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Pogka V, Papadopoulou G, Valiakou V, Sgouras DN, Mentis AF, Karamitros T. Targeted Virome Sequencing Enhances Unbiased Detection and Genome Assembly of Known and Emerging Viruses-The Example of SARS-CoV-2. Viruses 2022; 14:1272. [PMID: 35746743 PMCID: PMC9227943 DOI: 10.3390/v14061272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 06/08/2022] [Accepted: 06/08/2022] [Indexed: 12/10/2022] Open
Abstract
Targeted virome enrichment and sequencing (VirCapSeq-VERT) utilizes a pool of oligos (baits) to enrich all known—up to 2015—vertebrate-infecting viruses, increasing their detection sensitivity. The hybridisation of the baits to the target sequences can be partial, thus enabling the detection and genomic reconstruction of novel pathogens with <40% genetic diversity compared to the strains used for the baits’ design. In this study, we deploy this method in multiplexed mixes of viral extracts, and we assess its performance in the unbiased detection of DNA and RNA viruses after cDNA synthesis. We further assess its efficiency in depleting various background genomic material. Finally, as a proof-of-concept, we explore the potential usage of the method for the characterization of unknown, emerging human viruses, such as SARS-CoV-2, which may not be included in the baits’ panel. We mixed positive samples of equimolar DNA/RNA viral extracts from SARS-CoV-2, coronavirus OC43, cytomegalovirus, influenza A virus H3N2, parvovirus B19, respiratory syncytial virus, adenovirus C and coxsackievirus A16. Targeted virome enrichment was performed on a dsDNA mix, followed by sequencing on the NextSeq500 (Illumina) and the portable MinION sequencer, to evaluate its usability as a point-of-care (PoC) application. Genome mapping assembly was performed using viral reference sequences. The untargeted libraries contained less than 1% of total reads mapped on most viral genomes, while RNA viruses remained undetected. In the targeted libraries, the percentage of viral-mapped reads were substantially increased, allowing full genome assembly in most cases. Targeted virome sequencing can enrich a broad range of viruses, potentially enabling the discovery of emerging viruses.
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Affiliation(s)
- Vasiliki Pogka
- Laboratory of Medical Microbiology, Department of Microbiology, Hellenic Pasteur Institute, 11521 Athens, Greece; (V.P.); (D.N.S.); (A.F.M.)
- Bioinformatics and Applied Genomics Unit, Department of Microbiology, Hellenic Pasteur Institute, 11521 Athens, Greece; (G.P.); (V.V.)
| | - Gethsimani Papadopoulou
- Bioinformatics and Applied Genomics Unit, Department of Microbiology, Hellenic Pasteur Institute, 11521 Athens, Greece; (G.P.); (V.V.)
| | - Vaia Valiakou
- Bioinformatics and Applied Genomics Unit, Department of Microbiology, Hellenic Pasteur Institute, 11521 Athens, Greece; (G.P.); (V.V.)
| | - Dionyssios N. Sgouras
- Laboratory of Medical Microbiology, Department of Microbiology, Hellenic Pasteur Institute, 11521 Athens, Greece; (V.P.); (D.N.S.); (A.F.M.)
| | - Andreas F. Mentis
- Laboratory of Medical Microbiology, Department of Microbiology, Hellenic Pasteur Institute, 11521 Athens, Greece; (V.P.); (D.N.S.); (A.F.M.)
| | - Timokratis Karamitros
- Laboratory of Medical Microbiology, Department of Microbiology, Hellenic Pasteur Institute, 11521 Athens, Greece; (V.P.); (D.N.S.); (A.F.M.)
- Bioinformatics and Applied Genomics Unit, Department of Microbiology, Hellenic Pasteur Institute, 11521 Athens, Greece; (G.P.); (V.V.)
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2
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Burridge AJ, Winfield MO, Wilkinson PA, Przewieslik-Allen AM, Edwards KJ, Barker GLA. The Use and Limitations of Exome Capture to Detect Novel Variation in the Hexaploid Wheat Genome. FRONTIERS IN PLANT SCIENCE 2022; 13:841855. [PMID: 35498663 PMCID: PMC9039655 DOI: 10.3389/fpls.2022.841855] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 02/28/2022] [Indexed: 06/14/2023]
Abstract
The bread wheat (Triticum aestivum) pangenome is a patchwork of variable regions, including translocations and introgressions from progenitors and wild relatives. Although a large number of these have been documented, it is likely that many more remain unknown. To map these variable regions and make them more traceable in breeding programs, wheat accessions need to be genotyped or sequenced. The wheat genome is large and complex and consequently, sequencing efforts are often targeted through exome capture. In this study, we employed exome capture prior to sequencing 12 wheat varieties; 10 elite T. aestivum cultivars and two T. aestivum landrace accessions. Sequence coverage across chromosomes was greater toward distal regions of chromosome arms and lower in centromeric regions, reflecting the capture probe distribution which itself is determined by the known telomere to centromere gene gradient. Superimposed on this general pattern, numerous drops in sequence coverage were observed. Several of these corresponded with reported introgressions. Other drops in coverage could not be readily explained and may point to introgressions that have not, to date, been documented.
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Affiliation(s)
| | - Mark O. Winfield
- School of Life Sciences, University of Bristol, Bristol, United Kingdom
| | - Paul A. Wilkinson
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | | | - Keith J. Edwards
- School of Life Sciences, University of Bristol, Bristol, United Kingdom
| | - Gary L. A. Barker
- School of Life Sciences, University of Bristol, Bristol, United Kingdom
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3
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Hou J, Lu D, Mason AS, Li B, An S, Li G, Cai D. Distribution of MITE family Monkey King in rapeseed (Brassica napus L) and its influence on gene expression. Genomics 2021; 113:2934-2943. [PMID: 34182079 DOI: 10.1016/j.ygeno.2021.06.034] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 05/06/2021] [Accepted: 06/24/2021] [Indexed: 10/21/2022]
Abstract
Miniature inverted-repeat transposable elements (MITEs) are a group of class II transposable elements. The MITE Monkey King (MK) was first discovered upstream of BnFLC.A10. In this study, genome resequencing of four selected B. napus accessions, revealed more than 4000 distributed copies of MKs constituting ~2.4 Mb of the B. napus genomic sequence and caused 677 polymorphisms among the four accessions. MK -polymorphism-related markers across 128 natural and 58 synthetic accessions revealed more polymorphic MKs in natural than synthetic accessions. Ten MK -induced indels significantly affected the expression levels of the nearest gene based on RNAseq analysis, six of these effects were subsequently confirmed using qRT-PCR. Decreased expression pattern of MK -derived miRNA-bna-miR6031 was also observed under various stress treatments. Further research focused on the MITE families should promote not only our understanding of gene regulatory networks but also inform crop improvement efforts.
