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Kummeling GJM, Baas AF, Harakalova M, van der Smagt JJ, Asselbergs FW. Cardiovascular genetics: technological advancements and applicability for dilated cardiomyopathy. Neth Heart J 2015; 23:356-62. [PMID: 26031632 PMCID: PMC4497982 DOI: 10.1007/s12471-015-0700-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Genetics plays an important role in the pathophysiology of cardiovascular diseases, and is increasingly being integrated into clinical practice. Since 2008, both capacity and cost-efficiency of mutation screening of DNA have been increased magnificently due to the technological advancement obtained by next-generation sequencing. Hence, the discovery rate of genetic defects in cardiovascular genetics has grown rapidly and the financial threshold for gene diagnostics has been lowered, making large-scale DNA sequencing broadly accessible. In this review, the genetic variants, mutations and inheritance models are briefly introduced, after which an overview is provided of current clinical and technological applications in gene diagnostics and research for cardiovascular disease and in particular, dilated cardiomyopathy. Finally, a reflection on the future perspectives in cardiogenetics is given.
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Affiliation(s)
- G J M Kummeling
- Department of Cardiology, Division Heart and Lungs, University Medical Center Utrecht, Room E03.511, PO Box 85500, 3508 GA, Utrecht, The Netherlands,
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Behzad H, Gojobori T, Mineta K. Challenges and opportunities of airborne metagenomics. Genome Biol Evol 2015; 7:1216-26. [PMID: 25953766 PMCID: PMC4453059 DOI: 10.1093/gbe/evv064] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/06/2015] [Indexed: 01/09/2023] Open
Abstract
Recent metagenomic studies of environments, such as marine and soil, have significantly enhanced our understanding of the diverse microbial communities living in these habitats and their essential roles in sustaining vast ecosystems. The increase in the number of publications related to soil and marine metagenomics is in sharp contrast to those of air, yet airborne microbes are thought to have significant impacts on many aspects of our lives from their potential roles in atmospheric events such as cloud formation, precipitation, and atmospheric chemistry to their major impact on human health. In this review, we will discuss the current progress in airborne metagenomics, with a special focus on exploring the challenges and opportunities of undertaking such studies. The main challenges of conducting metagenomic studies of airborne microbes are as follows: 1) Low density of microorganisms in the air, 2) efficient retrieval of microorganisms from the air, 3) variability in airborne microbial community composition, 4) the lack of standardized protocols and methodologies, and 5) DNA sequencing and bioinformatics-related challenges. Overcoming these challenges could provide the groundwork for comprehensive analysis of airborne microbes and their potential impact on the atmosphere, global climate, and our health. Metagenomic studies offer a unique opportunity to examine viral and bacterial diversity in the air and monitor their spread locally or across the globe, including threats from pathogenic microorganisms. Airborne metagenomic studies could also lead to discoveries of novel genes and metabolic pathways relevant to meteorological and industrial applications, environmental bioremediation, and biogeochemical cycles.
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Affiliation(s)
- Hayedeh Behzad
- Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
| | - Takashi Gojobori
- Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
| | - Katsuhiko Mineta
- Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia Computer, Electrical, and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
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Tsukagoshi H, Suzuki T, Nishikawa K, Agarie S, Ishiguro S, Higashiyama T. RNA-seq analysis of the response of the halophyte, Mesembryanthemum crystallinum (ice plant) to high salinity. PLoS One 2015; 10:e0118339. [PMID: 25706745 PMCID: PMC4338230 DOI: 10.1371/journal.pone.0118339] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Accepted: 01/14/2015] [Indexed: 01/08/2023] Open
Abstract
Understanding the molecular mechanisms that convey salt tolerance in plants is a crucial issue for increasing crop yield. The ice plant (Mesembryanthemum crystallinum) is a halophyte that is capable of growing under high salt conditions. For example, the roots of ice plant seedlings continue to grow in 140 mM NaCl, a salt concentration that completely inhibits Arabidopsis thaliana root growth. Identifying the molecular mechanisms responsible for this high level of salt tolerance in a halophyte has the potential of revealing tolerance mechanisms that have been evolutionarily successful. In the present study, deep sequencing (RNAseq) was used to examine gene expression in ice plant roots treated with various concentrations of NaCl. Sequencing resulted in the identification of 53,516 contigs, 10,818 of which were orthologs of Arabidopsis genes. In addition to the expression analysis, a web-based ice plant database was constructed that allows broad public access to the data. The results obtained from an analysis of the RNAseq data were confirmed by RT-qPCR. Novel patterns of gene expression in response to high salinity within 24 hours were identified in the ice plant when the RNAseq data from the ice plant was compared to gene expression data obtained from Arabidopsis plants exposed to high salt. Although ABA responsive genes and a sodium transporter protein (HKT1), are up-regulated and down-regulated respectively in both Arabidopsis and the ice plant; peroxidase genes exhibit opposite responses. The results of this study provide an important first step towards analyzing environmental tolerance mechanisms in a non-model organism and provide a useful dataset for predicting novel gene functions.
