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Kuhl H, Strassert JFH, Čertnerová D, Varga E, Kreuz E, Lamatsch DK, Wuertz S, Köhler J, Monaghan MT, Stöck M. The haplotype-resolved Prymnesium parvum (type B) microalga genome reveals the genetic basis of its fish-killing toxins. Curr Biol 2024:S0960-9822(24)00817-0. [PMID: 38986615 DOI: 10.1016/j.cub.2024.06.033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 05/13/2024] [Accepted: 06/11/2024] [Indexed: 07/12/2024]
Abstract
The catastrophic loss of aquatic life in the Central European Oder River in 2022, caused by a toxic bloom of the haptophyte microalga Prymnesium parvum (in a wide sense, s.l.), underscores the need to improve our understanding of the genomic basis of the toxin. Previous morphological, phylogenetic, and genomic studies have revealed cryptic diversity within P. parvum s.l. and uncovered three clade-specific (types A, B, and C) prymnesin toxins. Here, we used state-of-the-art long-read sequencing and assembled the first haplotype-resolved diploid genome of a P. parvum type B from the strain responsible for the Oder disaster. Comparative analyses with type A genomes uncovered a genome-size expansion driven by repetitive elements in type B. We also found conserved synteny but divergent evolution in several polyketide synthase (PKS) genes, which are known to underlie toxin production in combination with environmental cues. We identified an approximately 20-kbp deletion in the largest PKS gene of type B that we link to differences in the chemical structure of types A and B prymnesins. Flow cytometry and electron microscopy analyses confirmed diploidy in the Oder River strain and revealed differences to closely related strains in both ploidy and morphology. Our results provide unprecedented resolution of strain diversity in P. parvum s.l. and a better understanding of the genomic basis of toxin variability in haptophytes. The reference-quality genome will enable us to better understand changes in microbial diversity in the face of increasing environmental pressures and provides a basis for strain-level monitoring of invasive Prymnesium in the future.
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Affiliation(s)
- Heiner Kuhl
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany
| | - Jürgen F H Strassert
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany
| | - Dora Čertnerová
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic; Research Department for Limnology, Mondsee, University of Innsbruck, Mondsee, Austria
| | - Elisabeth Varga
- Department of Food Chemistry and Toxicology, University of Vienna, Vienna, Austria; Unit Food Hygiene and Technology, Centre for Food Science and Veterinary Public Health, Clinical Department for Farm Animals and Food System Science, University of Veterinary Medicine, Vienna, Austria
| | - Eva Kreuz
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany
| | - Dunja K Lamatsch
- Research Department for Limnology, Mondsee, University of Innsbruck, Mondsee, Austria
| | - Sven Wuertz
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany
| | - Jan Köhler
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany
| | - Michael T Monaghan
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany; Institut für Biologie, Freie Universität Berlin, Berlin, Germany.
| | - Matthias Stöck
- Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany.
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Iwasaki Y, Ikemura T, Wada K, Wada Y, Abe T. Comparative genomic analysis of the human genome and six bat genomes using unsupervised machine learning: Mb-level CpG and TFBS islands. BMC Genomics 2022; 23:497. [PMID: 35804296 PMCID: PMC9264310 DOI: 10.1186/s12864-022-08664-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 05/31/2022] [Indexed: 11/25/2022] Open
Abstract
Background Emerging infectious disease-causing RNA viruses, such as the SARS-CoV-2 and Ebola viruses, are thought to rely on bats as natural reservoir hosts. Since these zoonotic viruses pose a great threat to humans, it is important to characterize the bat genome from multiple perspectives. Unsupervised machine learning methods for extracting novel information from big sequence data without prior knowledge or particular models are highly desirable for obtaining unexpected insights. We previously established a batch-learning self-organizing map (BLSOM) of the oligonucleotide composition that reveals novel genome characteristics from big sequence data. Results In this study, using the oligonucleotide BLSOM, we conducted a comparative genomic study of humans and six bat species. BLSOM is an explainable-type machine learning algorithm that reveals the diagnostic oligonucleotides contributing to sequence clustering (self-organization). When unsupervised machine learning reveals unexpected and/or characteristic features, these features can be studied in more detail via the much simpler and more direct standard distribution map method. Based on this combined strategy, we identified the Mb-level enrichment of CG dinucleotide (Mb-level CpG islands) around the termini of bat long-scaffold sequences. In addition, a class of CG-containing oligonucleotides were enriched in the centromeric and pericentromeric regions of human chromosomes. Oligonucleotides longer than tetranucleotides often represent binding motifs for a wide variety of proteins (e.g., transcription factor binding sequences (TFBSs)). By analyzing the penta- and hexanucleotide composition, we observed the evident enrichment of a wide range of hexanucleotide TFBSs in centromeric and pericentromeric heterochromatin regions on all human chromosomes. Conclusion Function of transcription factors (TFs) beyond their known regulation of gene expression (e.g., TF-mediated looping interactions between two different genomic regions) has received wide attention. The Mb-level TFBS and CpG islands are thought to be involved in the large-scale nuclear organization, such as centromere and telomere clustering. TFBSs, which are enriched in centromeric and pericentromeric heterochromatin regions, are thought to play an important role in the formation of nuclear 3D structures. Our machine learning-based analysis will help us to understand the differential features of nuclear 3D structures in the human and bat genomes. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08664-9.
