/HLA Database release 3.24.0 (April 2016; prior to the submission of the sequences described here), only 5.2% of all known HLA alleles have been fully characterised together with intronic and UTR sequences. So far, we have applied our strategy to characterise and submit 1056 HLA alleles, thereby more than doubling the number of fully characterised alleles. Given the increasing application of next generation sequencing (NGS) for full gene characterisation in clinical practice, extending the HLA database concomitantly is highly desirable. Therefore, we propose this dual redundant sequencing strategy as a workflow for submission of novel full‐length alleles and characterisation of sequences that are as yet incomplete. This would help to mitigate the predominance of partially known alleles in the database.
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Affiliation(s)
| | | | | | - K Lang
- DKMS Life Science Lab, Dresden, Germany
| | - G Schöfl
- DKMS Life Science Lab, Dresden, Germany
| | - A Dahl
- Deep Sequencing Group, CRTD - Center for Regenerative Therapies Dresden, Dresden, Germany
| | - S Winkler
- DNA Sequencing, Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - V Lange
- DKMS Life Science Lab, Dresden, Germany
| | - I Böhme
- DKMS Life Science Lab, Dresden, Germany
| | - A H Schmidt
- DKMS Life Science Lab, Dresden, Germany.,DKMS, Tübingen, Germany
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Hänniger S, Dumas P, Schöfl G, Gebauer-Jung S, Vogel H, Unbehend M, Heckel DG, Groot AT. Genetic basis of allochronic differentiation in the fall armyworm. BMC Evol Biol 2017; 17:68. [PMID: 28264650 PMCID: PMC5339952 DOI: 10.1186/s12862-017-0911-5] [Citation(s) in RCA: 30] [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: 09/06/2016] [Accepted: 02/14/2017] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Very little is known on how changes in circadian rhythms evolve. The noctuid moth Spodoptera frugiperda (Lepidoptera: Noctuidae) consists of two strains that exhibit allochronic differentiation in their mating time, which acts as a premating isolation barrier between the strains. We investigated the genetic basis of the strain-specific timing differences to identify the molecular mechanisms of differentiation in circadian rhythms. RESULTS Through QTL analyses we identified one major Quantitative trait chromosome (QTC) underlying differentiation in circadian timing of mating activity. Using RADtags, we identified this QTC to be homologous to Bombyx mori C27, on which the clock gene vrille is located, which thus became the major candidate gene. In S. frugiperda, vrille showed strain-specific polymorphisms. Also, vrille expression differed significantly between the strains, with the rice-strain showing higher expression levels than the corn-strain. In addition, RT-qPCR experiments with the other main clock genes showed that pdp1, antagonist of vrille in the modulatory feedback loop of the circadian clock, showed higher expression levels in the rice-strain than in the corn-strain. CONCLUSIONS Together, our results indicate that the allochronic differentiation in the two strains of S. frugiperda is associated with differential transcription of vrille or a cis-acting gene close to vrille, which contributes to the evolution of prezygotic isolation in S. frugiperda.
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Affiliation(s)
- Sabine Hänniger
- Max Planck Institute for Chemical Ecology, Entomology, Hans-Knöll-Str. 8, 07745 Jena, Germany
| | - Pascaline Dumas
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Gerhard Schöfl
- DKMS Life Science Lab, Fiedlerstr, 34, 01307 Dresden, Germany
| | - Steffi Gebauer-Jung
- Max Planck Institute for Chemical Ecology, Entomology, Hans-Knöll-Str. 8, 07745 Jena, Germany
| | - Heiko Vogel
- Max Planck Institute for Chemical Ecology, Entomology, Hans-Knöll-Str. 8, 07745 Jena, Germany
| | - Melanie Unbehend
- Max Planck Institute for Chemical Ecology, Entomology, Hans-Knöll-Str. 8, 07745 Jena, Germany
| | - David G. Heckel
- Max Planck Institute for Chemical Ecology, Entomology, Hans-Knöll-Str. 8, 07745 Jena, Germany
| | - Astrid T. Groot
- Max Planck Institute for Chemical Ecology, Entomology, Hans-Knöll-Str. 8, 07745 Jena, Germany
- DKMS Life Science Lab, Fiedlerstr, 34, 01307 Dresden, Germany
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21
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Schöfl G, Lang K, Quenzel P, Böhme I, Sauter J, Hofmann JA, Pingel J, Schmidt AH, Lange V. 2.7 million samples genotyped for HLA by next generation sequencing: lessons learned. BMC Genomics 2017; 18:161. [PMID: 28196473 PMCID: PMC5309984 DOI: 10.1186/s12864-017-3575-z] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [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: 12/13/2016] [Accepted: 02/09/2017] [Indexed: 11/10/2022] Open
Abstract
Background At the DKMS Life Science Lab, Next Generation Sequencing (NGS) has been used for ultra-high-volume high-resolution genotyping of HLA loci for the last three and a half years. Here, we report on our experiences in genotyping the HLA, CCR5, ABO, RHD and KIR genes using a direct amplicon sequencing approach on Illumina MiSeq and HiSeq 2500 instruments. Results Between January 2013 and June 2016, 2,714,110 samples largely from German, Polish and UK-based potential stem cell donors have been processed. 98.9% of all alleles for the targeted HLA loci (HLA-A, -B, -C, -DRB1, -DQB1 and -DPB1) were typed at high resolution or better. Initially a simple three-step workflow based on nanofluidic chips in conjunction with 4-primer amplicon tagging was used. Over time, we found that this setup results in PCR artefacts such as primer dimers and PCR-mediated recombination, which may necessitate repeat typing. Split workflows for low- and high-DNA-concentration samples helped alleviate these problems and reduced average per-locus repeat rates from 3.1 to 1.3%. Further optimisations of the workflow included the use of phosphorothioate oligos to reduce primer degradation and primer dimer formation, and employing statistical models to predict read yield from initial template DNA concentration to avoid intermediate quantification of PCR products. Finally, despite the populations typed at DKMS Life Science Lab being relatively homogenous genetically, an analysis of 1.4 million donors processed between January 2015 and May 2016 led to the discovery of 1,919 distinct novel HLA alleles. Conclusions Amplicon-based NGS HLA genotyping workflows have become the workhorse in high-volume tissue typing of registry donors. The optimisation of workflow practices over multiple years has led to insights and solutions that improve the efficiency and robustness of short amplicon based genotyping workflows. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3575-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Gerhard Schöfl
- DKMS Life Science Lab, Blasewitzerstr. 43, 01307, Dresden, Germany.