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Affiliation(s)
- Jinna Hou
- Henan Academy of Agricultural Sciences, Zhengzhou 450002, China.
| | - Dandan Lu
- Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Annaliese S Mason
- Chair of Plant Breeding, Institute of Crop Science and Resource Conservation, University of Bonn, Bonn, Germany.
| | - Baoquan Li
- Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Sufang An
- Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Gaoyuan Li
- Bioinformatic Institute, Huazhong Agricultural University, Wuhan 430071, China.
| | - Dongfang Cai
- Henan Academy of Agricultural Sciences, Zhengzhou 450002, China.
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4
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Bragina MK, Afonnikov DA, Salina EA. Progress in plant genome sequencing: research directions. Vavilovskii Zhurnal Genet Selektsii 2019. [DOI: 10.18699/vj19.459] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Since the first plant genome of Arabidopsis thaliana has been sequenced and published, genome sequencing technologies have undergone significant changes. New algorithms, sequencing technologies and bioinformatic approaches were adopted to obtain genome, transcriptome and exome sequences for model and crop species, which have permitted deep inferences into plant biology. As a result of an improved genome assembly and analysis methods, genome sequencing costs plummeted and the number of high-quality plant genome sequences is constantly growing. Consequently, more than 300 plant genome sequences have been published over the past twenty years. Although many of the published genomes are considered incomplete, they proved to be a valuable tool for identifying genes involved in the formation of economically valuable plant traits, for marker-assisted and genomic selection and for comparative analysis of plant genomes in order to determine the basic patterns of origin of various plant species. Since a high coverage and resolution of a genome sequence is not enough to detect all changes in complex samples, targeted sequencing, which consists in the isolation and sequencing of a specific region of the genome, has begun to develop. Targeted sequencing has a higher detection power (the ability to identify new differences/variants) and resolution (up to one basis). In addition, exome sequencing (the method of sequencing only protein-coding genes regions) is actively developed, which allows for the sequencing of non-expressed alleles and genes that cannot be found with RNA-seq. In this review, an analysis of sequencing technologies development and the construction of “reference” genomes of plants is performed. A comparison of the methods of targeted sequencing based on the use of the reference DNA sequence is accomplished.
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Affiliation(s)
| | - D. A. Afonnikov
- Institute of Cytology and Genetics, SB RAS; Novosibirsk State University
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Abstract
Understanding how crop plants evolved from their wild relatives and spread around the world can inform about the origins of agriculture. Here, we review how the rapid development of genomic resources and tools has made it possible to conduct genetic mapping and population genetic studies to unravel the molecular underpinnings of domestication and crop evolution in diverse crop species. We propose three future avenues for the study of crop evolution: establishment of high-quality reference genomes for crops and their wild relatives; genomic characterization of germplasm collections; and the adoption of novel methodologies such as archaeogenetics, epigenomics, and genome editing.
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Affiliation(s)
- Mona Schreiber
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstraße 3, 06466, Seeland, Germany
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstraße 3, 06466, Seeland, Germany
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstraße 3, 06466, Seeland, Germany.
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103, Leipzig, Germany.
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Mable BK, Brysting AK, Jørgensen MH, Carbonell AKZ, Kiefer C, Ruiz-Duarte P, Lagesen K, Koch MA. Adding Complexity to Complexity: Gene Family Evolution in Polyploids. Front Ecol Evol 2018. [DOI: 10.3389/fevo.2018.00114] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
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7
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Klonowska K, Handschuh L, Swiercz A, Figlerowicz M, Kozlowski P. MTTE: an innovative strategy for the evaluation of targeted/exome enrichment efficiency. Oncotarget 2018; 7:67266-67276. [PMID: 27572310 PMCID: PMC5341873 DOI: 10.18632/oncotarget.11646] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2016] [Accepted: 07/28/2016] [Indexed: 02/06/2023] Open
Abstract
Although currently available strategies for the preparation of exome-enriched libraries are well established, a final validation of the libraries in terms of exome enrichment efficiency prior to the sequencing step is of considerable importance. Here, we present a strategy for the evaluation of exome enrichment, i.e., the Multipoint Test for Targeted-enrichment Efficiency (MTTE), PCR-based approach utilizing multiplex ligation-dependent probe amplification with capillary electrophoresis separation. We used MTTE for the analysis of subsequent steps of the Illumina TruSeq Exome Enrichment procedure. The calculated values of enrichment-associated parameters (i.e., relative enrichment, relative clearance, overall clearance, and fold enrichment) and the comparison of MTTE results with the actual enrichment revealed the high reliability of our assay. Additionally, the MTTE assay enabled the determination of the sequence-associated features that may confer bias in the enrichment of different targets. Importantly, the MTTE is low cost method that can be easily adapted to the region of interest important for a particular project. Thus, the MTTE strategy is attractive for post-capture validation in a variety of targeted/exome enrichment NGS projects.
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Affiliation(s)
- Katarzyna Klonowska
- European Centre for Bioinformatics and Genomics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
| | - Luiza Handschuh
- European Centre for Bioinformatics and Genomics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland.,Department of Hematology and Bone Marrow Transplantation, Poznan University of Medical Sciences, 60-569 Poznan, Poland
| | - Aleksandra Swiercz
- European Centre for Bioinformatics and Genomics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland.,Institute of Computing Science, Poznan University of Technology, 60-965 Poznan, Poland
| | - Marek Figlerowicz
- European Centre for Bioinformatics and Genomics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland.,Institute of Computing Science, Poznan University of Technology, 60-965 Poznan, Poland
| | - Piotr Kozlowski
- European Centre for Bioinformatics and Genomics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland.,Institute of Technology and Chemical Engineering, Poznan University of Technology, 60-965 Poznan, Poland
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8
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Peng Z, Fan W, Wang L, Paudel D, Leventini D, Tillman BL, Wang J. Target enrichment sequencing in cultivated peanut (Arachis hypogaea L.) using probes designed from transcript sequences. Mol Genet Genomics 2017; 292:955-965. [PMID: 28492983 DOI: 10.1007/s00438-017-1327-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Accepted: 05/07/2017] [Indexed: 11/29/2022]
Abstract
Enabled by the next generation sequencing, target enrichment sequencing (TES) is a powerful method to enrich genomic regions of interest and to identify sequence variations. The objective of this study was to explore the feasibility of probe design from transcript sequences for TES application in calling sequence variants in peanut, an important allotetraploid crop with a large genome size. In this study, we applied an in-solution hybridization method to enrich DNA sequences of seven peanut genotypes. Our results showed that it is feasible to apply TES with probes designed from transcript sequences in polyploid peanut. Using a set of 31,123 probes, a total of 5131 and 7521 genes were targeted in peanut A and B genomes, respectively. For each genotype used in this study, the probe target capture regions were efficiently covered with high depth. The average on-target rate of sequencing reads was 42.47%, with a significant amount of off-target reads coming from genomic regions homologous to target regions. In this study, when given predefined genomic regions of interest and the same amount of sequencing data, TES provided the highest coverage of target regions when compared to whole genome sequencing, RNA sequencing, and genotyping by sequencing. Single nucleotide polymorphism (SNP) calling and subsequent validation revealed a high validation rate (85.71%) of homozygous SNPs, providing valuable markers for peanut genotyping. This study demonstrated the success of applying TES for SNP identification in peanut, which shall provide valuable suggestions for TES application in other non-model species without a genome reference available.
