scholarly journals Estimating the quality of eukaryotic genomes recovered from metagenomic analysis with EukCC

2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Paul Saary ◽  
Alex L. Mitchell ◽  
Robert D. Finn
Keyword(s):  
Marker Gene ◽  
Single Copy ◽  
High Quality ◽  
Dynamic Selection ◽  
Microbial Eukaryotes ◽  
Gene Sets ◽  
Current Availability ◽  
Eukaryotic Genomes ◽  
Selection Of

Abstract Microbial eukaryotes constitute a significant fraction of biodiversity and have recently gained more attention, but the recovery of high-quality metagenomic assembled eukaryotic genomes is limited by the current availability of tools. To help address this, we have developed EukCC, a tool for estimating the quality of eukaryotic genomes based on the automated dynamic selection of single copy marker gene sets. We demonstrate that our method outperforms current genome quality estimators, particularly for estimating contamination, and have applied EukCC to datasets derived from two different environments to enable the identification of novel eukaryote genomes, including one from the human skin.

scholarly journals Estimating the quality of eukaryotic genomes recovered from metagenomic analysis

2019 ◽  
Author(s):  
Paul Saary ◽  
Alex L. Mitchell ◽  
Robert D. Finn
Keyword(s):  
Large Fraction ◽  
Marker Gene ◽  
Single Copy ◽  
Dynamic Selection ◽  
Microbial Eukaryotes ◽  
Gene Sets ◽  
Eukaryotic Genomes ◽  
Eukaryote Genome ◽  
Selection Of

AbstractEukaryotes make up a large fraction of microbial biodiversity. However, the field of metagenomics has been heavily biased towards the study of just the prokaryotic fraction. This focus has driven the necessary methodological developments to enable the recovery of prokaryotic genomes from metagenomes, which has reliably yielded genomes from thousands of novel species. More recently, microbial eukaryotes have gained more attention, but there is yet to be a parallel explosion in the number of eukaryotic genomes recovered from metagenomic samples. One of the current deficiencies is the lack of a universally applicable and reliable tool for the estimation of eukaryote genome quality. To address this need, we have developed EukCC, a tool for estimating the quality of eukaryotic genomes based on the dynamic selection of single copy marker gene sets, with the aim of applying it to metagenomics datasets. We demonstrate that our method outperforms current genome quality estimators and have applied EukCC to datasets from two different biomes to enable the identification of novel genomes, including a eukaryote found on the human skin and a Bathycoccus species obtained from a marine sample.

scholarly journals GENETIC VARIATION OF HUMPBACK GROUPER (Cromileptes altivelis) ON F1 AND F3 GENERATIONS

2013 ◽  
Vol 5 (1) ◽  
Author(s):  
Sari Budi Moria Sembiring ◽  
Tridjoko Tridjoko ◽  
Haryanti Haryanti
Keyword(s):  
Body Weight ◽  
Genetic Variation ◽  
Body Length ◽  
Quantitative Characteristic ◽  
Breeding Program ◽  
High Quality ◽  
Culture Technology ◽  
Selection Of ◽  
Rapd Method

Hatchery and culture technology of Humpback grouper has been developed. However,  sometimes it is still found constraint in sedd production and caused instability of production due to failure by many factors. Breeding program become necessary to provide seed with high quality and good genetic variation. Quantitative characteristic selection is one of breeding program to improve productivity in grouper aquaculture. The aim of this research was to produce good phenotyphic and genotypic quality of Humpback grouper candidate broodstock. Selection of Humpback grouper F1 and F3 was done based on quantitative characteristic (body length and weight) and genotyphic characteristic by using ramdom amplified polymorphism DNA (RAPD) method.  The results of conventional selection were found candidate broodstock of Humpback grouper F1 and F3 with body weight range from 170-210 g and 160-170 g consecutively.  Heterozygosity values of Humpback grouper analized by RAPD of F1 and F3 were 0.7940 and 0.7749 consecutively and it was not significantly different. This value emphasis that population of this F3 Humpback grouper was still good to grow for broodstock. Keywords: genetic variation, humpback grouper, F1, F3.

scholarly journals QUALITY PREDICTION OF DENSE POINTS GENERATED BY STRUCTURE FROM MOTION FOR HIGH-QUALITY AND EFFICIENT AS-IS MODEL RECONSTRUCTION