| | - Kathrin Lang
- DKMS Life Science Lab, Blasewitzerstr. 43, 01307, Dresden, Germany
| | - Philipp Quenzel
- DKMS Life Science Lab, Blasewitzerstr. 43, 01307, Dresden, Germany
| | - Irina Böhme
- DKMS Life Science Lab, Blasewitzerstr. 43, 01307, Dresden, Germany
| | | | | | | | - Alexander H Schmidt
- DKMS Life Science Lab, Blasewitzerstr. 43, 01307, Dresden, Germany.,DKMS, Kressbach 1, 72072, Tübingen, Germany
| | - Vinzenz Lange
- DKMS Life Science Lab, Blasewitzerstr. 43, 01307, Dresden, Germany
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22
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Lang K, Wagner I, Schöne B, Schöfl G, Birkner K, Hofmann JA, Sauter J, Pingel J, Böhme I, Schmidt AH, Lange V. ABO allele-level frequency estimation based on population-scale genotyping by next generation sequencing. BMC Genomics 2016; 17:374. [PMID: 27207383 PMCID: PMC4874024 DOI: 10.1186/s12864-016-2687-1] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [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: 01/11/2016] [Accepted: 04/28/2016] [Indexed: 03/15/2023] Open
Abstract
BACKGROUND The characterization of the ABO blood group status is vital for blood transfusion and solid organ transplantation. Several methods for the molecular characterization of the ABO gene, which encodes the alleles that give rise to the different ABO blood groups, have been described. However, the application of those methods has so far been restricted to selected samples and not been applied to population-scale analysis. RESULTS We describe a cost-effective method for high-throughput genotyping of the ABO system by next generation sequencing. Sample specific barcodes and sequencing adaptors are introduced during PCR, rendering the products suitable for direct sequencing on Illumina MiSeq or HiSeq instruments. Complete sequence coverage of exons 6 and 7 enables molecular discrimination of the ABO subgroups and many alleles. The workflow was applied to ABO genotype more than a million samples. We report the allele group frequencies calculated on a subset of more than 110,000 sampled individuals of German origin. Further we discuss the potential of the workflow for high resolution genotyping taking the observed allele group frequencies into account. Finally, sequence analysis revealed 287 distinct so far not described alleles of which the most abundant one was identified in 174 samples. CONCLUSIONS The described workflow delivers high resolution ABO genotyping at low cost enabling population-scale molecular ABO characterization.
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Affiliation(s)
- Kathrin Lang
- DKMS Life Science Lab, Blasewitzer Str. 43, 01307, Dresden, Germany
| | - Ines Wagner
- DKMS Life Science Lab, Blasewitzer Str. 43, 01307, Dresden, Germany
| | - Bianca Schöne
- DKMS Life Science Lab, Blasewitzer Str. 43, 01307, Dresden, Germany
| | - Gerhard Schöfl
- DKMS Life Science Lab, Blasewitzer Str. 43, 01307, Dresden, Germany
| | - Kerstin Birkner
- DKMS Life Science Lab, Blasewitzer Str. 43, 01307, Dresden, Germany
| | | | | | | | - Irina Böhme
- DKMS Life Science Lab, Blasewitzer Str. 43, 01307, Dresden, Germany
| | - Alexander H Schmidt
- DKMS Life Science Lab, Blasewitzer Str. 43, 01307, Dresden, Germany.,DKMS, Kressbach 1, 72072, Tübingen, Germany
| | - Vinzenz Lange
- DKMS Life Science Lab, Blasewitzer Str. 43, 01307, Dresden, Germany.
