1
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Clark ML, Salas L, Baligar S, Quinn CA, Snyder RL, Leland D, Schackwitz W, Goetz SJ, Newsam S. The effect of soundscape composition on bird vocalization classification in a citizen science biodiversity monitoring project. ECOL INFORM 2023. [DOI: 10.1016/j.ecoinf.2023.102065] [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: 03/18/2023]
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2
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Wakao S, Shih PM, Guan K, Schackwitz W, Ye J, Patel D, Shih RM, Dent RM, Chovatia M, Sharma A, Martin J, Wei CL, Niyogi KK. Discovery of photosynthesis genes through whole-genome sequencing of acetate-requiring mutants of Chlamydomonas reinhardtii. PLoS Genet 2021; 17:e1009725. [PMID: 34492001 PMCID: PMC8448359 DOI: 10.1371/journal.pgen.1009725] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [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: 03/02/2021] [Revised: 09/17/2021] [Accepted: 07/19/2021] [Indexed: 11/18/2022] Open
Abstract
Large-scale mutant libraries have been indispensable for genetic studies, and the development of next-generation genome sequencing technologies has greatly advanced efforts to analyze mutants. In this work, we sequenced the genomes of 660 Chlamydomonas reinhardtii acetate-requiring mutants, part of a larger photosynthesis mutant collection previously generated by insertional mutagenesis with a linearized plasmid. We identified 554 insertion events from 509 mutants by mapping the plasmid insertion sites through paired-end sequences, in which one end aligned to the plasmid and the other to a chromosomal location. Nearly all (96%) of the events were associated with deletions, duplications, or more complex rearrangements of genomic DNA at the sites of plasmid insertion, and together with deletions that were unassociated with a plasmid insertion, 1470 genes were identified to be affected. Functional annotations of these genes were enriched in those related to photosynthesis, signaling, and tetrapyrrole synthesis as would be expected from a library enriched for photosynthesis mutants. Systematic manual analysis of the disrupted genes for each mutant generated a list of 253 higher-confidence candidate photosynthesis genes, and we experimentally validated two genes that are essential for photoautotrophic growth, CrLPA3 and CrPSBP4. The inventory of candidate genes includes 53 genes from a phylogenomically defined set of conserved genes in green algae and plants. Altogether, 70 candidate genes encode proteins with previously characterized functions in photosynthesis in Chlamydomonas, land plants, and/or cyanobacteria; 14 genes encode proteins previously shown to have functions unrelated to photosynthesis. Among the remaining 169 uncharacterized genes, 38 genes encode proteins without any functional annotation, signifying that our results connect a function related to photosynthesis to these previously unknown proteins. This mutant library, with genome sequences that reveal the molecular extent of the chromosomal lesions and resulting higher-confidence candidate genes, will aid in advancing gene discovery and protein functional analysis in photosynthesis.
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Affiliation(s)
- Setsuko Wakao
- Division of Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- Department of Plant and Microbial Biology, University of California, Berkeley, California, United States of America
| | - Patrick M. Shih
- Department of Plant and Microbial Biology, University of California, Berkeley, California, United States of America
- Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- Feedstocks Division, Joint BioEnergy Institute, Emeryville, California, United States of America
- Innovative Genomics Institute, University of California, Berkeley, California, United States of America
| | - Katharine Guan
- Department of Plant and Microbial Biology, University of California, Berkeley, California, United States of America
- Howard Hughes Medical Institute, University of California, Berkeley, California, United States of America
| | - Wendy Schackwitz
- Joint Genome Institute, Berkeley, California, United States of America
| | - Joshua Ye
- Department of Plant and Microbial Biology, University of California, Berkeley, California, United States of America
- Howard Hughes Medical Institute, University of California, Berkeley, California, United States of America
| | - Dhruv Patel
- Department of Plant and Microbial Biology, University of California, Berkeley, California, United States of America
| | - Robert M. Shih
- Division of Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Rachel M. Dent
- Department of Plant and Microbial Biology, University of California, Berkeley, California, United States of America
| | - Mansi Chovatia
- Joint Genome Institute, Berkeley, California, United States of America
| | - Aditi Sharma
- Joint Genome Institute, Berkeley, California, United States of America
| | - Joel Martin
- Joint Genome Institute, Berkeley, California, United States of America
| | - Chia-Lin Wei
- Joint Genome Institute, Berkeley, California, United States of America
| | - Krishna K. Niyogi
- Division of Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- Department of Plant and Microbial Biology, University of California, Berkeley, California, United States of America
- Howard Hughes Medical Institute, University of California, Berkeley, California, United States of America
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3
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Álvarez-Escribano I, Sasse C, Bok JW, Na H, Amirebrahimi M, Lipzen A, Schackwitz W, Martin J, Barry K, Gutiérrez G, Cea-Sánchez S, Marcos AT, Grigoriev IV, Keller NP, Braus GH, Cánovas D. Genome sequencing of evolved aspergilli populations reveals robust genomes, transversions in A. flavus, and sexual aberrancy in non-homologous end-joining mutants. BMC Biol 2019; 17:88. [PMID: 31711484 PMCID: PMC6844060 DOI: 10.1186/s12915-019-0702-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [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: 07/15/2019] [Accepted: 09/19/2019] [Indexed: 01/19/2023] Open
Abstract
Background Aspergillus spp. comprises a very diverse group of lower eukaryotes with a high relevance for industrial applications and clinical implications. These multinucleate species are often cultured for many generations in the laboratory, which can unknowingly propagate hidden genetic mutations. To assess the likelihood of such events, we studied the genome stability of aspergilli by using a combination of mutation accumulation (MA) lines and whole genome sequencing. Results We sequenced the whole genomes of 30 asexual and 10 sexual MA lines of three Aspergillus species (A. flavus, A. fumigatus and A. nidulans) and estimated that each MA line accumulated mutations for over 4000 mitoses during asexual cycles. We estimated mutation rates of 4.2 × 10−11 (A. flavus), 1.1 × 10−11 (A. fumigatus) and 4.1 × 10−11 (A. nidulans) per site per mitosis, suggesting that the genomes are very robust. Unexpectedly, we found a very high rate of GC → TA transversions only in A. flavus. In parallel, 30 asexual lines of the non-homologous end-joining (NHEJ) mutants of the three species were also allowed to accumulate mutations for the same number of mitoses. Sequencing of these NHEJ MA lines gave an estimated mutation rate of 5.1 × 10−11 (A. flavus), 2.2 × 10−11 (A. fumigatus) and 4.5 × 10−11 (A. nidulans) per base per mitosis, which is slightly higher than in the wild-type strains and some ~ 5–6 times lower than in the yeasts. Additionally, in A. nidulans, we found a NHEJ-dependent interference of the sexual cycle that is independent of the accumulation of mutations. Conclusions We present for the first time direct counts of the mutation rate of filamentous fungal species and find that Aspergillus genomes are very robust. Deletion of the NHEJ machinery results in a slight increase in the mutation rate, but at a rate we suggest is still safe to use for biotechnology purposes. Unexpectedly, we found GC→TA transversions predominated only in the species A. flavus, which could be generated by the hepatocarcinogen secondary metabolite aflatoxin. Lastly, a strong effect of the NHEJ mutation in self-crossing was observed and an increase in the mutations of the asexual lines was quantified.
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Affiliation(s)
- Isidro Álvarez-Escribano
- Department of Genetics, Faculty of Biology, University of Seville, Seville, Spain.,Present Address: Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas y Universidad de Sevilla, Seville, Spain
| | - Christoph Sasse
- Department of Molecular Microbiology and Genetics and Göttingen Center for Molecular Biosciences (GZMB), Georg-August-University, Göttingen, Germany
| | - Jin Woo Bok
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI, USA
| | - Hyunsoo Na
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | | | - Anna Lipzen
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Wendy Schackwitz
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Joel Martin
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Kerrie Barry
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Gabriel Gutiérrez
- Department of Genetics, Faculty of Biology, University of Seville, Seville, Spain
| | - Sara Cea-Sánchez
- Department of Genetics, Faculty of Biology, University of Seville, Seville, Spain
| | - Ana T Marcos
- Department of Genetics, Faculty of Biology, University of Seville, Seville, Spain.,Present Address: Instituto para el Estudio de la Reproducción Humana (Inebir), Avda de la Cruz Roja 1, 41009, Sevilla, Spain
| | - Igor V Grigoriev
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA.,Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA
| | - Nancy P Keller
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI, USA.,Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
| | - Gerhard H Braus
- Department of Molecular Microbiology and Genetics and Göttingen Center for Molecular Biosciences (GZMB), Georg-August-University, Göttingen, Germany
| | - David Cánovas
- Department of Genetics, Faculty of Biology, University of Seville, Seville, Spain.
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4
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Labbé J, Muchero W, Czarnecki O, Wang J, Wang X, Bryan AC, Zheng K, Yang Y, Xie M, Zhang J, Wang D, Meidl P, Wang H, Morrell-Falvey JL, Cope KR, Maia LGS, Ané JM, Mewalal R, Jawdy SS, Gunter LE, Schackwitz W, Martin J, Le Tacon F, Li T, Zhang Z, Ranjan P, Lindquist E, Yang X, Jacobson DA, Tschaplinski TJ, Barry K, Schmutz J, Chen JG, Tuskan GA. Mediation of plant-mycorrhizal interaction by a lectin receptor-like kinase. Nat Plants 2019; 5:676-680. [PMID: 31285560 DOI: 10.1038/s41477-019-0469-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Accepted: 06/04/2019] [Indexed: 05/21/2023]
Abstract
The molecular mechanisms underlying mycorrhizal symbioses, the most ubiquitous and impactful mutualistic plant-microbial interaction in nature, are largely unknown. Through genetic mapping, resequencing and molecular validation, we demonstrate that a G-type lectin receptor-like kinase (lecRLK) mediates the symbiotic interaction between Populus and the ectomycorrhizal fungus Laccaria bicolor. This finding uncovers an important molecular step in the establishment of symbiotic plant-fungal associations and provides a molecular target for engineering beneficial mycorrhizal relationships.
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Affiliation(s)
- Jessy Labbé
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | | | - Olaf Czarnecki
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Juan Wang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Xiaoping Wang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Anthony C Bryan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Kaijie Zheng
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Yongil Yang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Meng Xie
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Jin Zhang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Dongfang Wang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Peter Meidl
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Hemeng Wang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | | | - Kevin R Cope
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
- Department of Agronomy, University of Wisconsin-Madison, Madison, WI, USA
| | - Lucas G S Maia
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
- Department of Agronomy, University of Wisconsin-Madison, Madison, WI, USA
| | - Jean-Michel Ané
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
- Department of Agronomy, University of Wisconsin-Madison, Madison, WI, USA
| | - Ritesh Mewalal
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Sara S Jawdy
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Lee E Gunter
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Wendy Schackwitz
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Joel Martin
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - François Le Tacon
- Institut National de la Recherche Agronomique et Université de Lorraine, Labex ARBRE, Champenoux, France
| | - Ting Li
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Zhihao Zhang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Priya Ranjan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Erika Lindquist
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Xiaohan Yang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Daniel A Jacobson
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | | | - Kerrie Barry
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Jeremy Schmutz
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Jin-Gui Chen
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA.
| | - Gerald A Tuskan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
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5
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Abstract
Whole-genome resequencing is a method for determining the differences between individuals and a reference genome. The experiments are performed by sequencing the individuals, aligning generated reads to a common reference and discovering variation within the data set by analysis of the alignment with software tools. When correlated with phenotypic information, sites of causative genomic variation may be putatively assigned.While the analysis is generally straightforward, there are many nuances, and we aim to help you understand how to generate an initial result, sift through it to identify likely candidates for a phenotype of interest, and flag false positive calls.