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Affiliation(s)
- Yuki Iwasaki
- Department of Bioscience, Nagahama Institute of Bio-Science and Technology, Tamura-cho 1266, Nagahama-shi, Shiga-ken, 526-0829, Japan
| | - Toshimichi Ikemura
- Department of Bioscience, Nagahama Institute of Bio-Science and Technology, Tamura-cho 1266, Nagahama-shi, Shiga-ken, 526-0829, Japan.
| | - Kennosuke Wada
- Department of Bioscience, Nagahama Institute of Bio-Science and Technology, Tamura-cho 1266, Nagahama-shi, Shiga-ken, 526-0829, Japan
| | - Yoshiko Wada
- Department of Bioscience, Nagahama Institute of Bio-Science and Technology, Tamura-cho 1266, Nagahama-shi, Shiga-ken, 526-0829, Japan
| | - Takashi Abe
- Smart Information Systems, Faculty of Engineering, Niigata University, Niigata-ken, 950-2181, Japan.
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Valeri MP, Dias GB, do Espírito Santo AA, Moreira CN, Yonenaga-Yassuda Y, Sommer IB, Kuhn GCS, Svartman M. First Description of a Satellite DNA in Manatees' Centromeric Regions. Front Genet 2021; 12:694866. [PMID: 34504514 PMCID: PMC8421680 DOI: 10.3389/fgene.2021.694866] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 07/30/2021] [Indexed: 11/18/2022] Open
Abstract
Trichechus manatus and Trichechus inunguis are the two Sirenia species that occur in the Americas. Despite their increasing extinction risk, many aspects of their biology remain understudied, including the repetitive DNA fraction of their genomes. Here we used the sequenced genome of T. manatus and TAREAN to identify satellite DNAs (satDNAs) in this species. We report the first description of TMAsat, a satDNA comprising ~0.87% of the genome, with ~684bp monomers and centromeric localization. In T. inunguis, TMAsat showed similar monomer length, chromosome localization and conserved CENP-B box-like motifs as in T. manatus. We also detected this satDNA in the Dugong dugon and in the now extinct Hydrodamalis gigas genomes. The neighbor-joining tree shows that TMAsat sequences from T. manatus, T. inunguis, D. dugon, and H. gigas lack species-specific clusters, which disagrees with the predictions of concerted evolution. We detected a divergent TMAsat-like homologous sequence in elephants and hyraxes, but not in other mammals, suggesting this sequence was already present in the common ancestor of Paenungulata, and later became a satDNA in the Sirenians. This is the first description of a centromeric satDNA in manatees and will facilitate the inclusion of Sirenia in future studies of centromeres and satDNA biology.
