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Yu X, Jiang W, Shi Y, Ye H, Lin J. Applications of sequencing technology in clinical microbial infection. J Cell Mol Med 2019; 23:7143-7150. [PMID: 31475453 PMCID: PMC6815769 DOI: 10.1111/jcmm.14624] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 07/25/2019] [Indexed: 12/29/2022] Open
Abstract
Infectious diseases are a type of disease caused by pathogenic microorganisms. Although the discovery of antibiotics changed the treatment of infectious diseases and reduced the mortality of bacterial infections, resistant bacterial strains have emerged. Anti‐infective therapy based on aetiological evidence is the gold standard for clinical treatment, but the time lag and low positive culture rate of traditional methods of pathogen diagnosis leads to relative difficulty in obtaining the evidence of pathogens. Compared with traditional methods of pathogenic diagnosis, next‐generation and third‐generation sequencing technologies have many advantages in the detection of pathogenic microorganisms. In this review, we mainly introduce recent progress in research on pathogenic diagnostic technology and the applications of sequencing technology in the diagnosis of pathogenic microorganisms. This review provides new insights into the application of sequencing technology in the clinical diagnosis of microorganisms.
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Affiliation(s)
- Xiaoling Yu
- Department of Infectious Diseases, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, China
| | - Wenqian Jiang
- Department of Infectious Diseases, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, China
| | - Yang Shi
- Institute of Apply Genomics, Fuzhou University, Fuzhou, China
| | - Hanhui Ye
- Department of Infectious Diseases, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, China
| | - Jun Lin
- Institute of Apply Genomics, Fuzhou University, Fuzhou, China.,School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China.,Fujian Key Laboratory of Marine Enzyme Engineering, Fuzhou University, Fuzhou, China
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52
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Piper AM, Batovska J, Cogan NOI, Weiss J, Cunningham JP, Rodoni BC, Blacket MJ. Prospects and challenges of implementing DNA metabarcoding for high-throughput insect surveillance. Gigascience 2019; 8:giz092. [PMID: 31363753 PMCID: PMC6667344 DOI: 10.1093/gigascience/giz092] [Citation(s) in RCA: 82] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 06/25/2019] [Accepted: 07/09/2019] [Indexed: 12/21/2022] Open
Abstract
Trap-based surveillance strategies are widely used for monitoring of invasive insect species, aiming to detect newly arrived exotic taxa as well as track the population levels of established or endemic pests. Where these surveillance traps have low specificity and capture non-target endemic species in excess of the target pests, the need for extensive specimen sorting and identification creates a major diagnostic bottleneck. While the recent development of standardized molecular diagnostics has partly alleviated this requirement, the single specimen per reaction nature of these methods does not readily scale to the sheer number of insects trapped in surveillance programmes. Consequently, target lists are often restricted to a few high-priority pests, allowing unanticipated species to avoid detection and potentially establish populations. DNA metabarcoding has recently emerged as a method for conducting simultaneous, multi-species identification of complex mixed communities and may lend itself ideally to rapid diagnostics of bulk insect trap samples. Moreover, the high-throughput nature of recent sequencing platforms could enable the multiplexing of hundreds of diverse trap samples on a single flow cell, thereby providing the means to dramatically scale up insect surveillance in terms of both the quantity of traps that can be processed concurrently and number of pest species that can be targeted. In this review of the metabarcoding literature, we explore how DNA metabarcoding could be tailored to the detection of invasive insects in a surveillance context and highlight the unique technical and regulatory challenges that must be considered when implementing high-throughput sequencing technologies into sensitive diagnostic applications.
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Affiliation(s)
- Alexander M Piper
- Agriculture Victoria Research, AgriBio Centre, 5 Ring Road, Bundoora 3083, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora 3083, VIC, Australia
| | - Jana Batovska
- Agriculture Victoria Research, AgriBio Centre, 5 Ring Road, Bundoora 3083, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora 3083, VIC, Australia
| | - Noel O I Cogan
- Agriculture Victoria Research, AgriBio Centre, 5 Ring Road, Bundoora 3083, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora 3083, VIC, Australia
| | - John Weiss
- Agriculture Victoria Research, AgriBio Centre, 5 Ring Road, Bundoora 3083, VIC, Australia
| | - John Paul Cunningham
- Agriculture Victoria Research, AgriBio Centre, 5 Ring Road, Bundoora 3083, VIC, Australia
| | - Brendan C Rodoni
- Agriculture Victoria Research, AgriBio Centre, 5 Ring Road, Bundoora 3083, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora 3083, VIC, Australia
| | - Mark J Blacket
- Agriculture Victoria Research, AgriBio Centre, 5 Ring Road, Bundoora 3083, VIC, Australia
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Genetic testing and PGD for unexplained recurrent fetal malformations with MAGEL2 gene mutation. SCIENCE CHINA-LIFE SCIENCES 2019; 62:886-894. [PMID: 31152388 DOI: 10.1007/s11427-019-9541-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2019] [Accepted: 04/15/2019] [Indexed: 12/31/2022]
Abstract
Birth defects are caused by multiple factors, such as chromosome abnormality, environmental factors, and maternal factors. In this study, we focused on exploring the genetic causes of a non-consanguineous couple who suffered from four times of unsuccessful pregnancy due to unexplained recurrent fetal malformations with similar symptoms and normal chromosome copy number variations. Using trio-whole exome sequencing (trio-WES) for this couple and one of the affected fetuses, we found a mutation, c.1996delC on the maternal imprinted gene MAGEL2 that was carried by the affected fetus and husband, leading to Schaaf-Yang syndrome. To screen this mutation, we further performed preimplantation genetic diagnosis (PGD) strategy followed by a gene pedigree validation and pathogenicity analysis. After the transfer of a PGD-screened embryo, a normal newborn without previous abnormal symptoms was born (February 15, 2019). We present the first data that identified a pathogenic gene (MAGEL2 c.1996delC) in a fetus with Schaaf-Yang syndrome in the EAS (East Asian) database and overcame this genetic defect by using processed PGD for this couple based on the WES results.
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Bethune K, Mariac C, Couderc M, Scarcelli N, Santoni S, Ardisson M, Martin J, Montúfar R, Klein V, Sabot F, Vigouroux Y, Couvreur TLP. Long-fragment targeted capture for long-read sequencing of plastomes. APPLICATIONS IN PLANT SCIENCES 2019; 7:e1243. [PMID: 31139509 PMCID: PMC6526642 DOI: 10.1002/aps3.1243] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 03/21/2019] [Indexed: 05/09/2023]
Abstract
PREMISE Third-generation sequencing methods generate significantly longer reads than those produced using alternative sequencing methods. This provides increased possibilities for the study of biodiversity, phylogeography, and population genetics. We developed a protocol for in-solution enrichment hybridization capture of long DNA fragments applicable to complete plastid genomes. METHODS AND RESULTS The protocol uses cost-effective in-house probes developed via long-range PCR and was used in six non-model monocot species (Poaceae: African rice, pearl millet, fonio; and three palm species). DNA was extracted from fresh and silica gel-dried leaves. Our protocol successfully captured long-read plastome fragments (3151 bp median on average), with an enrichment rate ranging from 15% to 98%. DNA extracted from silica gel-dried leaves led to low-quality plastome assemblies when compared to DNA extracted from fresh tissue. CONCLUSIONS Our protocol could also be generalized to capture long sequences from specific nuclear fragments.
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Affiliation(s)
| | | | | | | | - Sylvain Santoni
- UMR AGAP, Equipe Diversité et Adaptation de la Vigne et des Espèces MéditerranéennesINRA2 Place Viala34060MontpellierFrance
| | - Morgane Ardisson
- UMR AGAP, Equipe Diversité et Adaptation de la Vigne et des Espèces MéditerranéennesINRA2 Place Viala34060MontpellierFrance
| | | | - Rommel Montúfar
- Facultad de Ciencias Exactas y NaturalesPontificia Universidad Católica del EcuadorQuitoEcuador
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55
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Adams CIM, Knapp M, Gemmell NJ, Jeunen GJ, Bunce M, Lamare MD, Taylor HR. Beyond Biodiversity: Can Environmental DNA (eDNA) Cut It as a Population Genetics Tool? Genes (Basel) 2019; 10:E192. [PMID: 30832286 PMCID: PMC6470983 DOI: 10.3390/genes10030192] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 02/19/2019] [Accepted: 02/26/2019] [Indexed: 01/23/2023] Open
Abstract
Population genetic data underpin many studies of behavioral, ecological, and evolutionary processes in wild populations and contribute to effective conservation management. However, collecting genetic samples can be challenging when working with endangered, invasive, or cryptic species. Environmental DNA (eDNA) offers a way to sample genetic material non-invasively without requiring visual observation. While eDNA has been trialed extensively as a biodiversity and biosecurity monitoring tool with a strong taxonomic focus, it has yet to be fully explored as a means for obtaining population genetic information. Here, we review current research that employs eDNA approaches for the study of populations. We outline challenges facing eDNA-based population genetic methodologies, and suggest avenues of research for future developments. We advocate that with further optimizations, this emergent field holds great potential as part of the population genetics toolkit.
