scholarly journals Quick and efficient approach to develop genomic resources in orphan species: application in Lavandula angustifolia

2018 ◽  
Author(s):  
Berline Fopa Fomeju ◽  
Dominique Brunel ◽  
Aurélie Bérard ◽  
Jean-Baptiste Rivoal ◽  
Philippe Gallois ◽  
...  
Keyword(s):  
Large Scale ◽  
De Novo ◽  
Rapid Development ◽  
Genetic Distances ◽  
Lavandula Angustifolia ◽  
Alternative Medicines ◽  
Snp Development ◽  
High Level ◽  
The Cost ◽  
Next Generation Sequencing Ngs

AbstractNext-Generation Sequencing (NGS) technologies, by reducing the cost and increasing the throughput of sequencing, have opened doors of research efforts to generate genomic data to a range of previously poorly studied species. In this study, we proposed a method for the rapid development of a large scale molecular resources for orphan species. We studied as an example Lavandula angustifolia, a perennial sub-shrub plant native from the Mediterranean region and whose essential oil have numerous applications in cosmetics, pharmaceuticals, and alternative medicines.We first built a ‘Maillette’ reference Unigene, compound of coding sequences, thanks to de novo RNA-seq assembly. Then, we reconstructed the complete genes sequences (with exons and introns) using a transcriptome-guided DNA-seq assembly approach in order to maximize the possibilities of finding polymorphism between genetically close individuals. Finally, we used these resources for SNP mining within a collection of 16 lavender clones and tested the SNP within the scope of a phylogeny analysis. We obtained a cleaned reference of 8, 030 functionally annotated ‘genes’ (in silico annotation). We found up to 400K polymorphic sites, depending on the genotype analyzed, and observed a high SNP frequency (mean of 1 SNP per 90 bp) and a high level of heterozygosity (more than 60% of heterozygous SNP per genotype). We found similar genetic distances between pairs of clones, related to the out-crossing nature of the species, the restricted area of cultivation and the clonal propagation of the varieties.The method propose is transferable to other orphan species, requires little bioinformatics resources and can be realized within a year. This is the first reported large-scale SNP development on Lavandula angustifolia. All this data provides a rich pool of molecular resource to explore and exploit biodiversity in breeding programs.

scholarly journals Quick and efficient approach to develop genomic resources in orphan species: Application in Lavandula angustifolia

PLoS ONE ◽  
2020 ◽  
Vol 15 (12) ◽  
pp. e0243853
Author(s):  
Berline Fopa Fomeju ◽  
Dominique Brunel ◽  
Aurélie Bérard ◽  
Jean-Baptiste Rivoal ◽  
Philippe Gallois ◽  
...  
Keyword(s):  
Large Scale ◽  
De Novo ◽  
Rapid Development ◽  
Genetic Distances ◽  
Lavandula Angustifolia ◽  
Distance Analysis ◽  
Alternative Medicines ◽  
Dna And Rna ◽  
Snp Development ◽  
High Level

Next-Generation Sequencing (NGS) technologies, by reducing the cost and increasing the throughput of sequencing, have opened doors to generate genomic data in a range of previously poorly studied species. In this study, we propose a method for the rapid development of a large-scale molecular resources for orphan species. We studied as an example the true lavender (Lavandula angustifolia Mill.), a perennial sub-shrub plant native from the Mediterranean region and whose essential oil have numerous applications in cosmetics, pharmaceuticals, and alternative medicines. The heterozygous clone “Maillette” was used as a reference for DNA and RNA sequencing. We first built a reference Unigene, compound of coding sequences, thanks to de novo RNA-seq assembly. Then, we reconstructed the complete genes sequences (with introns and exons) using an Unigene-guided DNA-seq assembly approach. This aimed to maximize the possibilities of finding polymorphism between genetically close individuals despite the lack of a reference genome. Finally, we used these resources for SNP mining within a collection of 16 commercial lavender clones and tested the SNP within the scope of a genetic distance analysis. We obtained a cleaned reference of 8, 030 functionally in silico annotated genes. We found 359K polymorphic sites and observed a high SNP frequency (mean of 1 SNP per 90 bp) and a high level of heterozygosity (more than 60% of heterozygous SNP per genotype). On overall, we found similar genetic distances between pairs of clones, which is probably related to the out-crossing nature of the species and the restricted area of cultivation. The proposed method is transferable to other orphan species, requires little bioinformatics resources and can be realized within a year. This is also the first reported large-scale SNP development on Lavandula angustifolia. All the genomics resources developed herein are publicly available and provide a rich pool of molecular resources to explore and exploit lavender genetic diversity in breeding programs.