2019 ◽  
Vol XLII-2/W13 ◽  
pp. 95-101
Author(s):  
R. Moritani ◽  
S. Kanai ◽  
H. Date ◽  
Y. Niina ◽  
R. Honma
Keyword(s):  
Structure From Motion ◽  
Point Clouds ◽  
Quality Prediction ◽  
Construction Site ◽  
Model Reconstruction ◽  
High Quality ◽  
Bridge Column ◽  
Dense Point ◽  
Selection Of

<p><strong>Abstract.</strong> In this paper, we introduce a method for predicting the quality of dense points and selecting low-quality regions on the points generated by the structure from motion (SfM) and multi-view stereo (MVS) pipeline to realize high-quality and efficient as-is model reconstruction, using only results from the former: sparse point clouds and camera poses. The method was shown to estimate the quality of the final dense points as the quality predictor on an approximated model obtained from SfM only, without requiring the time-consuming MVS process. Moreover, the predictors can be used for selection of low-quality regions on the approximated model to estimate the next-best optimum camera poses which could improve quality. Furthermore, the method was applied to the prediction of dense point quality generated from the image sets of a concrete bridge column and construction site, and the prediction was validated in a time much shorter than using MVS. Finally, we discussed the correlation between the predictors and the final dense point quality.</p>

scholarly journals High-quality assembly of sweet basil genome

2018 ◽  
Author(s):  
Nativ Dudai ◽  
Marie-Jeanne Carp ◽  
Renana Milavski ◽  
David Chaimovitsh ◽  
Alona Shachter ◽  
...  
Keyword(s):  
Reference Genome ◽  
Single Copy ◽  
High Quality ◽  
Sweet Basil ◽  
Independent Analysis ◽  
Aroma Production ◽  
Culinary Uses ◽  
Underlying Mechanisms ◽  
Sequencing Platforms

AbstractSweet basil, sometimes called the King of Herbs, is well known for its culinary uses, especially in the Italian sauce ‘Pesto’. It is also used in traditional medicine, as a source for essential oils and as an ornamental plant. So far, basil was bred by classical and traditional methods due to lack of a reference genome that will allow optimized application of the most up-to-date sequencing techniques. Here, we report on the first completion of the sweet basil genome of the cultivar ‘Perrie’, a fresh-cut Genovese-type basil, using several next generation sequencing platforms followed by genome assembly with NRGENE’s DeNovoMAGIC assembly tool. We determined that the genome size of sweet basil is 2.13 Gbp and assembled it into 12,212 scaffolds. The high-quality of the assembly is reflected in that more than 90% of the assembly size is composed of only 107 scaffolds. An independent analysis of single copy orthologues genes showed a 93% completeness which reveal also that 74% of them were duplicated, indicating that the sweet basil is a tetraploid organism. A reference genome of sweet basil will enable to develop precise molecular markers for various agricultural important traits such as disease resistance and tolerance to various environmental conditions. We will gain a better understanding of the underlying mechanisms of various metabolic processes such as aroma production and pigment accumulation. Finally, it will save time and money for basil breeders and scientists and ensure higher throughput and robustness in future studies.

scholarly journals Testing of tomato hybrids of the breeding of the company "Gavrish" in JSC "Teplichnoye" of the Tambov region

2019 ◽  
pp. 64-67
Author(s):  
Konstantin A. Chupkin ◽  
Vera I. Terekhova ◽  
Anastasiya V. Konstantinovich
Keyword(s):  
Vegetable Crops ◽  
High Quality ◽  
Traditional Form ◽  
Original Shape ◽  
Tomato Breeding ◽  
Extended Circulation ◽  
The Rose ◽  
Selection Of