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Affiliation(s)
- Mirela Pelizaro Valeri
- Laboratório de Citogenômica Evolutiva, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Guilherme Borges Dias
- Department of Genetics and Institute of Bioinformatics, University of Georgia, Athens, GA, United States
| | - Alice Alves do Espírito Santo
- Laboratório de Citogenômica Evolutiva, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Camila Nascimento Moreira
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Yatiyo Yonenaga-Yassuda
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Iara Braga Sommer
- Centro Nacional de Pesquisa e Conservação da Biodiversidade Marinha do Nordeste, Instituto Chico Mendes de Conservação da Biodiversidade, Brasília, Brazil
| | - Gustavo C. S. Kuhn
- Laboratório de Citogenômica Evolutiva, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Marta Svartman
- Laboratório de Citogenômica Evolutiva, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
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Brown J, Barry C, Schmitz MT, Argus C, Bolin JM, Schwartz MP, Van Aartsen A, Steill J, Swanson S, Stewart R, Thomson JA, Kendziorski C. Interspecies chimeric conditions affect the developmental rate of human pluripotent stem cells. PLoS Comput Biol 2021; 17:e1008778. [PMID: 33647016 PMCID: PMC7951976 DOI: 10.1371/journal.pcbi.1008778] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 03/11/2021] [Accepted: 02/08/2021] [Indexed: 12/17/2022] Open
Abstract
Human pluripotent stem cells hold significant promise for regenerative medicine. However, long differentiation protocols and immature characteristics of stem cell-derived cell types remain challenges to the development of many therapeutic applications. In contrast to the slow differentiation of human stem cells in vitro that mirrors a nine-month gestation period, mouse stem cells develop according to a much faster three-week gestation timeline. Here, we tested if co-differentiation with mouse pluripotent stem cells could accelerate the differentiation speed of human embryonic stem cells. Following a six-week RNA-sequencing time course of neural differentiation, we identified 929 human genes that were upregulated earlier and 535 genes that exhibited earlier peaked expression profiles in chimeric cell cultures than in human cell cultures alone. Genes with accelerated upregulation were significantly enriched in Gene Ontology terms associated with neurogenesis, neuron differentiation and maturation, and synapse signaling. Moreover, chimeric mixed samples correlated with in utero human embryonic samples earlier than human cells alone, and acceleration was dose-dependent on human-mouse co-culture ratios. The altered gene expression patterns and developmental rates described in this report have implications for accelerating human stem cell differentiation and the use of interspecies chimeric embryos in developing human organs for transplantation.
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Affiliation(s)
- Jared Brown
- Department of Statistics, University of Wisconsin-Madison, Wisconsin, United States of America
- * E-mail: (JB); (CK)
| | - Christopher Barry
- Morgridge Institute for Research, Madison, Wisconsin, United States of America
| | - Matthew T. Schmitz
- Morgridge Institute for Research, Madison, Wisconsin, United States of America
| | - Cara Argus
- Morgridge Institute for Research, Madison, Wisconsin, United States of America
| | - Jennifer M. Bolin
- Morgridge Institute for Research, Madison, Wisconsin, United States of America
| | - Michael P. Schwartz
- NSF Center for Sustainable Nanotechnology, Department of Chemistry, University of Wisconsin-Madison, Wisconsin, United States of America
| | - Amy Van Aartsen
- Morgridge Institute for Research, Madison, Wisconsin, United States of America
| | - John Steill
- Morgridge Institute for Research, Madison, Wisconsin, United States of America
| | - Scott Swanson
- Morgridge Institute for Research, Madison, Wisconsin, United States of America
| | - Ron Stewart
- Morgridge Institute for Research, Madison, Wisconsin, United States of America
| | - James A. Thomson
- Morgridge Institute for Research, Madison, Wisconsin, United States of America
- Department of Cell and Regenerative Biology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, United States of America
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, California, United States of America
| | - Christina Kendziorski
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Wisconsin, United States of America
- * E-mail: (JB); (CK)
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5
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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] [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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6
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Kasai F, O'Brien PCM, Ferguson-Smith MA. Squamate Chromosome Size and GC Content Assessed by Flow Karyotyping. Cytogenet Genome Res 2019; 157:46-52. [PMID: 30904910 DOI: 10.1159/000497265] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Chromosome homologies in reptiles have been investigated extensively by gene mapping and chromosome painting. Relative chromosome size can be estimated roughly from conventional karyotypes, but chromosome GC content cannot be evaluated by any of these approaches. However, GC content can be obtained by whole-genome sequencing, although complete data are available only for a limited number of reptilian species. Chromosomes can be characterized by size and GC content in bivariate flow karyotypes, in which the distribution of peaks represents the differences. We have analysed flow karyotypes from 9 representative squamate species and show chromosome profiles for each species based on the relationship between size and GC content. Our results reveal that the GC content of macrochromosomes is invariable in the 9 species. A higher GC content was found in microchromosomes, similar to profiles previously determined in crocodile, turtle, and chicken. The findings suggest that karyotype evolution in reptiles is characterized by unique features of chromosome GC content.