scholarly journals TnClone: high-throughput clonal analysis using Tn5-mediated library construction and de novo assembly

2018 ◽  
Author(s):  
Byungjin Hwang ◽  
Sunghoon Heo ◽  
Namjin Cho ◽  
Duhee Bang
Keyword(s):  
Sanger Sequencing ◽  
Large Scale ◽  
De Novo ◽  
Low Frequency ◽  
Clonal Analysis ◽  
Hands On ◽  
The Cost ◽  
Next Generation Sequencing Ngs ◽  
User Friendly ◽  
Analysis Platform

ABSTRACTA typical molecular cloning procedure requires Sanger sequencing for validation, which becomes cost-prohibitive and labour-intensive for large-scale clonal analysis of genotype-phenotype studies. Here we present a Tn5-mediated clonal analysis platform TnClone, which uses next-generation sequencing (NGS) to rapidly and cost-effectively analyze a large number of clones. We also developed a user-friendly graphical user interface and have provided general guidelines for conducting validation experiments. Using TnClone, we achieved more than 20-fold cost reduction compared with the cost incurred using conventional Sanger sequencing and detected low-frequency mutant clones (~10%) in mixed samples. We tested our programme and achieved 99.4% sensitivity. Our platform provides rapid turnaround with minimal hands-on time for secondary evaluation as NGS technology continues to evolve.

scholarly journals Comparative genomics and pangenome-oriented studies reveal high homogeneity of the agronomically relevant enterobacterial plant pathogen Dickeya solani

2020 ◽  
Author(s):  
Agata Motyka-Pomagruk ◽  
Sabina Zoledowska ◽  
Agnieszka Emilia Misztak ◽  
Wojciech Sledz ◽  
Alessio Mengoni ◽  
...  
Keyword(s):  
Comparative Genomics ◽  
Large Scale ◽  
De Novo ◽  
Genetic Material ◽  
Soft Rot ◽  
Potato Production ◽  
Core Gene ◽  
Ecological Niches ◽  
Dickeya Solani ◽  
High Level

Abstract Background: Dickeya solani is an important plant pathogenic bacterium causing severe losses in European potato production. This species draws a lot of attention due to its remarkable virulence, great devastating potential and easier spread in contrast to other Dickeya spp. In view of a high need for extensive studies on economically important soft rot Pectobacteriaceae , we performed a comparative genomics analysis on D. solani strains to search for genetic foundations that would explain the differences in the observed virulence levels within the D. solani population. Results: High quality assemblies of 8 de novo sequenced D. solani genomes have been obtained. Whole-sequence comparison, ANIb, ANIm, Tetra and pangenome-oriented analyses performed on these genomes and the sequences of 14 additional strains revealed an exceptionally high level of homogeneity among the studied genetic material of D. solani strains. With the use of 22 genomes, the pangenome of D. solani , comprising 84.7% core, 7.2% accessory and 8.1% unique genes, has been almost completely determined, suggesting the presence of a nearly closed pangenome structure. Attribution of the genes included in the D. solani pangenome fractions to functional COG categories showed that higher percentages of accessory and unique pangenome parts in contrast to the core section are encountered in phage/mobile elements- and transcription- associated groups with the genome of RNS 05.1.2A strain having the most significant impact. Also, the first D. solani large-scale genome-wide phylogeny computed on concatenated core gene alignments is herein reported. Conclusions: The almost closed status of D. solani pangenome achieved in this work points to the fact that the unique gene pool of this species should no longer expand. Such a feature is characteristic of taxa whose representatives either occupy isolated ecological niches or lack efficient mechanisms for gene exchange and recombination, which seems rational concerning a strictly pathogenic species with clonal population structure. Finally, no obvious correlations between the geographical origin of D. solani strains and their phylogeny were found, which might reflect the specificity of the international seed potato market.