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Affiliation(s)
- Clare I M Adams
- Department of Anatomy, University of Otago, 270 Great King Street, Dunedin, Otago 9016, New Zealand.
| | - Michael Knapp
- Department of Anatomy, University of Otago, 270 Great King Street, Dunedin, Otago 9016, New Zealand.
| | - Neil J Gemmell
- Department of Anatomy, University of Otago, 270 Great King Street, Dunedin, Otago 9016, New Zealand.
| | - Gert-Jan Jeunen
- Department of Anatomy, University of Otago, 270 Great King Street, Dunedin, Otago 9016, New Zealand.
| | - Michael Bunce
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Bentley, Perth, WA 6102, Australia.
| | - Miles D Lamare
- Department of Marine Science, University of Otago, 310 Castle Street, Dunedin, Otago 9016, New Zealand.
| | - Helen R Taylor
- Department of Anatomy, University of Otago, 270 Great King Street, Dunedin, Otago 9016, New Zealand.
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Characterization and evolutionary dynamics of complex regions in eukaryotic genomes. SCIENCE CHINA-LIFE SCIENCES 2019; 62:467-488. [PMID: 30810961 DOI: 10.1007/s11427-018-9458-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 11/05/2018] [Indexed: 01/07/2023]
Abstract
Complex regions in eukaryotic genomes are typically characterized by duplications of chromosomal stretches that often include one or more genes repeated in a tandem array or in relatively close proximity. Nevertheless, the repetitive nature of these regions, together with the often high sequence identity among repeats, have made complex regions particularly recalcitrant to proper molecular characterization, often being misassembled or completely absent in genome assemblies. This limitation has prevented accurate functional and evolutionary analyses of these regions. This is becoming increasingly relevant as evidence continues to support a central role for complex genomic regions in explaining human disease, developmental innovations, and ecological adaptations across phyla. With the advent of long-read sequencing technologies and suitable assemblers, the development of algorithms that can accommodate sample heterozygosity, and the adoption of a pangenomic-like view of these regions, accurate reconstructions of complex regions are now within reach. These reconstructions will finally allow for accurate functional and evolutionary studies of complex genomic regions, underlying the generation of genotype-phenotype maps of unprecedented resolution.
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58
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Wu M, Kostyun JL, Moyle LC. Genome Sequence of Jaltomata Addresses Rapid Reproductive Trait Evolution and Enhances Comparative Genomics in the Hyper-Diverse Solanaceae. Genome Biol Evol 2019; 11:335-349. [PMID: 30608583 PMCID: PMC6368146 DOI: 10.1093/gbe/evy274] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/16/2018] [Indexed: 12/11/2022] Open
Abstract
Within the economically important plant family Solanaceae, Jaltomata is a rapidly evolving genus that has extensive diversity in flower size and shape, as well as fruit and nectar color, among its ∼80 species. Here, we report the whole-genome sequencing, assembly, and annotation, of one representative species (Jaltomata sinuosa) from this genus. Combining PacBio long reads (25×) and Illumina short reads (148×) achieved an assembly of ∼1.45 Gb, spanning ∼96% of the estimated genome. Ninety-six percent of curated single-copy orthologs in plants were detected in the assembly, supporting a high level of completeness of the genome. Similar to other Solanaceous species, repetitive elements made up a large fraction (∼80%) of the genome, with the most recently active element, Gypsy, expanding across the genome in the last 1–2 Myr. Computational gene prediction, in conjunction with a merged transcriptome data set from 11 tissues, identified 34,725 protein-coding genes. Comparative phylogenetic analyses with six other sequenced Solanaceae species determined that Jaltomata is most likely sister to Solanum, although a large fraction of gene trees supported a conflicting bipartition consistent with substantial introgression between Jaltomata and Capsicum after these species split. We also identified gene family dynamics specific to Jaltomata, including expansion of gene families potentially involved in novel reproductive trait development, and loss of gene families that accompanied the loss of self-incompatibility. This high-quality genome will facilitate studies of phenotypic diversification in this rapidly radiating group and provide a new point of comparison for broader analyses of genomic evolution across the Solanaceae.
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Affiliation(s)
- Meng Wu
- Department of Biology, Indiana University Bloomington
| | - Jamie L Kostyun
- Department of Biology, Indiana University Bloomington.,Department of Plant Biology, University of Vermont
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Kistenich S, Halvorsen R, Schrøder-Nielsen A, Thorbek L, Timdal E, Bendiksby M. DNA Sequencing Historical Lichen Specimens. Front Ecol Evol 2019. [DOI: 10.3389/fevo.2019.00005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
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60
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Formenti G, Chiara M, Poveda L, Francoijs KJ, Bonisoli-Alquati A, Canova L, Gianfranceschi L, Horner DS, Saino N. SMRT long reads and Direct Label and Stain optical maps allow the generation of a high-quality genome assembly for the European barn swallow (Hirundo rustica rustica). Gigascience 2019; 8:5202456. [PMID: 30496513 PMCID: PMC6324554 DOI: 10.1093/gigascience/giy142] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 11/14/2018] [Indexed: 11/12/2022] Open
Abstract
Background The barn swallow (Hirundo rustica) is a migratory bird that has been the focus of a large number of ecological, behavioral, and genetic studies. To facilitate further population genetics and genomic studies, we present a reference genome assembly for the European subspecies (H. r. rustica). Findings As part of the Genome10K effort on generating high-quality vertebrate genomes (Vertebrate Genomes Project), we have assembled a highly contiguous genome assembly using single molecule real-time (SMRT) DNA sequencing and several Bionano optical map technologies. We compared and integrated optical maps derived from both the Nick, Label, Repair, and Stain technology and from the Direct Label and Stain (DLS) technology. As proposed by Bionano, DLS more than doubled the scaffold N50 with respect to the nickase. The dual enzyme hybrid scaffold led to a further marginal increase in scaffold N50 and an overall increase of confidence in the scaffolds. After removal of haplotigs, the final assembly is approximately 1.21 Gbp in size, with a scaffold N50 value of more than 25.95 Mbp. Conclusions This high-quality genome assembly represents a valuable resource for future studies of population genetics and genomics in the barn swallow and for studies concerning the evolution of avian genomes. It also represents one of the very first genomes assembled by combining SMRT long-read sequencing with the new Bionano DLS technology for scaffolding. The quality of this assembly demonstrates the potential of this methodology to substantially increase the contiguity of genome assemblies.
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Affiliation(s)
- Giulio Formenti
- Department of Environmental Science and Policy, University of Milan, via celoria 2, Milan, 20133, Italy
| | - Matteo Chiara
- Department of Biosciences, University of Milan, via celoria 26, Milan, 20133, Italy
| | - Lucy Poveda
- Functional Genomics Center of Zurich, University of Zurich, Winterthurerstrasse 190, Zürich, 8057, Switzerland
| | | | - Andrea Bonisoli-Alquati
- Department of Biological Sciences, California State Polytechnic University, 3801 West Temple Avenue, Pomona, California, 91768, USA
| | - Luca Canova
- Department of Biochemistry, University of Pavia, Via Taramelli 12, Pavia, 27100, Italy
| | - Luca Gianfranceschi
- Department of Biosciences, University of Milan, via celoria 26, Milan, 20133, Italy
| | - David Stephen Horner
- Department of Biosciences, University of Milan, via celoria 26, Milan, 20133, Italy
| | - Nicola Saino
- Department of Environmental Science and Policy, University of Milan, via celoria 2, Milan, 20133, Italy
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Golparian D, Donà V, Sánchez-Busó L, Foerster S, Harris S, Endimiani A, Low N, Unemo M. Antimicrobial resistance prediction and phylogenetic analysis of Neisseria gonorrhoeae isolates using the Oxford Nanopore MinION sequencer. Sci Rep 2018; 8:17596. [PMID: 30514867 PMCID: PMC6279828 DOI: 10.1038/s41598-018-35750-4] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 11/10/2018] [Indexed: 11/09/2022] Open
Abstract
Antimicrobial resistance (AMR) in Neisseria gonorrhoeae is common, compromising gonorrhoea treatment internationally. Rapid characterisation of AMR strains could ensure appropriate and personalised treatment, and support identification and investigation of gonorrhoea outbreaks in nearly real-time. Whole-genome sequencing is ideal for investigation of emergence and dissemination of AMR determinants, predicting AMR, in the gonococcal population and spread of AMR strains in the human population. The novel, rapid and revolutionary long-read sequencer MinION is a small hand-held device that generates bacterial genomes within one day. However, accuracy of MinION reads has been suboptimal for many objectives and the MinION has not been evaluated for gonococci. In this first MinION study for gonococci, we show that MinION-derived sequences analysed with existing open-access, web-based sequence analysis tools are not sufficiently accurate to identify key gonococcal AMR determinants. Nevertheless, using an in house-developed CLC Genomics Workbench including de novo assembly and optimised BLAST algorithms, we show that 2D ONT-derived sequences can be used for accurate prediction of decreased susceptibility or resistance to recommended antimicrobials in gonococcal isolates. We also show that the 2D ONT-derived sequences are useful for rapid phylogenomic-based molecular epidemiological investigations, and, in hybrid assemblies with Illumina sequences, for producing contiguous assemblies and finished reference genomes.