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Lang K, Schöfl G, Zweiniger C, König C, Penning M, Rozemuller E, Clausing S, Duport Y, Gscheidel N, Winkler S, Lange V, Boehme I, Schmidt AH. Phased full Length SMRT sequencing of HLA-DPB1. Hum Immunol 2015. [DOI: 10.1016/j.humimm.2015.07.159] [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: 11/29/2022]
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Abdul-Aziz MA, Schöfl G, Mrotzek G, Haryanti H, Sugama K, Saluz HP. Population structure of the Indonesian giant tiger shrimp Penaeus monodon: a window into evolutionary similarities between paralogous mitochondrial DNA sequences and their genomes. Ecol Evol 2015; 5:3570-84. [PMID: 26380687 PMCID: PMC4567862 DOI: 10.1002/ece3.1616] [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: 04/28/2015] [Revised: 06/22/2015] [Accepted: 06/22/2015] [Indexed: 11/16/2022] Open
Abstract
Here we used both microsatellites and mtCR (mitochondrial DNA control region) sequences as genetic markers to examine the genetic diversity and population structure of Penaeus monodon shrimp from six Indonesian regions. The microsatellite data showed that shrimp from the Indian and the Pacific Ocean were genetically distinct from each other. It has been reported previously that P. monodon mtCR sequences from the Indo-Pacific group into two major paralogous clades of unclear origin. Here we show that the population structure inferred from mtCR sequences matches the microsatellite-based population structure for one of these clades. This is consistent with the notion that this mtCR clade shares evolutionary history with nuclear DNA and may thus represent nuclear mitochondrial pseudogenes (Numts).
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Affiliation(s)
- Muslihudeen A Abdul-Aziz
- Leibniz Institute for Natural Product Research and Infection BiologyBeutenbergstr. 11a, 07745, Jena, Germany
- Friedrich Schiller University JenaJena, Germany
| | - Gerhard Schöfl
- Leibniz Institute for Natural Product Research and Infection BiologyBeutenbergstr. 11a, 07745, Jena, Germany
- DKMS Life Science Lab GmbHFiedlerstr. 34, 01277, Dresden, Germany
| | - Grit Mrotzek
- Leibniz Institute for Natural Product Research and Infection BiologyBeutenbergstr. 11a, 07745, Jena, Germany
| | - Haryanti Haryanti
- Institute for Mariculture Research and Development – IMRAD, Ds PenyabanganBr. Gondol PO. Box 140, Singaraja, Bali, 81101, Indonesia
| | - Ketut Sugama
- Research and Development Center for AquacultureJL Ragunan 20, Pasar Minggu, Jakarta Selatan, 12540, Indonesia
| | - Hans Peter Saluz
- Leibniz Institute for Natural Product Research and Infection BiologyBeutenbergstr. 11a, 07745, Jena, Germany
- Friedrich Schiller University JenaJena, Germany
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25
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Krügel H, Klimina KM, Mrotzek G, Tretyakov A, Schöfl G, Saluz HP, Brantl S, Poluektova EU, Danilenko VN. Expression of the toxin-antitoxin genes yefM(Lrh), yoeB(Lrh) in human Lactobacillus rhamnosus isolates. J Basic Microbiol 2015; 55:982-91. [PMID: 25832734 DOI: 10.1002/jobm.201400904] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [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: 11/29/2014] [Accepted: 03/13/2015] [Indexed: 11/07/2022]
Abstract
Lactobacilli are important microorganisms in various activities, for example, diary products, meat ripening, bread and pickles, but, moreover, are associated directly with human skin and cavities (e.g., mouth, gut, or vagina). Some of them are used as probiotics. Therefore, the molecular biological investigation of these bacteria is important. Earlier we described several toxin antitoxin systems (type II) in lactobacilli. Here, we describe the structure and transcriptional regulation of genes, encoding TA system YefM-YoeB(Lrh) in three strains of Lactobacillus rhamnosus comparing stationary and exponential growth phases, the influence of stress factors and mRNA stability. The same TA system is responding to physiological and stress conditions differently in related strains. Using primer extension and RLM-RACE methods we determined three transcription start sites of RNAs in the operon. The promoter region of the operon is preceded by a conserved BOX element occurring at multiple positions in the genomes of L. rhamnosus strains. Downstream of and partially overlapping with the 3' end of the yoeB(Lrh) toxin gene, a divergently transcribed unexpected RNA was detected.