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Affiliation(s)
- Ze Peng
- Agronomy Department, University of Florida, Gainesville, FL, 32610, USA
| | - Wen Fan
- Agronomy Department, University of Florida, Gainesville, FL, 32610, USA
| | - Liping Wang
- Agronomy Department, University of Florida, Gainesville, FL, 32610, USA
| | - Dev Paudel
- Agronomy Department, University of Florida, Gainesville, FL, 32610, USA
| | - Dante Leventini
- Agronomy Department, University of Florida, Gainesville, FL, 32610, USA
| | - Barry L Tillman
- Agronomy Department, University of Florida, Gainesville, FL, 32610, USA
| | - Jianping Wang
- Agronomy Department, University of Florida, Gainesville, FL, 32610, USA.
- Genetics Institute, Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL, 32610, USA.
- Center for Genomics and Biotechnology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China.
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9
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Boutte J, Ferreira de Carvalho J, Rousseau-Gueutin M, Poulain J, Da Silva C, Wincker P, Ainouche M, Salmon A. Reference Transcriptomes and Detection of Duplicated Copies in Hexaploid and Allododecaploid Spartina Species (Poaceae). Genome Biol Evol 2016; 8:3030-3044. [PMID: 27614235 PMCID: PMC5633685 DOI: 10.1093/gbe/evw209] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/20/2016] [Indexed: 01/19/2023] Open
Abstract
In this study, we report the assembly and annotation of five reference transcriptomes for the European hexaploid Spartina species (S. maritima, S. alterniflora and their homoploid hybrids S. x townsendii and S. x neyrautii) and the allododecaploid invasive species S. anglica These transcriptomes were constructed from various leaf and root cDNA libraries that were sequenced using both Roche-454 and Illumina technologies. Considering the high ploidy levels of the Spartina genomes under study, and considering the absence of diploid reference genome and the need of an appropriate analytical strategy, we developed generic bioinformatics tools to (1) detect different haplotypes of each gene within each species and (2) assign a parental origin to haplotypes detected in the hexaploid hybrids and the neo-allopolyploid. The approach described here allows the detection of putative homeologs from sets of short reads. Synonymous substitution rate (KS) comparisons between haplotypes from the hexaploid species revealed the presence of one KS peak (likely resulting from the tetraploid duplication event). The procedure developed in this study can be applied for future differential gene expression or genomics experiments to study the fate of duplicated genes in the invasive allododecaploid S. anglica.
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Affiliation(s)
- Julien Boutte
- UMR CNRS 6553 Ecobio, OSUR (Observatoire des Sciences de l'Univers de Rennes), University of Rennes 1, Rennes Cedex, France
| | - Julie Ferreira de Carvalho
- UMR CNRS 6553 Ecobio, OSUR (Observatoire des Sciences de l'Univers de Rennes), University of Rennes 1, Rennes Cedex, France
| | - Mathieu Rousseau-Gueutin
- UMR CNRS 6553 Ecobio, OSUR (Observatoire des Sciences de l'Univers de Rennes), University of Rennes 1, Rennes Cedex, France UMR Institut de Génétique, Environnement et Protection des Plantes, Institut National de la Recherche Agronomique, Le Rheu Cedex, France
| | | | | | | | - Malika Ainouche
- UMR CNRS 6553 Ecobio, OSUR (Observatoire des Sciences de l'Univers de Rennes), University of Rennes 1, Rennes Cedex, France
| | - Armel Salmon
- UMR CNRS 6553 Ecobio, OSUR (Observatoire des Sciences de l'Univers de Rennes), University of Rennes 1, Rennes Cedex, France
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10
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Glover NM, Redestig H, Dessimoz C. Homoeologs: What Are They and How Do We Infer Them? TRENDS IN PLANT SCIENCE 2016; 21:609-621. [PMID: 27021699 PMCID: PMC4920642 DOI: 10.1016/j.tplants.2016.02.005] [Citation(s) in RCA: 102] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Revised: 02/09/2016] [Accepted: 02/20/2016] [Indexed: 05/18/2023]
Abstract
The evolutionary history of nearly all flowering plants includes a polyploidization event. Homologous genes resulting from allopolyploidy are commonly referred to as 'homoeologs', although this term has not always been used precisely or consistently in the literature. With several allopolyploid genome sequencing projects under way, there is a pressing need for computational methods for homoeology inference. Here we review the definition of homoeology in historical and modern contexts and propose a precise and testable definition highlighting the connection between homoeologs and orthologs. In the second part, we survey experimental and computational methods of homoeolog inference, considering the strengths and limitations of each approach. Establishing a precise and evolutionarily meaningful definition of homoeology is essential for understanding the evolutionary consequences of polyploidization.
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Affiliation(s)
- Natasha M Glover
- Bayer CropScience NV, Technologiepark 38, 9052 Gent, Belgium; University College London, Gower Street, London WC1E 6BT, UK
| | | | - Christophe Dessimoz
- University College London, Gower Street, London WC1E 6BT, UK; University of Lausanne, Biophore, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, Biophore, 1015 Lausanne, Switzerland.
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11
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Bombarely A, Moser M, Amrad A, Bao M, Bapaume L, Barry CS, Bliek M, Boersma MR, Borghi L, Bruggmann R, Bucher M, D'Agostino N, Davies K, Druege U, Dudareva N, Egea-Cortines M, Delledonne M, Fernandez-Pozo N, Franken P, Grandont L, Heslop-Harrison JS, Hintzsche J, Johns M, Koes R, Lv X, Lyons E, Malla D, Martinoia E, Mattson NS, Morel P, Mueller LA, Muhlemann J, Nouri E, Passeri V, Pezzotti M, Qi Q, Reinhardt D, Rich M, Richert-Pöggeler KR, Robbins TP, Schatz MC, Schranz ME, Schuurink RC, Schwarzacher T, Spelt K, Tang H, Urbanus SL, Vandenbussche M, Vijverberg K, Villarino GH, Warner RM, Weiss J, Yue Z, Zethof J, Quattrocchio F, Sims TL, Kuhlemeier C. Insight into the evolution of the Solanaceae from the parental genomes of Petunia hybrida. NATURE PLANTS 2016; 2:16074. [PMID: 27255838 DOI: 10.1038/nplants.2016.74] [Citation(s) in RCA: 214] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Accepted: 04/22/2016] [Indexed: 05/21/2023]
Abstract
Petunia hybrida is a popular bedding plant that has a long history as a genetic model system. We report the whole-genome sequencing and assembly of inbred derivatives of its two wild parents, P. axillaris N and P. inflata S6. The assemblies include 91.3% and 90.2% coverage of their diploid genomes (1.4 Gb; 2n = 14) containing 32,928 and 36,697 protein-coding genes, respectively. The genomes reveal that the Petunia lineage has experienced at least two rounds of hexaploidization: the older gamma event, which is shared with most Eudicots, and a more recent Solanaceae event that is shared with tomato and other solanaceous species. Transcription factors involved in the shift from bee to moth pollination reside in particularly dynamic regions of the genome, which may have been key to the remarkable diversity of floral colour patterns and pollination systems. The high-quality genome sequences will enhance the value of Petunia as a model system for research on unique biological phenomena such as small RNAs, symbiosis, self-incompatibility and circadian rhythms.