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Affiliation(s)
- Daniel Golparian
- WHO Collaborating Centre for Gonorrhoea and other Sexually Transmitted Infections, Department of Laboratory Medicine, Clinical Microbiology, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Valentina Donà
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
- Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Leonor Sánchez-Busó
- Pathogen Genomics, The Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, United Kingdom
| | - Sunniva Foerster
- WHO Collaborating Centre for Gonorrhoea and other Sexually Transmitted Infections, Department of Laboratory Medicine, Clinical Microbiology, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Simon Harris
- Pathogen Genomics, The Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, United Kingdom
| | - Andrea Endimiani
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Nicola Low
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
| | - Magnus Unemo
- WHO Collaborating Centre for Gonorrhoea and other Sexually Transmitted Infections, Department of Laboratory Medicine, Clinical Microbiology, Faculty of Medicine and Health, Örebro University, Örebro, Sweden.
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Dahlö M, Scofield DG, Schaal W, Spjuth O. Tracking the NGS revolution: managing life science research on shared high-performance computing clusters. Gigascience 2018; 7:4962406. [PMID: 29659792 PMCID: PMC5928410 DOI: 10.1093/gigascience/giy028] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 03/22/2018] [Indexed: 02/06/2023] Open
Abstract
Background Next-generation sequencing (NGS) has transformed the life sciences, and many research groups are newly dependent upon computer clusters to store and analyze large datasets. This creates challenges for e-infrastructures accustomed to hosting computationally mature research in other sciences. Using data gathered from our own clusters at UPPMAX computing center at Uppsala University, Sweden, where core hour usage of ∼800 NGS and ∼200 non-NGS projects is now similar, we compare and contrast the growth, administrative burden, and cluster usage of NGS projects with projects from other sciences. Results The number of NGS projects has grown rapidly since 2010, with growth driven by entry of new research groups. Storage used by NGS projects has grown more rapidly since 2013 and is now limited by disk capacity. NGS users submit nearly twice as many support tickets per user, and 11 more tools are installed each month for NGS projects than for non-NGS projects. We developed usage and efficiency metrics and show that computing jobs for NGS projects use more RAM than non-NGS projects, are more variable in core usage, and rarely span multiple nodes. NGS jobs use booked resources less efficiently for a variety of reasons. Active monitoring can improve this somewhat. Conclusions Hosting NGS projects imposes a large administrative burden at UPPMAX due to large numbers of inexperienced users and diverse and rapidly evolving research areas. We provide a set of recommendations for e-infrastructures that host NGS research projects. We provide anonymized versions of our storage, job, and efficiency databases.
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Affiliation(s)
- Martin Dahlö
- Science for Life Laboratory, Uppsala University, Uppsala, SE-750 03, Sweden.,Uppsala Multidisciplinary Center for Advanced Computational Science, Uppsala University, Uppsala, SE-751 05, Sweden.,Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, SE-751 24, Sweden
| | - Douglas G Scofield
- Uppsala Multidisciplinary Center for Advanced Computational Science, Uppsala University, Uppsala, SE-751 05, Sweden.,Department of Ecology and Genetics: Evolutionary Biology, Uppsala University, Uppsala, SE-752 36, Sweden
| | - Wesley Schaal
- Science for Life Laboratory, Uppsala University, Uppsala, SE-750 03, Sweden.,Uppsala Multidisciplinary Center for Advanced Computational Science, Uppsala University, Uppsala, SE-751 05, Sweden.,Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, SE-751 24, Sweden
| | - Ola Spjuth
- Science for Life Laboratory, Uppsala University, Uppsala, SE-750 03, Sweden.,Uppsala Multidisciplinary Center for Advanced Computational Science, Uppsala University, Uppsala, SE-751 05, Sweden.,Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, SE-751 24, Sweden
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Gros-Balthazard M, Hazzouri KM, Flowers JM. Genomic Insights into Date Palm Origins. Genes (Basel) 2018; 9:genes9100502. [PMID: 30336633 PMCID: PMC6211059 DOI: 10.3390/genes9100502] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2018] [Revised: 10/03/2018] [Accepted: 10/03/2018] [Indexed: 11/16/2022] Open
Abstract
With the development of next-generation sequencing technology, the amount of date palm (Phoenix dactylifera L.) genomic data has grown rapidly and yielded new insights into this species and its origins. Here, we review advances in understanding of the evolutionary history of the date palm, with a particular emphasis on what has been learned from the analysis of genomic data. We first record current genomic resources available for date palm including genome assemblies and resequencing data. We discuss new insights into its domestication and diversification history based on these improved genomic resources. We further report recent discoveries such as the existence of wild ancestral populations in remote locations of Oman and high differentiation between African and Middle Eastern populations. While genomic data are consistent with the view that domestication took place in the Gulf region, they suggest that the process was more complex involving multiple gene pools and possibly a secondary domestication. Many questions remain unanswered, especially regarding the genetic architecture of domestication and diversification. We provide a road map to future studies that will further clarify the domestication history of this iconic crop.
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Affiliation(s)
- Muriel Gros-Balthazard
- Center for Genomics and Systems Biology, New York University Abu Dhabi, Saadiyat Island, P.O. Box 129188, Abu Dhabi, UAE.
| | - Khaled Michel Hazzouri
- Khalifa Center for Genetic Engineering and Biotechnology (KCGEB), United Arab Emirates University, P.O. Box 15551, Al Ain, UAE.
| | - Jonathan Mark Flowers
- Center for Genomics and Systems Biology, New York University Abu Dhabi, Saadiyat Island, P.O. Box 129188, Abu Dhabi, UAE.
- Department of Biology, Center for Genomics and Systems Biology, 12 Waverly Place, New York University, New York, NY 10003, USA.
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Larridon I, Walter HE, Rosas M, Vandomme V, Guerrero PC. Evolutionary trends in the columnar cactus genus Eulychnia (Cactaceae) based on molecular phylogenetics, morphology, distribution, and habitat. SYST BIODIVERS 2018. [DOI: 10.1080/14772000.2018.1473898] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Isabel Larridon
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
- Department of Biology, Research Group Spermatophytes, Ghent University, K.L. Ledeganckstraat 35, 9000 Gent, Belgium
| | - Helmut E. Walter
- The EXSIS Project: Cactaceae Ex-Situ & In-Situ Conservation, 31860, Emmerthal, Germany
| | - Marcelo Rosas
- Departamento de Botánica, Facultad de Ciencias Naturales & Oceanográficas, Universidad de Concepción, Casilla 160C, Concepción, Chile
| | - Viki Vandomme
- Department of Biology, Research Group Spermatophytes, Ghent University, K.L. Ledeganckstraat 35, 9000 Gent, Belgium
| | - Pablo C. Guerrero
- Departamento de Botánica, Facultad de Ciencias Naturales & Oceanográficas, Universidad de Concepción, Casilla 160C, Concepción, Chile
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65
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Li WV, Li JJ. Modeling and analysis of RNA-seq data: a review from a statistical perspective. QUANTITATIVE BIOLOGY 2018; 6:195-209. [PMID: 31456901 PMCID: PMC6711375 DOI: 10.1007/s40484-018-0144-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 02/23/2018] [Accepted: 03/29/2018] [Indexed: 12/21/2022]
Abstract
BACKGROUND Since the invention of next-generation RNA sequencing (RNA-seq) technologies, they have become a powerful tool to study the presence and quantity of RNA molecules in biological samples and have revolutionized transcriptomic studies. The analysis of RNA-seq data at four different levels (samples, genes, transcripts, and exons) involve multiple statistical and computational questions, some of which remain challenging up to date. RESULTS We review RNA-seq analysis tools at the sample, gene, transcript, and exon levels from a statistical perspective. We also highlight the biological and statistical questions of most practical considerations. CONCLUSIONS The development of statistical and computational methods for analyzing RNA-seq data has made significant advances in the past decade. However, methods developed to answer the same biological question often rely on diverse statistical models and exhibit different performance under different scenarios. This review discusses and compares multiple commonly used statistical models regarding their assumptions, in the hope of helping users select appropriate methods as needed, as well as assisting developers for future method development.