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Affiliation(s)
- Joel Martin
- United States Department of Energy Joint Genome Institute, Walnut Creek, CA, USA.
| | - Wendy Schackwitz
- United States Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Anna Lipzen
- United States Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
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6
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Blanc-Mathieu R, Krasovec M, Hebrard M, Yau S, Desgranges E, Martin J, Schackwitz W, Kuo A, Salin G, Donnadieu C, Desdevises Y, Sanchez-Ferandin S, Moreau H, Rivals E, Grigoriev IV, Grimsley N, Eyre-Walker A, Piganeau G. Population genomics of picophytoplankton unveils novel chromosome hypervariability. Sci Adv 2017; 3:e1700239. [PMID: 28695208 PMCID: PMC5498103 DOI: 10.1126/sciadv.1700239] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 05/25/2017] [Indexed: 05/18/2023]
Abstract
Tiny photosynthetic microorganisms that form the picoplankton (between 0.3 and 3 μm in diameter) are at the base of the food web in many marine ecosystems, and their adaptability to environmental change hinges on standing genetic variation. Although the genomic and phenotypic diversity of the bacterial component of the oceans has been intensively studied, little is known about the genomic and phenotypic diversity within each of the diverse eukaryotic species present. We report the level of genomic diversity in a natural population of Ostreococcus tauri (Chlorophyta, Mamiellophyceae), the smallest photosynthetic eukaryote. Contrary to the expectations of clonal evolution or cryptic species, the spectrum of genomic polymorphism observed suggests a large panmictic population (an effective population size of 1.2 × 107) with pervasive evidence of sexual reproduction. De novo assemblies of low-coverage chromosomes reveal two large candidate mating-type loci with suppressed recombination, whose origin may pre-date the speciation events in the class Mamiellophyceae. This high genetic diversity is associated with large phenotypic differences between strains. Strikingly, resistance of isolates to large double-stranded DNA viruses, which abound in their natural environment, is positively correlated with the size of a single hypervariable chromosome, which contains 44 to 156 kb of strain-specific sequences. Our findings highlight the role of viruses in shaping genome diversity in marine picoeukaryotes.
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Affiliation(s)
- Romain Blanc-Mathieu
- Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
- CNRS, Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, F-66650 Banyuls-sur-Mer, France
| | - Marc Krasovec
- CNRS, Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, F-66650 Banyuls-sur-Mer, France
- Sorbonne Universités, Université Pierre et Marie Curie, UMR7232, BIOM, Observatoire Océanologique, F-66650 Banyuls-sur-Mer, France
| | - Maxime Hebrard
- Laboratoire d’Informatique, de Robotique et de Microélectronique de Montpellier, CNRS, and Université de Montpellier, 161 rue Ada, 34095 Montpellier Cedex 5, France
- Institut de Biologie Computationnelle, CNRS, and Université de Montpellier, 860 rue Saint Priest, 34095 Montpellier Cedex 5, France
| | - Sheree Yau
- CNRS, Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, F-66650 Banyuls-sur-Mer, France
- Sorbonne Universités, Université Pierre et Marie Curie, UMR7232, BIOM, Observatoire Océanologique, F-66650 Banyuls-sur-Mer, France
| | - Elodie Desgranges
- CNRS, Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, F-66650 Banyuls-sur-Mer, France
- Sorbonne Universités, Université Pierre et Marie Curie, UMR7232, BIOM, Observatoire Océanologique, F-66650 Banyuls-sur-Mer, France
| | - Joel Martin
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Wendy Schackwitz
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Alan Kuo
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Gerald Salin
- INRA, plateforme Génome et Transcriptome (GeT-PlaGe), GenoToul, Castanet-Tolosan, France
| | - Cecile Donnadieu
- INRA, plateforme Génome et Transcriptome (GeT-PlaGe), GenoToul, Castanet-Tolosan, France
| | - Yves Desdevises
- CNRS, Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, F-66650 Banyuls-sur-Mer, France
- Sorbonne Universités, Université Pierre et Marie Curie, UMR7232, BIOM, Observatoire Océanologique, F-66650 Banyuls-sur-Mer, France
| | - Sophie Sanchez-Ferandin
- CNRS, Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, F-66650 Banyuls-sur-Mer, France
- Sorbonne Universités, Université Pierre et Marie Curie, UMR7232, BIOM, Observatoire Océanologique, F-66650 Banyuls-sur-Mer, France
| | - Hervé Moreau
- CNRS, Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, F-66650 Banyuls-sur-Mer, France
- Sorbonne Universités, Université Pierre et Marie Curie, UMR7232, BIOM, Observatoire Océanologique, F-66650 Banyuls-sur-Mer, France
| | - Eric Rivals
- Laboratoire d’Informatique, de Robotique et de Microélectronique de Montpellier, CNRS, and Université de Montpellier, 161 rue Ada, 34095 Montpellier Cedex 5, France
- Institut de Biologie Computationnelle, CNRS, and Université de Montpellier, 860 rue Saint Priest, 34095 Montpellier Cedex 5, France
| | - Igor V. Grigoriev
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, 111 Koshland Hall, Berkeley, CA 94720, USA
| | - Nigel Grimsley
- CNRS, Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, F-66650 Banyuls-sur-Mer, France
- Sorbonne Universités, Université Pierre et Marie Curie, UMR7232, BIOM, Observatoire Océanologique, F-66650 Banyuls-sur-Mer, France
| | - Adam Eyre-Walker
- School of Life Sciences, University of Sussex, Brighton BN1 9QG, UK
| | - Gwenael Piganeau
- CNRS, Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, F-66650 Banyuls-sur-Mer, France
- Sorbonne Universités, Université Pierre et Marie Curie, UMR7232, BIOM, Observatoire Océanologique, F-66650 Banyuls-sur-Mer, France
- School of Life Sciences, University of Sussex, Brighton BN1 9QG, UK
- Corresponding author.
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7
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Bendall ML, Stevens SLR, Chan LK, Malfatti S, Schwientek P, Tremblay J, Schackwitz W, Martin J, Pati A, Bushnell B, Froula J, Kang D, Tringe SG, Bertilsson S, Moran MA, Shade A, Newton RJ, McMahon KD, Malmstrom RR. Genome-wide selective sweeps and gene-specific sweeps in natural bacterial populations. ISME J 2016; 10:1589-601. [PMID: 26744812 PMCID: PMC4918448 DOI: 10.1038/ismej.2015.241] [Citation(s) in RCA: 142] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Revised: 10/22/2015] [Accepted: 11/18/2015] [Indexed: 12/30/2022]
Abstract
Multiple models describe the formation and evolution of distinct microbial phylogenetic groups. These evolutionary models make different predictions regarding how adaptive alleles spread through populations and how genetic diversity is maintained. Processes predicted by competing evolutionary models, for example, genome-wide selective sweeps vs gene-specific sweeps, could be captured in natural populations using time-series metagenomics if the approach were applied over a sufficiently long time frame. Direct observations of either process would help resolve how distinct microbial groups evolve. Here, from a 9-year metagenomic study of a freshwater lake (2005-2013), we explore changes in single-nucleotide polymorphism (SNP) frequencies and patterns of gene gain and loss in 30 bacterial populations. SNP analyses revealed substantial genetic heterogeneity within these populations, although the degree of heterogeneity varied by >1000-fold among populations. SNP allele frequencies also changed dramatically over time within some populations. Interestingly, nearly all SNP variants were slowly purged over several years from one population of green sulfur bacteria, while at the same time multiple genes either swept through or were lost from this population. These patterns were consistent with a genome-wide selective sweep in progress, a process predicted by the 'ecotype model' of speciation but not previously observed in nature. In contrast, other populations contained large, SNP-free genomic regions that appear to have swept independently through the populations prior to the study without purging diversity elsewhere in the genome. Evidence for both genome-wide and gene-specific sweeps suggests that different models of bacterial speciation may apply to different populations coexisting in the same environment.
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Affiliation(s)
| | - Sarah LR Stevens
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
| | | | | | | | | | | | - Joel Martin
- DOE Joint Genome Institute, Walnut Creek, CA, USA
| | - Amrita Pati
- DOE Joint Genome Institute, Walnut Creek, CA, USA
| | | | - Jeff Froula
- DOE Joint Genome Institute, Walnut Creek, CA, USA
| | - Dongwan Kang
- DOE Joint Genome Institute, Walnut Creek, CA, USA
| | | | - Stefan Bertilsson
- Department of Ecology and Genetics, Limnology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Mary A Moran
- Department of Marine Sciences, University of Georgia, Athens, GA, USA
| | - Ashley Shade
- Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
| | - Ryan J Newton
- School of Freshwater Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - Katherine D McMahon
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
- Civil and Environmental Engineering, University of Wisconsin-Madison, Madison, WI, USA
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8
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Corrochano LM, Kuo A, Marcet-Houben M, Polaino S, Salamov A, Villalobos-Escobedo JM, Grimwood J, Álvarez MI, Avalos J, Bauer D, Benito EP, Benoit I, Burger G, Camino LP, Cánovas D, Cerdá-Olmedo E, Cheng JF, Domínguez A, Eliáš M, Eslava AP, Glaser F, Gutiérrez G, Heitman J, Henrissat B, Iturriaga EA, Lang BF, Lavín JL, Lee SC, Li W, Lindquist E, López-García S, Luque EM, Marcos AT, Martin J, McCluskey K, Medina HR, Miralles-Durán A, Miyazaki A, Muñoz-Torres E, Oguiza JA, Ohm RA, Olmedo M, Orejas M, Ortiz-Castellanos L, Pisabarro AG, Rodríguez-Romero J, Ruiz-Herrera J, Ruiz-Vázquez R, Sanz C, Schackwitz W, Shahriari M, Shelest E, Silva-Franco F, Soanes D, Syed K, Tagua VG, Talbot NJ, Thon MR, Tice H, de Vries RP, Wiebenga A, Yadav JS, Braun EL, Baker SE, Garre V, Schmutz J, Horwitz BA, Torres-Martínez S, Idnurm A, Herrera-Estrella A, Gabaldón T, Grigoriev IV. Expansion of Signal Transduction Pathways in Fungi by Extensive Genome Duplication. Curr Biol 2016; 26:1577-1584. [PMID: 27238284 DOI: 10.1016/j.cub.2016.04.038] [Citation(s) in RCA: 131] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Revised: 03/22/2016] [Accepted: 04/13/2016] [Indexed: 02/03/2023]
Abstract
Plants and fungi use light and other signals to regulate development, growth, and metabolism. The fruiting bodies of the fungus Phycomyces blakesleeanus are single cells that react to environmental cues, including light, but the mechanisms are largely unknown [1]. The related fungus Mucor circinelloides is an opportunistic human pathogen that changes its mode of growth upon receipt of signals from the environment to facilitate pathogenesis [2]. Understanding how these organisms respond to environmental cues should provide insights into the mechanisms of sensory perception and signal transduction by a single eukaryotic cell, and their role in pathogenesis. We sequenced the genomes of P. blakesleeanus and M. circinelloides and show that they have been shaped by an extensive genome duplication or, most likely, a whole-genome duplication (WGD), which is rarely observed in fungi [3-6]. We show that the genome duplication has expanded gene families, including those involved in signal transduction, and that duplicated genes have specialized, as evidenced by differences in their regulation by light. The transcriptional response to light varies with the developmental stage and is still observed in a photoreceptor mutant of P. blakesleeanus. A phototropic mutant of P. blakesleeanus with a heterozygous mutation in the photoreceptor gene madA demonstrates that photosensor dosage is important for the magnitude of signal transduction. We conclude that the genome duplication provided the means to improve signal transduction for enhanced perception of environmental signals. Our results will help to understand the role of genome dynamics in the evolution of sensory perception in eukaryotes.