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Affiliation(s)
- Aureliano Bombarely
- Department of Horticulture, Virginia Polytechnic Institute and State University, 490 West Campus Dr., Blacksburg, Virginia 24061, USA
| | - Michel Moser
- Institute of Plant Sciences, University of Bern, Altenbergrain 21, 3013 Bern, Switzerland
| | - Avichai Amrad
- Institute of Plant Sciences, University of Bern, Altenbergrain 21, 3013 Bern, Switzerland
| | - Manzhu Bao
- Huazhong Agricultural University, Wuhan 430070, P. R. China
| | - Laure Bapaume
- Department of Biology, University of Fribourg, Fribourg, Switzerland, 6 Rte Albert Gockel, CH-1700 Fribourg, Switzerland
| | - Cornelius S Barry
- Department of Horticulture, Michigan State University, East Lansing, Michigan 48824, USA
| | - Mattijs Bliek
- Department of Plant Development and (Epi)Genetics, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
| | - Maaike R Boersma
- Department of Plant Physiology, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
| | - Lorenzo Borghi
- Institute of Plant and Microbiology, University of Zürich, Zollikerstr. 107, CH-8008 Zürich, Switzerland
| | - Rémy Bruggmann
- Interfaculty Bioinformatics Unit, University of Bern, Baltzerstrasse 6, CH-3012 Bern, Switzerland
| | - Marcel Bucher
- Cologne Biocenter, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Zuelpicher Straße 47b, 50674 Cologne, Germany
| | - Nunzio D'Agostino
- Consiglio per la Ricerca in Agricoltura e l'analisi dell'economia agraria, Centro di Ricerca per l'Orticoltura (CREA-ORT), via Cavalleggeri 25, 84098 Pontecagnano (Sa) Italy
| | - Kevin Davies
- Department of Breeding and Genomics, Plant and Food Research, Auckland, 120 Mt Albert Road, Mount Albert, Sandringham 1142, New Zealand
| | - Uwe Druege
- Department of Plant Propagation, Leibniz Institute of Vegetable and Ornamental Crops (IGZ), Kühnhäuserstr. 101, 99090 Erfurt, Germany
| | - Natalia Dudareva
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907-2063, USA
| | - Marcos Egea-Cortines
- Instituto de Biotecnología Vegetal, Universidad Politécnica de Cartagena, 30202, Cartagena, Spain
| | - Massimo Delledonne
- Dipartimento di Biotecnologie, Universita degli Studi di Verona, Strada le Grazie 15, 37134 Verona, Italy
| | - Noe Fernandez-Pozo
- Boyce Thompson Institute for Plant Research, 533 Tower Rd, Ithaca, New York 14853, USA
| | - Philipp Franken
- Department of Plant Propagation, Leibniz Institute of Vegetable and Ornamental Crops (IGZ), Kühnhäuserstr. 101, 99090 Erfurt, Germany
| | - Laurie Grandont
- Biosystematics Group, Wageningen University and Research Center, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - J S Heslop-Harrison
- Department of Genetics, University of Leicester, University Road, Leicester LE1 7RH, UK
| | - Jennifer Hintzsche
- Department of Biological Sciences, Northern Illinois University, DeKalb, Illinois 60115, USA
| | - Mitrick Johns
- Department of Biological Sciences, Northern Illinois University, DeKalb, Illinois 60115, USA
| | - Ronald Koes
- Department of Plant Development and (Epi)Genetics, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
| | - Xiaodan Lv
- Beijing Genomics Institute, Shenzhen 518083, China
| | - Eric Lyons
- School of Plant Sciences, iPlant Collaborative, University of Arizona, Tucson, Arizona 85721, USA
| | - Diwa Malla
- Department of Biological Sciences, Northern Illinois University, DeKalb, Illinois 60115, USA
| | - Enrico Martinoia
- Institute of Plant and Microbiology, University of Zürich, Zollikerstr. 107, CH-8008 Zürich, Switzerland
| | - Neil S Mattson
- School of Integrative Plant Science, Cornell University, Cornell University, Ithaca, New York 14853, USA
| | - Patrice Morel
- Laboratoire Reproduction et Développement des Plantes (RDP), ENS de Lyon/CNRS/INRA/UCBL, 46 Allée d'Italie, 69364 Lyon, France
| | - Lukas A Mueller
- Boyce Thompson Institute for Plant Research, 533 Tower Rd, Ithaca, New York 14853, USA
| | - Joëlle Muhlemann
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907-2063, USA
| | - Eva Nouri
- Department of Biology, University of Fribourg, Fribourg, Switzerland, 4 Rte Albert Gockel, CH-1700 Fribourg, Switzerland
| | - Valentina Passeri
- Department of Plant Development and (Epi)Genetics, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
| | - Mario Pezzotti
- Dipartimento di Biotecnologie, Universita degli Studi di Verona, Strada le Grazie 15, 37134 Verona, Italy
| | - Qinzhou Qi
- Department of Biological Sciences, Northern Illinois University, DeKalb, Illinois 60115, USA
| | - Didier Reinhardt
- Department of Biology, University of Fribourg, Fribourg, Switzerland, 3 Rte Albert Gockel, CH-1700 Fribourg, Switzerland
| | - Melanie Rich
- Department of Biology, University of Fribourg, Fribourg, Switzerland, 5 Rte Albert Gockel, CH-1700 Fribourg, Switzerland
| | - Katja R Richert-Pöggeler
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn-Institut (JKI), Federal Research Centre for Cultivated Plants, Messeweg 11-12, 38104 Braunschweig, Germany
| | - Tim P Robbins
- Department of Crop and Plant Sciences, University of Nottingham, Sutton Bonington, Leicestershire, UL LE12 5RD, UK
| | - Michael C Schatz
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, New York 11724, USA
| | - M Eric Schranz
- Biosystematics Group, Wageningen University and Research Center, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Robert C Schuurink
- Department of Plant Physiology, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
| | - Trude Schwarzacher
- Department of Genetics, University of Leicester, University Road, Leicester LE1 7RH, UK
| | - Kees Spelt
- Department of Plant Development and (Epi)Genetics, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
| | - Haibao Tang
- School of Plant Sciences, iPlant Collaborative, University of Arizona, Tucson, Arizona 85721, USA
| | - Susan L Urbanus
- Department of Plant Development and (Epi)Genetics, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
| | - Michiel Vandenbussche
- Laboratoire Reproduction et Développement des Plantes (RDP), ENS de Lyon/CNRS/INRA/UCBL, 46 Allée d'Italie, 69364 Lyon, France
| | - Kitty Vijverberg
- Radboud University, FNWI, IWWR, Heyendaalseweg 135, 6525AJ Nijmegen, The Netherlands
| | - Gonzalo H Villarino
- School of Integrative Plant Science, Cornell University, Cornell University, Ithaca, New York 14853, USA
| | - Ryan M Warner
- Department of Horticulture, Michigan State University, East Lansing, Michigan 48824, USA
| | - Julia Weiss
- Instituto de Biotecnología Vegetal, Universidad Politécnica de Cartagena, 30202, Cartagena, Spain
| | - Zhen Yue
- Beijing Genomics Institute, Shenzhen 518083, China
| | - Jan Zethof
- Radboud University, FNWI, IWWR, Heyendaalseweg 135, 6525AJ Nijmegen, The Netherlands
| | - Francesca Quattrocchio