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Affiliation(s)
- Hans Krügel
- Leibniz Institute for Natural Product Research and Infection Biology, Hans-Knöll-Institute, Jena, Germany
| | - Ksenia M Klimina
- Department of Post-genomic Biotechnology, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Grit Mrotzek
- Leibniz Institute for Natural Product Research and Infection Biology, Hans-Knöll-Institute, Jena, Germany
| | - Alexander Tretyakov
- Leibniz Institute for Natural Product Research and Infection Biology, Hans-Knöll-Institute, Jena, Germany
| | - Gerhard Schöfl
- Leibniz Institute for Natural Product Research and Infection Biology, Hans-Knöll-Institute, Jena, Germany
| | - Hans-Peter Saluz
- Leibniz Institute for Natural Product Research and Infection Biology, Hans-Knöll-Institute, Jena, Germany.,Friedrich-Schiller-University Jena, Jena, Germany
| | | | - Elena U Poluektova
- Department of Post-genomic Biotechnology, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Valery N Danilenko
- Department of Post-genomic Biotechnology, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
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26
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Knittler MR, Berndt A, Böcker S, Dutow P, Hänel F, Heuer D, Kägebein D, Klos A, Koch S, Liebler-Tenorio E, Ostermann C, Reinhold P, Saluz HP, Schöfl G, Sehnert P, Sachse K. Chlamydia psittaci: New insights into genomic diversity, clinical pathology, host–pathogen interaction and anti-bacterial immunity. Int J Med Microbiol 2014; 304:877-93. [DOI: 10.1016/j.ijmm.2014.06.010] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
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27
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Groot AT, Schöfl G, Inglis O, Donnerhacke S, Classen A, Schmalz A, Santangelo RG, Emerson J, Gould F, Schal C, Heckel DG. Within-population variability in a moth sex pheromone blend: genetic basis and behavioural consequences. Proc Biol Sci 2014; 281:20133054. [PMID: 24500170 PMCID: PMC3924083 DOI: 10.1098/rspb.2013.3054] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Accepted: 01/14/2014] [Indexed: 11/12/2022] Open
Abstract
Evolutionary diversification of sexual communication systems in moths is perplexing because signal and response are under stabilizing selection in many species, and this is expected to constrain evolutionary change. In the moth Heliothis virescens, we consistently found high phenotypic variability in the female sex pheromone blend within each of four geographically distant populations. Here, we assess the heritability, genetic basis and behavioural consequences of this variation. Artificial selection with field-collected moths dramatically increased the relative amount of the saturated compound 16:Ald and decreased its unsaturated counterpart Z11-16:Ald, the major sex pheromone component (high line). In a cross between the high- and low-selected lines, one quantitative trait locus (QTL) explained 11-21% of the phenotypic variance in the 16:Ald/Z11-16:Ald ratio. Because changes in activity of desaturase enzymes could affect this ratio, we measured their expression levels in pheromone glands and mapped desaturase genes onto our linkage map. A delta-11-desaturase had lower expression in females producing less Z11-16:Ald; however, this gene mapped to a different chromosome than the QTL. A model in which the QTL is a trans-acting repressor of delta-11 desaturase expression explains many features of the data. Selection favouring heterozygotes which produce more unsaturated components could maintain a polymorphism at this locus.
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Affiliation(s)
- Astrid T. Groot
- IBED, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
- Department Entomology, Max Planck Institute for Chemical Ecology, Hans Knöll Strasse 8, Jena 07745, Germany
- Department Entomology, North Carolina State University, 100 Derieux Place, Raleigh, NC 27695-7613, USA
- W. M. Keck Center for Behavioral Biology, North Carolina State University, Raleigh, NC 27695-7617, USA
| | - Gerhard Schöfl
- Leibniz Institute for Natural Product Research and Infection Biology, Beutenbergstrasse 11A, Jena 07745, Germany
| | - Ollie Inglis
- Department Entomology, North Carolina State University, 100 Derieux Place, Raleigh, NC 27695-7613, USA
| | - Susanne Donnerhacke
- Department Entomology, Max Planck Institute for Chemical Ecology, Hans Knöll Strasse 8, Jena 07745, Germany
| | - Alice Classen
- Department Entomology, Max Planck Institute for Chemical Ecology, Hans Knöll Strasse 8, Jena 07745, Germany
| | - Antje Schmalz
- Department Entomology, Max Planck Institute for Chemical Ecology, Hans Knöll Strasse 8, Jena 07745, Germany
| | - Richard G. Santangelo
- Department Entomology, North Carolina State University, 100 Derieux Place, Raleigh, NC 27695-7613, USA
| | - Jennifer Emerson
- Department Entomology, North Carolina State University, 100 Derieux Place, Raleigh, NC 27695-7613, USA
| | - Fred Gould
- Department Entomology, North Carolina State University, 100 Derieux Place, Raleigh, NC 27695-7613, USA
- W. M. Keck Center for Behavioral Biology, North Carolina State University, Raleigh, NC 27695-7617, USA
| | - Coby Schal
- Department Entomology, North Carolina State University, 100 Derieux Place, Raleigh, NC 27695-7613, USA
- W. M. Keck Center for Behavioral Biology, North Carolina State University, Raleigh, NC 27695-7617, USA
| | - David G. Heckel
- Department Entomology, Max Planck Institute for Chemical Ecology, Hans Knöll Strasse 8, Jena 07745, Germany
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Bleicher A, Schöfl G, Rodicio MDR, Saluz HP. The plasmidome of a Salmonella enterica serovar Derby isolated from pork meat. Plasmid 2013; 69:202-10. [PMID: 23333216 DOI: 10.1016/j.plasmid.2013.01.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2012] [Revised: 01/04/2013] [Accepted: 01/06/2013] [Indexed: 10/27/2022]
Abstract
The complete nucleotide sequences of four plasmids hosted by a Salmonella enterica serovar. Derby strain 6MK1 isolated from pork were determined by shotgun Sanger sequencing. A 107,637 base pairs (bp) conjugative plasmid pSD107 containing 150 putative coding sequences (CDS) could be assigned to the narrow host range incompatibility group IncI1. A detailed annotation of all CDS was carried out, revealing the presence of genes needed for plasmid replication, conjugal transfer, plasmid partitioning and stability as well as resistance to antimicrobials. The resistance determinants dhfrA1, aadA1, qacEΔ1, sul1 (supplied by a class 1 integron), blaTEM-1b (carried by a truncated Tn2 flanked by IS26), sul2 and strAB confer multidrug resistance to the host bacterium. In addition to pSD107, three small cryptic plasmids pSD4.0, pSD4.6 and pSD5.6 were identified, showing significant sequence similarities to already known replicons of Escherichia coli and S. enterica. In conjugation experiments performed on solid medium, pSD107 was successfully transferred to a nalidixic acid resistant E. coli DH5α, mobilizing pSD4.0 and, more infrequently, also pSD4.6. All transferred plasmids were stably propagated in the recipient strain without selective pressure for approximately 66 generations. The absolute plasmid copy numbers were determined in real time PCR experiments, revealing an approximate 1:1:1:1 ratio of the four replicons compared to the chromosome. The evolutionary position of pSD107 within the IncI1 family of plasmids was inferred from a maximum likelihood phylogenetic tree and by comparison of genetic key elements in a set of 17 IncI1 reference plasmids.
