scholarly journals The haplotype-resolved reference genome of lemon (Citrus limon L. Burm f.)

2021 ◽  
Author(s):  
Mario Di Guardo ◽  
Marco Moretto ◽  
Mirko Moser ◽  
Chiara Catalano ◽  
Michela Troggio ◽  
...  
Keyword(s):  
Reference Genome ◽  
Perfect Match ◽  
In Silico Analysis ◽  
Mature Mirnas ◽  
Citrus Limon ◽  
Oxford Nanopore ◽  
A Genome ◽  
Set Up ◽  
Definition Of

Lemon (Citrus limon (L.) Burm. f.) is an evergreen tree belonging to the genus Citrus. The fruits are particularly prized for their organoleptic and nutraceutical properties of the juice. Herein we report, for the first time, the release of a high-quality reference genome of the two haplotypes of lemon. The sequencing has been carried out coupling Illumina short reads and Oxford Nanopore data leading to the definition of a primary and an alternative assembly characterized by a genome size of 312.8 Mb and 324.74 Mb respectively. The analysis of the long terminal repeat (LTR) allowed the identification of 1921 regions on the primary and 1911 on the alternative assembly distributed across the nine chromosomes. Furthermore, an in-silico analysis of the microRNA genes was carried out using 246 mature miRNA and the respective pre-miRNA hairpin sequences of C. sinensis. Such analysis highlighted a high conservation between the two species with 233 mature miRNAs and 51 pre-miRNA stem-loops aligning with perfect match on the lemon genome. In parallel, total RNA was extracted from fruit, flower, leaf and root enabling the detection of 38,205 and 37,753 predicted transcripts on primary and alternative assemblies respectively. Among those, the highest and lowest number of tissue-specific transcripts were detected in flower (2.73% and 2.71% in primary and alternative assemblies respectively) and leaf (0.7% and 0.68%) while gene ontology analysis enables a more precise characterization of the expressed genes based on their function. The availability of a reference genome is an important prerequisite both for the set-up of high-throughput genotyping analysis and for functional genomic approaches toward the characterization of the genetic determinism of traits of agronomic interest.

scholarly journals Constructing a Reference Genome in a Single Lab: The Possibility to Use Oxford Nanopore Technology

Plants ◽  
2019 ◽  
Vol 8 (8) ◽  
pp. 270 ◽  
Author(s):  
Yun Gyeong Lee ◽  
Sang Chul Choi ◽  
Yuna Kang ◽  
Kyeong Min Kim ◽  
Chon-Sik Kang ◽  
...  
Keyword(s):  
Plant Species ◽  
Genome Sequencing ◽  
Reference Genome ◽  
Genome Structure ◽  
Plant Genome ◽  
Sequence Information ◽  
Sequencing Analysis ◽  
Oxford Nanopore ◽  
A Genome ◽  
Long Read

The whole genome sequencing (WGS) has become a crucial tool in understanding genome structure and genetic variation. The MinION sequencing of Oxford Nanopore Technologies (ONT) is an excellent approach for performing WGS and it has advantages in comparison with other Next-Generation Sequencing (NGS): It is relatively inexpensive, portable, has simple library preparation, can be monitored in real-time, and has no theoretical limits on reading length. Sorghum bicolor (L.) Moench is diploid (2n = 2x = 20) with a genome size of about 730 Mb, and its genome sequence information is released in the Phytozome database. Therefore, sorghum can be used as a good reference. However, plant species have complex and large genomes when compared to animals or microorganisms. As a result, complete genome sequencing is difficult for plant species. MinION sequencing that produces long-reads can be an excellent tool for overcoming the weak assembly of short-reads generated from NGS by minimizing the generation of gaps or covering the repetitive sequence that appears on the plant genome. Here, we conducted the genome sequencing for S. bicolor cv. BTx623 while using the MinION platform and obtained 895,678 reads and 17.9 gigabytes (Gb) (ca. 25× coverage of reference) from long-read sequence data. A total of 6124 contigs (covering 45.9%) were generated from Canu, and a total of 2661 contigs (covering 50%) were generated from Minimap and Miniasm with a Racon through a de novo assembly using two different tools and mapped assembled contigs against the sorghum reference genome. Our results provide an optimal series of long-read sequencing analysis for plant species while using the MinION platform and a clue to determine the total sequencing scale for optimal coverage that is based on various genome sizes.