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Affiliation(s)
- Luis M Corrochano
- Department of Genetics, University of Seville, Avenida Reina Mercedes s/n, 41012 Seville, Spain.
| | - Alan Kuo
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
| | - Marina Marcet-Houben
- Centre for Genomic Regulation (CRG), Doctor Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Doctor Aiguader 88, 08003 Barcelona, Spain
| | - Silvia Polaino
- School of Biological Sciences, University of Missouri-Kansas City, 5007 Rockhill Road, Kansas City, MO 64110, USA
| | - Asaf Salamov
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
| | - José M Villalobos-Escobedo
- Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO), Centro de Investigación y Estudios Avanzados, Kilómetro 9.6 Libramiento Norte, Carretera Irapuato-León, 36821 Irapuato, Guanajuato, México
| | - Jane Grimwood
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA; HudsonAlpha Institute of Biotechnology, 601 Genome Way Northwest, Huntsville, AL 35806, USA
| | - M Isabel Álvarez
- Departamento de Microbiología y Genética, Universidad de Salamanca, Plaza de los doctores de la Reina s/n, 37007 Salamanca, Spain
| | - Javier Avalos
- Department of Genetics, University of Seville, Avenida Reina Mercedes s/n, 41012 Seville, Spain
| | - Diane Bauer
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
| | - Ernesto P Benito
- Departamento de Microbiología y Genética, Universidad de Salamanca, Plaza de los doctores de la Reina s/n, 37007 Salamanca, Spain; Instituto Hispano-Luso de Investigaciones Agrarias (CIALE), Universidad de Salamanca, Río Duero 12, 37185 Salamanca, Spain
| | - Isabelle Benoit
- CBS-KNAW Fungal Biodiversity Centre and Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - Gertraud Burger
- Universite de Montreal, Pavillon Roger-Gaudry, Biochimie, CP 6128, Succursale Centre-Ville, Montreal QC, H3C 3J7, Canada
| | - Lola P Camino
- Department of Genetics, University of Seville, Avenida Reina Mercedes s/n, 41012 Seville, Spain
| | - David Cánovas
- Department of Genetics, University of Seville, Avenida Reina Mercedes s/n, 41012 Seville, Spain
| | - Enrique Cerdá-Olmedo
- Department of Genetics, University of Seville, Avenida Reina Mercedes s/n, 41012 Seville, Spain
| | - Jan-Fang Cheng
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
| | - Angel Domínguez
- Departamento de Microbiología y Genética, Universidad de Salamanca, Plaza de los doctores de la Reina s/n, 37007 Salamanca, Spain
| | - Marek Eliáš
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Chittussiho 10, 710 00 Ostrava, Czech Republic
| | - Arturo P Eslava
- Departamento de Microbiología y Genética, Universidad de Salamanca, Plaza de los doctores de la Reina s/n, 37007 Salamanca, Spain
| | - Fabian Glaser
- Lokey Interdisciplinary Center for Life Sciences and Engineering, Technion - Israel Institute of Technology, Haifa 3200003, Israel
| | - Gabriel Gutiérrez
- Department of Genetics, University of Seville, Avenida Reina Mercedes s/n, 41012 Seville, Spain
| | - Joseph Heitman
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Research Drive, Durham, NC 27710, USA
| | - Bernard Henrissat
- Centre National de la Recherche Scientifique (CNRS), UMR7257, Université Aix-Marseille, 163 Avenue de Luminy, 13288 Marseille, France; Department of Biological Sciences, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia
| | - Enrique A Iturriaga
- Departamento de Microbiología y Genética, Universidad de Salamanca, Plaza de los doctores de la Reina s/n, 37007 Salamanca, Spain
| | - B Franz Lang
- Universite de Montreal, Pavillon Roger-Gaudry, Biochimie, CP 6128, Succursale Centre-Ville, Montreal QC, H3C 3J7, Canada
| | - José L Lavín
- Genome Analysis Platform, CIC bioGUNE, Bizkaia Technology Park, 48160 Derio, Bizkaia, Spain
| | - Soo Chan Lee
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Research Drive, Durham, NC 27710, USA
| | - Wenjun Li
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Research Drive, Durham, NC 27710, USA
| | - Erika Lindquist
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
| | - Sergio López-García
- Departamento de Genética y Microbiología, Universidad de Murcia, 30071 Murcia, Spain
| | - Eva M Luque
- Department of Genetics, University of Seville, Avenida Reina Mercedes s/n, 41012 Seville, Spain
| | - Ana T Marcos
- Department of Genetics, University of Seville, Avenida Reina Mercedes s/n, 41012 Seville, Spain
| | - Joel Martin
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
| | - Kevin McCluskey
- Department of Plant Pathology, Kansas State University, 4024 Throckmorton Plant Sciences Center, Manhattan, KS 66506, USA
| | - Humberto R Medina
- Department of Genetics, University of Seville, Avenida Reina Mercedes s/n, 41012 Seville, Spain
| | | | - Atsushi Miyazaki
- Department of Biological Sciences, Faculty of Science and Engineering, Ishinomaki Senshu University, Ishinomaki 986-8580, Japan
| | - Elisa Muñoz-Torres
- Departamento de Biología Celular y Patología, Facultad de Medicina, Universidad de Salamanca, Avenida Campus Miguel de Unamuno, 37007 Salamanca, Spain
| | - José A Oguiza
- Department of Agrarian Production, Public University of Navarre, 31006 Pamplona, Spain
| | - Robin A Ohm
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
| | - María Olmedo
- Department of Genetics, University of Seville, Avenida Reina Mercedes s/n, 41012 Seville, Spain
| | - Margarita Orejas
- Instituto de Agroquímica y Tecnología de Alimentos, Consejo Superior de Investigaciones Científicas (IATA-CSIC), Avenida Catedrático Agustín Escardino 7, 46980 Paterna, Valencia, Spain
| | - Lucila Ortiz-Castellanos
- Departamento de Ingeniería Genética, Unidad Irapuato, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Kilómetro 9.6 Libramiento Norte, Carretera Irapuato-León, 36821 Irapuato, Guanajuato, Mexico
| | - Antonio G Pisabarro
- Department of Agrarian Production, Public University of Navarre, 31006 Pamplona, Spain
| | - Julio Rodríguez-Romero
- Department of Genetics, University of Seville, Avenida Reina Mercedes s/n, 41012 Seville, Spain
| | - José Ruiz-Herrera
- Departamento de Ingeniería Genética, Unidad Irapuato, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Kilómetro 9.6 Libramiento Norte, Carretera Irapuato-León, 36821 Irapuato, Guanajuato, Mexico
| | - Rosa Ruiz-Vázquez
- Departamento de Genética y Microbiología, Universidad de Murcia, 30071 Murcia, Spain
| | - Catalina Sanz
- Departamento de Microbiología y Genética, Universidad de Salamanca, Plaza de los doctores de la Reina s/n, 37007 Salamanca, Spain
| | - Wendy Schackwitz
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
| | - Mahdi Shahriari
- Departamento de Microbiología y Genética, Universidad de Salamanca, Plaza de los doctores de la Reina s/n, 37007 Salamanca, Spain
| | - Ekaterina Shelest
- Leibniz Institute for Natural Product Research and Infection Biology (Hans Knoell Institute), Beutenbergstrasse 11a, 07745 Jena, Germany
| | - Fátima Silva-Franco
- Departamento de Genética y Microbiología, Universidad de Murcia, 30071 Murcia, Spain
| | - Darren Soanes
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Stocker Road, Exeter EX4 4QD, UK
| | - Khajamohiddin Syed
- Department of Environmental Health, University of Cincinnati College of Medicine, 160 Panzeca Way, Cincinnati, OH 45267-0056, USA
| | - Víctor G Tagua
- Department of Genetics, University of Seville, Avenida Reina Mercedes s/n, 41012 Seville, Spain
| | - Nicholas J Talbot
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Stocker Road, Exeter EX4 4QD, UK
| | - Michael R Thon
- Departamento de Microbiología y Genética, Universidad de Salamanca, Plaza de los doctores de la Reina s/n, 37007 Salamanca, Spain; Instituto Hispano-Luso de Investigaciones Agrarias (CIALE), Universidad de Salamanca, Río Duero 12, 37185 Salamanca, Spain
| | - Hope Tice
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
| | - Ronald P de Vries
- CBS-KNAW Fungal Biodiversity Centre and Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - Ad Wiebenga
- CBS-KNAW Fungal Biodiversity Centre and Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - Jagjit S Yadav
- Department of Environmental Health, University of Cincinnati College of Medicine, 160 Panzeca Way, Cincinnati, OH 45267-0056, USA
| | - Edward L Braun
- Department of Biology, University of Florida, P.O. Box 118525, Gainesville, FL 32611-8525, USA
| | - Scott E Baker
- Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA 99352, USA
| | - Victoriano Garre
- Departamento de Genética y Microbiología, Universidad de Murcia, 30071 Murcia, Spain
| | - Jeremy Schmutz
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA; HudsonAlpha Institute of Biotechnology, 601 Genome Way Northwest, Huntsville, AL 35806, USA
| | - Benjamin A Horwitz
- Department of Biology, Technion - Israel Institute of Technology, Haifa 32000, Israel
| | | | - Alexander Idnurm
- School of Biological Sciences, University of Missouri-Kansas City, 5007 Rockhill Road, Kansas City, MO 64110, USA; School of BioSciences, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Alfredo Herrera-Estrella
- Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO), Centro de Investigación y Estudios Avanzados, Kilómetro 9.6 Libramiento Norte, Carretera Irapuato-León, 36821 Irapuato, Guanajuato, México
| | - Toni Gabaldón
- Centre for Genomic Regulation (CRG), Doctor Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Doctor Aiguader 88, 08003 Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain
| | - Igor V Grigoriev
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
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9
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McCarthy S, Johnson T, Pavlik BJ, Payne S, Schackwitz W, Martin J, Lipzen A, Keffeler E, Blum P. Expanding the Limits of Thermoacidophily in the Archaeon Sulfolobus solfataricus by Adaptive Evolution. Appl Environ Microbiol 2016; 82:857-67. [PMID: 26590281 PMCID: PMC4725277 DOI: 10.1128/aem.03225-15] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Accepted: 11/15/2015] [Indexed: 11/20/2022] Open
Abstract
Extremely thermoacidophilic Crenarchaeota belonging to the order Sulfolobales flourish in hot acidic habitats that are strongly oxidizing. The pH extremes of these habitats, however, often exceed the acid tolerance of type species and strains. Here, adaptive laboratory evolution was used over a 3-year period to test whether such organisms harbor additional thermoacidophilic capacity. Three distinct cell lines derived from a single type species were subjected to high-temperature serial passage while culture acidity was gradually increased. A 178-fold increase in thermoacidophily was achieved after 29 increments of shifted culture pH resulting in growth at pH 0.8 and 80°C. These strains were named super-acid-resistant Crenarchaeota (SARC). Mathematical modeling using growth parameters predicted the limits of acid resistance, while genome resequencing and transcriptome resequencing were conducted for insight into mechanisms responsible for the evolved trait. Among the mutations that were detected, a set of eight nonsynonymous changes may explain the heritability of increased acid resistance despite an unexpected lack of transposition. Four multigene components of the SARC transcriptome implicated oxidative stress as a primary challenge accompanying growth at acid extremes. These components included accelerated membrane biogenesis, induction of the mer operon, and an increased capacity for the generation of energy and reductant.