scholarly journals LeafGo: Leaf to Genome, a quick workflow to produce high-quality De novo genomes with Third Generation Sequencing technology

2021 ◽  
Author(s):  
Patrick Driguez ◽  
Salim Bougouffa ◽  
Karen Carty ◽  
Alexander Putra ◽  
Kamel Jabbari ◽  
...  
Keyword(s):  
De Novo ◽  
Rapid Development ◽  
Plant Genome ◽  
Plant Genomics ◽  
High Quality ◽  
High Molecular Weight Dna ◽  
Tissue Samples ◽  
Sequencing Technologies ◽  
The Cost ◽  
New Generation

AbstractRecent years have witnessed a rapid development of sequencing technologies. Fundamental differences and limitations among various platforms impact the time, the cost and the accuracy for sequencing whole genomes. Here we designed a complete de novo plant genome generation workflow that starts from plant tissue samples and produces high-quality draft genomes with relatively modest laboratory and bioinformatic resources within seven days. To optimize our workflow we selected different species of plants which were used to extract high molecular weight DNA, to make PacBio and ONT libraries for sequencing with the Sequel I, Sequel II and GridION platforms. We assembled high-quality draft genomes of two different Eucalyptus species E. rudis, and E. camaldulensis to chromosome level without using additional scaffolding technologies. For the rapid production of de novo genome assembly of plant species we showed that our DNA extraction protocol followed by PacBio high fidelity sequencing, and assembly with new generation assemblers such as hifiasm produce excellent results. Our findings will be a valuable benchmark for groups planning wet- and dry-lab plant genomics research and for high throughput plant genomics initiatives.

scholarly journals Views on Differential Management in Safety Supervision of Construction Engineering

2018 ◽  
Vol 2 (2) ◽  
Author(s):  
Song Yinghua
Keyword(s):  
Large Scale ◽  
Rapid Development ◽  
Science And Technology ◽  
Deep Foundation ◽  
Safety Risk ◽  
Construction Engineering ◽  
Engineering Construction ◽  
Engineering Structure ◽  
High Level ◽  
Socialist Market

Given the advances in science and technology, rapid development of socialist market economy and continuous advance of urbanization, it is necessary to enlarge the scale of engineering construction. As the form of engineering structure becomes more complex, large-scale and high-level projects with deep foundation have appeared in engineering construction. For construction engineering, one of its technologies includes solving the difficulties in construction. It is required to deal with the safety risk of construction in time to guarantee safety construction, timely solve the management difficulties and contradictory problems of the project and ensure both the safety of engineering construction and the rationalization of the institution setting of the safety supervision on the project. 

scholarly journals Using Greedy Random Adaptive Procedure to Solve the User Selection Problem in Mobile Crowdsourcing

Sensors ◽  
2019 ◽  
Vol 19 (14) ◽  
pp. 3158
Author(s):  
Jian Yang ◽  
Xiaojuan Ban ◽  
Chunxiao Xing
Keyword(s):  
Mobile Networks ◽  
Large Scale ◽  
Rapid Development ◽  
Synthetic Data ◽  
Data Sets ◽  
User Selection ◽  
Adaptive Procedure ◽  
Mobile Crowdsourcing ◽  
Marginal Gain ◽  
The Cost