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Affiliation(s)
- Anne Bleicher
- Leibniz-Institute for Natural Product Research and Infection Biology, Beutenbergstrasse 11a, Cell and Molecular Biology, D-07745 Jena, Germany.
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Groot AT, Staudacher H, Barthel A, Inglis O, Schöfl G, Santangelo RG, Gebauer-Jung S, Vogel H, Emerson J, Schal C, Heckel DG, Gould F. One quantitative trait locus for intra- and interspecific variation in a sex pheromone. Mol Ecol 2013; 22:1065-80. [PMID: 23294019 DOI: 10.1111/mec.12171] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2012] [Revised: 11/08/2012] [Accepted: 11/08/2012] [Indexed: 12/27/2022]
Abstract
Even though premating isolation is hypothesized to be a major driving force in speciation, its genetic basis is poorly known. In the noctuid moth Heliothis subflexa, one group of sex pheromone components, the acetates, emitted by the female, plays a crucial isolating role in preventing interspecific matings to males of the closely related Heliothis virescens, in which females do not produce acetates and males are repelled by them. We previously found intraspecific variation in acetates in H. subflexa: females in eastern North America contain significantly more acetates than females in Western Mexico. Here we describe the persistence of this intraspecific variation in laboratory-reared strains and the identification of one major quantitative trait locus (QTL), explaining 40% of the variance in acetate amounts. We homologized this intraspecific QTL to our previously identified interspecific QTL using restriction-associated DNA (RAD) tags. We found that a major intraspecific QTL overlaps with one of the two major interspecific QTL. To identify candidate genes underlying the acetate variation, we investigated a number of gene families with known or suspected acetyl- or acyltransferase activity. The most likely candidate genes did not map to our QTL, so that we currently hypothesize that a transcription factor underlies this QTL. Finding a single, large QTL that impacts variation in pheromone blends between and within species is, to our knowledge, the first such example for traits that have been demonstrated to affect premating isolation.
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Affiliation(s)
- A T Groot
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands.
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Abstract
BACKGROUND Chlamydiaceae are a family of obligate intracellular pathogens causing a wide range of diseases in animals and humans, and facing unique evolutionary constraints not encountered by free-living prokaryotes. To investigate genomic aspects of infection, virulence and host preference we have sequenced Chlamydia psittaci, the pathogenic agent of ornithosis. RESULTS A comparison of the genome of the avian Chlamydia psittaci isolate 6BC with the genomes of other chlamydial species, C. trachomatis, C. muridarum, C. pneumoniae, C. abortus, C. felis and C. caviae, revealed a high level of sequence conservation and synteny across taxa, with the major exception of the human pathogen C. trachomatis. Important differences manifest in the polymorphic membrane protein family specific for the Chlamydiae and in the highly variable chlamydial plasticity zone. We identified a number of psittaci-specific polymorphic membrane proteins of the G family that may be related to differences in host-range and/or virulence as compared to closely related Chlamydiaceae. We calculated non-synonymous to synonymous substitution rate ratios for pairs of orthologous genes to identify putative targets of adaptive evolution and predicted type III secreted effector proteins. CONCLUSIONS This study is the first detailed analysis of the Chlamydia psittaci genome sequence. It provides insights in the genome architecture of C. psittaci and proposes a number of novel candidate genes mostly of yet unknown function that may be important for pathogen-host interactions.