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Affiliation(s)
- Samuel McCarthy
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Tyler Johnson
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Benjamin J Pavlik
- Department of Chemical and Biomolecular Engineering, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Sophie Payne
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Wendy Schackwitz
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, California, USA
| | - Joel Martin
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, California, USA
| | - Anna Lipzen
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, California, USA
| | - Erica Keffeler
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Paul Blum
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska, USA Department of Chemical and Biomolecular Engineering, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
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10
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Lichius A, Bidard F, Buchholz F, Le Crom S, Martin J, Schackwitz W, Austerlitz T, Grigoriev IV, Baker SE, Margeot A, Seiboth B, Kubicek CP. Erratum to: Genome sequencing of the Trichoderma reesei QM9136 mutant identifies a truncation of the transcriptional regulator XYR1 as the cause for its cellulase-negative phenotype. BMC Genomics 2015; 16:725. [PMID: 26395946 PMCID: PMC4580284 DOI: 10.1186/s12864-015-1917-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Accepted: 09/10/2015] [Indexed: 11/10/2022] Open
Affiliation(s)
- Alexander Lichius
- Research Division Biotechnology and Microbiology, Institute of Chemical Engineering, Vienna University of Technology, A-1060, Vienna, Austria
| | - Frédérique Bidard
- IFP Energies Nouvelles, 1-4 Avenue de Bois-Préau, 92852, Rueil-Malmaison, France
| | - Franziska Buchholz
- Research Division Biotechnology and Microbiology, Institute of Chemical Engineering, Vienna University of Technology, A-1060, Vienna, Austria
| | - Stéphane Le Crom
- Sorbonne Universités, UPMC Université Paris 06, Institut de Biologie Paris Seine (IBPS), FR 3631, Département des Plateforme, F-75005, Paris, France
| | - Joel Martin
- US Department of Energy Joint Genome Institute, 2800 Mitchell Avenue, Walnut Creek, CA, 94598, USA
| | - Wendy Schackwitz
- US Department of Energy Joint Genome Institute, 2800 Mitchell Avenue, Walnut Creek, CA, 94598, USA
| | - Tina Austerlitz
- Research Division Biotechnology and Microbiology, Institute of Chemical Engineering, Vienna University of Technology, A-1060, Vienna, Austria
| | - Igor V Grigoriev
- US Department of Energy Joint Genome Institute, 2800 Mitchell Avenue, Walnut Creek, CA, 94598, USA
| | - Scott E Baker
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Antoine Margeot
- IFP Energies Nouvelles, 1-4 Avenue de Bois-Préau, 92852, Rueil-Malmaison, France
| | - Bernhard Seiboth
- Research Division Biotechnology and Microbiology, Institute of Chemical Engineering, Vienna University of Technology, A-1060, Vienna, Austria.
| | - Christian P Kubicek
- Research Division Biotechnology and Microbiology, Institute of Chemical Engineering, Vienna University of Technology, A-1060, Vienna, Austria
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11
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Zhou A, Hillesland KL, He Z, Schackwitz W, Tu Q, Zane GM, Ma Q, Qu Y, Stahl DA, Wall JD, Hazen TC, Fields MW, Arkin AP, Zhou J. Rapid selective sweep of pre-existing polymorphisms and slow fixation of new mutations in experimental evolution of Desulfovibrio vulgaris. ISME J 2015; 9:2360-72. [PMID: 25848870 DOI: 10.1038/ismej.2015.45] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Revised: 02/07/2015] [Accepted: 02/26/2015] [Indexed: 01/19/2023]
Abstract
To investigate the genetic basis of microbial evolutionary adaptation to salt (NaCl) stress, populations of Desulfovibrio vulgaris Hildenborough (DvH), a sulfate-reducing bacterium important for the biogeochemical cycling of sulfur, carbon and nitrogen, and potentially the bioremediation of toxic heavy metals and radionuclides, were propagated under salt stress or non-stress conditions for 1200 generations. Whole-genome sequencing revealed 11 mutations in salt stress-evolved clone ES9-11 and 14 mutations in non-stress-evolved clone EC3-10. Whole-population sequencing data suggested the rapid selective sweep of the pre-existing polymorphisms under salt stress within the first 100 generations and the slow fixation of new mutations. Population genotyping data demonstrated that the rapid selective sweep of pre-existing polymorphisms was common in salt stress-evolved populations. In contrast, the selection of pre-existing polymorphisms was largely random in EC populations. Consistently, at 100 generations, stress-evolved population ES9 showed improved salt tolerance, namely increased growth rate (2.0-fold), higher biomass yield (1.8-fold) and shorter lag phase (0.7-fold) under higher salinity conditions. The beneficial nature of several mutations was confirmed by site-directed mutagenesis. All four tested mutations contributed to the shortened lag phases under higher salinity condition. In particular, compared with the salt tolerance improvement in ES9-11, a mutation in a histidine kinase protein gene lytS contributed 27% of the growth rate increase and 23% of the biomass yield increase while a mutation in hypothetical gene DVU2472 contributed 24% of the biomass yield increase. Our results suggested that a few beneficial mutations could lead to dramatic improvements in salt tolerance.
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Affiliation(s)
- Aifen Zhou
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
| | | | - Zhili He
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
| | - Wendy Schackwitz
- Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Qichao Tu
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
| | - Grant M Zane
- Departments of Biochemistry and Molecular Microbiology and Immunology, University of Missouri-Columbia, Columbia, MO, USA
| | - Qiao Ma
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA.,Key Laboratory of Industrial Ecology and Environmental Engineering (MOE), School of Environmental Science and Technology, Dalian University of Technology, Dalian, China
| | - Yuanyuan Qu
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA.,Key Laboratory of Industrial Ecology and Environmental Engineering (MOE), School of Environmental Science and Technology, Dalian University of Technology, Dalian, China
| | - David A Stahl
- Civil and Environmental Engineering, University of Washington, Seattle, WA, USA
| | - Judy D Wall
- Departments of Biochemistry and Molecular Microbiology and Immunology, University of Missouri-Columbia, Columbia, MO, USA
| | - Terry C Hazen
- Department of Civil and Environmental Engineering, The University of Tennessee, Knoxville, TN, USA.,Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Matthew W Fields
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, USA
| | - Adam P Arkin
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jizhong Zhou
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA.,Earth Science Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
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12
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Muchero W, Guo J, DiFazio SP, Chen JG, Ranjan P, Slavov GT, Gunter LE, Jawdy S, Bryan AC, Sykes R, Ziebell A, Klápště J, Porth I, Skyba O, Unda F, El-Kassaby YA, Douglas CJ, Mansfield SD, Martin J, Schackwitz W, Evans LM, Czarnecki O, Tuskan GA. High-resolution genetic mapping of allelic variants associated with cell wall chemistry in Populus. BMC Genomics 2015; 16:24. [PMID: 25613058 PMCID: PMC4307895 DOI: 10.1186/s12864-015-1215-z] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2014] [Accepted: 01/02/2015] [Indexed: 11/13/2022] Open
Abstract
Background QTL cloning for the discovery of genes underlying polygenic traits has historically been cumbersome in long-lived perennial plants like Populus. Linkage disequilibrium-based association mapping has been proposed as a cloning tool, and recent advances in high-throughput genotyping and whole-genome resequencing enable marker saturation to levels sufficient for association mapping with no a priori candidate gene selection. Here, multiyear and multienvironment evaluation of cell wall phenotypes was conducted in an interspecific P. trichocarpa x P. deltoides pseudo-backcross mapping pedigree and two partially overlapping populations of unrelated P. trichocarpa genotypes using pyrolysis molecular beam mass spectrometry, saccharification, and/ or traditional wet chemistry. QTL mapping was conducted using a high-density genetic map with 3,568 SNP markers. As a fine-mapping approach, chromosome-wide association mapping targeting a QTL hot-spot on linkage group XIV was performed in the two P. trichocarpa populations. Both populations were genotyped using the 34 K Populus Infinium SNP array and whole-genome resequencing of one of the populations facilitated marker-saturation of candidate intervals for gene identification. Results Five QTLs ranging in size from 0.6 to 1.8 Mb were mapped on linkage group XIV for lignin content, syringyl to guaiacyl (S/G) ratio, 5- and 6-carbon sugars using the mapping pedigree. Six candidate loci exhibiting significant associations with phenotypes were identified within QTL intervals. These associations were reproducible across multiple environments, two independent genotyping platforms, and different plant growth stages. cDNA sequencing for allelic variants of three of the six loci identified polymorphisms leading to variable length poly glutamine (PolyQ) stretch in a transcription factor annotated as an ANGUSTIFOLIA C-terminus Binding Protein (CtBP) and premature stop codons in a KANADI transcription factor as well as a protein kinase. Results from protoplast transient expression assays suggested that each of the polymorphisms conferred allelic differences in the activation of cellulose, hemicelluloses, and lignin pathway marker genes. Conclusion This study illustrates the utility of complementary QTL and association mapping as tools for gene discovery with no a priori candidate gene selection. This proof of concept in a perennial organism opens up opportunities for discovery of novel genetic determinants of economically important but complex traits in plants. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1215-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Wellington Muchero
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.
| | - Jianjun Guo
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA. .,Current address: Department of Plant Biology, Carnegie Institute for Science, Stanford, CA, 94305, USA.
| | - Stephen P DiFazio
- Department of Biology, West Virginia University, Morgantown, WV, 26506, USA.
| | - Jin-Gui Chen
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.
| | - Priya Ranjan
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.
| | - Gancho T Slavov
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, SY23 3EB, UK.
| | - Lee E Gunter
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.
| | - Sara Jawdy
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.
| | - Anthony C Bryan
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.
| | - Robert Sykes
- Bioscience Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401, USA.
| | - Angela Ziebell
- Bioscience Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401, USA.
| | - Jaroslav Klápště
- Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, Forest Sciences Centre, 2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada. .,Department of Genetics and Physiology of Forest Trees, Faculty of Forestry and Wood Sciences, Czech University of Life Sciences in Prague, Kamýcká 129, 165 21, Praha 6, Czech Republic.
| | - Ilga Porth
- Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, Forest Sciences Centre, 2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada.
| | - Oleksandr Skyba
- Department of Wood Science, Faculty of Forestry, University of British Columbia, Forest Sciences Centre, 2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada.
| | - Faride Unda
- Department of Wood Science, Faculty of Forestry, University of British Columbia, Forest Sciences Centre, 2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada.
| | - Yousry A El-Kassaby
- Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, Forest Sciences Centre, 2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada.
| | - Carl J Douglas
- Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada.
| | - Shawn D Mansfield
- Department of Wood Science, Faculty of Forestry, University of British Columbia, Forest Sciences Centre, 2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada.
| | - Joel Martin
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA, 94598, USA.
| | - Wendy Schackwitz
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA, 94598, USA.
| | - Luke M Evans
- Department of Biology, West Virginia University, Morgantown, WV, 26506, USA.
| | - Olaf Czarnecki
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.
| | - Gerald A Tuskan
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.
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13
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Blanc-Mathieu R, Verhelst B, Derelle E, Rombauts S, Bouget FY, Carré I, Château A, Eyre-Walker A, Grimsley N, Moreau H, Piégu B, Rivals E, Schackwitz W, Van de Peer Y, Piganeau G. An improved genome of the model marine alga Ostreococcus tauri unfolds by assessing Illumina de novo assemblies. BMC Genomics 2014; 15:1103. [PMID: 25494611 PMCID: PMC4378021 DOI: 10.1186/1471-2164-15-1103] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Accepted: 11/19/2014] [Indexed: 12/17/2022] Open
Abstract
Background Cost effective next generation sequencing technologies now enable the production of genomic datasets for many novel planktonic eukaryotes, representing an understudied reservoir of genetic diversity. O. tauri is the smallest free-living photosynthetic eukaryote known to date, a coccoid green alga that was first isolated in 1995 in a lagoon by the Mediterranean sea. Its simple features, ease of culture and the sequencing of its 13 Mb haploid nuclear genome have promoted this microalga as a new model organism for cell biology. Here, we investigated the quality of genome assemblies of Illumina GAIIx 75 bp paired-end reads from Ostreococcus tauri, thereby also improving the existing assembly and showing the genome to be stably maintained in culture. Results The 3 assemblers used, ABySS, CLCBio and Velvet, produced 95% complete genomes in 1402 to 2080 scaffolds with a very low rate of misassembly. Reciprocally, these assemblies improved the original genome assembly by filling in 930 gaps. Combined with additional analysis of raw reads and PCR sequencing effort, 1194 gaps have been solved in total adding up to 460 kb of sequence. Mapping of RNAseq Illumina data on this updated genome led to a twofold reduction in the proportion of multi-exon protein coding genes, representing 19% of the total 7699 protein coding genes. The comparison of the DNA extracted in 2001 and 2009 revealed the fixation of 8 single nucleotide substitutions and 2 deletions during the approximately 6000 generations in the lab. The deletions either knocked out or truncated two predicted transmembrane proteins, including a glutamate-receptor like gene. Conclusion High coverage (>80 fold) paired-end Illumina sequencing enables a high quality 95% complete genome assembly of a compact ~13 Mb haploid eukaryote. This genome sequence has remained stable for 6000 generations of lab culture. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-1103) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | - Gwenaël Piganeau
- CNRS, UMR 7232, Observatoire Océanologique, Avenue du Fontaulé, BP44, 66650 Banyuls-sur-Mer, France.