- Department of Plant Development and (Epi)Genetics, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
| | - Thomas L Sims
- Department of Biological Sciences, Northern Illinois University, DeKalb, Illinois 60115, USA
| | - Cris Kuhlemeier
- Institute of Plant Sciences, University of Bern, Altenbergrain 21, 3013 Bern, Switzerland
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12
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Kellogg EA. Has the connection between polyploidy and diversification actually been tested? CURRENT OPINION IN PLANT BIOLOGY 2016; 30:25-32. [PMID: 26855304 DOI: 10.1016/j.pbi.2016.01.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Revised: 01/09/2016] [Accepted: 01/17/2016] [Indexed: 05/07/2023]
Abstract
Many major clades of angiosperms have several whole genome duplications (polyploidization events) in their distant past, suggesting that polyploidy drives or at least permits diversification. However, data on recently diverged groups are more equivocal, finding little evidence of elevated diversification following polyploidy. The discrepancy may be attributable at least in part to methodology. Many studies use indirect methods, such as chromosome numbers, genome size, and Ks plots, to test polyploidy, although these approaches can be misleading, and often lack sufficient resolution. A direct test of diversification following polyploidy requires a sequence-based approach that traces the history of nuclear genomes rather than species. These methods identify the point of coalescence of ancestral genomes, but may be misleading about the time and thus the extent of diversification. Limitations of existing methods mean that the connection between polyploidy and diversification has not been rigorously tested and remains unknown.
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Affiliation(s)
- Elizabeth A Kellogg
- Donald Danforth Plant Science Center, 975 North Warson Rd., St. Louis, MO 63132, USA.
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13
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Jones MR, Good JM. Targeted capture in evolutionary and ecological genomics. Mol Ecol 2016; 25:185-202. [PMID: 26137993 PMCID: PMC4823023 DOI: 10.1111/mec.13304] [Citation(s) in RCA: 203] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Revised: 06/19/2015] [Accepted: 06/24/2015] [Indexed: 12/17/2022]
Abstract
The rapid expansion of next-generation sequencing has yielded a powerful array of tools to address fundamental biological questions at a scale that was inconceivable just a few years ago. Various genome-partitioning strategies to sequence select subsets of the genome have emerged as powerful alternatives to whole-genome sequencing in ecological and evolutionary genomic studies. High-throughput targeted capture is one such strategy that involves the parallel enrichment of preselected genomic regions of interest. The growing use of targeted capture demonstrates its potential power to address a range of research questions, yet these approaches have yet to expand broadly across laboratories focused on evolutionary and ecological genomics. In part, the use of targeted capture has been hindered by the logistics of capture design and implementation in species without established reference genomes. Here we aim to (i) increase the accessibility of targeted capture to researchers working in nonmodel taxa by discussing capture methods that circumvent the need of a reference genome, (ii) highlight the evolutionary and ecological applications where this approach is emerging as a powerful sequencing strategy and (iii) discuss the future of targeted capture and other genome-partitioning approaches in the light of the increasing accessibility of whole-genome sequencing. Given the practical advantages and increasing feasibility of high-throughput targeted capture, we anticipate an ongoing expansion of capture-based approaches in evolutionary and ecological research, synergistic with an expansion of whole-genome sequencing.
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Affiliation(s)
- Matthew R. Jones
- University of Montana, Division of Biological Sciences, 32 Campus Dr. HS104, Missoula, MT 59812, USA
| | - Jeffrey M. Good
- University of Montana, Division of Biological Sciences, 32 Campus Dr. HS104, Missoula, MT 59812, USA
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14
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Nicholls JA, Pennington RT, Koenen EJM, Hughes CE, Hearn J, Bunnefeld L, Dexter KG, Stone GN, Kidner CA. Using targeted enrichment of nuclear genes to increase phylogenetic resolution in the neotropical rain forest genus Inga (Leguminosae: Mimosoideae). FRONTIERS IN PLANT SCIENCE 2015; 6:710. [PMID: 26442024 PMCID: PMC4584976 DOI: 10.3389/fpls.2015.00710] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Accepted: 08/25/2015] [Indexed: 05/20/2023]
Abstract
Evolutionary radiations are prominent and pervasive across many plant lineages in diverse geographical and ecological settings; in neotropical rainforests there is growing evidence suggesting that a significant fraction of species richness is the result of recent radiations. Understanding the evolutionary trajectories and mechanisms underlying these radiations demands much greater phylogenetic resolution than is currently available for these groups. The neotropical tree genus Inga (Leguminosae) is a good example, with ~300 extant species and a crown age of 2-10 MY, yet over 6 kb of plastid and nuclear DNA sequence data gives only poor phylogenetic resolution among species. Here we explore the use of larger-scale nuclear gene data obtained though targeted enrichment to increase phylogenetic resolution within Inga. Transcriptome data from three Inga species were used to select 264 nuclear loci for targeted enrichment and sequencing. Following quality control to remove probable paralogs from these sequence data, the final dataset comprised 259,313 bases from 194 loci for 24 accessions representing 22 Inga species and an outgroup (Zygia). Bayesian phylogenies reconstructed using either all loci concatenated or a gene-tree/species-tree approach yielded highly resolved phylogenies. We used coalescent approaches to show that the same targeted enrichment data also have significant power to discriminate among alternative within-species population histories within the widespread species I. umbellifera. In either application, targeted enrichment simplifies the informatics challenge of identifying orthologous loci associated with de novo genome sequencing. We conclude that targeted enrichment provides the large volumes of phylogenetically-informative sequence data required to resolve relationships within recent plant species radiations, both at the species level and for within-species phylogeographic studies.