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Affiliation(s)
- Hironaka Tsukagoshi
- The Center for Gene Research, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, Japan
- Program for leading graduate schools, PhD Professional: Gateway to Success in Frontier Asia, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, Japan
- PRESTO, JST, Honcho, Kawaguchi, Saitama, Japan
| | - Takamasa Suzuki
- Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, Japan
- JST, ERATO, Higashiyama Live-Holonics Project, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, Japan
| | - Kouki Nishikawa
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, Japan
| | - Sakae Agarie
- Faculty of Agriculture, Kagawa university, Saiwaicho 1-1, Takamatsu, Kagawa, Japan
| | - Sumie Ishiguro
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, Japan
| | - Tetsuya Higashiyama
- Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, Japan
- JST, ERATO, Higashiyama Live-Holonics Project, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, Japan
- WPI-ITbM, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, Japan
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Gallus S, Hallström BM, Kumar V, Dodt WG, Janke A, Schumann GG, Nilsson MA. Evolutionary histories of transposable elements in the genome of the largest living marsupial carnivore, the Tasmanian devil. Mol Biol Evol 2015; 32:1268-83. [PMID: 25633377 PMCID: PMC4408412 DOI: 10.1093/molbev/msv017] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The largest living carnivorous marsupial, the Tasmanian devil (Sarcophilus harrisii), is the sole survivor of a lineage originating about 12 Ma. We set out to investigate the spectrum of transposable elements found in the Tasmanian devil genome, the first high-coverage genome of an Australian marsupial. Marsupial genomes have been shown to have the highest amount of transposable elements among vertebrates. We analyzed the horizontally transmitted DNA transposons OC1 and hAT-1_MEu in the Tasmanian devil genome. OC1 is present in all carnivorous marsupials, while having a very limited distribution among the remaining Australian marsupial orders. In contrast, hAT-1_MEu is present in all Australian marsupial orders, and has so far only been identified in a few placental mammals. We screened 158 introns for phylogenetically informative retrotransposons in the order Dasyuromorphia, and found that the youngest SINE (Short INterspersed Element), WSINE1, is no longer active in the subfamily Dasyuridae. The lack of detectable WSINE1 activity in this group may be due to a retrotransposon inactivation event approximately 30 Ma. We found that the Tasmanian devil genome contains a relatively low number of continuous full-length LINE-1 (Long INterspersed Element 1, L1) retrotransposons compared with the opossum genome. Furthermore, all L1 elements in the Tasmanian devil appeared to be nonfunctional. Hidden Markov Model approaches suggested that other potential sources of functional reverse transcriptase are absent from the genome. We discuss the issues associated with assembling long, highly similar L1 copies from short read Illumina data and describe how assembly artifacts can potentially lead to erroneous conclusions.