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14
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Evans LM, Slavov GT, Rodgers-Melnick E, Martin J, Ranjan P, Muchero W, Brunner AM, Schackwitz W, Gunter L, Chen JG, Tuskan GA, DiFazio SP. Population genomics of Populus trichocarpa identifies signatures of selection and adaptive trait associations. Nat Genet 2014; 46:1089-96. [DOI: 10.1038/ng.3075] [Citation(s) in RCA: 250] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Accepted: 07/30/2014] [Indexed: 12/16/2022]
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15
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Gordon SP, Priest H, Des Marais DL, Schackwitz W, Figueroa M, Martin J, Bragg JN, Tyler L, Lee CR, Bryant D, Wang W, Messing J, Manzaneda AJ, Barry K, Garvin DF, Budak H, Tuna M, Mitchell-Olds T, Pfender WF, Juenger TE, Mockler TC, Vogel JP. Genome diversity in Brachypodium distachyon: deep sequencing of highly diverse inbred lines. Plant J 2014; 79:361-74. [PMID: 24888695 DOI: 10.1111/tpj.12569] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2013] [Revised: 05/20/2014] [Accepted: 05/23/2014] [Indexed: 05/08/2023]
Abstract
Brachypodium distachyon is small annual grass that has been adopted as a model for the grasses. Its small genome, high-quality reference genome, large germplasm collection, and selfing nature make it an excellent subject for studies of natural variation. We sequenced six divergent lines to identify a comprehensive set of polymorphisms and analyze their distribution and concordance with gene expression. Multiple methods and controls were utilized to identify polymorphisms and validate their quality. mRNA-Seq experiments under control and simulated drought-stress conditions, identified 300 genes with a genotype-dependent treatment response. We showed that large-scale sequence variants had extremely high concordance with altered expression of hundreds of genes, including many with genotype-dependent treatment responses. We generated a deep mRNA-Seq dataset for the most divergent line and created a de novo transcriptome assembly. This led to the discovery of >2400 previously unannotated transcripts and hundreds of genes not present in the reference genome. We built a public database for visualization and investigation of sequence variants among these widely used inbred lines.
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Affiliation(s)
- Sean P Gordon
- USDA-ARS Western Regional Research Center, 800 Buchanan St., Albany, CA, 94710, USA
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16
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Mukherjee S, Thompson LK, Godin S, Schackwitz W, Lipzen A, Martin J, Blanchard JL. Population level analysis of evolved mutations underlying improvements in plant hemicellulose and cellulose fermentation by Clostridium phytofermentans. PLoS One 2014; 9:e86731. [PMID: 24466216 PMCID: PMC3899296 DOI: 10.1371/journal.pone.0086731] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [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: 06/15/2013] [Accepted: 12/16/2013] [Indexed: 12/17/2022] Open
Abstract
Background The complexity of plant cell walls creates many challenges for microbial decomposition. Clostridium phytofermentans, an anaerobic bacterium isolated from forest soil, directly breaks down and utilizes many plant cell wall carbohydrates. The objective of this research is to understand constraints on rates of plant decomposition by Clostridium phytofermentans and identify molecular mechanisms that may overcome these limitations. Results Experimental evolution via repeated serial transfers during exponential growth was used to select for C. phytofermentans genotypes that grow more rapidly on cellobiose, cellulose and xylan. To identify the underlying mutations an average of 13,600,000 paired-end reads were generated per population resulting in ∼300 fold coverage of each site in the genome. Mutations with allele frequencies of 5% or greater could be identified with statistical confidence. Many mutations are in carbohydrate-related genes including the promoter regions of glycoside hydrolases and amino acid substitutions in ABC transport proteins involved in carbohydrate uptake, signal transduction sensors that detect specific carbohydrates, proteins that affect the export of extracellular enzymes, and regulators of unknown specificity. Structural modeling of the ABC transporter complex proteins suggests that mutations in these genes may alter the recognition of carbohydrates by substrate-binding proteins and communication between the intercellular face of the transmembrane and the ATPase binding proteins. Conclusions Experimental evolution was effective in identifying molecular constraints on the rate of hemicellulose and cellulose fermentation and selected for putative gain of function mutations that do not typically appear in traditional molecular genetic screens. The results reveal new strategies for evolving and engineering microorganisms for faster growth on plant carbohydrates.
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Affiliation(s)
- Supratim Mukherjee
- Department of Microbiobiology, University of Massachusetts, Amherst, Massachusetts, United States of America
| | - Lynmarie K. Thompson
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts, United States of America
| | - Stephen Godin
- Biology Department, University of Massachusetts, Amherst, Massachusetts, United States of America
| | - Wendy Schackwitz
- Genomic Technologies, Joint Genome Institute, Walnut Creek, California, United States of America
| | - Anna Lipzen
- Genomic Technologies, Joint Genome Institute, Walnut Creek, California, United States of America
| | - Joel Martin
- Genomic Technologies, Joint Genome Institute, Walnut Creek, California, United States of America
| | - Jeffrey L. Blanchard
- Department of Microbiobiology, University of Massachusetts, Amherst, Massachusetts, United States of America
- Biology Department, University of Massachusetts, Amherst, Massachusetts, United States of America
- * E-mail:
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17
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Condon BJ, Leng Y, Wu D, Bushley KE, Ohm RA, Otillar R, Martin J, Schackwitz W, Grimwood J, MohdZainudin N, Xue C, Wang R, Manning VA, Dhillon B, Tu ZJ, Steffenson BJ, Salamov A, Sun H, Lowry S, LaButti K, Han J, Copeland A, Lindquist E, Barry K, Schmutz J, Baker SE, Ciuffetti LM, Grigoriev IV, Zhong S, Turgeon BG. Comparative genome structure, secondary metabolite, and effector coding capacity across Cochliobolus pathogens. PLoS Genet 2013; 9:e1003233. [PMID: 23357949 PMCID: PMC3554632 DOI: 10.1371/journal.pgen.1003233] [Citation(s) in RCA: 148] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2012] [Accepted: 11/14/2012] [Indexed: 11/17/2022] Open
Abstract
The genomes of five Cochliobolus heterostrophus strains, two Cochliobolus sativus strains, three additional Cochliobolus species (Cochliobolus victoriae, Cochliobolus carbonum, Cochliobolus miyabeanus), and closely related Setosphaeria turcica were sequenced at the Joint Genome Institute (JGI). The datasets were used to identify SNPs between strains and species, unique genomic regions, core secondary metabolism genes, and small secreted protein (SSP) candidate effector encoding genes with a view towards pinpointing structural elements and gene content associated with specificity of these closely related fungi to different cereal hosts. Whole-genome alignment shows that three to five percent of each genome differs between strains of the same species, while a quarter of each genome differs between species. On average, SNP counts among field isolates of the same C. heterostrophus species are more than 25× higher than those between inbred lines and 50× lower than SNPs between Cochliobolus species. The suites of nonribosomal peptide synthetase (NRPS), polyketide synthase (PKS), and SSP-encoding genes are astoundingly diverse among species but remarkably conserved among isolates of the same species, whether inbred or field strains, except for defining examples that map to unique genomic regions. Functional analysis of several strain-unique PKSs and NRPSs reveal a strong correlation with a role in virulence.
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Affiliation(s)
- Bradford J. Condon
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, New York, United States of America
| | - Yueqiang Leng
- Department of Plant Pathology, North Dakota State University, Fargo, North Dakota, United States of America
| | - Dongliang Wu
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, New York, United States of America
| | - Kathryn E. Bushley
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
| | - Robin A. Ohm
- United States Department of Energy (DOE) Joint Genome Institute (JGI), Walnut Creek, California, United States of America
| | - Robert Otillar
- United States Department of Energy (DOE) Joint Genome Institute (JGI), Walnut Creek, California, United States of America
| | - Joel Martin
- United States Department of Energy (DOE) Joint Genome Institute (JGI), Walnut Creek, California, United States of America
| | - Wendy Schackwitz
- United States Department of Energy (DOE) Joint Genome Institute (JGI), Walnut Creek, California, United States of America
| | - Jane Grimwood
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, United States of America
| | - NurAinIzzati MohdZainudin
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, New York, United States of America
- Department of Biology, Faculty of Science, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Chunsheng Xue
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, New York, United States of America
- College of Plant Protection, Shenyang Agricultural University, Shenyang, China
| | - Rui Wang
- Department of Plant Pathology, North Dakota State University, Fargo, North Dakota, United States of America
| | - Viola A. Manning
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
| | - Braham Dhillon
- Department of Forest Sciences, University of British Columbia, Vancouver, Canada
| | - Zheng Jin Tu
- Supercomputing Institute for Advanced Computational Research, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Brian J. Steffenson
- Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Asaf Salamov
- United States Department of Energy (DOE) Joint Genome Institute (JGI), Walnut Creek, California, United States of America
| | - Hui Sun
- United States Department of Energy (DOE) Joint Genome Institute (JGI), Walnut Creek, California, United States of America
| | - Steve Lowry
- United States Department of Energy (DOE) Joint Genome Institute (JGI), Walnut Creek, California, United States of America
| | - Kurt LaButti
- United States Department of Energy (DOE) Joint Genome Institute (JGI), Walnut Creek, California, United States of America
| | - James Han
- United States Department of Energy (DOE) Joint Genome Institute (JGI), Walnut Creek, California, United States of America
| | - Alex Copeland
- United States Department of Energy (DOE) Joint Genome Institute (JGI), Walnut Creek, California, United States of America
| | - Erika Lindquist
- United States Department of Energy (DOE) Joint Genome Institute (JGI), Walnut Creek, California, United States of America
| | - Kerrie Barry
- United States Department of Energy (DOE) Joint Genome Institute (JGI), Walnut Creek, California, United States of America
| | - Jeremy Schmutz
- United States Department of Energy (DOE) Joint Genome Institute (JGI), Walnut Creek, California, United States of America
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, United States of America
| | - Scott E. Baker
- Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Lynda M. Ciuffetti
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
| | - Igor V. Grigoriev
- United States Department of Energy (DOE) Joint Genome Institute (JGI), Walnut Creek, California, United States of America
| | - Shaobin Zhong
- Department of Plant Pathology, North Dakota State University, Fargo, North Dakota, United States of America
| | - B. Gillian Turgeon
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, New York, United States of America
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18
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Geraldes A, Difazio SP, Slavov GT, Ranjan P, Muchero W, Hannemann J, Gunter LE, Wymore AM, Grassa CJ, Farzaneh N, Porth I, McKown AD, Skyba O, Li E, Fujita M, Klápště J, Martin J, Schackwitz W, Pennacchio C, Rokhsar D, Friedmann MC, Wasteneys GO, Guy RD, El-Kassaby YA, Mansfield SD, Cronk QCB, Ehlting J, Douglas CJ, Tuskan GA. A 34K SNP genotyping array for Populus trichocarpa: design, application to the study of natural populations and transferability to other Populus species. Mol Ecol Resour 2013; 13:306-23. [PMID: 23311503 DOI: 10.1111/1755-0998.12056] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2012] [Revised: 11/30/2012] [Accepted: 12/03/2012] [Indexed: 02/03/2023]
Abstract
Genetic mapping of quantitative traits requires genotypic data for large numbers of markers in many individuals. For such studies, the use of large single nucleotide polymorphism (SNP) genotyping arrays still offers the most cost-effective solution. Herein we report on the design and performance of a SNP genotyping array for Populus trichocarpa (black cottonwood). This genotyping array was designed with SNPs pre-ascertained in 34 wild accessions covering most of the species latitudinal range. We adopted a candidate gene approach to the array design that resulted in the selection of 34 131 SNPs, the majority of which are located in, or within 2 kb of, 3543 candidate genes. A subset of the SNPs on the array (539) was selected based on patterns of variation among the SNP discovery accessions. We show that more than 95% of the loci produce high quality genotypes and that the genotyping error rate for these is likely below 2%. We demonstrate that even among small numbers of samples (n = 10) from local populations over 84% of loci are polymorphic. We also tested the applicability of the array to other species in the genus and found that the number of polymorphic loci decreases rapidly with genetic distance, with the largest numbers detected in other species in section Tacamahaca. Finally, we provide evidence for the utility of the array to address evolutionary questions such as intraspecific studies of genetic differentiation, species assignment and the detection of natural hybrids.