With the rapid development of mobile networks and smart terminals, mobile crowdsourcing has aroused the interest of relevant scholars and industries. In this paper, we propose a new solution to the problem of user selection in mobile crowdsourcing system. The existing user selection schemes mainly include: (1) find a subset of users to maximize crowdsourcing quality under a given budget constraint; (2) find a subset of users to minimize cost while meeting minimum crowdsourcing quality requirement. However, these solutions have deficiencies in selecting users to maximize the quality of service of the task and minimize costs. Inspired by the marginalism principle in economics, we wish to select a new user only when the marginal gain of the newly joined user is higher than the cost of payment and the marginal cost associated with integration. We modeled the scheme as a marginalism problem of mobile crowdsourcing user selection (MCUS-marginalism). We rigorously prove the MCUS-marginalism problem to be NP-hard, and propose a greedy random adaptive procedure with annealing randomness (GRASP-AR) to achieve maximize the gain and minimize the cost of the task. The effectiveness and efficiency of our proposed approaches are clearly verified by a large scale of experimental evaluations on both real-world and synthetic data sets.

Targeted Resequencing of Putative Growth-Related Genes Using Whole Exome Sequencing in Patients with Severe Primary IGF-I Deficiency

2017 ◽  
Vol 88 (6) ◽  
pp. 408-417 ◽  
Author(s):  
Greta Grosse ◽  
Alina Hilger ◽  
Michael Ludwig ◽  
Heiko Reutter ◽  
Franziska Lorenzen ◽  
...  
Keyword(s):  
Large Scale ◽  
De Novo ◽  
Targeted Resequencing ◽  
Targeted Next Generation Sequencing ◽  
Increased Risk ◽  
Igf I ◽  
Novel Variant ◽  
Unaffected Parent ◽  
Next Generation Sequencing Ngs ◽  
Clinical Phenotyping

Background/Aims: To elucidate the genetic causes of severe primary insulin-like growth factor-I deficiency (SPIGFD) by systematic, targeted, next-generation sequencing (NGS)-based resequencing of growth-related genes. Methods: Clinical phenotyping followed by NGS in 17 families including 6 affected sib pairs. Results: We identified disease-causing, heterozygous, de novo variants in HRAS (p.Gly13Cys) and FAM111A (p.Arg569His) in 2 male patients with syndromic SPIGFD. A previously described homozygous GHR nonsense variant was detected in 2 siblings of a consanguineous family (p.Glu198*). Furthermore, we identified an inherited novel variant in the IGF2 gene (p.Arg156Cys) of a maternally imprinted gene in a less severely affected father and his affected daughter. We detected 2 other novel missense variants in SH2B1 and SOCS2, both were inherited from an unaffected parent. Conclusions: Screening of growth-related genes using NGS-based, large-scale, targeted resequencing identified disease-causing variants in HRAS, FAM111A, and GHR. Considering the increased risk of subjects with HRAS mutations for neoplasms, close clinical monitoring and a thorough discussion of the risk/benefit ratio of the treatment with recombinant IGF-I is mandatory. Segregation analysis proved to be critical in the interpretation of potential SPIGFD-associated gene variations.

scholarly journals A parallel computational framework for ultra-large-scale sequence clustering analysis

2018 ◽  
Vol 35 (3) ◽  
pp. 380-388 ◽  
Author(s):  
Wei Zheng ◽  
Qi Mao ◽  
Robert J Genco ◽  
Jean Wactawski-Wende ◽  
Michael Buck ◽  
...  
Keyword(s):  
Parallel Computing ◽  
High Performance ◽  
Large Scale ◽  
De Novo ◽  
Rapid Development ◽  
Operational Taxonomic Unit ◽  
Supplementary Information ◽  
Computational Framework ◽  
Speed Up ◽  
Scale Sequence