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Affiliation(s)
- Susanne Gallus
- Division of Medical Biotechnology, Paul Ehrlich Institute, Langen, Germany LOEWE Biodiversity and Climate Research Centre (BiK-F), Senckenberg Gesellschaft für Naturforschung, Frankfurt am Main, Germany
| | - Björn M Hallström
- Division of Medical Biotechnology, Paul Ehrlich Institute, Langen, Germany LOEWE Biodiversity and Climate Research Centre (BiK-F), Senckenberg Gesellschaft für Naturforschung, Frankfurt am Main, Germany Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Vikas Kumar
- LOEWE Biodiversity and Climate Research Centre (BiK-F), Senckenberg Gesellschaft für Naturforschung, Frankfurt am Main, Germany
| | - William G Dodt
- LOEWE Biodiversity and Climate Research Centre (BiK-F), Senckenberg Gesellschaft für Naturforschung, Frankfurt am Main, Germany School of Earth, Environmental and Biological Sciences, Queensland University of Technology, Brisbane, Qld, Australia
| | - Axel Janke
- LOEWE Biodiversity and Climate Research Centre (BiK-F), Senckenberg Gesellschaft für Naturforschung, Frankfurt am Main, Germany Institute for Ecology, Evolution & Diversity, Biologicum, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Gerald G Schumann
- Division of Medical Biotechnology, Paul Ehrlich Institute, Langen, Germany
| | - Maria A Nilsson
- LOEWE Biodiversity and Climate Research Centre (BiK-F), Senckenberg Gesellschaft für Naturforschung, Frankfurt am Main, Germany
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Escalante AE, Jardón Barbolla L, Ramírez-Barahona S, Eguiarte LE. The study of biodiversity in the era of massive sequencing. REV MEX BIODIVERS 2014. [DOI: 10.7550/rmb.43498] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
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Karam MJ, Lefèvre F, Dagher-Kharrat MB, Pinosio S, Vendramin G. Genomic exploration and molecular marker development in a large and complex conifer genome using RADseq and mRNAseq. Mol Ecol Resour 2014; 15:601-12. [DOI: 10.1111/1755-0998.12329] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Revised: 08/30/2014] [Accepted: 09/05/2014] [Indexed: 01/05/2023]
Affiliation(s)
- M.-J. Karam
- INRA; UR 629 Ecologie des Forêts Méditerranéennes; URFM; Avignon France
| | - F. Lefèvre
- INRA; UR 629 Ecologie des Forêts Méditerranéennes; URFM; Avignon France
| | - M. Bou Dagher-Kharrat
- Laboratoire Caractérisation Génomique des Plantes; Département Sciences de la Vie et de la Terre; Faculté des Sciences; Campus Sciences et Technologies; Université Saint-Joseph; Mar Roukos Mkalles Lebanon
| | - S. Pinosio
- Istituto di Genomica Applicata (IGA); Udine Italy
- Institute of Biosciences and Bioresources; National Research Council; Florence Italy
| | - G.G. Vendramin
- Institute of Biosciences and Bioresources; National Research Council; Florence Italy
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Validation and assessment of variant calling pipelines for next-generation sequencing. Hum Genomics 2014; 8:14. [PMID: 25078893 PMCID: PMC4129436 DOI: 10.1186/1479-7364-8-14] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Accepted: 07/15/2014] [Indexed: 02/07/2023] Open
Abstract
Background The processing and analysis of the large scale data generated by next-generation sequencing (NGS) experiments is challenging and is a burgeoning area of new methods development. Several new bioinformatics tools have been developed for calling sequence variants from NGS data. Here, we validate the variant calling of these tools and compare their relative accuracy to determine which data processing pipeline is optimal. Results We developed a unified pipeline for processing NGS data that encompasses four modules: mapping, filtering, realignment and recalibration, and variant calling. We processed 130 subjects from an ongoing whole exome sequencing study through this pipeline. To evaluate the accuracy of each module, we conducted a series of comparisons between the single nucleotide variant (SNV) calls from the NGS data and either gold-standard Sanger sequencing on a total of 700 variants or array genotyping data on a total of 9,935 single-nucleotide polymorphisms. A head to head comparison showed that Genome Analysis Toolkit (GATK) provided more accurate calls than SAMtools (positive predictive value of 92.55% vs. 80.35%, respectively). Realignment of mapped reads and recalibration of base quality scores before SNV calling proved to be crucial to accurate variant calling. GATK HaplotypeCaller algorithm for variant calling outperformed the UnifiedGenotype algorithm. We also showed a relationship between mapping quality, read depth and allele balance, and SNV call accuracy. However, if best practices are used in data processing, then additional filtering based on these metrics provides little gains and accuracies of >99% are achievable. Conclusions Our findings will help to determine the best approach for processing NGS data to confidently call variants for downstream analyses. To enable others to implement and replicate our results, all of our codes are freely available at http://metamoodics.org/wes.