scholarly journals Highly Contiguous Nanopore Genome Assembly of Chlamydomonas reinhardtii CC-1690

2020 ◽  
Vol 9 (37) ◽  
Author(s):  
Samuel O’Donnell ◽  
Frederic Chaux ◽  
Gilles Fischer
Keyword(s):  
Chlamydomonas Reinhardtii ◽  
Genome Size ◽  
Genome Assembly ◽  
Reference Genome ◽  
De Novo ◽  
Content Type ◽  
Oxford Nanopore ◽  
A Genome ◽  
Reference Quality

ABSTRACT The current Chlamydomonas reinhardtii reference genome remains fragmented due to gaps stemming from large repetitive regions. To overcome the vast majority of these gaps, publicly available Oxford Nanopore Technology data were used to create a new reference-quality de novo genome assembly containing only 21 contigs, 30/34 telomeric ends, and a genome size of 111 Mb.

scholarly journals Constructing a Reference Genome in a Single Lab: The Possibility to Use Oxford Nanopore Technology

2019 ◽  
Author(s):  
Yun Gyeong Lee ◽  
Sang Chul Choi ◽  
Yuna Kang ◽  
Kyeong Min Kim ◽  
Chon-Sik Kang ◽  
...  
Keyword(s):  
Plant Species ◽  
Genome Sequencing ◽  
Reference Genome ◽  
Plant Genome ◽  
Read Length ◽  
Sequence Information ◽  
Sequencing Analysis ◽  
Oxford Nanopore ◽  
A Genome ◽  
Long Read

The whole genome sequencing (WGS) has become a crucial tool to understand genome structure and genetic variation. The MinION sequencing of Oxford Nanopore Technologies (ONT) is an excellent approach for performing WGS and has advantages in comparison with other Next-Generation Sequencing (NGS): It is relatively inexpensive, portable, has simple library preparation, can be monitored in real-time, and has no theoretical limits on read length. Sorghum bicolor (L.) Moench is diploid (2n = 2x = 20) with a genome size of about 730 Mb, and its genome sequence information is released in the Phytozome database. Therefore, sorghum can be be used as a good reference. However, plant species have complex and large genomes compared to animals or microorganisms. As a result, complete genome sequencing is difficult for plant species. MinION sequencing that produces long-reads can be an excellent tool to overcome the weak assembly of short-reads generated from NGS by minimizing the generation of gaps or covering the repetitive sequence that appears on the plant genome. Here, we conducted the genome sequencing for S. bicolor cv. BTx623 using the MinION platform and obtained 895,678 reads and 17.9 gigabytes(Gb) (ca. 25X coverage of reference) from long-read sequence data. Through a de novo assembly using two different tools and mapped assembled contigs against the sorghum reference genome, a total of 6,124 contigs (covering 45.9%) were generated from Canu, and a total of 2,661 contigs (covering 50%) were generated from Minimap and Miniasm with a Racon pipeline. Our results provide a pipeline of long-read sequencing analysis for plant species using the MinION platform and a clue to determine the total sequencing scale for optimal coverage based on various genome sizes.

scholarly journals Genetic characterization of an almond germplasm collection and volatilome profiling of raw and roasted kernels

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
M. Di Guardo ◽  
B. Farneti ◽  
I. Khomenko ◽  
G. Modica ◽  
A. Mosca ◽  
...  
Keyword(s):  
Snp Array ◽  
Germplasm Collection ◽  
Phenotypic Characterization ◽  
South Italy ◽  
Genome Wide ◽  
A Genome ◽  
Genetic Stratification ◽  
Set Up ◽  
High Level