Abstract Motivation The rapid development of sequencing technology has led to an explosive accumulation of genomic data. Clustering is often the first step to be performed in sequence analysis. However, existing methods scale poorly with respect to the unprecedented growth of input data size. As high-performance computing systems are becoming widely accessible, it is highly desired that a clustering method can easily scale to handle large-scale sequence datasets by leveraging the power of parallel computing. Results In this paper, we introduce SLAD (Separation via Landmark-based Active Divisive clustering), a generic computational framework that can be used to parallelize various de novo operational taxonomic unit (OTU) picking methods and comes with theoretical guarantees on both accuracy and efficiency. The proposed framework was implemented on Apache Spark, which allows for easy and efficient utilization of parallel computing resources. Experiments performed on various datasets demonstrated that SLAD can significantly speed up a number of popular de novo OTU picking methods and meanwhile maintains the same level of accuracy. In particular, the experiment on the Earth Microbiome Project dataset (∼2.2B reads, 437 GB) demonstrated the excellent scalability of the proposed method. Availability and implementation Open-source software for the proposed method is freely available at https://www.acsu.buffalo.edu/~yijunsun/lab/SLAD.html. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals The Development of an Ordinary Least Squares Parametric Model to Estimate the Cost Per Flying Hour of ‘Unknown’ Aircraft Types and a Comparative Application †

Aerospace ◽  
2018 ◽  
Vol 5 (4) ◽  
pp. 104 ◽  
Author(s):  
Ilias Lappas ◽  
Michail Bozoudis
Keyword(s):  
Least Squares ◽  
Large Scale ◽  
Ordinary Least Squares ◽  
Parametric Model ◽  
Development Programs ◽  
Cost Estimating ◽  
Life Cycle Stages ◽  
Wide Range ◽  
High Level ◽  
The Cost

The development of a parametric model for the variable portion of the Cost Per Flying Hour (CPFH) of an ‘unknown’ aircraft platform and its application to diverse types of fixed and rotary wing aircraft development programs (F-35A, Su-57, Dassault Rafale, T-X candidates, AW189, Airbus RACER among others) is presented. The novelty of this paper lies in the utilization of a diverse sample of aircraft types, aiming to obtain a ‘universal’ Cost Estimating Relationship (CER) applicable to a wide range of platforms. Moreover, the model does not produce absolute cost figures but rather analogy ratios versus the F-16’s CPFH, broadening the model’s applicability. The model will enable an analyst to carry out timely and reliable Operational and Support (O&S) cost estimates for a wide range of ‘unknown’ aircraft platforms at their early stages of conceptual design, despite the lack of actual data from the utilization and support life cycle stages. The statistical analysis is based on Ordinary Least Squares (OLS) regression, conducted with R software (v5.3.1, released on 2 July 2018). The model’s output is validated against officially published CPFH data of several existing ‘mature’ aircraft platforms, including one of the most prolific fighter jet types all over the world, the F-16C/D, which is also used as a reference to compare CPFH estimates of various next generation aircraft platforms. Actual CPFH data of the Hellenic Air Force (HAF) have been used to develop the parametric model, the application of which is expected to significantly inform high level decision making regarding aircraft procurement, budgeting and future force structure planning, including decisions related to large scale aircraft modifications and upgrades.

A Review of Distribution Network Planning with Large-Scale Intermittent Renewable Energy Access to Distribution Network

2014 ◽  
Vol 1008-1009 ◽  
pp. 723-728 ◽  
Author(s):  
Xu Dong Song ◽  
Nan Hua Yu ◽  
Jun Jun Liang ◽  
Cheng Jun Xia
Keyword(s):  
Renewable Energy ◽  
Large Scale ◽  
Rapid Development ◽  
Distribution Network ◽  
Research Direction ◽  
Absorption Capacity ◽  
Energy Access ◽  
Multiple Sources ◽  
Unique Source ◽  
The Cost

With the rapid development of DG, especially the access of large-scale renewable energy, traditional simple distribution network with unique source turns into ADN with multiple sources, making the distribution network more complicated. In this paper, The power source and grid planning of traditional and intelligent distribution network are discussed, based on which the problems ADN faces and the research difficulty are focused on. The key technology of ADN planning is analyzed, including the uncertainty of load forecasting, the ADN absorption capacity for DG and the cost-effectiveness of ADN planning. Some suggestions for the research direction of ADN in the future are made at the end, providing reference for the ADN planning with large-scale renewable energy access.

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