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Aguilar-Pontes MV, de Vries RP, Zhou M. (Post-)genomics approaches in fungal research. Brief Funct Genomics 2014; 13:424-39. [PMID: 25037051 DOI: 10.1093/bfgp/elu028] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
To date, hundreds of fungal genomes have been sequenced and many more are in progress. This wealth of genomic information has provided new directions to study fungal biodiversity. However, to further dissect and understand the complicated biological mechanisms involved in fungal life styles, functional studies beyond genomes are required. Thanks to the developments of current -omics techniques, it is possible to produce large amounts of fungal functional data in a high-throughput fashion (e.g. transcriptome, proteome, etc.). The increasing ease of creating -omics data has also created a major challenge for downstream data handling and analysis. Numerous databases, tools and software have been created to meet this challenge. Facing such a richness of techniques and information, hereby we provide a brief roadmap on current wet-lab and bioinformatics approaches to study functional genomics in fungi.
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Polimanti R, Iorio A, Piacentini S, Manfellotto D, Fuciarelli M. Human pharmacogenomic variation of antihypertensive drugs: from population genetics to personalized medicine. Pharmacogenomics 2014; 15:157-67. [DOI: 10.2217/pgs.13.231] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Aim: To investigate the human pharmacogenetic variation related to antihypertensive drugs, providing a survey of functional interpopulation differences in hypertension pharmacogenes. Materials & methods: The study was divided into two stages. In the first stage, we analyzed 1249 variants located in 57 hypertension pharmacogenes. This first-stage analysis confirmed that geographic origin strongly affects hypertension pharmacogenomic variation and that 31 pharmacogenes are geographically differentiated. In the second stage, we focused our attention on the ethnic-differentiated pharmacogenes, investigating 55,521 genetic variants. In silico analyses were performed to predict the effect of genetic variation. Results: Our analyses indicated functional interpopulation differences, suggesting insight into the mechanisms of antihypertensive drug response. Moreover, our data suggested that rare variants mainly determine the functionality of genes related to antihypertensive drugs. Conclusion: Our study provided important knowledge about the genetics of the antihypertensive drug response, suggesting that next-generation sequencing technologies may develop reliable pharmacogenetic tests for antihypertensive drugs. Original submitted 19 September 2013; Revision submitted 14 November 2013
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Affiliation(s)
- Renato Polimanti
- Department of Biology, University of Rome “Tor Vergata”, Via della Ricerca Scientifica 1, Rome, Italy
| | - Andrea Iorio
- Clinical Pathophysiology Center, AFaR – “San Giovanni Calibita” Fatebenefratelli Hospital, Isola Tiberina, Rome, Italy
| | - Sara Piacentini
- Department of Biology, University of Rome “Tor Vergata”, Via della Ricerca Scientifica 1, Rome, Italy
| | - Dario Manfellotto
- Clinical Pathophysiology Center, AFaR – “San Giovanni Calibita” Fatebenefratelli Hospital, Isola Tiberina, Rome, Italy
| | - Maria Fuciarelli
- Department of Biology, University of Rome “Tor Vergata”, Via della Ricerca Scientifica 1, Rome, Italy
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Abstract
The genomic revolution promises great advances in the search for useful biocatalysts. Function-based metagenomic approaches have identified several enzymes with properties that make them useful candidates for a variety of bioprocesses. As DNA sequencing costs continue to decline, the volume of genomic data, along with their corresponding predicted protein sequences, will continue to increase dramatically, necessitating new approaches to leverage this information for gene-based bioprospecting efforts. Additionally, as new functions are discovered and correlated with this sequence information, the knowledge of the often complex relationship between a protein's sequence and function will improve. This in turn will lead to better gene-based bioprospecting approaches and facilitate the tailoring of desired properties through protein engineering projects. In this chapter, we discuss a number of recent advances in bioprospecting within the context of the genomic age.
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Affiliation(s)
- Michael A Hicks
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Kristala L J Prather
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA; Synthetic Biology Engineering Research Center (SynBERC), Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.