AbstractAlmond is appreciated for its nutraceutical value and for the aromatic profile of the kernels. In this work, an almond collection composed of 96 Sicilian accessions complemented with 10 widely cultivated cultivars was phenotyped for the production of volatile organic compounds using a proton-transfer time-of-flight mass spectrometer and genotyped using the Illumina Infinium®18 K Peach SNP array. The profiling of the aroma was carried out on fresh and roasted kernels enabling the detection of 150 mass peaks. Sixty eight, for the most related with sulfur compounds, furan containing compounds, and aldehydes formed by Strecker degradation, significantly increased during roasting, while the concentration of fifty-four mass peaks, for the most belonging to alcohols and terpenes, significantly decreased. Four hundred and seventy-one robust SNPs were selected and employed for population genetic studies. Structure analysis detected three subpopulations with the Sicilian accessions characterized by a different genetic stratification compared to those collected in Apulia (South Italy) and the International cultivars. The linkage-disequilibrium (LD) decay across the genome was equal to r2 = 0.083. Furthermore, a high level of collinearity (r2 = 0.96) between almond and peach was registered confirming the high synteny between the two genomes. A preliminary application of a genome-wide association analysis allowed the detection of significant marker-trait associations for 31 fresh and 33 roasted almond mass peaks respectively. An accurate genetic and phenotypic characterization of novel germplasm can represent a valuable tool for the set-up of marker-assisted selection of novel cultivars with an enhanced aromatic profile.

scholarly journals Chromosome scale reference genome of Cluster bean (Cyamopsis tetragonoloba (L.) Taub.)

2020 ◽  
Author(s):  
Kishor Gaikwad ◽  
G. Ramakrishna ◽  
Harsha Srivastava ◽  
Swati Saxena ◽  
Tanvi Kaila ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Reference Genome ◽  
Guar Gum ◽  
Western India ◽  
Cyamopsis Tetragonoloba ◽  
Protein Coding ◽  
Cluster Bean ◽  
Gas Drilling ◽  
Oxford Nanopore ◽  
A Genome

AbstractClusterbean (Cyamopsis tetragonoloba (L.) Taub.), also known as Guar is a widely cultivated dryland legume of Western India and parts of Africa. Apart from being a vegetable crop, it is also an abundant source of a natural hetero-polysaccharide called guar gum or galactomannan which is widely used in cosmetics, pharmaceuticals, food processing, shale gas drilling etc. Here, for the first time we are reporting a chromosome-scale reference genome assembly of clusterbean, from a high galactomannan containing popular guar cultivar, RGC-936, by combining sequenced reads from Illumina, 10x Chromium and Oxford Nanopore technologies. The initial assembly of 1580 scaffolds with an N50 value of 7.12 Mbp was generated. Then, the final genome assembly was obtained by anchoring these scaffolds to a high density SNP map. Finally, a genome assembly of 550.31 Mbp was obtained in 7 pseudomolecules corresponding to 7 chromosomes with a very high N50 of 78.27 Mbp. We finally predicted 34,680 protein-coding genes in the guar genome. The high-quality chromosome-scale cluster bean genome assembly will facilitate understanding of the molecular basis of galactomannan biosynthesis and aid in genomics-assisted breeding of superior cultivars.

The specifics of mergers and acquisitions of innovative and technological companies

2020 ◽  
Vol 26 (5) ◽  
pp. 1186-1204
Author(s):  
A.V. Fedorov ◽  
Zh.S. Peredera
Keyword(s):  
Digital Technology ◽  
Comprehensive Analysis ◽  
Methodological Framework ◽  
Comparison Study ◽  
Technology Sector ◽  
Theoretical Perspectives ◽  
Innovation And Technology ◽  
Set Up ◽  
Definition Of ◽  
Traditional Approaches

Subject. The article reviews distinctions of M&A deals in innovation and technology. Objectives. We determine the specifics of innovative and technological companies and its impact on the synergy, process, finance, valuation of M&A deals. Methods. The article employs methods of generalization, comprehensive analysis, systematization, specification, comparison, study into trends and the structure. Graphics and tables are used to display the findings. Results. We conducted the content analysis of the term Mergers & Acquisitions, thus finding the divergence of foreign and the Russian approaches. We provide our own definition of the concept and analyzed the dynamics of the overall M&A market and the innovation and technological sector. The article describes operational distinctions of innovative and technological companies and compares them with conventional sectors. The article determined the specifics of synergy, process, finance, valuation of M&A deals in innovation and technology. Conclusions and Relevance. The innovation and technology sector saw M&A deals become more frequent for the recent five years. What distinguishes them is the number of startups and infant businesses, large M&A deals in order to develop their ecosystems, involve digital technology companies. Traditional approaches should be adapted for structuring M&A deals, their arrangement, financing and valuation of target companies. The findings can lay the groundwork for further studies into the specifics of the innovation and technology sector, M&A deals, and set up the methodological framework for the valuation of innovative and technological companies. The findings can also immediately support parties of M&A deals from theoretical perspectives.