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Affiliation(s)
- Anja Voigt
- Leibniz-Institute for Natural Product Research and Infection Biology, Jena, Germany
| | - Gerhard Schöfl
- Leibniz-Institute for Natural Product Research and Infection Biology, Jena, Germany
| | - Hans Peter Saluz
- Leibniz-Institute for Natural Product Research and Infection Biology, Jena, Germany
- Friedrich Schiller University, Jena, Germany
- * E-mail:
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Groot AT, Classen A, Inglis O, Blanco CA, López J, Téran Vargas A, Schal C, Heckel DG, Schöfl G. Genetic differentiation across North America in the generalist moth Heliothis virescens and the specialist H. subflexa. Mol Ecol 2011; 20:2676-92. [PMID: 21615579 DOI: 10.1111/j.1365-294x.2011.05129.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The two moth species Heliothis virescens (Hv) and H. subflexa (Hs) are closely related, but have vastly different feeding habits. Hv is a generalist and an important pest in many crops in the USA, while Hs is a specialist feeding only on plants in the genus Physalis. In this study, we conducted a comparative population genetic analysis to assess whether and how generalist and specialist life styles are reflected in differences in population structures. In Hv 98% of the total variation occurred within populations. The overall differentiation (F(ST) ) between regions was 0.006 and even lower between years (0.0039) and hosts (0.0028). Analyses of population structure suggest that all individuals form one genetically homogeneous population, except for at most 12 individuals (6%) that diverged from this cluster. Population homogeneity likely results from the high mobility of Hv and its generalist feeding behaviour. Hs exhibited substantially more population structure. Even though 96% of the total variation was attributable to within-population variability, F(ST) -values between Hs populations were 10 times higher than between Hv populations. Hs populations showed significant isolation by distance. Analyses of Hs population structure suggest at least two subpopulations and thus some degree of metapopulation structure. We speculate that the patchy distribution of Physalis- the exclusive food source of Hs - contributes to differences in population structure between these closely related species. The finding that the specialist shows more population differentiation than the generalist corroborates the notion that host specialization is not an evolutionary dead end but a dynamic trait.
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Affiliation(s)
- A T Groot
- Department of Entomology, Max Planck Institute for Chemical Ecology, Hans-Knöll Strasse 8, 07745 Jena, Germany.
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Loxdale HD, Massonnet B, Schöfl G, Weisser WW. Evidence for a quiet revolution: seasonal variation in colonies of the specialist tansy aphid, Macrosiphoniella tanacetaria (Kaltenbach) (Hemiptera: Aphididae) studied using microsatellite markers. Bull Entomol Res 2011; 101:221-239. [PMID: 21062524 DOI: 10.1017/s0007485310000477] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
In cyclical parthenogens, clonal diversity is expected to decrease due to selection and drift during the asexual phase per number of asexual generations. The decrease in diversity may be counteracted by immigration of new genotypes. We analysed temporal variation in clonal diversity in colonies of the monophagous tansy aphid, Macrosiphoniella tanacetaria (Kaltenbach), sampled four times over the course of a growing season. In a related field study, we recorded aphid colony sizes and the occurrence of winged dispersers throughout the season. The number of colonies increased from April, when asexual stem mothers hatched from the sexually produced eggs, to the end of June. The proportion of colonies with winged individuals also increased over this period. After a severe reduction in colony sizes in late summer, a second expansion phase occurred in October when sexuals were produced. At the season's end, the only winged forms were males. A linked genetic study showed that the number of microsatellite multilocus genotypes and genetic variability assessed at three polymorphic loci per colony decreased from June to October. Overall, the relatedness of wingless to winged individuals within colonies was lower than average relatedness among wingless individuals, suggesting that winged forms mainly originated in different colonies. The results demonstrate that patterns of genetic diversity within colonies can be explained by the antagonistic forces of clonal selection, migration and genetic drift (largely due to midsummer population bottlenecks). We further suggest that the males emigrate over comparatively longer distances than winged asexual females.
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Affiliation(s)
- H D Loxdale
- Institute of Ecology, Friedrich-Schiller-University, Dornburger Strasse 159, Jena, Germany.
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Schöfl G, Dill A, Heckel DG, Groot AT. Allochronic Separation versus Mate Choice: Nonrandom Patterns of Mating between Fall Armyworm Host Strains. Am Nat 2011; 177:470-85. [DOI: 10.1086/658904] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Henniges-Janssen K, Schöfl G, Reineke A, Heckel DG, Groot AT. Oviposition of diamondback moth in the presence and absence of a novel host plant. Bull Entomol Res 2011; 101:99-105. [PMID: 20569516 DOI: 10.1017/s0007485310000234] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
The diamondback moth (DBM, Plutella xylostella L. (Lepidoptera: Plutellidae)) consumes a wide variety of brassicaceous host plants and is a common pest of crucifer crops worldwide. A highly unusual infestation of a sugar pea crop was recorded in Kenya in 1999, which persisted for two consecutive years. A strain (DBM-P) from this population was established in the laboratory and is the only one of several strains tested that can complete larval development on sugar peas. The oviposition acceptance and preference of the DBM-P strain was assessed in the presence of cabbage plants, sugar pea plants or both, in comparison to another strain (DBM-Cj) that was collected from cabbage and is unable to grow on pea plants. As expected, DBM-Cj females preferred to oviposit on cabbage plants. Surprisingly, DBM-P females also laid most eggs on cabbage and very few on peas. However, they laid significantly more eggs on the cabbage plant when pea plants were present. Our findings suggest that DBM-P manifested the initial stages of an evolutionary host range expansion, which is incomplete due to lack of oviposition fidelity on pea plants.
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Affiliation(s)
- K Henniges-Janssen
- Max Planck Institute for Chemical Ecology, Department of Entomology, Hans-Knöll-Str. 8, 07745 Jena, Germany.