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Rubinstein ND, Feldstein T, Shenkar N, Botero-Castro F, Griggio F, Mastrototaro F, Delsuc F, Douzery EJ, Gissi C, Huchon D. Deep sequencing of mixed total DNA without barcodes allows efficient assembly of highly plastic ascidian mitochondrial genomes. Genome Biol Evol 2013; 5:1185-99. [PMID: 23709623 PMCID: PMC3698926 DOI: 10.1093/gbe/evt081] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Ascidians or sea squirts form a diverse group within chordates, which includes a few thousand members of marine sessile filter-feeding animals. Their mitochondrial genomes are characterized by particularly high evolutionary rates and rampant gene rearrangements. This extreme variability complicates standard polymerase chain reaction (PCR) based techniques for molecular characterization studies, and consequently only a few complete Ascidian mitochondrial genome sequences are available. Using the standard PCR and Sanger sequencing approach, we produced the mitochondrial genome of Ascidiella aspersa only after a great effort. In contrast, we produced five additional mitogenomes (Botrylloides aff. leachii, Halocynthia spinosa, Polycarpa mytiligera, Pyura gangelion, and Rhodosoma turcicum) with a novel strategy, consisting in sequencing the pooled total DNA samples of these five species using one Illumina HiSeq 2000 flow cell lane. Each mitogenome was efficiently assembled in a single contig using de novo transcriptome assembly, as de novo genome assembly generally performed poorly for this task. Each of the new six mitogenomes presents a different and novel gene order, showing that no syntenic block has been conserved at the ordinal level (in Stolidobranchia and in Phlebobranchia). Phylogenetic analyses support the paraphyly of both Ascidiacea and Phlebobranchia, with Thaliacea nested inside Phlebobranchia, although the deepest nodes of the Phlebobranchia-Thaliacea clade are not well resolved. The strategy described here thus provides a cost-effective approach to obtain complete mitogenomes characterized by a highly plastic gene order and a fast nucleotide/amino acid substitution rate.
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Affiliation(s)
- Nimrod D. Rubinstein
- Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Israel
- Present address: Department of Molecular and Cellular Biology, Harvard University
| | - Tamar Feldstein
- Department of Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Israel
- The Steinhardt National Collections of Natural History Tel Aviv University, Ramat Aviv, Israel
| | - Noa Shenkar
- Department of Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Israel
| | - Fidel Botero-Castro
- Institut des Sciences de l'Evolution de Montpellier (ISEM), UMR 5554 - CNRS, Université Montpellier II, Montpellier, France
| | | | | | - Frédéric Delsuc
- Institut des Sciences de l'Evolution de Montpellier (ISEM), UMR 5554 - CNRS, Université Montpellier II, Montpellier, France
| | - Emmanuel J.P. Douzery
- Institut des Sciences de l'Evolution de Montpellier (ISEM), UMR 5554 - CNRS, Université Montpellier II, Montpellier, France
| | - Carmela Gissi
- Dip. di Bioscienze, Università degli Studi di Milano, Milano, Italy
- *Corresponding authors: E-mail: ;
| | - Dorothée Huchon
- Department of Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Israel
- *Corresponding authors: E-mail: ;
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Seok HS, Sim M, Lee D, Kim J. A clustering method for next-generation sequences of bacterial genomes through multiomics data mapping. Genes Genomics 2013. [DOI: 10.1007/s13258-013-0155-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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Veras AADO, de Sá PHCG, Azevedo V, Silva A, Ramos RTJ. AutoAssemblyD: a graphical user interface system for several genome assemblers. Bioinformation 2013; 9:840-1. [PMID: 24143057 PMCID: PMC3796888 DOI: 10.6026/97320630009840] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2013] [Accepted: 08/28/2013] [Indexed: 11/23/2022] Open
Abstract
UNLABELLED Next-generation sequencing technologies have increased the amount of biological data generated. Thus, bioinformatics has become important because new methods and algorithms are necessary to manipulate and process such data. However, certain challenges have emerged, such as genome assembly using short reads and high-throughput platforms. In this context, several algorithms have been developed, such as Velvet, Abyss, Euler-SR, Mira, Edna, Maq, SHRiMP, Newbler, ALLPATHS, Bowtie and BWA. However, most such assemblers do not have a graphical interface, which makes their use difficult for users without computing experience given the complexity of the assembler syntax. Thus, to make the operation of such assemblers accessible to users without a computing background, we developed AutoAssemblyD, which is a graphical tool for genome assembly submission and remote management by multiple assemblers through XML templates. AVAILABILITY AssemblyD is freely available at https://sourceforge.net/projects/autoassemblyd. It requires Sun jdk 6 or higher.