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Affiliation(s)
- James A. Nicholls
- Ashworth Labs, Institute of Evolutionary Biology, School of Biological Sciences, University of EdinburghEdinburgh, UK
- Royal Botanic Garden EdinburghEdinburgh, UK
| | | | - Erik J. M. Koenen
- Institute of Systematic Botany, University of ZurichZürich, Switzerland
| | - Colin E. Hughes
- Institute of Systematic Botany, University of ZurichZürich, Switzerland
| | - Jack Hearn
- Ashworth Labs, Institute of Evolutionary Biology, School of Biological Sciences, University of EdinburghEdinburgh, UK
| | - Lynsey Bunnefeld
- Ashworth Labs, Institute of Evolutionary Biology, School of Biological Sciences, University of EdinburghEdinburgh, UK
| | - Kyle G. Dexter
- School of Geosciences, University of EdinburghEdinburgh, UK
| | - Graham N. Stone
- Ashworth Labs, Institute of Evolutionary Biology, School of Biological Sciences, University of EdinburghEdinburgh, UK
| | - Catherine A. Kidner
- Royal Botanic Garden EdinburghEdinburgh, UK
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of EdinburghEdinburgh, UK
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15
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Wang B, Zhang Y, Wei P, Sun M, Ma X, Zhu X. Identification of nuclear low-copy genes and their phylogenetic utility in rosids. Genome 2015; 57:547-54. [PMID: 25761707 DOI: 10.1139/gen-2014-0138] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
By far, the interordinal relationships in rosids remain poorly resolved. Previous studies based on chloroplast, mitochondrial, and nuclear DNA has produced conflicting phylogenetic resolutions that has become a widely concerned problem in recent phylogenetic studies. Here, a total of 96 single-copy nuclear gene loci were identified from the KOG (eukaryotic orthologous groups) database, most of which were first used for phylogenetic analysis of angiosperms. The orthologous sequence datasets from completely sequenced genomes of rosids were assembled for the resolution of the position of the COM (Celastrales-Oxalidales-Malpighiales) clade in rosids. Our analysis revealed strong and consistent support for CM topology (the COM clade as sister to the malvids). Our results will contribute to further exploring the underlying cause of conflict between chloroplast, mitochondrial, and nuclear data. In addition, our study identified a few novel nuclear molecular markers with potential to investigate the deep phylogenetic relationship of plants or other eukaryotic taxonomical groups.
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Affiliation(s)
- Baohua Wang
- School of Life Sciences, Nantong University, Nantong 226019, China
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16
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Nicholls JA, Pennington RT, Koenen EJM, Hughes CE, Hearn J, Bunnefeld L, Dexter KG, Stone GN, Kidner CA. Using targeted enrichment of nuclear genes to increase phylogenetic resolution in the neotropical rain forest genus Inga (Leguminosae: Mimosoideae). FRONTIERS IN PLANT SCIENCE 2015. [PMID: 26442024 DOI: 10.5061/dryad.r9c12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Evolutionary radiations are prominent and pervasive across many plant lineages in diverse geographical and ecological settings; in neotropical rainforests there is growing evidence suggesting that a significant fraction of species richness is the result of recent radiations. Understanding the evolutionary trajectories and mechanisms underlying these radiations demands much greater phylogenetic resolution than is currently available for these groups. The neotropical tree genus Inga (Leguminosae) is a good example, with ~300 extant species and a crown age of 2-10 MY, yet over 6 kb of plastid and nuclear DNA sequence data gives only poor phylogenetic resolution among species. Here we explore the use of larger-scale nuclear gene data obtained though targeted enrichment to increase phylogenetic resolution within Inga. Transcriptome data from three Inga species were used to select 264 nuclear loci for targeted enrichment and sequencing. Following quality control to remove probable paralogs from these sequence data, the final dataset comprised 259,313 bases from 194 loci for 24 accessions representing 22 Inga species and an outgroup (Zygia). Bayesian phylogenies reconstructed using either all loci concatenated or a gene-tree/species-tree approach yielded highly resolved phylogenies. We used coalescent approaches to show that the same targeted enrichment data also have significant power to discriminate among alternative within-species population histories within the widespread species I. umbellifera. In either application, targeted enrichment simplifies the informatics challenge of identifying orthologous loci associated with de novo genome sequencing. We conclude that targeted enrichment provides the large volumes of phylogenetically-informative sequence data required to resolve relationships within recent plant species radiations, both at the species level and for within-species phylogeographic studies.
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Affiliation(s)
- James A Nicholls
- Ashworth Labs, Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh Edinburgh, UK ; Royal Botanic Garden Edinburgh Edinburgh, UK
| | | | - Erik J M Koenen
- Institute of Systematic Botany, University of Zurich Zürich, Switzerland
| | - Colin E Hughes
- Institute of Systematic Botany, University of Zurich Zürich, Switzerland
| | - Jack Hearn
- Ashworth Labs, Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh Edinburgh, UK
| | - Lynsey Bunnefeld
- Ashworth Labs, Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh Edinburgh, UK
| | - Kyle G Dexter
- School of Geosciences, University of Edinburgh Edinburgh, UK
| | - Graham N Stone
- Ashworth Labs, Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh Edinburgh, UK
| | - Catherine A Kidner
- Royal Botanic Garden Edinburgh Edinburgh, UK ; Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh Edinburgh, UK
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Transcriptome and complexity-reduced, DNA-based identification of intraspecies single-nucleotide polymorphisms in the polyploid Gossypium hirsutum L. G3-GENES GENOMES GENETICS 2014; 4:1893-905. [PMID: 25106949 PMCID: PMC4199696 DOI: 10.1534/g3.114.012542] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Varietal single nucleotide polymorphisms (SNPs) are the differences within one of the two subgenomes between different tetraploid cotton varieties and have not been practically used in cotton genetics and breeding because they are difficult to identify due to low genetic diversity and very high sequence identity between homeologous genes in cotton. We have used transcriptome and restriction site-associated DNA sequencing to identify varietal SNPs among 18 G. hirsutum varieties based on the rationale that varietal SNPs can be more confidently called when flanked by subgenome-specific SNPs. Using transcriptome data, we successfully identified 37,413 varietal SNPs and, of these, 22,121 did not have an additional varietal SNP within their 20-bp flanking regions so can be used in most SNP genotyping assays. From restriction site-associated DNA sequencing data, we identified an additional 3090 varietal SNPs between two of the varieties. Of the 1583 successful SNP assays achieved using different genotyping platforms, 1363 were verified. Many of the SNPs behaved as dominant markers because of coamplification from homeologous loci, but the number of SNPs acting as codominant markers increased when one or more subgenome-specific SNP(s) were incorporated in their assay primers, giving them greater utility for breeding applications. A G. hirsutum genetic map with 1244 SNP markers was constructed covering 5557.42 centiMorgan and used to map qualitative and quantitative traits. This collection of G. hirsutum varietal SNPs complements existing intra-specific SNPs and provides the cotton community with a valuable marker resource applicable to genetic analyses and breeding programs.