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Kasai F, Pereira JC, Kohara A, Ferguson-Smith MA. Homologue-specific chromosome sequencing characterizes translocation junctions and permits allelic assignment. DNA Res 2018. [PMID: 29518182 PMCID: PMC6105103 DOI: 10.1093/dnares/dsy007] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Chromosome translocations can be detected by cytogenetic analysis, but it is hard to characterize the breakpoints at the sequence level. Chromosome sorting by flow cytometry produces flow karyotypes that enable the isolation of abnormal chromosomes and the generation of chromosome-specific DNA. In this study, a derivative chromosome t(9; 14) and its homologous normal chromosomes 9 and 14 from the Ishikawa 3-H-12 cell line were sorted to collect homologue-specific samples. Chromosome sequencing identified the breakpoint junction in the der(9) at 9p24.3 and 14q13.1 and uncovered the formation of a fusion gene, WASH1–NPAS3. Amplicon sequencing targeted for neighbouring genes at the fusion breakpoint revealed that the variant frequencies correlate with the allelic copy number. Sequencing of sorted chromosomes permits the assignment of allelic variants and can lead to the characterization of abnormal chromosomes. We show that allele-specific chromosome sequencing of homologues is a robust technique for distinguishing alleles and this provides an efficient approach for the comprehensive analysis of genomic changes.
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Affiliation(s)
- Fumio Kasai
- Japanese Collection of Research Bioresources (JCRB) Cell Bank, Laboratory of Cell Cultures, National Institutes of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka, Japan.,Cambridge Resource Centre for Comparative Genomics, Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Jorge C Pereira
- Cambridge Resource Centre for Comparative Genomics, Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Arihiro Kohara
- Japanese Collection of Research Bioresources (JCRB) Cell Bank, Laboratory of Cell Cultures, National Institutes of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka, Japan
| | - Malcolm A Ferguson-Smith
- Cambridge Resource Centre for Comparative Genomics, Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
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8
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Kasai F, O'Brien PCM, Pereira JC, Ferguson-Smith MA. Marsupial chromosome DNA content and genome size assessed from flow karyotypes: invariable low autosomal GC content. ROYAL SOCIETY OPEN SCIENCE 2018; 5:171539. [PMID: 30224977 PMCID: PMC6124049 DOI: 10.1098/rsos.171539] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 08/06/2018] [Indexed: 06/08/2023]
Abstract
Extensive chromosome homologies revealed by cross-species chromosome painting between marsupials have suggested a high level of genome conservation during evolution. Surprisingly, it has been reported that marsupial genome sizes vary by more than 1.2 Gb between species. We have shown previously that individual chromosome sizes and GC content can be measured in flow karyotypes, and have applied this method to compare four marsupial species. Chromosome sizes and GC content were calculated for the grey short-tailed opossum (2n = 18), tammar wallaby (2n = 16), Tasmanian devil (2n = 14) and fat-tailed dunnart (2n = 14), resulting in genome sizes of 3.41, 3.31, 3.17 and 3.25 Gb, respectively. The findings under the same conditions allow a comparison between the four species, indicating that the genomes of these four species are 1-8% larger than human. We show that marsupial genomes are characterized by a low GC content invariable between autosomes and distinct from the higher GC content of the marsupial × chromosome.
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Affiliation(s)
- Fumio Kasai
- Author for correspondence: Fumio Kasai e-mail:
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9
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Bourgeois S, Senn H, Kaden J, Taggart JB, Ogden R, Jeffery KJ, Bunnefeld N, Abernethy K, McEwing R. Single-nucleotide polymorphism discovery and panel characterization in the African forest elephant. Ecol Evol 2018; 8:2207-2217. [PMID: 29468037 PMCID: PMC5817121 DOI: 10.1002/ece3.3854] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2017] [Revised: 12/17/2017] [Accepted: 12/29/2017] [Indexed: 12/14/2022] Open
Abstract
The continuing decline in forest elephant (Loxodonta cyclotis) numbers due to poaching and habitat reduction is driving the search for new tools to inform management and conservation. For dense rainforest species, basic ecological data on populations and threats can be challenging and expensive to collect, impeding conservation action in the field. As such, genetic monitoring is being increasingly implemented to complement or replace more burdensome field techniques. Single-nucleotide polymorphisms (SNPs) are particularly cost-effective and informative markers that can be used for a range of practical applications, including population census, assessment of human impact on social and genetic structure, and investigation of the illegal wildlife trade. SNP resources for elephants are scarce, but next-generation sequencing provides the opportunity for rapid, inexpensive generation of SNP markers in nonmodel species. Here, we sourced forest elephant DNA from 23 samples collected from 10 locations within Gabon, Central Africa, and applied double-digest restriction-site-associated DNA (ddRAD) sequencing to discover 31,851 tags containing SNPs that were reduced to a set of 1,365 high-quality candidate SNP markers. A subset of 115 candidate SNPs was then selected for assay design and validation using 56 additional samples. Genotyping resulted in a high conversion rate (93%) and a low per allele error rate (0.07%). This study provides the first panel of 107 validated SNP markers for forest elephants. This resource presents great potential for new genetic tools to produce reliable data and underpin a step-change in conservation policies for this elusive species.