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Affiliation(s)
| | | | - Vasco Azevedo
- Institute of Biological Sciences, Federal University Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Artur Silva
- Institute of Biological Sciences, Federal University Pará, Belém, Pará, Brazil
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Bradnam KR, Fass JN, Alexandrov A, Baranay P, Bechner M, Birol I, Boisvert S, Chapman JA, Chapuis G, Chikhi R, Chitsaz H, Chou WC, Corbeil J, Del Fabbro C, Docking TR, Durbin R, Earl D, Emrich S, Fedotov P, Fonseca NA, Ganapathy G, Gibbs RA, Gnerre S, Godzaridis E, Goldstein S, Haimel M, Hall G, Haussler D, Hiatt JB, Ho IY, Howard J, Hunt M, Jackman SD, Jaffe DB, Jarvis ED, Jiang H, Kazakov S, Kersey PJ, Kitzman JO, Knight JR, Koren S, Lam TW, Lavenier D, Laviolette F, Li Y, Li Z, Liu B, Liu Y, Luo R, Maccallum I, Macmanes MD, Maillet N, Melnikov S, Naquin D, Ning Z, Otto TD, Paten B, Paulo OS, Phillippy AM, Pina-Martins F, Place M, Przybylski D, Qin X, Qu C, Ribeiro FJ, Richards S, Rokhsar DS, Ruby JG, Scalabrin S, Schatz MC, Schwartz DC, Sergushichev A, Sharpe T, Shaw TI, Shendure J, Shi Y, Simpson JT, Song H, Tsarev F, Vezzi F, Vicedomini R, Vieira BM, Wang J, Worley KC, Yin S, Yiu SM, Yuan J, Zhang G, Zhang H, Zhou S, Korf IF. Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species. Gigascience 2013; 2:10. [PMID: 23870653 PMCID: PMC3844414 DOI: 10.1186/2047-217x-2-10] [Citation(s) in RCA: 420] [Impact Index Per Article: 38.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Accepted: 07/15/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The process of generating raw genome sequence data continues to become cheaper, faster, and more accurate. However, assembly of such data into high-quality, finished genome sequences remains challenging. Many genome assembly tools are available, but they differ greatly in terms of their performance (speed, scalability, hardware requirements, acceptance of newer read technologies) and in their final output (composition of assembled sequence). More importantly, it remains largely unclear how to best assess the quality of assembled genome sequences. The Assemblathon competitions are intended to assess current state-of-the-art methods in genome assembly. RESULTS In Assemblathon 2, we provided a variety of sequence data to be assembled for three vertebrate species (a bird, a fish, and snake). This resulted in a total of 43 submitted assemblies from 21 participating teams. We evaluated these assemblies using a combination of optical map data, Fosmid sequences, and several statistical methods. From over 100 different metrics, we chose ten key measures by which to assess the overall quality of the assemblies. CONCLUSIONS Many current genome assemblers produced useful assemblies, containing a significant representation of their genes and overall genome structure. However, the high degree of variability between the entries suggests that there is still much room for improvement in the field of genome assembly and that approaches which work well in assembling the genome of one species may not necessarily work well for another.
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Kenny NJ, Quah S, Holland PWH, Tobe SS, Hui JHL. How are comparative genomics and the study of microRNAs changing our views on arthropod endocrinology and adaptations to the environment? Gen Comp Endocrinol 2013; 188:16-22. [PMID: 23480873 DOI: 10.1016/j.ygcen.2013.02.013] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/17/2012] [Accepted: 02/09/2013] [Indexed: 01/01/2023]
Abstract
As the last few decades of work has shown, precise regulation of biosynthesis and release of arthropod hormones is essential to cope with environmental stresses and challenges. In crustaceans and insects, the sesquiterpenoids methyl farnesoate (MF), farnesoic acid (FA) and juvenile hormone (JH) regulate many developmental, physiological, and reproductive processes. In this review, we discuss how comparative genomics has and will impact our views on arthropod endocrinology. We will also highlight the current knowledge of regulation of genes involved in arthropod hormone biosynthesis by microRNAs, and describe the potential insights into arthropod endocrinology, evolution, and adaptation that are likely to come from the study of microRNAs.