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Affiliation(s)
- Wei Vivian Li
- Department of Statistics, University of California, Los Angeles, Los Angeles, CA 90095-1554, USA
| | - Jingyi Jessica Li
- Department of Statistics, University of California, Los Angeles, Los Angeles, CA 90095-1554, USA
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA 90095-088, USA
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Overview of Trends in the Application of Metagenomic Techniques in the Analysis of Human Enteric Viral Diversity in Africa's Environmental Regimes. Viruses 2018; 10:v10080429. [PMID: 30110939 PMCID: PMC6115975 DOI: 10.3390/v10080429] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Revised: 08/03/2018] [Accepted: 08/10/2018] [Indexed: 12/19/2022] Open
Abstract
There has been an increase in the quest for metagenomics as an approach for the identification and study of the diversity of human viruses found in aquatic systems, both for their role as waterborne pathogens and as water quality indicators. In the last few years, environmental viral metagenomics has grown significantly and has enabled the identification, diversity and entire genome sequencing of viruses in environmental and clinical samples extensively. Prior to the arrival of metagenomics, traditional molecular procedures such as the polymerase chain reaction (PCR) and sequencing, were mostly used to identify and classify enteric viral species in different environmental milieu. After the advent of metagenomics, more detailed reports have emerged about the important waterborne viruses identified in wastewater treatment plant effluents and surface water. This paper provides a review of methods that have been used for the concentration, detection and identification of viral species from different environmental matrices. The review also takes into consideration where metagenomics has been explored in different African countries, as well as the limitations and challenges facing the approach. Procedures including sample processing, experimental design, sequencing technology, and bioinformatics analysis are discussed. The review concludes by summarising the current thinking and practices in the field and lays bare key issues that those venturing into this field need to consider and address.
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von Reumont BM. Studying Smaller and Neglected Organisms in Modern Evolutionary Venomics Implementing RNASeq (Transcriptomics)-A Critical Guide. Toxins (Basel) 2018; 10:toxins10070292. [PMID: 30012955 PMCID: PMC6070909 DOI: 10.3390/toxins10070292] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 07/06/2018] [Accepted: 07/13/2018] [Indexed: 12/20/2022] Open
Abstract
Venoms are evolutionary key adaptations that species employ for defense, predation or competition. However, the processes and forces that drive the evolution of venoms and their toxin components remain in many aspects understudied. In particular, the venoms of many smaller, neglected (mostly invertebrate) organisms are not characterized in detail, especially with modern methods. For the majority of these taxa, even their biology is only vaguely known. Modern evolutionary venomics addresses the question of how venoms evolve by applying a plethora of -omics methods. These recently became so sensitive and enhanced that smaller, neglected organisms are now more easily accessible to comparatively study their venoms. More knowledge about these taxa is essential to better understand venom evolution in general. The methodological core pillars of integrative evolutionary venomics are genomics, transcriptomics and proteomics, which are complemented by functional morphology and the field of protein synthesis and activity tests. This manuscript focuses on transcriptomics (or RNASeq) as one toolbox to describe venom evolution in smaller, neglected taxa. It provides a hands-on guide that discusses a generalized RNASeq workflow, which can be adapted, accordingly, to respective projects. For neglected and small taxa, generalized recommendations are difficult to give and conclusions need to be made individually from case to case. In the context of evolutionary venomics, this overview highlights critical points, but also promises of RNASeq analyses. Methodologically, these concern the impact of read processing, possible improvements by perfoming multiple and merged assemblies, and adequate quantification of expressed transcripts. Readers are guided to reappraise their hypotheses on venom evolution in smaller organisms and how robustly these are testable with the current transcriptomics toolbox. The complementary approach that combines particular proteomics but also genomics with transcriptomics is discussed as well. As recently shown, comparative proteomics is, for example, most important in preventing false positive identifications of possible toxin transcripts. Finally, future directions in transcriptomics, such as applying 3rd generation sequencing strategies to overcome difficulties by short read assemblies, are briefly addressed.
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Affiliation(s)
- Björn Marcus von Reumont
- Justus Liebig University of Giessen, Institute for Insect Biotechnology, Heinrich Buff Ring 58, 35392 Giessen, Germany.
- Natural History Museum, Department of Life Sciences, Cromwell Rd, London SW75BD, UK.
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68
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Vincent AT, Charette SJ. Completion of genome of Aeromonas salmonicida subsp. salmonicida 01-B526 reveals how sequencing technologies can influence sequence quality and result interpretations. New Microbes New Infect 2018; 25:24-26. [PMID: 29983988 PMCID: PMC6031243 DOI: 10.1016/j.nmni.2018.05.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2018] [Accepted: 05/24/2018] [Indexed: 12/14/2022] Open
Abstract
Aeromonas salmonicida subsp. salmonicida is a pathogen that primarily infects salmonids. A strain of this bacterium, 01-B526, has been used in several studies as a reference. The genomic sequence of this strain is available, but comes from pyrosequencing and is the second most fragmented assembly for this bacterium. We generated its closed genome sequence and found a pitfall in result interpretations associated with low-quality genomic sequences.
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Affiliation(s)
- A T Vincent
- INRS-Institut Armand-Frappier, Bacterial Symbionts Evolution, Laval City, QC, H7V 1B7, Canada
| | - S J Charette
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC, G1V 0A6, Canada.,Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Quebec City, QC, G1V 0A6, Canada.,Centre de recherche de l'Institut universitaire de cardiologie et de pneumologie de Québec (IUCPQ), Quebec City, QC, G1V 4G5, Canada
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69
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Thirugnanasambandam PP, Hoang NV, Henry RJ. The Challenge of Analyzing the Sugarcane Genome. FRONTIERS IN PLANT SCIENCE 2018; 9:616. [PMID: 29868072 PMCID: PMC5961476 DOI: 10.3389/fpls.2018.00616] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 04/18/2018] [Indexed: 05/04/2023]
Abstract
Reference genome sequences have become key platforms for genetics and breeding of the major crop species. Sugarcane is probably the largest crop produced in the world (in weight of crop harvested) but lacks a reference genome sequence. Sugarcane has one of the most complex genomes in crop plants due to the extreme level of polyploidy. The genome of modern sugarcane hybrids includes sub-genomes from two progenitors Saccharum officinarum and S. spontaneum with some chromosomes resulting from recombination between these sub-genomes. Advancing DNA sequencing technologies and strategies for genome assembly are making the sugarcane genome more tractable. Advances in long read sequencing have allowed the generation of a more complete set of sugarcane gene transcripts. This is supporting transcript profiling in genetic research. The progenitor genomes are being sequenced. A monoploid coverage of the hybrid genome has been obtained by sequencing BAC clones that cover the gene space of the closely related sorghum genome. The complete polyploid genome is now being sequenced and assembled. The emerging genome will allow comparison of related genomes and increase understanding of the functioning of this polyploidy system. Sugarcane breeding for traditional sugar and new energy and biomaterial uses will be enhanced by the availability of these genomic resources.
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Affiliation(s)
- Prathima P. Thirugnanasambandam
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, Australia
- ICAR - Sugarcane Breeding Institute, Coimbatore, India
| | - Nam V. Hoang
- College of Agriculture and Forestry, Hue University, Hue, Vietnam
| | - Robert J. Henry
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, Australia
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70
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Ghosh M, Sharma N, Singh AK, Gera M, Pulicherla KK, Jeong DK. Transformation of animal genomics by next-generation sequencing technologies: a decade of challenges and their impact on genetic architecture. Crit Rev Biotechnol 2018; 38:1157-1175. [PMID: 29631431 DOI: 10.1080/07388551.2018.1451819] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
For more than a quarter of a century, sequencing technologies from Sanger's method to next-generation high-throughput techniques have provided fascinating opportunities in the life sciences. The continuing upward trajectory of sequencing technologies will improve livestock research and expedite the development of various new genomic and technological studies with farm animals. The use of high-throughput technologies in livestock research has increased interest in metagenomics, epigenetics, genome-wide association studies, and identification of single nucleotide polymorphisms and copy number variations. Such studies are beginning to provide revolutionary insights into biological and evolutionary processes. Farm animals, such as cattle, swine, and horses, have played a dual role as economically and agriculturally important animals as well as biomedical research models. The first part of this study explores the current state of sequencing methods, many of which are already used in animal genomic studies, and the second part summarizes the state of cattle, swine, horse, and chicken genome sequencing and illustrates its achievements during the last few years. Finally, we describe several high-throughput sequencing approaches for the improved detection of known, unknown, and emerging infectious agents, leading to better diagnosis of infectious diseases. The insights from viral metagenomics and the advancement of next-generation sequencing will strongly support specific and efficient vaccine development and provide strategies for controlling infectious disease transmission among animal populations and/or between animals and humans. However, prospective sequencing technologies will require further research and in-field testing before reaching the marketplace.