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Affiliation(s)
- Stéphanie Bourgeois
- Agence Nationale des Parcs NationauxLibrevilleGabon
- WildGenes LaboratoryThe Royal Zoological Society of ScotlandEdinburgh ZooEdinburghUK
- Biological and Environmental SciencesFaculty of Natural SciencesUniversity of StirlingStirlingUK
| | - Helen Senn
- WildGenes LaboratoryThe Royal Zoological Society of ScotlandEdinburgh ZooEdinburghUK
| | - Jenny Kaden
- WildGenes LaboratoryThe Royal Zoological Society of ScotlandEdinburgh ZooEdinburghUK
| | - John B. Taggart
- Aquaculture Pathfoot BuildingUniversity of StirlingStirlingUK
| | - Rob Ogden
- TRACE Wildlife Forensics NetworkEdinburghUK
- Royal (Dick) School of Veterinary Studies & The Roslin InstituteUniversity of EdinburghEdinburghUK
| | - Kathryn J. Jeffery
- Agence Nationale des Parcs NationauxLibrevilleGabon
- Biological and Environmental SciencesFaculty of Natural SciencesUniversity of StirlingStirlingUK
- Institut de Recherche en Écologie TropicaleLibrevilleGabon
| | - Nils Bunnefeld
- Biological and Environmental SciencesFaculty of Natural SciencesUniversity of StirlingStirlingUK
| | - Katharine Abernethy
- Biological and Environmental SciencesFaculty of Natural SciencesUniversity of StirlingStirlingUK
- Institut de Recherche en Écologie TropicaleLibrevilleGabon
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Damas J, O'Connor R, Farré M, Lenis VPE, Martell HJ, Mandawala A, Fowler K, Joseph S, Swain MT, Griffin DK, Larkin DM. Upgrading short-read animal genome assemblies to chromosome level using comparative genomics and a universal probe set. Genome Res 2016; 27:875-884. [PMID: 27903645 PMCID: PMC5411781 DOI: 10.1101/gr.213660.116] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 11/16/2016] [Indexed: 02/07/2023]
Abstract
Most recent initiatives to sequence and assemble new species’ genomes de novo fail to achieve the ultimate endpoint to produce contigs, each representing one whole chromosome. Even the best-assembled genomes (using contemporary technologies) consist of subchromosomal-sized scaffolds. To circumvent this problem, we developed a novel approach that combines computational algorithms to merge scaffolds into chromosomal fragments, PCR-based scaffold verification, and physical mapping to chromosomes. Multigenome-alignment-guided probe selection led to the development of a set of universal avian BAC clones that permit rapid anchoring of multiple scaffolds to chromosomes on all avian genomes. As proof of principle, we assembled genomes of the pigeon (Columbia livia) and peregrine falcon (Falco peregrinus) to chromosome levels comparable, in continuity, to avian reference genomes. Both species are of interest for breeding, cultural, food, and/or environmental reasons. Pigeon has a typical avian karyotype (2n = 80), while falcon (2n = 50) is highly rearranged compared to the avian ancestor. By using chromosome breakpoint data, we established that avian interchromosomal breakpoints appear in the regions of low density of conserved noncoding elements (CNEs) and that the chromosomal fission sites are further limited to long CNE “deserts.” This corresponds with fission being the rarest type of rearrangement in avian genome evolution. High-throughput multiple hybridization and rapid capture strategies using the current BAC set provide the basis for assembling numerous avian (and possibly other reptilian) species, while the overall strategy for scaffold assembly and mapping provides the basis for an approach that (provided metaphases can be generated) could be applied to any animal genome.