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Affiliation(s)
- Nathan J Kenny
- Department of Zoology, University of Oxford, South Parks Road, OX1 3PS, UK
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Naito K, Kaga A, Tomooka N, Kawase M. De novo assembly of the complete organelle genome sequences of azuki bean (Vigna angularis) using next-generation sequencers. BREEDING SCIENCE 2013; 63:176-82. [PMID: 23853512 PMCID: PMC3688379 DOI: 10.1270/jsbbs.63.176] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2012] [Accepted: 02/05/2013] [Indexed: 05/09/2023]
Abstract
Since chloroplasts and mitochondria are maternally inherited and have unique features in evolution, DNA sequences of those organelle genomes have been broadly used in phylogenetic studies. Thanks to recent progress in next-generation sequencer (NGS) technology, whole-genome sequencing can be easily performed. Here, using NGS data generated by Roche GS Titanium and Illumina Hiseq 2000, we performed a hybrid assembly of organelle genome sequences of Vigna angularis (azuki bean). Both the mitochondrial genome (mtDNA) and the chloroplast genome (cpDNA) of V. angularis have very similar size and gene content to those of V. radiata (mungbean). However, in structure, mtDNA sequences have undergone many recombination events after divergence from the common ancestor of V. angularis and V. radiata, whereas cpDNAs are almost identical between the two. The stability of cpDNAs and the variability of mtDNAs was further confirmed by comparative analysis of Vigna organelles with model plants Lotus japonicus and Arabidopsis thaliana.
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Watson SP, Lowe GC, Lordkipanidzé M, Morgan NV. Genotyping and phenotyping of platelet function disorders. J Thromb Haemost 2013; 11 Suppl 1:351-63. [PMID: 23516995 DOI: 10.1111/jth.12199] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The majority of patients with platelet function disorders (PFDs) have normal platelet counts and mild day-to-day bleeding symptoms, but are at risk of major hemorrhage at times of trauma, surgery, or childbirth. This group is challenging to investigate, because the assays are often time-intensive and labour-intensive, and interpretation is difficult, especially in patients with mild disorders. In addition, interuser variability in performance of the assays, including the currently accepted gold standard, light transmission aggregometry, makes the results difficult to compare between laboratories. Furthermore, a similar pattern of mucocutaneous bleeding is seen in disorders in other components of the hemostatic pathway, including type 1 von Willebrand disease (VWD). We have undertaken an extensive investigation of patients with clinically diagnosed excessive bleeding, using a genotyping and platelet phenotyping approach based on lumi-aggregometry, and other specialist tests of platelet function, in combination with Sanger and next-generation sequencing (NGS). We found a functional defect in ~ 60% of patients, the majority being associated with feedback pathways of platelet activation. Function-disrupting mutations were identified in known and novel genes, and coinheritance with other genetic disorders of hemostasis, including type 1 VWD, was shown. A significant number of mutations are heterozygous and unlikely to cause extensive bleeding in isolation, consistent with incomplete penetrance of inheritance of bleeding disorders and a multifactorial etiology for excessive bleeding in many patients. Mucocutaneous bleeding is a complex trait, and this has important implications for NGS in the assessment of a PFD.
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Affiliation(s)
- S P Watson
- Centre for Cardiovascular Sciences, Institute of Biomedical Research, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK.
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Champagne A, Boutry M. Proteomics of nonmodel plant species. Proteomics 2013; 13:663-73. [PMID: 23125178 DOI: 10.1002/pmic.201200312] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2012] [Revised: 10/17/2012] [Accepted: 10/22/2012] [Indexed: 01/10/2023]
Abstract
Until recently, large scale proteomic investigations in the plant field have only been possible for a few model species for which the whole genome sequence had been fully determined. In contrast, for many other species with a strong economic interest as sources of human food and animal feed, as well as industrial and pharmacological molecules, little was known about their genome sequence and identifying the proteome in these species was still considered challenging. However, progress has been made as a result of several recent advances in proteomics tools, e.g. in MS technology and data search programs, and the increasing availability of genomic and cDNA sequences from various species. Moreover, next-generation sequencing technologies now make it possible to rapidly determine, at a reasonable cost, the genome or RNA sequence of species not currently considered as models, thus considerably expanding the plant sequence databases. This review will show how these advances make it possible to identify a large set of proteins, even for species for which few sequences are currently available.
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Affiliation(s)
- Antoine Champagne
- Institut des Sciences de la Vie, Université catholique de Louvain, Croix du Sud 4-15, Louvain-la-Neuve, Belgium
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