Relevance Currently, the requirements for modern tomato hybrids are increasing both from consumers and from producers. Modern tomato hybrids in extended circulation should yield at least 60 kg / m2, be distinguished by high quality of fruits, early ripeness, possess manufacturability, resistance to major diseases. Along with the traditional form of fruits, hybrids with original shape, color, taste and aroma are interesting for manufacturers. Methods The aim of the research was the variety study of indeterminant F1 hybrids of tomato breeding of the company "Gavrish" in JSC "Teplichnoye" of the Tambov region. Studies were conducted in 2017-2018 in the extended and summer-autumn turnover in the conditions of JSC "Teplichnoye" of the Tambov region in accordance with generally accepted recommendations for research with vegetable crops in greenhouses. The objects of the study in extended circulation were tomato hybrids: F1 Bao Bab, F1 Baloven, the F1 Torero hybrid was taken as a control. In the summerautumn turnover, a study was made of the rose hybrid – F1 Panthera; the Rosario F1 hybrid was used as a control; a hybrid with a plum-shaped fruit – F1 Armata, control – a hybrid F1 Lezghinka. Results According to the results of the study of tomato hybrids, the selection of the Gavrish company at the enterprise made the decision to grow it in extended circulation and increase the area under F1 Baloven, in the summer-autumn turnover under the F1 Panthera hybrid.

scholarly journals THE QUALITY ANALYSIS OF CHOCOLATE CONFECTIONERY PRODUCTS IN RESTAURANT BUSINESS

2018 ◽  
Vol 64 ◽  
Author(s):  
N.V. Bespalova ◽  
M.M. Gomola ◽  
T.I. Yakovleva
Keyword(s):  
Quality Control ◽  
Raw Materials ◽  
Quality Analysis ◽  
High Quality ◽  
Confectionery Products ◽  
Practical Recommendations ◽  
Selection Of

The article is devoted to the urgent theoretical and practical problems of the quality control of the chocolate confectionery products in cafes and restaurants. The authors analyze the modern approaches to the quality control of the chocolate confectionery products. The practical recommendations can be useful for the process of selection of the high quality raw materials. The criteria for the quality control of the chocolate confectionery products have been given. Some ways to improve the quality of he chocolate confectionery products have been discussed.

scholarly journals Ampelographic and oenological characterization of the ancient grapevine cv. Dobričić grown in the coastal region of Croatia

OENO One ◽  
2012 ◽  
Vol 46 (4) ◽  
pp. 263
Author(s):  
Goran Zdunić ◽  
Irena Budić-Leto ◽  
Urska Vrhovsek ◽  
Iva Tomić-Potrebuješ ◽  
Edi Maletić
Keyword(s):  
Coastal Region ◽  
Red Wines ◽  
High Quality ◽  
Virus Incidence ◽  
High Virus ◽  
First Time ◽  
Outstanding Quality ◽  
Selection Of

<p style="text-align: justify;"><strong>Aims</strong>:A four-year study (2007 through 2010) was carried out to determine agronomic, biological, and oenological characteristics of Dobričić grapevines so as to evaluate this cultivar and protect it from extinction.</p><p style="text-align: justify;"><strong>Methods and results</strong>: 38 characteristics from the OIV descriptor list were used to describe young shoot, mature leaf, cluster, and berry morphology of Dobričić grapevines. The dimensions of an average leaf were constructed from measured leaf variables. A typical Dobričić genotype at nine microsatellite loci is presented. ELISA analysis revealed high virus incidence and all samples tested were GLRaV-3 positive. The profile of different classes of polyphenols in Dobričić wine was determined using HPLC and spectrophotometry. The concentrations of polyphenols in Dobričić wine, especially anthocyanins, hydroxycinnamic acids and stilbenes, were high compared to major red wines reported in the literature. Descriptive sensory analysis was carried out to determine the aroma attributes describing a Dobričić monovarietal wine.</p><p style="text-align: justify;"><strong>Conclusion</strong>: Knowledge of the biodiversity of the grapevine cultivars of Croatia is still scant. This study provides for the first time ampelographic and oenological information on Dobričić grapevines and demonstrates its high quality potential.</p><p style="text-align: justify;"><strong>Significance and impact of the study</strong>: The results of the ampelographic characterization would be helpful in the identification and selection of Dobričić for cultivation in certain vine-growing areas. The outstanding quality of Dobričić makes it very promising for wine blending (colour improvement) and plant breeding purposes.</p>

scholarly journals GENETIC VARIATION OF HUMPBACK GROUPER (Cromileptes altivelis) ON F1 AND F3 GENERATIONS

2013 ◽  
Vol 5 (1) ◽  
Author(s):  
Sari Budi Moria Sembiring ◽  
Tridjoko Tridjoko ◽  
Haryanti Haryanti
Keyword(s):  
Body Weight ◽  
Genetic Variation ◽  
Body Length ◽  
Quantitative Characteristic ◽  
Breeding Program ◽  
High Quality ◽  
Culture Technology ◽  
Selection Of ◽  
Rapd Method