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Affiliation(s)
- A Geraldes
- Department of Botany, University of British Columbia, Vancouver, BC, V6T1Z4, Canada.
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19
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Manning VA, Pandelova I, Dhillon B, Wilhelm LJ, Goodwin SB, Berlin AM, Figueroa M, Freitag M, Hane JK, Henrissat B, Holman WH, Kodira CD, Martin J, Oliver RP, Robbertse B, Schackwitz W, Schwartz DC, Spatafora JW, Turgeon BG, Yandava C, Young S, Zhou S, Zeng Q, Grigoriev IV, Ma LJ, Ciuffetti LM. Comparative genomics of a plant-pathogenic fungus, Pyrenophora tritici-repentis, reveals transduplication and the impact of repeat elements on pathogenicity and population divergence. G3 (Bethesda) 2013; 3:41-63. [PMID: 23316438 PMCID: PMC3538342 DOI: 10.1534/g3.112.004044] [Citation(s) in RCA: 129] [Impact Index Per Article: 11.7] [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] [Subscribe] [Scholar Register] [Received: 08/16/2012] [Accepted: 11/02/2012] [Indexed: 12/31/2022]
Abstract
Pyrenophora tritici-repentis is a necrotrophic fungus causal to the disease tan spot of wheat, whose contribution to crop loss has increased significantly during the last few decades. Pathogenicity by this fungus is attributed to the production of host-selective toxins (HST), which are recognized by their host in a genotype-specific manner. To better understand the mechanisms that have led to the increase in disease incidence related to this pathogen, we sequenced the genomes of three P. tritici-repentis isolates. A pathogenic isolate that produces two known HSTs was used to assemble a reference nuclear genome of approximately 40 Mb composed of 11 chromosomes that encode 12,141 predicted genes. Comparison of the reference genome with those of a pathogenic isolate that produces a third HST, and a nonpathogenic isolate, showed the nonpathogen genome to be more diverged than those of the two pathogens. Examination of gene-coding regions has provided candidate pathogen-specific proteins and revealed gene families that may play a role in a necrotrophic lifestyle. Analysis of transposable elements suggests that their presence in the genome of pathogenic isolates contributes to the creation of novel genes, effector diversification, possible horizontal gene transfer events, identified copy number variation, and the first example of transduplication by DNA transposable elements in fungi. Overall, comparative analysis of these genomes provides evidence that pathogenicity in this species arose through an influx of transposable elements, which created a genetically flexible landscape that can easily respond to environmental changes.
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Affiliation(s)
- Viola A. Manning
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331
| | - Iovanna Pandelova
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331
| | - Braham Dhillon
- Department of Forest Sciences, University of British Columbia, Vancouver, British Columbia, Canada, V6T 1Z4
| | - Larry J. Wilhelm
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331
- Carbone/Ferguson Laboratories, Division of Neuroscience, Oregon National Primate Research Center (ONPRC), Beaverton, Oregon 97006
| | - Stephen B. Goodwin
- USDA–Agricultural Research Service, Purdue University, West Lafayette, Indiana 47907
| | | | - Melania Figueroa
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331
- USDA-Agricultural Research Service, Forage Seed and Cereal Research Unit, Oregon State University, Corvallis, Oregon 97331
| | - Michael Freitag
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331
- Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon 97331
| | - James K. Hane
- Commonwealth Scientific and Industrial Research Organization−Plant Industry, Centre for Environment and Life Sciences, Floreat, Western Australia 6014, Australia
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, Aix-Marseille Université, Centre National de la Recherche Scientifique, 13288 Marseille cedex 9, France
| | - Wade H. Holman
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331
| | - Chinnappa D. Kodira
- The Broad Institute, Cambridge, Massachusetts 02142
- Roche 454, Branford, Connecticut 06405
| | - Joel Martin
- US DOE Joint Genome Institute, Walnut Creek, California 94598
| | - Richard P. Oliver
- Australian Centre for Necrotrophic Fungal Pathogens, Department of Environment and Agriculture, Curtin University, Bentley, Western Australia 6845, Australia
| | - Barbara Robbertse
- Architecture et Fonction des Macromolécules Biologiques, Aix-Marseille Université, Centre National de la Recherche Scientifique, 13288 Marseille cedex 9, France
| | | | - David C. Schwartz
- Laboratory for Molecular and Computational Genomics, Department of Chemistry, Laboratory of Genetics, UW Biotechnology Center, University of Wisconsin–Madison, Madison, Wisconsin 53706
| | - Joseph W. Spatafora
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331
| | - B. Gillian Turgeon
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, New York 14850
| | | | - Sarah Young
- The Broad Institute, Cambridge, Massachusetts 02142
| | - Shiguo Zhou
- Laboratory for Molecular and Computational Genomics, Department of Chemistry, Laboratory of Genetics, UW Biotechnology Center, University of Wisconsin–Madison, Madison, Wisconsin 53706
| | | | | | - Li-Jun Ma
- The Broad Institute, Cambridge, Massachusetts 02142
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, Massachusetts 01003
| | - Lynda M. Ciuffetti
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331
- Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon 97331
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20
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Slavov GT, DiFazio SP, Martin J, Schackwitz W, Muchero W, Rodgers-Melnick E, Lipphardt MF, Pennacchio CP, Hellsten U, Pennacchio LA, Gunter LE, Ranjan P, Vining K, Pomraning KR, Wilhelm LJ, Pellegrini M, Mockler TC, Freitag M, Geraldes A, El-Kassaby YA, Mansfield SD, Cronk QCB, Douglas CJ, Strauss SH, Rokhsar D, Tuskan GA. Genome resequencing reveals multiscale geographic structure and extensive linkage disequilibrium in the forest tree Populus trichocarpa. New Phytol 2012; 196:713-725. [PMID: 22861491 DOI: 10.1111/j.1469-8137.2012.04258.x] [Citation(s) in RCA: 118] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
• Plant population genomics informs evolutionary biology, breeding, conservation and bioenergy feedstock development. For example, the detection of reliable phenotype-genotype associations and molecular signatures of selection requires a detailed knowledge about genome-wide patterns of allele frequency variation, linkage disequilibrium and recombination. • We resequenced 16 genomes of the model tree Populus trichocarpa and genotyped 120 trees from 10 subpopulations using 29,213 single-nucleotide polymorphisms. • Significant geographic differentiation was present at multiple spatial scales, and range-wide latitudinal allele frequency gradients were strikingly common across the genome. The decay of linkage disequilibrium with physical distance was slower than expected from previous studies in Populus, with r(2) dropping below 0.2 within 3-6 kb. Consistent with this, estimates of recent effective population size from linkage disequilibrium (N(e) ≈ 4000-6000) were remarkably low relative to the large census sizes of P. trichocarpa stands. Fine-scale rates of recombination varied widely across the genome, but were largely predictable on the basis of DNA sequence and methylation features. • Our results suggest that genetic drift has played a significant role in the recent evolutionary history of P. trichocarpa. Most importantly, the extensive linkage disequilibrium detected suggests that genome-wide association studies and genomic selection in undomesticated populations may be more feasible in Populus than previously assumed.
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Affiliation(s)
- Gancho T Slavov
- Department of Biology, West Virginia University, Morgantown, WV 26506-6057, USA
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, SY23 3EB, UK
| | - Stephen P DiFazio
- Department of Biology, West Virginia University, Morgantown, WV 26506-6057, USA
| | - Joel Martin
- US Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Wendy Schackwitz
- US Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Wellington Muchero
- BioSciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Eli Rodgers-Melnick
- Department of Biology, West Virginia University, Morgantown, WV 26506-6057, USA
| | - Mindie F Lipphardt
- Department of Biology, West Virginia University, Morgantown, WV 26506-6057, USA
| | | | - Uffe Hellsten
- US Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Len A Pennacchio
- US Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Lee E Gunter
- BioSciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Priya Ranjan
- BioSciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Kelly Vining
- Department of Forest Ecosystems and Society, Oregon State University, Corvallis, OR 97331-5752, USA
| | - Kyle R Pomraning
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331-7305, USA
| | | | - Matteo Pellegrini
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA 90095-1606, USA
| | - Todd C Mockler
- Donald Danforth Plant Science Center, Saint Louis, MO 63132, USA
| | - Michael Freitag
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331-7305, USA
| | - Armando Geraldes
- Department of Botany, University of British Columbia, Vancouver, BC, Canada, V6T 1Z4
| | - Yousry A El-Kassaby
- Department of Forest Sciences, University of British Columbia, Vancouver, BC, Canada, V6T 1Z4
| | - Shawn D Mansfield
- Department of Wood Science, University of British Columbia, Vancouver, BC, Canada, V6T 1Z4
| | - Quentin C B Cronk
- Department of Botany, University of British Columbia, Vancouver, BC, Canada, V6T 1Z4
| | - Carl J Douglas
- Department of Botany, University of British Columbia, Vancouver, BC, Canada, V6T 1Z4
| | - Steven H Strauss
- Department of Forest Ecosystems and Society, Oregon State University, Corvallis, OR 97331-5752, USA
| | - Dan Rokhsar
- US Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Gerald A Tuskan
- BioSciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
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21
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Cui Y, Lee MY, Huo N, Bragg J, Yan L, Yuan C, Li C, Holditch SJ, Xie J, Luo MC, Li D, Yu J, Martin J, Schackwitz W, Gu YQ, Vogel JP, Jackson AO, Liu Z, Garvin DF. Fine mapping of the Bsr1 barley stripe mosaic virus resistance gene in the model grass Brachypodium distachyon. PLoS One 2012; 7:e38333. [PMID: 22675544 PMCID: PMC3366947 DOI: 10.1371/journal.pone.0038333] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2012] [Accepted: 05/03/2012] [Indexed: 11/18/2022] Open
Abstract
The ND18 strain of Barley stripe mosaic virus (BSMV) infects several lines of Brachypodium distachyon, a recently developed model system for genomics research in cereals. Among the inbred lines tested, Bd3-1 is highly resistant at 20 to 25°C, whereas Bd21 is susceptible and infection results in an intense mosaic phenotype accompanied by high levels of replicating virus. We generated an F6∶7 recombinant inbred line (RIL) population from a cross between Bd3-1 and Bd21 and used the RILs, and an F2 population of a second Bd21 × Bd3-1 cross to evaluate the inheritance of resistance. The results indicate that resistance segregates as expected for a single dominant gene, which we have designated Barley stripe mosaic virus resistance 1 (Bsr1). We constructed a genetic linkage map of the RIL population using SNP markers to map this gene to within 705 Kb of the distal end of the top of chromosome 3. Additional CAPS and Indel markers were used to fine map Bsr1 to a 23 Kb interval containing five putative genes. Our study demonstrates the power of using RILs to rapidly map the genetic determinants of BSMV resistance in Brachypodium. Moreover, the RILs and their associated genetic map, when combined with the complete genomic sequence of Brachypodium, provide new resources for genetic analyses of many other traits.