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Walther E, Schöfl G, Mrotzek G, Haryanti, Sugama K, Saluz HP. Paralogous mitochondrial control region in the giant tiger shrimp, Penaeus monodon (F.) affects population genetics inference: A cautionary tale. Mol Phylogenet Evol 2010; 58:404-8. [PMID: 21145976 DOI: 10.1016/j.ympev.2010.11.028] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2010] [Revised: 11/29/2010] [Accepted: 11/30/2010] [Indexed: 10/18/2022]
Abstract
The mitochondrial control region (mtCR) is a widely used genetic marker for phylogenetic, phylogeographic and population genetic inference. The analysis of mtCR in 115 Indonesian specimens of the giant tiger shrimp, Penaeus monodon, revealed 26 individuals yielding a second - apparently paralogous - sequence in addition to the putatively authentic mitochondrial haplotype. The paralogous haplotypes fell into two major haplogroups that are highly diverged with respect to the authentic mitochondrial haplotypes (average pairwise sequence divergence of 12.5% and 5.0%, respectively). A comparison with published mtCR sequences of P. monodon showed that the paralogous contaminant sequences were inadvertently included in a series of recent population genetic studies, leading to seriously compromised conclusions about genetic diversity and differentiation. The prevalence of the paralogous haplotypes throughout the sampled Indo-Pacific populations is highly skewed: From African and Indian individuals only paralogs have been sequenced, while they are completely absent from Australian individuals. This suggests that geographically unequally distributed allelic variants at binding sites of the primer pair ordinarily used to amplify mtCR in P. monodon suppressed the amplification of authentic mtCR in a wide range of samples.
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Affiliation(s)
- Elisabeth Walther
- Leibniz Institute for Natural Product Research and Infection Biology, Jena, Germany
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Schöfl G, Heckel DG, Groot AT. Time-shifted reproductive behaviours among fall armyworm (Noctuidae: Spodoptera frugiperda) host strains: evidence for differing modes of inheritance. J Evol Biol 2009; 22:1447-59. [PMID: 19467132 DOI: 10.1111/j.1420-9101.2009.01759.x] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The noctuid moth Spodoptera frugiperda consists of two strains associated with different larval host plants (most notably corn and rice). These strains exhibit differential temporal patterns of female calling and copulation during scotophase, with the corn strain more active earlier in the night. We investigated strain-specific constraints in reproductive timing, mating interactions between the two strains, and the mode of inheritance of timing of female calling, male calling, copulation and oviposition. We observed an allochronic shift of all reproductive behaviours by approximately 3 h and a parallel shift of nonreproductive locomotor activity, suggesting involvement of the circadian clock. The corn strain was more variable in the timing of calling and copulation than the rice strain. Rice strain females were more restricted in the timing of copulation than rice strain males, while such differences between the sexes were not apparent in the corn strain. There were significant interactions between the strains affecting onset times of copulation and male calling. The four investigated reproductive traits differed in their modes of inheritance: timing of female and male calling exhibited strong maternal effects, timing of copulation was controlled by a combination of maternal effects and corn strain dominant autosomal factors, and timing of oviposition was inherited in a corn strain dominant fashion. We conclude that the allochronic separation of reproduction between fall armyworm strains is asymmetric, less pronounced than previously thought, and under complex genetic control.
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Affiliation(s)
- Gerhard Schöfl
- Department of Entomology, Max Planck Institute for Chemical Ecology, Jena, Germany.
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Groot AT, Marr M, Schöfl G, Lorenz S, Svatos A, Heckel DG. Host strain specific sex pheromone variation in Spodoptera frugiperda. Front Zool 2008; 5:20. [PMID: 19109878 PMCID: PMC2628650 DOI: 10.1186/1742-9994-5-20] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.5] [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: 09/17/2008] [Accepted: 12/25/2008] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The fall armyworm Spodoptera frugiperda (Lepidoptera; Noctuidae) consists of two distinct strains with different host plant preferences for corn and rice. To assess whether pheromonal-mediated behavioral isolation accompanies the habitat isolation on different host plants, we compared the sex pheromone composition among females of the two strains. Pheromone glands were extracted with or without injection of pheromone biosynthesis activating neuropeptide (PBAN). To assess the mode of inheritance of this variation, we also analyzed the pheromone composition of F1 hybrid females. RESULTS Relative to intra-strain variation, the pheromone composition of the two strains differed significantly. Corn strain females contained significantly more of the second most abundant pheromone compound Z11-16:Ac (m), and significantly less of most other compounds, than rice strain females. When females were injected with PBAN before their glands were extracted, the differences between the strains were less pronounced but still statistically significant. The pheromone composition of hybrid females showed a maternal inheritance of the major component Z9-14:Ac (M) as well as of Z11-16:Ac (m). Most other compounds showed an inheritance indicating genetic dominance of the corn strain. The within-strain phenotypic correlations among the various components were consistent with their hypothesized biosynthetic pathway, and between-strain differences in the correlation structure suggested candidate genes that may explain the pheromone differences between the two strains. These include Delta9- and Delta11 desaturases, and possibly also a Delta7-desaturase, although the latter has not been identified in insects so far. CONCLUSION The two host strains of S. frugiperda produce systematically differing female sex pheromone blends. Previously-documented geographic variation in the sexual communication of this species did not take strain identity into account, and thus may be partly explained by different strain occurrence in different regions. The finding of pheromone differences reinforces the possibility of incipient reproductive isolation among these strains, previously shown to differ in the timing of nocturnal mating activity and host plant use. Finding the genetic basis of the pheromone differences, as well as these other biological traits, will help to elucidate the role of premating isolation in the continuing differentiation of these two strains that may eventually lead to speciation.