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Affiliation(s)
- Mrinmoy Ghosh
- a Department of Animal Biotechnology , Jeju National University , Jeju-Do , Republic of Korea
| | - Neelesh Sharma
- b Department of Veterinary Science and Animal Husbandry , Sher-e-Kashmir University of Agricultural Sciences and Technology , R.S. Pura , India
| | - Amit Kumar Singh
- a Department of Animal Biotechnology , Jeju National University , Jeju-Do , Republic of Korea
| | - Meeta Gera
- a Department of Animal Biotechnology , Jeju National University , Jeju-Do , Republic of Korea
| | | | - Dong Kee Jeong
- a Department of Animal Biotechnology , Jeju National University , Jeju-Do , Republic of Korea
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71
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Vincent AT, Charette SJ, Barbeau J. Unexpected diversity in the mobilome of a Pseudomonas aeruginosa strain isolated from a dental unit waterline revealed by SMRT Sequencing. Genome 2018; 61:359-365. [PMID: 29546998 DOI: 10.1139/gen-2017-0239] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The Gram-negative bacterium Pseudomonas aeruginosa is found in several habitats, both natural and human-made, and is particularly known for its recurrent presence as a pathogen in the lungs of patients suffering from cystic fibrosis, a genetic disease. Given its clinical importance, several major studies have investigated the genomic adaptation of P. aeruginosa in lungs and its transition as acute infections become chronic. However, our knowledge about the diversity and adaptation of the P. aeruginosa genome to non-clinical environments is still fragmentary, in part due to the lack of accurate reference genomes of strains from the numerous environments colonized by the bacterium. Here, we used PacBio long-read technology to sequence the genome of PPF-1, a strain of P. aeruginosa isolated from a dental unit waterline. Generating this closed genome was an opportunity to investigate genomic features that are difficult to accurately study in a draft genome (contigs state). It was possible to shed light on putative genomic islands, some shared with other reference genomes, new prophages, and the complete content of insertion sequences. In addition, four different group II introns were also found, including two characterized here and not listed in the specialized group II intron database.
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Affiliation(s)
- Antony T Vincent
- a Institut de biologie intégrative et des systèmes (IBIS), Université Laval, Quebec City, QC, Canada.,b Centre de recherche de l'Institut universitaire de cardiologie et de pneumologie de Québec (CRIUCPQ), Quebec City, QC, Canada.,c Département de biochimie, de microbiologie et de bio-informatique, Université Laval, Quebec City, QC, Canada
| | - Steve J Charette
- a Institut de biologie intégrative et des systèmes (IBIS), Université Laval, Quebec City, QC, Canada.,b Centre de recherche de l'Institut universitaire de cardiologie et de pneumologie de Québec (CRIUCPQ), Quebec City, QC, Canada.,c Département de biochimie, de microbiologie et de bio-informatique, Université Laval, Quebec City, QC, Canada
| | - Jean Barbeau
- d Département de stomatologie, Faculté de médecine dentaire, Université de Montréal, Montreal, QC, Canada
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Zhang J, Ding X, Guan R, Zhu C, Xu C, Zhu B, Zhang H, Xiong Z, Xue Y, Tu J, Lu Z. Evaluation of different 16S rRNA gene V regions for exploring bacterial diversity in a eutrophic freshwater lake. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 618:1254-1267. [PMID: 29089134 DOI: 10.1016/j.scitotenv.2017.09.228] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2017] [Revised: 09/08/2017] [Accepted: 09/21/2017] [Indexed: 05/26/2023]
Abstract
Massive partial sequencing of 16S rRNA genes has become the predominant tool used for studying microbial ecology. However, determining which hypervariable regions and primer sets should be used for screening microbial communities requires extensive investigation if controversial results are to be avoided. Here, the performances of different variable regions of the 16S rRNA gene on bacterial diversity studies were evaluated in silico with respect to the SILVA non-redundant reference database (SILVA SSU Ref 123NR), and subsequently verified using samples from Lake Taihu in China, a eutrophic lake. We found that the bacterial community composition results were strongly impacted by the different V regions. The results show that V1-V2 and V1-V3 regions were the most reliable regions in the full-length 16S rRNA sequences, while most V3 to V6 regions (including V3, V4, V3-V4, V5, V4-V5, V6, V3-V6, V4-V6, and V5-V6) were more closely aligned with the SILVA SSU Ref 123NR database. Overall, V4 was the most prominent V region for achieving good domain specificity, higher coverage and a broader spectrum in the Bacteria domain, as confirmed by the validation experiments. S-D-Bact-0564-a-S-15/S-D-Bact-0785-b-A-18 is, therefore, a promising primer set for surveying bacterial diversity in eutrophic lakes.
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Affiliation(s)
- Junyi Zhang
- State Key Lab for Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China; Wuxi Environmental Monitoring Centre, Wuxi 214121, China
| | - Xiao Ding
- State Key Lab for Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Rui Guan
- State Key Lab for Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Congmin Zhu
- MOE Key Lab of Bioinformatics, Bioinformatics Division/Center for Synthetic and Systems Biology, TNLIST and Department of Automation, Tsinghua University, Beijing 100084, China
| | - Chao Xu
- Wuxi Environmental Monitoring Centre, Wuxi 214121, China
| | - Bingchuan Zhu
- Wuxi Environmental Monitoring Centre, Wuxi 214121, China
| | - Hu Zhang
- Wuxi Environmental Monitoring Centre, Wuxi 214121, China
| | - Zhipeng Xiong
- Lake Taihu Cyanobacterial Blooms Research Institute, Wuxi Metagene Science & Technology Co., Ltd, Wuxi 214135, China
| | - Yingang Xue
- Key Laboratory of Environmental Protection of Water Environment Biological Monitoring of Jiangsu Province, Changzhou Environmental Monitoring Center, Changzhou 213001, China
| | - Jing Tu
- State Key Lab for Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Zuhong Lu
- State Key Lab for Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China; Department of Biomedical Engineering, College of Engineering, Peking University, Beijing 100871, China.
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73
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Tedersoo L, Tooming-Klunderud A, Anslan S. PacBio metabarcoding of Fungi and other eukaryotes: errors, biases and perspectives. THE NEW PHYTOLOGIST 2018; 217:1370-1385. [PMID: 28906012 DOI: 10.1111/nph.14776] [Citation(s) in RCA: 109] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 07/31/2017] [Indexed: 05/04/2023]
Abstract
Second-generation, high-throughput sequencing methods have greatly improved our understanding of the ecology of soil microorganisms, yet the short barcodes (< 500 bp) provide limited taxonomic and phylogenetic information for species discrimination and taxonomic assignment. Here, we utilized the third-generation Pacific Biosciences (PacBio) RSII and Sequel instruments to evaluate the suitability of full-length internal transcribed spacer (ITS) barcodes and longer rRNA gene amplicons for metabarcoding Fungi, Oomycetes and other eukaryotes in soil samples. Metabarcoding revealed multiple errors and biases: Taq polymerase substitution errors and mis-incorporating indels in sequencing homopolymers constitute major errors; sequence length biases occur during PCR, library preparation, loading to the sequencing instrument and quality filtering; primer-template mismatches bias the taxonomic profile when using regular and highly degenerate primers. The RSII and Sequel platforms enable the sequencing of amplicons up to 3000 bp, but the sequence quality remains slightly inferior to Illumina sequencing especially in longer amplicons. The full ITS barcode and flanking rRNA small subunit gene greatly improve taxonomic identification at the species and phylum levels, respectively. We conclude that PacBio sequencing provides a viable alternative for metabarcoding of organisms that are of relatively low diversity, require > 500-bp barcode for reliable identification or when phylogenetic approaches are intended.
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Affiliation(s)
- Leho Tedersoo
- Natural History Museum, University of Tartu, 14a Ravila, Tartu, 50411, Estonia
| | - Ave Tooming-Klunderud
- Department of Biosciences, Norwegian Sequencing Centre and Centre for Ecological and Evolutionary Synthesis, University of Oslo, PO Box 1066, Blindern, Oslo, NO-0316, Norway
| | - Sten Anslan
- Institute of Ecology and Earth Sciences, University of Tartu, 14a Ravila, Tartu, 50411, Estonia
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74
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Abstract
In wine industry, there is a prevalent use of starter cultures to promote a controlled and efficient alcoholic fermentation preventing the growth of spoilage microbes. However, current trends in enology aim to combine the guaranteed success of monitored process and the complexity of fermentations either by inoculating autochthonous starters or by performing spontaneously to produce distinctive wines. To understand the complex roles of microorganisms on wine fermentation, we must understand their population dynamics and their relationships with wine quality and metabolome. Current metagenomics techniques based on massive sequencing are gaining relevance to study the diversity and evolution of microbial population on every stage of the wine making process. This new tool and technique increases the throughput and sensitivity to study microbial communities. This review focuses on the current knowledge about wine alcoholic fermentation, the contribution of massive sequencing techniques and the possibility of using this tool for microbial control.
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Abstract
A genome sequence of the Mycoplasma bovis Ningxia-1 strain was tested by Pacific Biosciences (PacBio) single-molecule real-time (SMRT) sequencing technology. The strain was isolated from a lesioned calf lung in 2013 in Pengyang, Ningxia, China. The single circular chromosome of 1,033,629 bp shows differences between complete Mycoplasma bovis genome in insertion-like sequences (ISs), integrative conjugative elements (ICEs), lipoproteins (LPs), variable surface lipoproteins (VSPs), pathogenicity islands (PAIs), etc.