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18
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Mandel JR, Dikow RB, Funk VA, Masalia RR, Staton SE, Kozik A, Michelmore RW, Rieseberg LH, Burke JM. A target enrichment method for gathering phylogenetic information from hundreds of loci: An example from the Compositae. APPLICATIONS IN PLANT SCIENCES 2014; 2:apps.1300085. [PMID: 25202605 PMCID: PMC4103609 DOI: 10.3732/apps.1300085] [Citation(s) in RCA: 105] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Accepted: 01/13/2014] [Indexed: 05/18/2023]
Abstract
UNLABELLED PREMISE OF THE STUDY The Compositae (Asteraceae) are a large and diverse family of plants, and the most comprehensive phylogeny to date is a meta-tree based on 10 chloroplast loci that has several major unresolved nodes. We describe the development of an approach that enables the rapid sequencing of large numbers of orthologous nuclear loci to facilitate efficient phylogenomic analyses. • METHODS AND RESULTS We designed a set of sequence capture probes that target conserved orthologous sequences in the Compositae. We also developed a bioinformatic and phylogenetic workflow for processing and analyzing the resulting data. Application of our approach to 15 species from across the Compositae resulted in the production of phylogenetically informative sequence data from 763 loci and the successful reconstruction of known phylogenetic relationships across the family. • CONCLUSIONS These methods should be of great use to members of the broader Compositae community, and the general approach should also be of use to researchers studying other families.
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Affiliation(s)
- Jennifer R. Mandel
- Department of Biological Sciences, University of Memphis, Memphis, Tennessee 38152 USA
| | - Rebecca B. Dikow
- Center for Conservation and Evolutionary Genetics, National Zoological Park and Division of Mammals, National Museum of Natural History, Smithsonian Institution, Washington, D.C. 20560 USA
| | - Vicki A. Funk
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, D.C. 20560 USA
| | - Rishi R. Masalia
- Department of Plant Biology, Miller Plant Sciences, University of Georgia, Athens, Georgia 30602 USA
| | - S. Evan Staton
- Department of Genetics, Davison Life Sciences Building, University of Georgia, Athens, Georgia 30602 USA
| | - Alex Kozik
- The Genome Center, University of California, Davis, California 95616 USA
| | | | - Loren H. Rieseberg
- Department of Botany, University of British Columbia, Vancouver, British Columbia V6T 1Z4 Canada
| | - John M. Burke
- Department of Plant Biology, Miller Plant Sciences, University of Georgia, Athens, Georgia 30602 USA
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19
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Mandel JR, Dikow RB, Funk VA, Masalia RR, Staton SE, Kozik A, Michelmore RW, Rieseberg LH, Burke JM. A target enrichment method for gathering phylogenetic information from hundreds of loci: An example from the Compositae. APPLICATIONS IN PLANT SCIENCES 2014. [PMID: 25202605 DOI: 10.5061/dryad.gr93t] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
PREMISE OF THE STUDY The Compositae (Asteraceae) are a large and diverse family of plants, and the most comprehensive phylogeny to date is a meta-tree based on 10 chloroplast loci that has several major unresolved nodes. We describe the development of an approach that enables the rapid sequencing of large numbers of orthologous nuclear loci to facilitate efficient phylogenomic analyses. • METHODS AND RESULTS We designed a set of sequence capture probes that target conserved orthologous sequences in the Compositae. We also developed a bioinformatic and phylogenetic workflow for processing and analyzing the resulting data. Application of our approach to 15 species from across the Compositae resulted in the production of phylogenetically informative sequence data from 763 loci and the successful reconstruction of known phylogenetic relationships across the family. • CONCLUSIONS These methods should be of great use to members of the broader Compositae community, and the general approach should also be of use to researchers studying other families.
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Affiliation(s)
- Jennifer R Mandel
- Department of Biological Sciences, University of Memphis, Memphis, Tennessee 38152 USA
| | - Rebecca B Dikow
- Center for Conservation and Evolutionary Genetics, National Zoological Park and Division of Mammals, National Museum of Natural History, Smithsonian Institution, Washington, D.C. 20560 USA
| | - Vicki A Funk
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, D.C. 20560 USA
| | - Rishi R Masalia
- Department of Plant Biology, Miller Plant Sciences, University of Georgia, Athens, Georgia 30602 USA
| | - S Evan Staton
- Department of Genetics, Davison Life Sciences Building, University of Georgia, Athens, Georgia 30602 USA
| | - Alex Kozik
- The Genome Center, University of California, Davis, California 95616 USA
| | | | - Loren H Rieseberg
- Department of Botany, University of British Columbia, Vancouver, British Columbia V6T 1Z4 Canada
| | - John M Burke
- Department of Plant Biology, Miller Plant Sciences, University of Georgia, Athens, Georgia 30602 USA
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20
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Clarke WE, Parkin IA, Gajardo HA, Gerhardt DJ, Higgins E, Sidebottom C, Sharpe AG, Snowdon RJ, Federico ML, Iniguez-Luy FL. Genomic DNA enrichment using sequence capture microarrays: a novel approach to discover sequence nucleotide polymorphisms (SNP) in Brassica napus L. PLoS One 2013; 8:e81992. [PMID: 24312619 PMCID: PMC3849492 DOI: 10.1371/journal.pone.0081992] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2013] [Accepted: 10/20/2013] [Indexed: 12/24/2022] Open
Abstract
Targeted genomic selection methodologies, or sequence capture, allow for DNA enrichment and large-scale resequencing and characterization of natural genetic variation in species with complex genomes, such as rapeseed canola (Brassica napus L., AACC, 2n=38). The main goal of this project was to combine sequence capture with next generation sequencing (NGS) to discover single nucleotide polymorphisms (SNPs) in specific areas of the B. napus genome historically associated (via quantitative trait loci –QTL– analysis) to traits of agronomical and nutritional importance. A 2.1 million feature sequence capture platform was designed to interrogate DNA sequence variation across 47 specific genomic regions, representing 51.2 Mb of the Brassica A and C genomes, in ten diverse rapeseed genotypes. All ten genotypes were sequenced using the 454 Life Sciences chemistry and to assess the effect of increased sequence depth, two genotypes were also sequenced using Illumina HiSeq chemistry. As a result, 589,367 potentially useful SNPs were identified. Analysis of sequence coverage indicated a four-fold increased representation of target regions, with 57% of the filtered SNPs falling within these regions. Sixty percent of discovered SNPs corresponded to transitions while 40% were transversions. Interestingly, fifty eight percent of the SNPs were found in genic regions while 42% were found in intergenic regions. Further, a high percentage of genic SNPs was found in exons (65% and 64% for the A and C genomes, respectively). Two different genotyping assays were used to validate the discovered SNPs. Validation rates ranged from 61.5% to 84% of tested SNPs, underpinning the effectiveness of this SNP discovery approach. Most importantly, the discovered SNPs were associated with agronomically important regions of the B. napus genome generating a novel data resource for research and breeding this crop species.