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Affiliation(s)
- Astrid T Groot
- Max Planck Institute for Chemical Ecology, Dept. Entomology, Hans-Knöll Strasse 8, 07745 Jena, Germany
| | - Melanie Marr
- Max Planck Institute for Chemical Ecology, Dept. Entomology, Hans-Knöll Strasse 8, 07745 Jena, Germany
| | - Gerhard Schöfl
- Max Planck Institute for Chemical Ecology, Dept. Entomology, Hans-Knöll Strasse 8, 07745 Jena, Germany
| | - Sybille Lorenz
- Max Planck Institute for Chemical Ecology, Research group Mass spectrometry, Hans-Knöll Strasse 8, 07745 Jena, Germany
| | - Ales Svatos
- Max Planck Institute for Chemical Ecology, Research group Mass spectrometry, Hans-Knöll Strasse 8, 07745 Jena, Germany
| | - David G Heckel
- Max Planck Institute for Chemical Ecology, Dept. Entomology, Hans-Knöll Strasse 8, 07745 Jena, Germany
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Abstract
Drosophila simulans originated in sub-Saharan Africa or Madagascar and colonized the rest of the world after the last glaciation about 10 000 years ago. Consistent with this demographic history, sub-Saharan African populations have been shown to harbour higher levels of microsatellite and sequence variation than cosmopolitan populations. Nevertheless, only limited information is available on the population structure of D. simulans. Here, we analysed X-linked and autosomal microsatellite loci in four sub-Saharan African, one North African, one Israeli, and two European D. simulans populations. Bayesian clustering algorithms combined the North African, Israeli, and European populations into a single cosmopolitan group. The four sub-Saharan populations were split into two separate groups. Pairwise F(ST) analysis, however, indicated significant population differentiation between all eight populations surveyed. A significant signal for population reduction in cosmopolitan populations was found only for X-linked loci.
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Affiliation(s)
- Gerhard Schöfl
- Institut für Tierzucht und Genetik, Veterinärmedizinische Universität Wien, Josef-Baumann Gasse 1, 1210 Wien, Austria
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Schöfl G, Catania F, Nolte V, Schlötterer C. African sequence variation accounts for most of the sequence polymorphism in non-African Drosophila melanogaster. Genetics 2005; 170:1701-9. [PMID: 15937137 PMCID: PMC1449792 DOI: 10.1534/genetics.104.037507] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We compared the sequence polymorphism of 12 genomic fragments in six geographically dispersed African populations to one European Drosophila melanogaster population. On the basis of one African and one European population half of these fragments have strongly reduced levels of variability outside of Africa. Despite this striking difference in European variation, we detected no significant difference in African variation between the two fragment classes. The joint analysis of all African populations indicated that all high-frequency European alleles are of African origin. We observed a negative Tajima's D in all African populations, with three populations deviating significantly from neutral equilibrium. Low, but statistically significant, population differentiation was observed among the African populations. Our results imply that the population structure and demographic past of African D. melanogaster populations need to be considered for the inference of footprints of selection in non-African populations.
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Affiliation(s)
- Gerhard Schöfl
- Institut für Tierzucht und Genetik, Veterinärmedizinische Universität, A-1210 Vienna, Austria
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Schöfl G, Schlötterer C. Patterns of Microsatellite Variability Among X Chromosomes and Autosomes Indicate a High Frequency of Beneficial Mutations in Non-African D. simulans. Mol Biol Evol 2004; 21:1384-90. [PMID: 15044592 DOI: 10.1093/molbev/msh132] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We analyzed microsatellite variability at 42 X-linked and 39 autosomal loci from African and European populations of Drosophila simulans. The African D. simulans harbored significantly more microsatellite variability than the European flies. In the European population, X-linked polymorphism was more reduced than autosomal variation, whereas there was no significant difference between chromosomes in the African population. Previous studies also observed a similar pattern but failed to distinguish between a demographic event and a selection scenario. We performed extensive computer simulations using a wide range of demographic scenarios to distinguish between the two hypotheses. Approximate summary likelihood estimates differed dramatically among X chromosomes and autosomes. Furthermore, our experimental data showed a surplus of X-linked microsatellites with a significantly reduced variability in non-African D. simulans. We conclude that our data are not compatible with a neutral scenario. Thus, the reduced variability at X-linked loci is most likely caused by selective sweeps associated with the out-of-Africa habitat expansion of D. simulans.
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Affiliation(s)
- Gerhard Schöfl
- Institut fur Tierzucht und Genetik, Veterinarmedizinische Universitat, Vienna, Austria
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