scholarly journals Evolution of plant genome architecture

2016 ◽  
Vol 17 (1) ◽  
Author(s):  
Jonathan F. Wendel ◽  
Scott A. Jackson ◽  
Blake C. Meyers ◽  
Rod A. Wing
Keyword(s):  
Plant Genome ◽  
Genome Architecture

scholarly journals Transposable Elements in the Organization and Diversification of the Genome of Aegilops speltoides Tausch (Poaceae, Triticeae)

2018 ◽  
Vol 2018 ◽  
pp. 1-9 ◽  
Author(s):  
Olga Raskina
Keyword(s):  
Transposable Elements ◽  
Mobile Element ◽  
Plant Genome ◽  
Aegilops Speltoides ◽  
Genome Architecture ◽  
Different Types ◽  
In The Wild ◽  
Species Specific ◽  
Current Species

Repetitive DNA—specifically, transposable elements (TEs)—is a prevailing genomic fraction in cereals that underlies extensive genome reshuffling and intraspecific diversification in the wild. Although large amounts of data have been accumulated, the effect of TEs on the genome architecture and functioning is not fully understood. Here, plant genome organization was addressed by means of cloning and sequencing TE fragments of different types, which compose the largest portion of the Aegilops speltoides genome. Individual genotypes were analyzed cytogenetically using the cloned TE fragments as the DNA probes for fluorescence in situ hybridization (FISH). The obtained TE sequences of the Ty1-copia, Ty3-gypsy, LINE, and CACTA superfamilies showed the relatedness of the Ae. speltoides genome to the Triticeae tribe and similarities to evolutionarily distant species. A significant number of clones consisted of intercalated fragments of TEs of various types, in which Fatima (Ty3-gypsy) sequences predominated. At the chromosomal level, different TE clones demonstrated sequence-specific patterning, emphasizing the effect of the TE fraction on the Ae. speltoides genome architecture and intraspecific diversification. Altogether, the obtained data highlight the current species-specific organization and patterning of the mobile element fraction and point to ancient evolutionary events in the genome of Ae. speltoides.

Comparative Assessment of Sporophyte and Gametophyte Thermal Resistance of Winter Rape

2019 ◽  
pp. 15-22
Keyword(s):  
Elevated Temperatures ◽  
Rapid Assessment ◽  
Temperature Stability ◽  
Temperature Factor ◽  
Plant Genome ◽  
Limiting Factors ◽  
Initial Assessment ◽  
High Temperature Stability ◽  
Winter Rape ◽  
High Yields

The temperature factor is one of the limiting factors for obtaining high yields of crops, so one of the main tasks of selection is to search for temperature-resistant genotypes and to create on their basis the banks of crops with high temperature stability. The first step to solving this problem is to conduct a rapid assessment of the temperature plasticity of large populations and to isolate breeding-valuable genotypes from them. There are numerous methods that allow, in the short term with minimal technical and material costs, to carry out an initial assessment of a large number of genotypes at sporophytic level and differentiate them by resistance to the temperature factor. These methods include the method of estimating pollen populations. These studies have repeatedly been conducted on many cultures, their correctness is due to the expression of a large part of the plant genome, both at the diploid and haploid levels of development and demonstrated by many studies in this direction. The aim of our study was to study the stability of gametophyte and sporophyte of collecting varieties and varieties of winter rape to elevated temperatures, to study the correlation between the heat resistance of sporophyte and gametophyte.

An Era of CRISPR/ Cas9 Mediated Plant Genome Editing

2018 ◽  
pp. 47-54 ◽  
Author(s):  
Haris Khurshid ◽  
Sohail Ahmad Jan ◽  
Zabta Khan Shinwari ◽  
Muhammad Jamal ◽  
Sabir Hussain Shah
Keyword(s):  
Genome Editing ◽  
Plant Genome

Methods for mapping three-dimensional genome architecture

Methods ◽  
2020 ◽  
Vol 170 ◽  
pp. 1-3
Author(s):  
Surabhi Chowdhary ◽  
Amoldeep S. Kainth ◽  
David S. Gross
Keyword(s):  
Three Dimensional ◽  
Genome Architecture

scholarly journals A convolution based computational approach towards DNA N6-methyladenine site identification and motif extraction in rice genome

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Chowdhury Rafeed Rahman ◽  
Ruhul Amin ◽  
Swakkhar Shatabda ◽  
Md. Sadrul Islam Toaha
Keyword(s):  
Operating Characteristic ◽  
Adenine Nucleotide ◽  
Characteristic Curve ◽  
Rice Genome ◽  
Plant Genome ◽  
Feature Importance ◽  
Importance Analysis ◽  
Motif Extraction ◽  
Site Identification ◽  
By Products

AbstractDNA N6-methylation (6mA) in Adenine nucleotide is a post replication modification responsible for many biological functions. Automated and accurate computational methods can help to identify 6mA sites in long genomes saving significant time and money. Our study develops a convolutional neural network (CNN) based tool i6mA-CNN capable of identifying 6mA sites in the rice genome. Our model coordinates among multiple types of features such as PseAAC (Pseudo Amino Acid Composition) inspired customized feature vector, multiple one hot representations and dinucleotide physicochemical properties. It achieves auROC (area under Receiver Operating Characteristic curve) score of 0.98 with an overall accuracy of 93.97% using fivefold cross validation on benchmark dataset. Finally, we evaluate our model on three other plant genome 6mA site identification test datasets. Results suggest that our proposed tool is able to generalize its ability of 6mA site identification on plant genomes irrespective of plant species. An algorithm for potential motif extraction and a feature importance analysis procedure are two by products of this research. Web tool for this research can be found at: https://cutt.ly/dgp3QTR.

scholarly journals Exosome/Liposome-like Nanoparticles: New Carriers for CRISPR Genome Editing in Plants

2021 ◽  
Vol 22 (14) ◽  
pp. 7456
Author(s):  
Mousa A. Alghuthaymi ◽  
Aftab Ahmad ◽  
Zulqurnain Khan ◽  
Sultan Habibullah Khan ◽  
Farah K. Ahmed ◽  
...  
Keyword(s):  
Genome Editing ◽  
Viral Vectors ◽  
Polymeric Materials ◽  
Inorganic Nanoparticles ◽  
Plant Genome ◽  
Delivery Methods ◽  
Detailed Consideration ◽  
Crispr System ◽  
Efficient Delivery ◽  
Low Cytotoxicity

Rapid developments in the field of plant genome editing using clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein (Cas) systems necessitate more detailed consideration of the delivery of the CRISPR system into plants. Successful and safe editing of plant genomes is partly based on efficient delivery of the CRISPR system. Along with the use of plasmids and viral vectors as cargo material for genome editing, non-viral vectors have also been considered for delivery purposes. These non-viral vectors can be made of a variety of materials, including inorganic nanoparticles, carbon nanotubes, liposomes, and protein- and peptide-based nanoparticles, as well as nanoscale polymeric materials. They have a decreased immune response, an advantage over viral vectors, and offer additional flexibility in their design, allowing them to be functionalized and targeted to specific sites in a biological system with low cytotoxicity. This review is dedicated to describing the delivery methods of CRISPR system into plants with emphasis on the use of non-viral vectors.

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