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Affiliation(s)
- Wayne E. Clarke
- Saskatoon Research Centre, Agriculture and Agri-Food Canada, Saskatoon, Saskatchewan, Canada
| | - Isobel A. Parkin
- Saskatoon Research Centre, Agriculture and Agri-Food Canada, Saskatoon, Saskatchewan, Canada
| | - Humberto A. Gajardo
- Genomics and Bioinformatics Unit, Agriaquaculture Nutritional Genomic Center (CGNA), Temuco, Louisiana, United States of America Araucanía, Chile
| | | | - Erin Higgins
- Saskatoon Research Centre, Agriculture and Agri-Food Canada, Saskatoon, Saskatchewan, Canada
| | - Christine Sidebottom
- Plant Biotechnology Institute, National Research Council Canada, Saskatoon, Saskatchewan, Canada
| | - Andrew G. Sharpe
- Plant Biotechnology Institute, National Research Council Canada, Saskatoon, Saskatchewan, Canada
| | - Rod J. Snowdon
- Department of Plant Breeding, Justus Liebig University, Giessen, Germany
| | - Maria L. Federico
- Genomics and Bioinformatics Unit, Agriaquaculture Nutritional Genomic Center (CGNA), Temuco, Louisiana, United States of America Araucanía, Chile
| | - Federico L. Iniguez-Luy
- Genomics and Bioinformatics Unit, Agriaquaculture Nutritional Genomic Center (CGNA), Temuco, Louisiana, United States of America Araucanía, Chile
- * E-mail:
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21
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Dufresne F, Stift M, Vergilino R, Mable BK. Recent progress and challenges in population genetics of polyploid organisms: an overview of current state-of-the-art molecular and statistical tools. Mol Ecol 2013; 23:40-69. [DOI: 10.1111/mec.12581] [Citation(s) in RCA: 248] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2013] [Revised: 10/29/2013] [Accepted: 10/30/2013] [Indexed: 12/19/2022]
Affiliation(s)
- France Dufresne
- Département de Biologie; Université du Québec à Rimouski; Québec QC Canada G5L 3A1
| | - Marc Stift
- Department of Biology; University of Konstanz; Konstanz D 78457 Germany
| | - Roland Vergilino
- Department of Integrative Biology; University of Guelph; Guelph ON Canada N1G 2W1
| | - Barbara K. Mable
- Institute of Biodiversity; Animal Health and Comparative Medicine; College of Medical, Veterinary and Life Sciences; University of Glasgow; Glasgow UK
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22
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Targeted sequence capture provides insight into genome structure and genetics of male sterility in a gynodioecious diploid strawberry, Fragaria vesca ssp. bracteata (Rosaceae). G3-GENES GENOMES GENETICS 2013; 3:1341-51. [PMID: 23749450 PMCID: PMC3737174 DOI: 10.1534/g3.113.006288] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Gynodioecy is a sexual system wherein females coexist with hermaphrodites. It is of interest not only because male-sterile plants are advantageous in plant breeding but also because it can be a crucial step in the evolutionary transition to entirely separate sexes (dioecy) from a hermaphroditic ancestor. The gynodioecious diploid wild strawberry, Fragaria vesca ssp. bracteata (Rosaceae), is a member of a clade with both dioecious and cultivated species, making it an ideal model in which to study the genetics of male sterility. To create a genetic map of F. v. ssp. bracteata, we identified informative polymorphisms from genomic sequencing (3−5x coverage) of two outbred plants from the same population. Using targeted enrichment, we sequenced 200 bp surrounding each of 6575 polymorphisms in 48 F1 offspring, yielding genotypes at 98% of targeted sites with mean coverage >100x, plus more than 600-kb high-coverage nontargeted sequence. With the resulting linkage map of 7802 stringently filtered markers (5417 targeted), we assessed recombination rates and genomic incongruities. Consistent with past work in strawberries, male sterility is dominant, segregates 1:1, and maps to a single location in the female. Further mapping an additional 55 offspring places male sterility in a gene-dense, 338-kb region of chromosome 4. The region is not syntenic with the sex-determining regions in the closely related octoploids, F. chiloensis and F. virginiana, suggesting either independent origins or translocation. The 57 genes in this region do not include protein families known to control male sterility and thus suggest alternate mechanisms for the suppression of male function.
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23
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Abstract
The emergence of new sequencing technologies has provided fast and cost-efficient strategies for high-resolution mapping of complex genomes. Although these approaches hold great promise to accelerate genome analysis, their application in studying genetic variation in wheat has been hindered by the complexity of its polyploid genome. Here, we applied the next-generation sequencing of a wheat doubled-haploid mapping population for high-resolution gene mapping and tested its utility for ordering shotgun sequence contigs of a flow-sorted wheat chromosome. A bioinformatical pipeline was developed for reliable variant analysis of sequence data generated for polyploid wheat mapping populations. The results of variant mapping were consistent with the results obtained using the wheat 9000 SNP iSelect assay. A reference map of the wheat genome integrating 2740 gene-associated single-nucleotide polymorphisms from the wheat iSelect assay, 1351 diversity array technology, 118 simple sequence repeat/sequence-tagged sites, and 416,856 genotyping-by-sequencing markers was developed. By analyzing the sequenced megabase-size regions of the wheat genome we showed that mapped markers are located within 40-100 kb from genes providing a possibility for high-resolution mapping at the level of a single gene. In our population, gene loci controlling a seed color phenotype cosegregated with 2459 markers including one that was located within the red seed color gene. We demonstrate that the high-density reference map presented here is a useful resource for gene mapping and linking physical and genetic maps of the wheat genome.
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del Viso F, Bhattacharya D, Kong Y, Gilchrist MJ, Khokha MK. Exon capture and bulk segregant analysis: rapid discovery of causative mutations using high-throughput sequencing. BMC Genomics 2012; 13:649. [PMID: 23171430 PMCID: PMC3526394 DOI: 10.1186/1471-2164-13-649] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2012] [Accepted: 11/15/2012] [Indexed: 11/21/2022] Open
Abstract
Background Exome sequencing has transformed human genetic analysis and may do the same for other vertebrate model systems. However, a major challenge is sifting through the large number of sequence variants to identify the causative mutation for a given phenotype. In models like Xenopus tropicalis, an incomplete and occasionally incorrect genome assembly compounds this problem. To facilitate cloning of X. tropicalis mutants identified in forward genetic screens, we sought to combine bulk segregant analysis and exome sequencing into a single step. Results Here we report the first use of exon capture sequencing to identify mutations in a non-mammalian, vertebrate model. We demonstrate that bulk segregant analysis coupled with exon capture sequencing is not only able to identify causative mutations but can also generate linkage information, facilitate the assembly of scaffolds, identify misassembles, and discover thousands of SNPs for fine mapping. Conclusion Exon capture sequencing and bulk segregant analysis is a rapid, inexpensive method to clone mutants identified in forward genetic screens. With sufficient meioses, this method can be generalized to any model system with a genome assembly, polished or unpolished, and in the latter case, it also provides many critical genomic resources.
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Affiliation(s)
- Florencia del Viso
- Department of Pediatrics and Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA
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