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76
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Brunetti AE, Carnevale Neto F, Vera MC, Taboada C, Pavarini DP, Bauermeister A, Lopes NP. An integrative omics perspective for the analysis of chemical signals in ecological interactions. Chem Soc Rev 2018; 47:1574-1591. [DOI: 10.1039/c7cs00368d] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
All living organisms emit, detect, and respond to chemical stimuli, thus creating an almost limitless number of interactions by means of chemical signals.
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Affiliation(s)
- A. E. Brunetti
- Physics and Chemistry Department
- School of Pharmaceutical Sciences of Ribeirão Preto
- University of São Paulo
- SP
- Brazil
| | - F. Carnevale Neto
- Physics and Chemistry Department
- School of Pharmaceutical Sciences of Ribeirão Preto
- University of São Paulo
- SP
- Brazil
| | - M. C. Vera
- Instituto de Herpetología
- Unidad Ejecutora Lillo
- CONICET
- Tucumán
- Argentina
| | - C. Taboada
- Physics and Chemistry Department
- School of Pharmaceutical Sciences of Ribeirão Preto
- University of São Paulo
- SP
- Brazil
| | - D. P. Pavarini
- Physics and Chemistry Department
- School of Pharmaceutical Sciences of Ribeirão Preto
- University of São Paulo
- SP
- Brazil
| | - A. Bauermeister
- Physics and Chemistry Department
- School of Pharmaceutical Sciences of Ribeirão Preto
- University of São Paulo
- SP
- Brazil
| | - N. P. Lopes
- Physics and Chemistry Department
- School of Pharmaceutical Sciences of Ribeirão Preto
- University of São Paulo
- SP
- Brazil
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Bleidorn C, Gerth M. A critical re-evaluation of multilocus sequence typing (MLST) efforts in Wolbachia. FEMS Microbiol Ecol 2017; 94:4654844. [DOI: 10.1093/femsec/fix163] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 11/22/2017] [Indexed: 01/10/2023] Open
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78
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Bartling P, Brinkmann H, Bunk B, Overmann J, Göker M, Petersen J. The Composite 259-kb Plasmid of Martelella mediterranea DSM 17316 T-A Natural Replicon with Functional RepABC Modules from Rhodobacteraceae and Rhizobiaceae. Front Microbiol 2017; 8:1787. [PMID: 28983283 PMCID: PMC5613091 DOI: 10.3389/fmicb.2017.01787] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Accepted: 09/05/2017] [Indexed: 12/13/2022] Open
Abstract
A multipartite genome organization with a chromosome and many extrachromosomal replicons (ECRs) is characteristic for Alphaproteobacteria. The best investigated ECRs of terrestrial rhizobia are the symbiotic plasmids for legume root nodulation and the tumor-inducing (Ti) plasmid of Agrobacterium tumefaciens. RepABC plasmids represent the most abundant alphaproteobacterial replicon type. The currently known homologous replication modules of rhizobia and Rhodobacteraceae are phylogenetically distinct. In this study, we surveyed type-strain genomes from the One Thousand Microbial Genomes (KMG-I) project and identified a roseobacter-specific RepABC-type operon in the draft genome of the marine rhizobium Martelella mediterranea DSM 17316T. PacBio genome sequencing demonstrated the presence of three circular ECRs with sizes of 593, 259, and 170-kb. The rhodobacteral RepABC module is located together with a rhizobial equivalent on the intermediate sized plasmid pMM259, which likely originated in the fusion of a pre-existing rhizobial ECR with a conjugated roseobacter plasmid. Further evidence for horizontal gene transfer (HGT) is given by the presence of a roseobacter-specific type IV secretion system on the 259-kb plasmid and the rhodobacteracean origin of 62% of the genes on this plasmid. Functionality tests documented that the genuine rhizobial RepABC module from the Martelella 259-kb plasmid is only maintained in A. tumefaciens C58 (Rhizobiaceae) but not in Phaeobacter inhibens DSM 17395 (Rhodobacteraceae). Unexpectedly, the roseobacter-like replication system is functional and stably maintained in both host strains, thus providing evidence for a broader host range than previously proposed. In conclusion, pMM259 is the first example of a natural plasmid that likely mediates genetic exchange between roseobacters and rhizobia.
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Affiliation(s)
- Pascal Bartling
- Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell CulturesBraunschweig, Germany
| | - Henner Brinkmann
- Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell CulturesBraunschweig, Germany
| | - Boyke Bunk
- Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell CulturesBraunschweig, Germany
| | - Jörg Overmann
- Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell CulturesBraunschweig, Germany
| | - Markus Göker
- Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell CulturesBraunschweig, Germany
| | - Jörn Petersen
- Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell CulturesBraunschweig, Germany
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Rozas J, Ferrer-Mata A, Sánchez-DelBarrio JC, Guirao-Rico S, Librado P, Ramos-Onsins SE, Sánchez-Gracia A. DnaSP 6: DNA Sequence Polymorphism Analysis of Large Data Sets. Mol Biol Evol 2017; 34:3299-3302. [DOI: 10.1093/molbev/msx248] [Citation(s) in RCA: 2494] [Impact Index Per Article: 356.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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80
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Fuentes-Pardo AP, Ruzzante DE. Whole-genome sequencing approaches for conservation biology: Advantages, limitations and practical recommendations. Mol Ecol 2017; 26:5369-5406. [PMID: 28746784 DOI: 10.1111/mec.14264] [Citation(s) in RCA: 152] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Revised: 06/23/2017] [Accepted: 06/28/2017] [Indexed: 12/14/2022]
Abstract
Whole-genome resequencing (WGR) is a powerful method for addressing fundamental evolutionary biology questions that have not been fully resolved using traditional methods. WGR includes four approaches: the sequencing of individuals to a high depth of coverage with either unresolved or resolved haplotypes, the sequencing of population genomes to a high depth by mixing equimolar amounts of unlabelled-individual DNA (Pool-seq) and the sequencing of multiple individuals from a population to a low depth (lcWGR). These techniques require the availability of a reference genome. This, along with the still high cost of shotgun sequencing and the large demand for computing resources and storage, has limited their implementation in nonmodel species with scarce genomic resources and in fields such as conservation biology. Our goal here is to describe the various WGR methods, their pros and cons and potential applications in conservation biology. WGR offers an unprecedented marker density and surveys a wide diversity of genetic variations not limited to single nucleotide polymorphisms (e.g., structural variants and mutations in regulatory elements), increasing their power for the detection of signatures of selection and local adaptation as well as for the identification of the genetic basis of phenotypic traits and diseases. Currently, though, no single WGR approach fulfils all requirements of conservation genetics, and each method has its own limitations and sources of potential bias. We discuss proposed ways to minimize such biases. We envision a not distant future where the analysis of whole genomes becomes a routine task in many nonmodel species and fields including conservation biology.
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81
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McCann JC, Elolimy AA, Loor JJ. Rumen Microbiome, Probiotics, and Fermentation Additives. Vet Clin North Am Food Anim Pract 2017; 33:539-553. [PMID: 28764865 DOI: 10.1016/j.cvfa.2017.06.009] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Abstract
Fermentation of a variety of feedstuffs by the ruminal microbiome is the distinctive feature of the ruminant digestive tract. The host derives energy and nutrients from microbiome activity; these organisms are essential to survival. Advances in DNA sequencing and bioinformatics have redefined the rumen microbial community. Current research seeks to connect our understanding of the rumen microbiome with nutritional strategies in ruminant livestock systems and their associated digestive disorders. These efforts align with a growing number of products designed to improve ruminal fermentation to benefit the overall efficiency of ruminant livestock production and health.
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Affiliation(s)
- Joshua C McCann
- Department of Animal Sciences, Division of Nutritional Sciences, University of Illinois, 1207 West Gregory Drive, Urbana, IL 61801, USA.
| | - Ahmed A Elolimy
- Department of Animal Sciences, Division of Nutritional Sciences, University of Illinois, 1207 West Gregory Drive, Urbana, IL 61801, USA
| | - Juan J Loor
- Department of Animal Sciences, Division of Nutritional Sciences, University of Illinois, 1207 West Gregory Drive, Urbana, IL 61801, USA.
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82
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Nkili-Meyong AA, Bigarré L, Labouba I, Vallaeys T, Avarre JC, Berthet N. Contribution of Next-Generation Sequencing to Aquatic and Fish Virology. Intervirology 2017; 59:285-300. [PMID: 28668959 DOI: 10.1159/000477808] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Accepted: 05/27/2017] [Indexed: 12/13/2022] Open
Abstract
The recent technological advances in nucleic acid sequencing, called next-generation sequencing (NGS), have revolutionized the field of genomics and have also influenced viral research. Aquatic viruses, and especially those infecting fish, have also greatly benefited from NGS technologies, which provide a huge amount of molecular information at a low cost in a relatively short period of time. Here, we review the use of the current high-throughput sequencing platforms with a special focus on the associated challenges (regarding sample preparation and bioinformatics) in their applications to the field of aquatic virology, especially for: (i) discovering novel viruses that may be associated with fish mortalities, (ii) elucidating the mechanisms of pathogenesis, and finally (iii) studying the molecular epidemiology of these pathogens.