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Affiliation(s)
- Yu Cui
- State Key Laboratory of Agro-Biotechnology, China Agricultural University, Beijing, China
- Department of Plant and Microbiology, University of California, Berkeley, California, United States of America
| | - Mi Yeon Lee
- Department of Plant and Microbiology, University of California, Berkeley, California, United States of America
| | - Naxin Huo
- USDA-ARS Western Regional Research Center, Albany, California, United States of America
| | - Jennifer Bragg
- USDA-ARS Western Regional Research Center, Albany, California, United States of America
| | - Lijie Yan
- State Key Laboratory of Agro-Biotechnology, China Agricultural University, Beijing, China
| | - Cheng Yuan
- State Key Laboratory of Agro-Biotechnology, China Agricultural University, Beijing, China
| | - Cui Li
- State Key Laboratory of Agro-Biotechnology, China Agricultural University, Beijing, China
| | - Sara J. Holditch
- Department of Plant and Microbiology, University of California, Berkeley, California, United States of America
| | - Jingzhong Xie
- State Key Laboratory of Agro-Biotechnology, China Agricultural University, Beijing, China
| | - Ming-Cheng Luo
- Department of Plant Sciences, University of California Davis, Davis, California, United States of America
| | - Dawei Li
- State Key Laboratory of Agro-Biotechnology, China Agricultural University, Beijing, China
| | - Jialin Yu
- State Key Laboratory of Agro-Biotechnology, China Agricultural University, Beijing, China
| | - Joel Martin
- US DOE Joint Genome Institute, Walnut Creek, California, United States of America
| | - Wendy Schackwitz
- US DOE Joint Genome Institute, Walnut Creek, California, United States of America
| | - Yong Qiang Gu
- USDA-ARS Western Regional Research Center, Albany, California, United States of America
| | - John P. Vogel
- USDA-ARS Western Regional Research Center, Albany, California, United States of America
| | - Andrew O. Jackson
- Department of Plant and Microbiology, University of California, Berkeley, California, United States of America
- * E-mail: (AOJ); (ZL)
| | - Zhiyong Liu
- State Key Laboratory of Agro-Biotechnology, China Agricultural University, Beijing, China
- * E-mail: (AOJ); (ZL)
| | - David F. Garvin
- USDA-ARS Plant Science Research Unit and Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota, United States of America
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22
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DiFazio S, Slavov G, Rodgers-Melnick E, Martin J, Schackwitz W, Priya R, Tuskan G. Inferring the evolutionary history of Populus trichocarpa from whole genome resequencing data. BMC Proc 2011. [PMCID: PMC3239878 DOI: 10.1186/1753-6561-5-s7-o1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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23
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Tuskan G, Slavov G, DiFazio S, Muchero W, Pryia R, Schackwitz W, Martin J, Rokhsar D, Sykes R, Davis M, Studer M, Wyman C. Populus resequencing: towards genome-wide association studies. BMC Proc 2011. [PMCID: PMC3239865 DOI: 10.1186/1753-6561-5-s7-i21] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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24
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Osbun N, Li J, O'Driscoll MC, Strominger Z, Wakahiro M, Rider E, Bukshpun P, Boland E, Spurrell CH, Schackwitz W, Pennacchio LA, Dobyns WB, Black GCM, Sherr EH. Genetic and functional analyses identify DISC1 as a novel callosal agenesis candidate gene. Am J Med Genet A 2011; 155A:1865-76. [PMID: 21739582 DOI: 10.1002/ajmg.a.34081] [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] [Received: 02/04/2011] [Accepted: 04/06/2011] [Indexed: 11/11/2022]
Abstract
Agenesis of the corpus callosum (AgCC) is a congenital brain malformation that occurs in approximately 1:1,000-1:6,000 births. Several syndromes associated with AgCC have been traced to single gene mutations; however, the majority of AgCC causes remain unidentified. We investigated a mother and two children who all shared complete AgCC and a chromosomal deletion at 1q42. We fine mapped this deletion and show that it includes Disrupted-in-Schizophrenia 1 (DISC1), a gene implicated in schizophrenia and other psychiatric disorders. Furthermore, we report a de novo chromosomal deletion at 1q42.13 to q44, which includes DISC1, in another individual with AgCC. We resequenced DISC1 in a cohort of 144 well-characterized AgCC individuals and identified 20 sequence changes, of which 4 are rare potentially pathogenic variants. Two of these variants were undetected in 768 control chromosomes. One of these is a splice site mutation at the 5' boundary of exon 11 that dramatically reduces full-length mRNA expression of DISC1, but not of shorter forms. We investigated the developmental expression of mouse DISC1 and find that it is highly expressed in the embryonic corpus callosum at a critical time for callosal formation. Taken together our results suggest a significant role for DISC1 in corpus callosum development.
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Affiliation(s)
- Nathan Osbun
- Department of Neurology, University of California San Francisco, San Francisco, California, USA
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25
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Woyke T, Tighe D, Mavromatis K, Clum A, Copeland A, Schackwitz W, Lapidus A, Wu D, McCutcheon JP, McDonald BR, Moran NA, Bristow J, Cheng JF. One bacterial cell, one complete genome. PLoS One 2010; 5:e10314. [PMID: 20428247 PMCID: PMC2859065 DOI: 10.1371/journal.pone.0010314] [Citation(s) in RCA: 194] [Impact Index Per Article: 13.9] [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: 03/02/2010] [Accepted: 03/11/2010] [Indexed: 12/03/2022] Open
Abstract
While the bulk of the finished microbial genomes sequenced to date are derived from cultured bacterial and archaeal representatives, the vast majority of microorganisms elude current culturing attempts, severely limiting the ability to recover complete or even partial genomes from these environmental species. Single cell genomics is a novel culture-independent approach, which enables access to the genetic material of an individual cell. No single cell genome has to our knowledge been closed and finished to date. Here we report the completed genome from an uncultured single cell of Candidatus Sulcia muelleri DMIN. Digital PCR on single symbiont cells isolated from the bacteriome of the green sharpshooter Draeculacephala minerva bacteriome allowed us to assess that this bacteria is polyploid with genome copies ranging from approximately 200–900 per cell, making it a most suitable target for single cell finishing efforts. For single cell shotgun sequencing, an individual Sulcia cell was isolated and whole genome amplified by multiple displacement amplification (MDA). Sanger-based finishing methods allowed us to close the genome. To verify the correctness of our single cell genome and exclude MDA-derived artifacts, we independently shotgun sequenced and assembled the Sulcia genome from pooled bacteriomes using a metagenomic approach, yielding a nearly identical genome. Four variations we detected appear to be genuine biological differences between the two samples. Comparison of the single cell genome with bacteriome metagenomic sequence data detected two single nucleotide polymorphisms (SNPs), indicating extremely low genetic diversity within a Sulcia population. This study demonstrates the power of single cell genomics to generate a complete, high quality, non-composite reference genome within an environmental sample, which can be used for population genetic analyzes.
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Affiliation(s)
- Tanja Woyke
- Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America
| | - Damon Tighe
- Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America
| | - Konstantinos Mavromatis
- Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America
| | - Alicia Clum
- Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America
| | - Alex Copeland
- Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America
| | - Wendy Schackwitz
- Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America
| | - Alla Lapidus
- Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America
| | - Dongying Wu
- Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America
| | - John P. McCutcheon
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona, United States of America
| | - Bradon R. McDonald
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona, United States of America
| | - Nancy A. Moran
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona, United States of America
| | - James Bristow
- Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America
| | - Jan-Fang Cheng
- Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America
- * E-mail:
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26
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Cordeddu V, Di Schiavi E, Pennacchio LA, Ma'ayan A, Sarkozy A, Fodale V, Cecchetti S, Cardinale A, Martin J, Schackwitz W, Lipzen A, Zampino G, Mazzanti L, Digilio MC, Martinelli S, Flex E, Lepri F, Bartholdi D, Kutsche K, Ferrero GB, Anichini C, Selicorni A, Rossi C, Tenconi R, Zenker M, Merlo D, Dallapiccola B, Iyengar R, Bazzicalupo P, Gelb BD, Tartaglia M. Mutation of SHOC2 promotes aberrant protein N-myristoylation and causes Noonan-like syndrome with loose anagen hair. Nat Genet 2009; 41:1022-6. [PMID: 19684605 PMCID: PMC2765465 DOI: 10.1038/ng.425] [Citation(s) in RCA: 296] [Impact Index Per Article: 19.7] [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: 04/01/2009] [Accepted: 06/22/2009] [Indexed: 11/15/2022]
Abstract
N-myristoylation is a common form of co-translational protein fatty acylation resulting from the attachment of myristate to a required N-terminal glycine residue. We show that aberrantly acquired N-myristoylation of SHOC2, a leucine-rich repeat-containing protein that positively modulates RAS-MAPK signal flow, underlies a clinically distinctive condition of the neuro-cardio-facial-cutaneous disorders family. Twenty-five subjects with a relatively consistent phenotype previously termed Noonan-like syndrome with loose anagen hair (MIM607721) shared the 4A>G missense change in SHOC2 (producing an S2G amino acid substitution) that introduces an N-myristoylation site, resulting in aberrant targeting of SHOC2 to the plasma membrane and impaired translocation to the nucleus upon growth factor stimulation. Expression of SHOC2(S2G) in vitro enhanced MAPK activation in a cell type-specific fashion. Induction of SHOC2(S2G) in Caenorhabditis elegans engendered protruding vulva, a neomorphic phenotype previously associated with aberrant signaling. These results document the first example of an acquired N-terminal lipid modification of a protein causing human disease.