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Affiliation(s)
- Joana Damas
- Department of Comparative Biomedical Sciences, Royal Veterinary College, University of London, London, NW1 0TU, United Kingdom
| | - Rebecca O'Connor
- School of Biosciences, University of Kent, Canterbury, CT2 7NY, United Kingdom
| | - Marta Farré
- Department of Comparative Biomedical Sciences, Royal Veterinary College, University of London, London, NW1 0TU, United Kingdom
| | - Vasileios Panagiotis E Lenis
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, SY23 3DA, United Kingdom
| | - Henry J Martell
- School of Biosciences, University of Kent, Canterbury, CT2 7NY, United Kingdom
| | - Anjali Mandawala
- School of Biosciences, University of Kent, Canterbury, CT2 7NY, United Kingdom.,School of Human and Life Sciences, Canterbury Christ Church University, Canterbury, CT1 1QU, United Kingdom
| | - Katie Fowler
- School of Human and Life Sciences, Canterbury Christ Church University, Canterbury, CT1 1QU, United Kingdom
| | - Sunitha Joseph
- School of Biosciences, University of Kent, Canterbury, CT2 7NY, United Kingdom
| | - Martin T Swain
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, SY23 3DA, United Kingdom
| | - Darren K Griffin
- School of Biosciences, University of Kent, Canterbury, CT2 7NY, United Kingdom
| | - Denis M Larkin
- Department of Comparative Biomedical Sciences, Royal Veterinary College, University of London, London, NW1 0TU, United Kingdom
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Ferguson-Smith MA. History and evolution of cytogenetics. Mol Cytogenet 2015; 8:19. [PMID: 25810762 PMCID: PMC4373004 DOI: 10.1186/s13039-015-0125-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Accepted: 03/04/2015] [Indexed: 11/21/2022] Open
Abstract
The events that have led to the development of cytogenetics as a specialty within the life sciences are described, with special attention to the early history of human cytogenetics. Improvements in the resolution of chromosome analysis has followed closely the introduction of innovative technology. The review provides a brief account of the structure of somatic and meiotic chromosomes, stressing the high conservation of structure in plants and animals, with emphasis on aspects that require further research. The future of molecular cytogenetics is likely to depend on a better knowledge of chromosome structure and function.
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Affiliation(s)
- Malcolm A Ferguson-Smith
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, CB3 0ES UK
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Abstract
Background Next generation sequencing (NGS) technologies have made it possible to exhaustively detect structural variations (SVs) in genomes. Although various methods for detecting SVs have been developed, the global structure of chromosomes, i.e., how segments in a reference genome are extracted and ordered in an unknown target genome, cannot be inferred by detecting only individual SVs. Results Here, we formulate the problem of inferring the global structure of chromosomes from SVs as an optimization problem on a bidirected graph. This problem takes into account the aberrant adjacencies of genomic regions, the copy numbers, and the number and length of chromosomes. Although the problem is NP-complete, we propose its polynomial-time solvable variation by restricting instances of the problem using a biologically meaningful condition, which we call the weakly connected constraint. We also explain how to obtain experimental data that satisfies the weakly connected constraint. Conclusion Our results establish a theoretical foundation for the development of practical computational tools that could be used to infer the global structure of chromosomes based on SVs. The computational complexity of the inference can be reduced by detecting the segments of the reference genome at the ends of the chromosomes of the target genome and also the segments that are known to exist in the target genome.
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The bat genome: GC-biased small chromosomes associated with reduction in genome size. Chromosoma 2013; 122:535-40. [PMID: 23881029 DOI: 10.1007/s00412-013-0426-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2013] [Revised: 06/28/2013] [Accepted: 06/28/2013] [Indexed: 12/31/2022]
Abstract
Bats are distinct from other mammals in their small genome size as well as their high metabolic rate, possibly related to flight ability. Although the genome sequence has been published in two species, the data lack cytogenetic information. In this study, the size and GC content of each chromosome are measured from the flow karyotype of the mouse-eared bat, Myotis myotis (MMY). The smaller chromosomes are GC-rich compared to the larger chromosomes, and the relative proportions of homologous segments between MMY and human differ among the MMY chromosomes. The MMY genome size calculated from the sum of the chromosome sizes is 2.25 Gb, and the total GC content is 42.3%, compared to human and dog with 41.0 and 41.2%, respectively. The GC-rich small MMY genome is characterised by GC-biased smaller chromosomes resulting from preferential loss of AT-rich sequences. Although the association between GC-rich small chromosomes and small genome size has been reported only in birds so far, we show in this paper, for the first time, that the same phenomenon is observed in at least one group of mammals, implying that this may be a mechanism common to genome evolution in general.
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