Developing capital accounting practices in the integrated reporting system of agricultural organizations

2020 ◽  
Vol 23 (8) ◽  
pp. 906-921
Author(s):  
R.A. Alborov ◽  
S.M. Kontsevaya ◽  
S.V. Kozmenkova
Keyword(s):  
Original Method ◽  
Theory And Practice ◽  
Integrated Reporting ◽  
Governance System ◽  
Analysis And Synthesis ◽  
Agricultural Organizations ◽  
Set Up ◽  
Definition Of ◽  
Methodological Aspects ◽  
Agricultural Organization

Subject. This article deals with the theory-and practice-relevant issues of classification and content definition of different types of capital used as sources of operations financing, and recommendations for developing their accounting in agricultural organizations. Objectives. The article aims to substantiate the organizational and methodological aspects of capital accounting development to generate information on value reserve and creation of value as new in the organization's integrated reporting. The article also aims to define the classification and content of capital types as sources of financing for the organization's activities and develop recommendations for developing the accounting of the availability, increase, reduction or transformation of the relevant types of capital in the organization's business activities. Methods. For the study, we used the methods of analysis and synthesis, induction and deduction, analogy, and comparison. The scientific works of domestic specialists and regulations, including the International Standard on Integrated Reporting (IR) are the methodological basis of this work. Results. The article defines conceptual provisions and offers practical recommendations on the set-up and development of capital flow accounting in the corporate governance system of the agricultural organization. It clarifies the classification and economic content of capital as a source of funding for the organization's reproduction activities. The article also offers an original method of accounting for the value reserve (balances) and capital changes. Conclusions and Relevance. The practical application of the developed recommendations for value accounting and capital changes will help generate all the necessary information in the integrated reporting of the agricultural organization to assess its reserves of value, create value as new, economic, environmental, and social efficiency of the organization's activities. The results of the study can be used to develop the theory, methodology and techniques of accounting of capital types as sources of financing of value creation as a result of the agricultural organization's business activities.

Rapid, Refined, and Robust Method for Expression, Purification, and Characterization of Recombinant Human Amyloid-beta M1-42

2019 ◽  
Author(s):  
Priya Prakash ◽  
Travis Lantz ◽  
Krupal P. Jethava ◽  
Gaurav Chopra
Keyword(s):  
Amyloid Beta ◽  
Western Blots ◽  
Force Microscopy ◽  
E Coli ◽  
Atomic Force ◽  
Set Up ◽  
Short Time

Amyloid plaques found in the brains of Alzheimer’s disease (AD) patients primarily consists of amyloid beta 1-42 (Ab42). Commercially, Ab42 is synthetized using peptide synthesizers. We describe a robust methodology for expression of recombinant human Ab(M1-42) in Rosetta(DE3)pLysS and BL21(DE3)pLysS competent E. coli with refined and rapid analytical purification techniques. The peptide is isolated and purified from the transformed cells using an optimized set-up for reverse-phase HPLC protocol, using commonly available C18 columns, yielding high amounts of peptide (~15-20 mg per 1 L culture) in a short time. The recombinant Ab(M1-42) forms characteristic aggregates similar to synthetic Ab42 aggregates as verified by western blots and atomic force microscopy to warrant future biological use. Our rapid, refined, and robust technique to purify human Ab(M1-42) can be used to synthesize chemical probes for several downstream in vitro and in vivo assays to facilitate AD research.