<p>Hatchery and culture technology of Humpback grouper has been developed. However,  sometimes it is still found constraint in sedd production and caused instability of production due to failure by many factors. Breeding program become necessary to provide seed with high quality and good genetic variation. Quantitative characteristic selection is one of breeding program to improve productivity in grouper aquaculture. The aim of this research was to produce good phenotyphic and genotypic quality of Humpback grouper candidate broodstock. Selection of Humpback grouper F1 and F3 was done based on quantitative characteristic (body length and weight) and genotyphic characteristic by using ramdom amplified polymorphism DNA (RAPD) method.  The results of conventional selection were found candidate broodstock of Humpback grouper F1 and F3 with body weight range from 170-210 g and 160-170 g consecutively.  Heterozygosity values of Humpback grouper analized by RAPD of F1 and F3 were 0.7940 and 0.7749 consecutively and it was not significantly different. This value emphasis that population of this F3 Humpback grouper was still good to grow for broodstock.</p> <p>Keywords: genetic variation, humpback grouper, F1, F3.</p>

scholarly journals Predicting Tomato Seedling Morphology by X-ray Analysis of Seeds

1994 ◽  
Vol 119 (2) ◽  
pp. 258-263 ◽  
Author(s):  
W.J. van der Burg ◽  
J.W. Aartse ◽  
R.A van Zwol ◽  
H. Jalink ◽  
R.J. Bino
Keyword(s):  
Free Space ◽  
Evaluation Procedure ◽  
Germination Test ◽  
High Quality ◽  
Seedling Morphology ◽  
Tomato Seedling ◽  
X Ray ◽  
Size And Morphology ◽  
Selection Of

Studies based on X-ray photographs were conducted to predict the morphology of tomato (Lycopersicon esculentum Mill.) seedlings at transplanting stage. Currently, seed-lot quality of tomato seeds for growing commercial transplants is determined with grow-out tests in the greenhouse because the standard germination test fails to predict the percentage of normal or usable transplants (UTs). These grow-out tests, however, are difficult to standardize. An X-ray evaluation procedure is presented as an alternative. X-ray images nondestructively provide information on embryo size and morphology and the amount of endosperm and the area of free space. These parameters correlate well with the morphology of 14-day old seedlings. Cotyledon morphology has the highest correlation with the percentage of UTs. A test based on the evaluation of X-ray images, classifying the cotyledon morphology and seed free space, predicts the percentage of UTs more accurately than the currently used germination test. A second method based on an equation that uses the probabilities of all X-ray categories proportionally predicts the percentage of UTs of primed seeds more accurately than the first method. Selecting individual seeds based on X-ray images has the potential to raise the percentage of UTs of seed lots. On the average, the percentage of UTs of control seeds was 22% higher after hand selection based on X-ray evaluation. Primed seeds gave 12% higher results. Hence, X-ray analysis can predict seedling performance and enable the selection of high-quality seeds.

scholarly journals Factors influencing consumer behaviour in the beer market in the Czech Republic

2021 ◽  
Vol 39 (No. 4) ◽  
pp. 319-328
Author(s):  
Veronika Svatošová ◽  
Petra Kosová ◽  
Zuzana Svobodová
Keyword(s):  
Czech Republic ◽  
Consumer Behaviour ◽  
Influential Factors ◽  
Influential Factor ◽  
High Quality ◽  
The Czech Republic ◽  
Beer Consumption ◽  
Factors Influencing ◽  
Selection Of

The aim of the paper is to identify the factors influencing consumers when beer consumption and when choosing restaurants for beer consumption in the Czech Republic (CR). A partial goal was to compare preferences and factors influencing beer consumers from the Vysočina Region and the South-Moravian Region. The survey included a questionnaire survey, which 408 respondents took part in. The results showed that the most influential factors in the selection of beer for consumers are taste, a high-quality brand, and Czech production. Surprisingly, price was not found to be an influential factor in beer selection but is rather neutral. Factors that influence consumers most when choosing a restaurant for beer consumption were also identified. Consumers are most influenced by the quality of the beer on offer and the environment in which it is consumed.

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