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Affiliation(s)
- Andriniaina Andy Nkili-Meyong
- Département Zoonoses et Maladies Emergentes, Centre International de Recherches Médicales de Franceville (CIRMF), Franceville, Gabon
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83
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Peham T, Steiner FM, Schlick‐Steiner BC, Arthofer W. Are we ready to detect nematode diversity by next generation sequencing? Ecol Evol 2017; 7:4147-4151. [PMID: 28649327 PMCID: PMC5478071 DOI: 10.1002/ece3.2998] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2016] [Revised: 03/16/2017] [Accepted: 03/20/2017] [Indexed: 12/28/2022] Open
Abstract
In a Technical Advance article, Porazinska et al. (2009, Molecular Ecology Resources, 9, 1439-1450) assessed next generation sequencing (NGS) as a method for metagenomic analysis of nematode diversity. We agree that NGS has great potential here. However, it is not an easy path to the successful implementation of NGS for environmental DNA analysis of nematodes. Here, we describe the method's limitations and discuss prospective research questions. For instance, only a few direct extraction kits are suitable for nematode DNA extraction from bulk samples without adaptation. They enable the analysis of extracellular nematode DNA. The most crucial and unresolved issue remains the limited availability of suitable primers.
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Affiliation(s)
- Thomas Peham
- Molecular Ecology GroupInstitute of EcologyUniversity of InnsbruckInnsbruckAustria
| | - Florian M. Steiner
- Molecular Ecology GroupInstitute of EcologyUniversity of InnsbruckInnsbruckAustria
| | | | - Wolfgang Arthofer
- Molecular Ecology GroupInstitute of EcologyUniversity of InnsbruckInnsbruckAustria
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84
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Batovska J, Lynch SE, Cogan NOI, Brown K, Darbro JM, Kho EA, Blacket MJ. Effective mosquito and arbovirus surveillance using metabarcoding. Mol Ecol Resour 2017; 18:32-40. [PMID: 28417591 PMCID: PMC5811807 DOI: 10.1111/1755-0998.12682] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Revised: 02/13/2017] [Accepted: 04/03/2017] [Indexed: 01/04/2023]
Abstract
Effective vector and arbovirus surveillance requires timely and accurate screening techniques that can be easily upscaled. Next-generation sequencing (NGS) is a high-throughput technology that has the potential to modernize vector surveillance. When combined with DNA barcoding, it is termed 'metabarcoding.' The aim of our study was to establish a metabarcoding protocol to characterize pools of mosquitoes and screen them for virus. Pools contained 100 morphologically identified individuals, including one Ross River virus (RRV) infected mosquito, with three species present at different proportions: 1, 5, 94%. Nucleic acid extracted from both crude homogenate and supernatant was used to amplify a 269-bp section of the mitochondrial cytochrome c oxidase subunit I (COI) locus. Additionally, a 67-bp region of the RRV E2 gene was amplified from synthesized cDNA to screen for RRV. Amplicon sequencing was performed using an Illumina MiSeq, and bioinformatic analysis was performed using a DNA barcode database of Victorian mosquitoes. Metabarcoding successfully detected all mosquito species and RRV in every positive sample tested. The limits of species detection were also examined by screening a pool of 1000 individuals, successfully identifying the species and RRV from a single mosquito. The primers used for amplification, number of PCR cycles and total number of individuals present all have effects on the quantification of species in mixed bulk samples. Based on the results, a number of recommendations for future metabarcoding studies are presented. Overall, metabarcoding shows great promise for providing a new alternative approach to screening large insect surveillance trap catches.
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Affiliation(s)
- J Batovska
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, Vic, Australia
| | - S E Lynch
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, Vic, Australia
| | - N O I Cogan
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, Vic, Australia.,School of Applied Systems Biology, La Trobe University, Bundoora, Vic, Australia
| | - K Brown
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, Vic, Australia
| | - J M Darbro
- Mosquito Control Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Qld, Australia
| | - E A Kho
- Mosquito Control Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Qld, Australia
| | - M J Blacket
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, Vic, Australia
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85
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Morgan HH, du Toit M, Setati ME. The Grapevine and Wine Microbiome: Insights from High-Throughput Amplicon Sequencing. Front Microbiol 2017; 8:820. [PMID: 28553266 PMCID: PMC5425579 DOI: 10.3389/fmicb.2017.00820] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2016] [Accepted: 04/21/2017] [Indexed: 12/21/2022] Open
Abstract
From the time when microbial activity in wine fermentation was first demonstrated, the microbial ecology of the vineyard, grape, and wine has been extensively investigated using culture-based methods. However, the last 2 decades have been characterized by an important change in the approaches used for microbial examination, due to the introduction of DNA-based community fingerprinting methods such as DGGE, SSCP, T-RFLP, and ARISA. These approaches allowed for the exploration of microbial community structures without the need to cultivate, and have been extensively applied to decipher the microbial populations associated with the grapevine as well as the microbial dynamics throughout grape berry ripening and wine fermentation. These techniques are well-established for the rapid more sensitive profiling of microbial communities; however, they often do not provide direct taxonomic information and possess limited ability to detect the presence of rare taxa and taxa with low abundance. Consequently, the past 5 years have seen an upsurge in the application of high-throughput sequencing methods for the in-depth assessment of the grapevine and wine microbiome. Although a relatively new approach in wine sciences, these methods reveal a considerably greater diversity than previously reported, and identified several species that had not yet been reported. The aim of the current review is to highlight the contribution of high-throughput next generation sequencing and metagenomics approaches to vineyard microbial ecology especially unraveling the influence of vineyard management practices on microbial diversity.
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Affiliation(s)
- Horatio H Morgan
- Department of Viticulture and Oenology, Institute for Wine Biotechnology, Stellenbosch UniversityStellenbosch, South Africa
| | - Maret du Toit
- Department of Viticulture and Oenology, Institute for Wine Biotechnology, Stellenbosch UniversityStellenbosch, South Africa
| | - Mathabatha E Setati
- Department of Viticulture and Oenology, Institute for Wine Biotechnology, Stellenbosch UniversityStellenbosch, South Africa
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86
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Pasipoularides A. Genomic translational research: Paving the way to individualized cardiac functional analyses and personalized cardiology. Int J Cardiol 2016; 230:384-401. [PMID: 28057368 DOI: 10.1016/j.ijcard.2016.12.097] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Revised: 11/27/2016] [Accepted: 12/17/2016] [Indexed: 01/08/2023]
Abstract
For most of Medicine's past, the best that physicians could do to cope with disease prevention and treatment was based on the expected response of an average patient. Currently, however, a more personalized/precise approach to cardiology and medicine in general is becoming possible, as the cost of sequencing a human genome has declined substantially. As a result, we are witnessing an era of precipitous advances in biomedicine and bourgeoning understanding of the genetic basis of cardiovascular and other diseases, reminiscent of the resurgence of innovations in physico-mathematical sciences and biology-anatomy-cardiology in the Renaissance, a parallel time of radical change and reformation of medical knowledge, education and practice. Now on the horizon is an individualized, diverse patient-centered, approach to medical practice that encompasses the development of new, gene-based diagnostics and preventive medicine tactics, and offers the broadest range of personalized therapies based on pharmacogenetics. Over time, translation of genomic and high-tech approaches unquestionably will transform clinical practice in cardiology and medicine as a whole, with the adoption of new personalized medicine approaches and procedures. Clearly, future prospects far outweigh present accomplishments, which are best viewed as a promising start. It is now essential for pluridisciplinary health care providers to examine the drivers and barriers to the clinical adoption of this emerging revolutionary paradigm, in order to expedite the realization of its potential. So, we are not there yet, but we are definitely on our way.
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Affiliation(s)
- Ares Pasipoularides
- Department of Surgery, Duke University School of Medicine, Durham, NC, 27710, USA.
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87
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Maddison DR. The rapidly changing landscape of insect phylogenetics. CURRENT OPINION IN INSECT SCIENCE 2016; 18:77-82. [PMID: 27939714 DOI: 10.1016/j.cois.2016.09.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 09/23/2016] [Indexed: 06/06/2023]
Abstract
Insect phylogenetics is being profoundly changed by many innovations. Although rapid developments in genomics have center stage, key progress has been made in phenomics, field and museum science, digital databases and pipelines, analytical tools, and the culture of science. The importance of these methodological and cultural changes to the pace of inference of the hexapod Tree of Life is discussed. The innovations have the potential, when synthesized and mobilized in ways as yet unforeseen, to shine light on the million or more clades in insects, and infer their composition with confidence. There are many challenges to overcome before insects can enter the 'phylocognisant age', but because of the promise of genomics, phenomics, and informatics, that is now an imaginable future.
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Affiliation(s)
- David R Maddison
- Department of Integrative Biology, 3029 Cordley Hall, Oregon State University, Corvallis, OR 97331, USA.