Isolation and characterization of oleochemical compounds from watermelon seed

2020 ◽  
Vol 10 (4) ◽  
pp. 79-82
Author(s):  
Madhubhushan M ◽  
Seshaiah S ◽  
Chandrudu J ◽  
Sagar R ◽  
Akila CR
Keyword(s):  
Cutting Tool ◽  
Citrullus Lanatus ◽  
Fatty Esters ◽  
Mineral Oils ◽  
Light Yellow ◽  
Isolation And Characterization ◽  
The Common ◽  
Set Up ◽  
Natural Gradation

The common watermelon item (Citrullus lanatus) seeds were gained from castoffs verdant nourishments for use by decorating, sun ventilation and pulverizing. Light yellow-toned oil was gotten by dissolvable withdrawal using oil atmosphere and the going with traits were gotten using oil ether: pH, refractive rundown, thickness, dissolvable miscibility, coagulating temperature, fire nature, express gravity, streak point and warmth of consuming. With a shallow level of unsaturation, stepped level of smoothness, and proximity of raised degree of the sensible proportion of free unsaturated fats. The low assessment of the solidifying temperature of the oil offered a hint that the oil can be managed in various areas paying little heed to the qualification in temperature. The following level of linoleic destructive of the oil offers a hint of natural gradation of solidarity. Fatty esters are increasing expanding significance as a biodegradable swap for mineral oils. In some request regions, for example, cutting tool oil, gearbox, pressure-driven oils, and greases for raw petroleum creation, the oleochemical items are set up. Nonetheless, certain particular wellsprings of fatty esters are hitherto to be abused for this comparative reason. This exploration subsequently tests into one of the less used wellsprings of fatty esters in watermelon. The oil from the kernels demonstrations a top-notch yield presents significant utilitarian gatherings for change and thus was utilized to set up an assortment of oleochemicals which demonstrated excellence materials in contrast with the routinely utilized oils feed frameworks for oleochemicals after portrayal. The photopolymers acquired indicated piercing vinyl protons for consistent polymerize.

In-Vitro and In-Silico Characterization of Xylose Reductase from Emericella nidulans

2019 ◽  
Vol 13 (2) ◽  
pp. 159-170 ◽  
Author(s):  
Vishal Ahuja ◽  
Aashima Sharma ◽  
Ranju Kumari Rathour ◽  
Vaishali Sharma ◽  
Nidhi Rana ◽  
...  
Keyword(s):  
Production Process ◽  
In Silico ◽  
Xylose Reductase ◽  
In Silico Analysis ◽  
Emericella Nidulans ◽  
Higher Temperature ◽  
In Silico Characterization ◽  
Silico Analysis

Background: Lignocellulosic residues generated by various anthropogenic activities can be a potential raw material for many commercial products such as biofuels, organic acids and nutraceuticals including xylitol. Xylitol is a low-calorie nutritive sweetener for diabetic patients. Microbial production of xylitol can be helpful in overcoming the drawbacks of traditional chemical production process and lowring cost of production. Objective: Designing efficient production process needs the characterization of required enzyme/s. Hence current work was focused on in-vitro and in-silico characterization of xylose reductase from Emericella nidulans. Methods: Xylose reductase from one of the hyper-producer isolates, Emericella nidulans Xlt-11 was used for in-vitro characterization. For in-silico characterization, XR sequence (Accession No: Q5BGA7) was used. Results: Xylose reductase from various microorganisms has been studied but the quest for better enzymes, their stability at higher temperature and pH still continues. Xylose reductase from Emericella nidulans Xlt-11 was found NADH dependent and utilizes xylose as its sole substrate for xylitol production. In comparison to whole cells, enzyme exhibited higher enzyme activity at lower cofactor concentration and could tolerate higher substrate concentration. Thermal deactivation profile showed that whole cell catalysts were more stable than enzyme at higher temperature. In-silico analysis of XR sequence from Emericella nidulans (Accession No: Q5BGA7) suggested that the structure was dominated by random coiling. Enzyme sequences have conserved active site with net negative charge and PI value in acidic pH range. Conclusion: Current investigation supported the enzyme’s specific application i.e. bioconversion of xylose to xylitol due to its higher selectivity. In-silico analysis may provide significant structural and physiological information for modifications and improved stability.

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