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Affiliation(s)
- Viviana Cordeddu
- Dipartimento di Ematologia, Oncologia e Medicina Molecolare, Istituto Superiore di Sanità, 00161 Rome, Italy
| | - Elia Di Schiavi
- Istituto di Genetica e Biofisica “A. Buzzati Traverso”, Consiglio Nazionale delle Ricerche, 80131 Naples, Italy
| | - Len A. Pennacchio
- Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
- US Department of Energy Joint Genome Institute, Walnut Creek, CA 94598
| | - Avi Ma'ayan
- Department of Pharmacology and Systems Therapeutics, Systems Biology Center New York (SBCNY), Mount Sinai School of Medicine, New York, NY 10029
| | - Anna Sarkozy
- IRCCS-Casa Sollievo della Sofferenza, San Giovanni Rotondo and Istituto Mendel, 00198, Rome, Italy
| | - Valentina Fodale
- Dipartimento di Ematologia, Oncologia e Medicina Molecolare, Istituto Superiore di Sanità, 00161 Rome, Italy
- Department of Experimental Medicine, University “La Sapienza”, 00198, Rome, Italy
| | - Serena Cecchetti
- Dipartimento di Biologia Cellulare e Neuroscienze, Istituto Superiore di Sanità, 00161 Rome, Italy
| | | | - Joel Martin
- US Department of Energy Joint Genome Institute, Walnut Creek, CA 94598
| | - Wendy Schackwitz
- US Department of Energy Joint Genome Institute, Walnut Creek, CA 94598
| | - Anna Lipzen
- US Department of Energy Joint Genome Institute, Walnut Creek, CA 94598
| | - Giuseppe Zampino
- Istituto di Clinica Pediatrica, Università, Cattolica del Sacro Cuore, 00168, Rome, Italy
| | - Laura Mazzanti
- Dipartimento di Pediatria, Università degli Studi di Bologna, 40138 Bologna, Italy
| | - Maria C. Digilio
- Sezione di Genetica Medica, Ospedale Bambino Gesù, 00165, Rome, Italy
| | - Simone Martinelli
- Dipartimento di Ematologia, Oncologia e Medicina Molecolare, Istituto Superiore di Sanità, 00161 Rome, Italy
| | - Elisabetta Flex
- Dipartimento di Ematologia, Oncologia e Medicina Molecolare, Istituto Superiore di Sanità, 00161 Rome, Italy
| | - Francesca Lepri
- IRCCS-Casa Sollievo della Sofferenza, San Giovanni Rotondo and Istituto Mendel, 00198, Rome, Italy
| | - Deborah Bartholdi
- Institute of Medical Genetics, University of Zurich, 8603 Schwerzenbach, Switzerland
| | - Kerstin Kutsche
- Institut für Humangenetik, Universitätsklinikum Hamburg-Eppendorf, 20246, Hamburg, Germany
| | | | - Cecilia Anichini
- Dipartimento di Pediatria, Ostetricia e Medicina della Riproduzione, Università di Siena, Siena, 53100, Italy
| | - Angelo Selicorni
- I Clinica Pediatrica, IRCCS Fondazione Policlinico Milano, 20122 Milan, Italy
| | - Cesare Rossi
- U.O. Genetica Medica, Policlinico S. Orsola-Malpighi, 40138 Bologna, Italy
| | - Romano Tenconi
- Dipartimento di Pediatria, Università di Padova, 35128 Padua, Italy
| | - Martin Zenker
- Institute of Human Genetics, University Hospital Erlangen, University of Erlangen-Nuremberg, 91054 Erlangen, Germany
| | - Daniela Merlo
- Dipartimento di Biologia Cellulare e Neuroscienze, Istituto Superiore di Sanità, 00161 Rome, Italy
- IRCCS-San Raffaele Pisana, 00163, Rome, Italy
| | - Bruno Dallapiccola
- IRCCS-Casa Sollievo della Sofferenza, San Giovanni Rotondo and Istituto Mendel, 00198, Rome, Italy
- Department of Experimental Medicine, University “La Sapienza”, 00198, Rome, Italy
| | - Ravi Iyengar
- Department of Pharmacology and Systems Therapeutics, Systems Biology Center New York (SBCNY), Mount Sinai School of Medicine, New York, NY 10029
| | - Paolo Bazzicalupo
- Istituto di Genetica e Biofisica “A. Buzzati Traverso”, Consiglio Nazionale delle Ricerche, 80131 Naples, Italy
| | - Bruce D. Gelb
- Center for Molecular Cardiology and Departments of Pediatrics and Genetics & Genomic Sciences, Mount Sinai School of Medicine, New York, NY 10029
| | - Marco Tartaglia
- Dipartimento di Ematologia, Oncologia e Medicina Molecolare, Istituto Superiore di Sanità, 00161 Rome, Italy
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27
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Pandit B, Sarkozy A, Pennacchio LA, Carta C, Oishi K, Martinelli S, Pogna EA, Schackwitz W, Ustaszewska A, Landstrom A, Bos JM, Ommen SR, Esposito G, Lepri F, Faul C, Mundel P, López Siguero JP, Tenconi R, Selicorni A, Rossi C, Mazzanti L, Torrente I, Marino B, Digilio MC, Zampino G, Ackerman MJ, Dallapiccola B, Tartaglia M, Gelb BD. Gain-of-function RAF1 mutations cause Noonan and LEOPARD syndromes with hypertrophic cardiomyopathy. Nat Genet 2007; 39:1007-12. [PMID: 17603483 DOI: 10.1038/ng2073] [Citation(s) in RCA: 468] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2006] [Accepted: 05/17/2007] [Indexed: 01/06/2023]
Abstract
Noonan and LEOPARD syndromes are developmental disorders with overlapping features, including cardiac abnormalities, short stature and facial dysmorphia. Increased RAS signaling owing to PTPN11, SOS1 and KRAS mutations causes approximately 60% of Noonan syndrome cases, and PTPN11 mutations cause 90% of LEOPARD syndrome cases. Here, we report that 18 of 231 individuals with Noonan syndrome without known mutations (corresponding to 3% of all affected individuals) and two of six individuals with LEOPARD syndrome without PTPN11 mutations have missense mutations in RAF1, which encodes a serine-threonine kinase that activates MEK1 and MEK2. Most mutations altered a motif flanking Ser259, a residue critical for autoinhibition of RAF1 through 14-3-3 binding. Of 19 subjects with a RAF1 mutation in two hotspots, 18 (or 95%) showed hypertrophic cardiomyopathy (HCM), compared with the 18% prevalence of HCM among individuals with Noonan syndrome in general. Ectopically expressed RAF1 mutants from the two HCM hotspots had increased kinase activity and enhanced ERK activation, whereas non-HCM-associated mutants were kinase impaired. Our findings further implicate increased RAS signaling in pathological cardiomyocyte hypertrophy.
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Affiliation(s)
- Bhaswati Pandit
- Center for Molecular Cardiology, Department of Pediatrics and Department of Genetics and Genomic Sciences, Mount Sinai School of Medicine, One Gustave L. Levy Place, New York, New York 10029, USA
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28
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Ahituv N, Kavaslar N, Schackwitz W, Ustaszewska A, Martin J, Hebert S, Doelle H, Ersoy B, Kryukov G, Schmidt S, Yosef N, Ruppin E, Sharan R, Vaisse C, Sunyaev S, Dent R, Cohen J, McPherson R, Pennacchio LA. Medical sequencing at the extremes of human body mass. Am J Hum Genet 2007; 80:779-91. [PMID: 17357083 PMCID: PMC1852707 DOI: 10.1086/513471] [Citation(s) in RCA: 182] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2005] [Accepted: 01/16/2007] [Indexed: 01/19/2023] Open
Abstract
Body weight is a quantitative trait with significant heritability in humans. To identify potential genetic contributors to this phenotype, we resequenced the coding exons and splice junctions of 58 genes in 379 obese and 378 lean individuals. Our 96-Mb survey included 21 genes associated with monogenic forms of obesity in humans or mice, as well as 37 genes that function in body weight-related pathways. We found that the monogenic obesity-associated gene group was enriched for rare nonsynonymous variants unique to the obese population compared with the lean population. In addition, computational analysis predicted a greater fraction of deleterious variants within the obese cohort. Together, these data suggest that multiple rare alleles contribute to obesity in the population and provide a medical sequencing-based approach to detect them.
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Affiliation(s)
- Nadav Ahituv
- Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
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29
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Tartaglia M, Pennacchio LA, Zhao C, Yadav KK, Fodale V, Sarkozy A, Pandit B, Oishi K, Martinelli S, Schackwitz W, Ustaszewska A, Martin J, Bristow J, Carta C, Lepri F, Neri C, Vasta I, Gibson K, Curry CJ, Siguero JPL, Digilio MC, Zampino G, Dallapiccola B, Bar-Sagi D, Gelb BD. Erratum: Corrigendum: Gain-of-function SOS1 mutations cause a distinctive form of Noonan syndrome. Nat Genet 2007. [DOI: 10.1038/ng0207-276a] [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: 11/09/2022]
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30
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Tartaglia M, Pennacchio LA, Zhao C, Yadav KK, Fodale V, Sarkozy A, Pandit B, Oishi K, Martinelli S, Schackwitz W, Ustaszewska A, Martin J, Bristow J, Carta C, Lepri F, Neri C, Vasta I, Gibson K, Curry CJ, Siguero JPL, Digilio MC, Zampino G, Dallapiccola B, Bar-Sagi D, Gelb BD. Gain-of-function SOS1 mutations cause a distinctive form of Noonan syndrome. Nat Genet 2006; 39:75-9. [PMID: 17143282 DOI: 10.1038/ng1939] [Citation(s) in RCA: 397] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2006] [Accepted: 11/07/2006] [Indexed: 12/26/2022]
Abstract
Noonan syndrome is a developmental disorder characterized by short stature, facial dysmorphia, congenital heart defects and skeletal anomalies. Increased RAS-mitogen-activated protein kinase (MAPK) signaling due to PTPN11 and KRAS mutations causes 50% of cases of Noonan syndrome. Here, we report that 22 of 129 individuals with Noonan syndrome without PTPN11 or KRAS mutation have missense mutations in SOS1, which encodes a RAS-specific guanine nucleotide exchange factor. SOS1 mutations cluster at codons encoding residues implicated in the maintenance of SOS1 in its autoinhibited form. In addition, ectopic expression of two Noonan syndrome-associated mutants induces enhanced RAS and ERK activation. The phenotype associated with SOS1 defects lies within the Noonan syndrome spectrum but is distinctive, with a high prevalence of ectodermal abnormalities but generally normal development and linear growth. Our findings implicate gain-of-function mutations in a RAS guanine nucleotide exchange factor in disease for the first time and define a new mechanism by which upregulation of the RAS pathway can profoundly change human development.
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Affiliation(s)
- Marco Tartaglia
- Dipartimento di Biologia Cellulare e Neuroscienze, Istituto Superiore di Sanità, Viale Regina Elena, 299, 00161 Rome, Italy.
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31
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Ahituv N, Kavaslar N, Schackwitz W, Ustaszewska A, Collier JM, Hébert S, Doelle H, Dent R, Pennacchio LA, McPherson R. A PYY Q62P variant linked to human obesity. Hum Mol Genet 2005; 15:387-91. [PMID: 16368708 DOI: 10.1093/hmg/ddi455] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [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: 11/14/2022] Open
Abstract
Peptide YY (PYY) has been implicated in the control of food intake through functional studies in rodents and humans. To investigate whether genetic alterations within this gene result in abnormal weight in humans, we sequenced its coding exons and splice sites in a large cohort of extremely obese [n = 379; average body mass index (BMI), 49.0 kg/m2] and lean (n = 378; average BMI, 19.5 kg/m2) individuals. In total, three rare non-synonymous variants were identified, only one of which, PYY Q62P, exhibited familial segregation with body mass. Through serendipity, previous studies based on cell culture revealed this precise variant to have altered receptor-binding selectivity in vitro. We further show, using mouse peptide injection experiments, that while the wild-type PYY peptide reduces food intake, the mutant PYY 62P had an insignificant effect in reducing food intake in vivo. Taken together, these results are the first to support that rare sequence variants within PYY can influence human susceptibility to obesity.
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Affiliation(s)
- Nadav Ahituv
- Genomics Division, One Cyclotron Road, MS 84-171, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
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32
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Weng L, Kavaslar N, Ustaszewska A, Doelle H, Schackwitz W, Hébert S, Cohen JC, McPherson R, Pennacchio LA. Lack of MEF2A mutations in coronary artery disease. J Clin Invest 2005; 115:1016-20. [PMID: 15841183 PMCID: PMC1070426 DOI: 10.1172/jci24186] [Citation(s) in RCA: 89] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2004] [Accepted: 01/25/2005] [Indexed: 12/12/2022] Open
Abstract
Mutations in MEF2A have been implicated in an autosomal dominant form of coronary artery disease (adCAD1). In this study we sought to determine whether severe mutations in MEF2A might also explain sporadic cases of coronary artery disease (CAD). To do this, we resequenced the coding sequence and splice sites of MEF2A in approximately 300 patients with premature CAD and failed to find causative mutations in the CAD cohort. However, we did identify the 21-bp MEF2A coding sequence deletion originally implicated in adCAD1 in 1 of 300 elderly control subjects without CAD. Further screening of approximately 1,500 additional individuals without CAD revealed 2 more subjects with the MEF2A 21-bp deletion. Genotyping of 19 family members of the 3 probands with the 21-bp deletion in MEF2A revealed that the mutation did not cosegregate with early CAD. These studies support that MEF2A mutations are not a common cause of CAD in white people and argue strongly against a role for the MEF2A 21-bp deletion in autosomal dominant CAD.
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Affiliation(s)
- Li Weng
- US Department of Energy, Joint Genome Institute, Walnut Creek, California, USA
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