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88
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De Oliveira AL, Wollesen T, Kristof A, Scherholz M, Redl E, Todt C, Bleidorn C, Wanninger A. Comparative transcriptomics enlarges the toolkit of known developmental genes in mollusks. BMC Genomics 2016; 17:905. [PMID: 27832738 PMCID: PMC5103448 DOI: 10.1186/s12864-016-3080-9] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 09/08/2016] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND Mollusks display a striking morphological disparity, including, among others, worm-like animals (the aplacophorans), snails and slugs, bivalves, and cephalopods. This phenotypic diversity renders them ideal for studies into animal evolution. Despite being one of the most species-rich phyla, molecular and in silico studies concerning specific key developmental gene families are still scarce, thus hampering deeper insights into the molecular machinery that governs the development and evolution of the various molluscan class-level taxa. RESULTS Next-generation sequencing was used to retrieve transcriptomes of representatives of seven out of the eight recent class-level taxa of mollusks. Similarity searches, phylogenetic inferences, and a detailed manual curation were used to identify and confirm the orthology of numerous molluscan Hox and ParaHox genes, which resulted in a comprehensive catalog that highlights the evolution of these genes in Mollusca and other metazoans. The identification of a specific molluscan motif in the Hox paralog group 5 and a lophotrochozoan ParaHox motif in the Gsx gene is described. Functional analyses using KEGG and GO tools enabled a detailed description of key developmental genes expressed in important pathways such as Hedgehog, Wnt, and Notch during development of the respective species. The KEGG analysis revealed Wnt8, Wnt11, and Wnt16 as Wnt genes hitherto not reported for mollusks, thereby enlarging the known Wnt complement of the phylum. In addition, novel Hedgehog (Hh)-related genes were identified in the gastropod Lottia cf. kogamogai, demonstrating a more complex gene content in this species than in other mollusks. CONCLUSIONS The use of de novo transcriptome assembly and well-designed in silico protocols proved to be a robust approach for surveying and mining large sequence data in a wide range of non-model mollusks. The data presented herein constitute only a small fraction of the information retrieved from the analysed molluscan transcriptomes, which can be promptly employed in the identification of novel genes and gene families, phylogenetic inferences, and other studies using molecular tools. As such, our study provides an important framework for understanding some of the underlying molecular mechanisms involved in molluscan body plan diversification and hints towards functions of key developmental genes in molluscan morphogenesis.
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Affiliation(s)
- A. L. De Oliveira
- Department of Integrative Zoology, Faculty of Life Sciences, University of Vienna, Althanstraße 14, Vienna, 1090 Austria
| | - T. Wollesen
- Department of Integrative Zoology, Faculty of Life Sciences, University of Vienna, Althanstraße 14, Vienna, 1090 Austria
| | - A. Kristof
- Department of Integrative Zoology, Faculty of Life Sciences, University of Vienna, Althanstraße 14, Vienna, 1090 Austria
| | - M. Scherholz
- Department of Integrative Zoology, Faculty of Life Sciences, University of Vienna, Althanstraße 14, Vienna, 1090 Austria
| | - E. Redl
- Department of Integrative Zoology, Faculty of Life Sciences, University of Vienna, Althanstraße 14, Vienna, 1090 Austria
| | - C. Todt
- University of Bergen, University Museum, The Natural History Collections, Allégaten 41, 5007 Bergen, Norway
| | - C. Bleidorn
- Museo Nacional de Ciencias Naturales, Spanish National Research Council (CSIC), José Gutiérrez Abascal 2, Madrid, 28006 Spain
- Institute of Biology, University of Leipzig, Leipzig, 04103 Germany
| | - A. Wanninger
- Department of Integrative Zoology, Faculty of Life Sciences, University of Vienna, Althanstraße 14, Vienna, 1090 Austria
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89
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Che J, Shi J, Gao Z, Zhang Y. Transcriptome Analysis Reveals the Genetic Basis of the Resveratrol Biosynthesis Pathway in an Endophytic Fungus (Alternaria sp. MG1) Isolated from Vitis vinifera. Front Microbiol 2016; 7:1257. [PMID: 27588016 PMCID: PMC4988973 DOI: 10.3389/fmicb.2016.01257] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Accepted: 07/29/2016] [Indexed: 12/19/2022] Open
Abstract
Alternaria sp. MG1, an endophytic fungus previously isolated from Merlot grape, produces resveratrol from glucose, showing similar metabolic flux to the phenylpropanoid biosynthesis pathway, currently found solely in plants. In order to identify the resveratrol biosynthesis pathway in this strain at the gene level, de novo transcriptome sequencing was conducted using Illumina paired-end sequencing. A total of 22,954,434 high-quality reads were assembled into contigs and 18,570 unigenes were identified. Among these unigenes, 14,153 were annotated in the NCBI non-redundant protein database and 5341 were annotated in the Swiss-Prot database. After KEGG mapping, 2701 unigenes were mapped onto 115 pathways. Eighty-four unigenes were annotated in major pathways from glucose to resveratrol, coding 20 enzymes for glycolysis, 10 for phenylalanine biosynthesis, 4 for phenylpropanoid biosynthesis, and 4 for stilbenoid biosynthesis. Chalcone synthase was identified for resveratrol biosynthesis in this strain, due to the absence of stilbene synthase. All the identified enzymes indicated a reasonable biosynthesis pathway from glucose to resveratrol via glycolysis, phenylalanine biosynthesis, phenylpropanoid biosynthesis, and stilbenoid pathways. These results provide essential evidence for the occurrence of resveratrol biosynthesis in Alternaria sp. MG1 at the gene level, facilitating further elucidation of the molecular mechanisms involved in this strain's secondary metabolism.
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Affiliation(s)
- Jinxin Che
- College of Food Science and Engineering, Northwest A & F University Yangling, China
| | - Junling Shi
- Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University Xi'an, China
| | - Zhenhong Gao
- College of Food Science and Engineering, Northwest A & F University Yangling, China
| | - Yan Zhang
- College of Food Science and Engineering, Northwest A & F University Yangling, China
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90
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Liu H, Li S, Wang X, Zhu J, Wei Y, Wang Y, Wen Y, Wang L, Huang Y, Zhang B, Shang S, Zhang Y. DNA methylation dynamics: identification and functional annotation. Brief Funct Genomics 2016; 15:470-484. [PMID: 27515490 DOI: 10.1093/bfgp/elw029] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
DNA methylation is an epigenetic modification of cytosines that undergoes dynamic changes in a temporal, spatial and cell-type-specific manner. Recent advances in technology have permitted the profiling of high-throughput methylomes in large numbers of biological samples. Various computational tools have been developed to identify and analyze DNA methylation dynamics in a variety of critical biological processes. As DNA methylation is becoming increasingly viewed as a dynamic process, the mechanisms governing DNA methylation dynamics and its roles in the transcriptional regulatory network are of great interest. It has been reported that DNA methylation dynamics plays essential roles in multiple biological processes, including development and cancer. As a functional event, the dynamics of DNA methylation have become increasingly relevant to many researchers. Here, we review state-of-the-art advances at three levels (genome-wide identification, regulatory mechanism investigation and the functional annotation) in the field of DNA methylation dynamics, as well as the future perspective of DNA methylation dynamics.
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91
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Recent Perspective of Next Generation Sequencing: Applications in Molecular Plant Biology and Crop Improvement. ACTA ACUST UNITED AC 2016. [DOI: 10.1007/s40011-016-0770-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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92
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Li C, Cao C, Tu J, Sun X. An accurate clone-based haplotyping method by overlapping pool sequencing. Nucleic Acids Res 2016; 44:e112. [PMID: 27095193 PMCID: PMC4937318 DOI: 10.1093/nar/gkw284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Accepted: 04/07/2016] [Indexed: 11/25/2022] Open
Abstract
Chromosome-long haplotyping of human genomes is important to identify genetic variants with differing gene expression, in human evolution studies, clinical diagnosis, and other biological and medical fields. Although several methods have realized haplotyping based on sequencing technologies or population statistics, accuracy and cost are factors that prohibit their wide use. Borrowing ideas from group testing theories, we proposed a clone-based haplotyping method by overlapping pool sequencing. The clones from a single individual were pooled combinatorially and then sequenced. According to the distinct pooling pattern for each clone in the overlapping pool sequencing, alleles for the recovered variants could be assigned to their original clones precisely. Subsequently, the clone sequences could be reconstructed by linking these alleles accordingly and assembling them into haplotypes with high accuracy. To verify the utility of our method, we constructed 130 110 clones in silico for the individual NA12878 and simulated the pooling and sequencing process. Ultimately, 99.9% of variants on chromosome 1 that were covered by clones from both parental chromosomes were recovered correctly, and 112 haplotype contigs were assembled with an N50 length of 3.4 Mb and no switch errors. A comparison with current clone-based haplotyping methods indicated our method was more accurate.
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Affiliation(s)
- Cheng Li
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, Jiangsu 210002, China
| | - Changchang Cao
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, Jiangsu 210002, China
| | - Jing Tu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, Jiangsu 210002, China
| | - Xiao Sun
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, Jiangsu 210002, China
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