The Review of Bioinformatics Tool for 3D Plant Genomics Research

2019 ◽  
pp. 16-27
Author(s):  
Xiangyu Yang ◽  
Zhenghao Li ◽  
Jingtian Zhao ◽  
Tao Ma ◽  
Pengchao Li ◽  
...  
Keyword(s):  
Plant Genomics ◽  
Bioinformatics Tool ◽  
Genomics Research

scholarly journals Aquatic Plant Genomics: Advances, Applications, and Prospects

2017 ◽  
Vol 2017 ◽  
pp. 1-9
Author(s):  
Shiqi Hu ◽  
Gaojie Li ◽  
Jingjing Yang ◽  
Hongwei Hou
Keyword(s):  
Molecular Markers ◽  
Comparative Study ◽  
Stress Tolerance ◽  
Transcriptome Sequencing ◽  
Aquatic Plant ◽  
Plant Genomics ◽  
Sequencing Technology ◽  
Genome Composition ◽  
Genomics Research ◽  
Biological Methods

Genomics is a discipline in genetics that studies the genome composition of organisms and the precise structure of genes and their expression and regulation. Genomics research has resolved many problems where other biological methods have failed. Here, we summarize advances in aquatic plant genomics with a focus on molecular markers, the genes related to photosynthesis and stress tolerance, comparative study of genomes and genome/transcriptome sequencing technology.

scholarly journals UK CropNet

Yeast ◽  
2000 ◽  
Vol 1 (3) ◽  
pp. 244-254
Author(s):  
Jo Wixon
Keyword(s):  
Comparative Mapping ◽  
Genome Mapping ◽  
Software Tools ◽  
Research Community ◽  
Plant Genomics ◽  
Kind Permission ◽  
Genomics Research ◽  
The Uk

This review explores the UK CropNet site. The project is aimed at aiding the comparative mapping of cereal and other crop genomes. The site provides software tools for use by those working on genome mapping, and access to an array of databases that will be of interest to all members of the plant genomics research community, using several ACeDB interfaces. All screen views from the website are reproduced with the kind permission of Dr Sean May, Director, Nottingham Arabidopsis Stock Centre (NASC).

scholarly journals Populus trichocarpa (Black Cottonwood) As a Model for Plant Genomic Studies: A Review

2021 ◽  
pp. 270-275
Author(s):  
Navjit Kaur ◽  
Divya Dhawal Bhandari
Keyword(s):  
Populus Trichocarpa ◽  
Duplication Event ◽  
Plant Genomics ◽  
Black Cottonwood ◽  
Genome Duplication Event ◽  
Protein Coding ◽  
Model Plant ◽  
Genomics Research ◽  
Genomic Studies ◽  
Medicinal Properties

Numerous plants have been the subject of recent research in the pharmacological, cosmetic, and agro-alimentary domains due to their chemical composition and multiple therapeutic capabilities. Populus trichocarpa is one of the most common trees found in deciduous forests (Salicaceae family). The current study examines Populus trichocarpa as a model plant for plant genomics research, as well as the most recent findings on phytochemical composition and medicinal potential. More than 45,000 potential protein-coding genes were discovered. In the Populus genome, a whole-genome duplication event was discovered, with approximately 8,000 pairs of duplicated genes surviving. Furthermore, the reproductive biology of Populus provides new opportunities and challenges in the study and analysis of natural genetic and phenotypic variation. In the present review, we endeavour to describe and compile the available knowledge on Populus trichocarpa as a model plant for genomic investigations and to bring that material up to date of Populus trichocarpa's phytochemical and medicinal properties.

KEGG Bioinformatics Resource for Plant Genomics Research

2007 ◽  
pp. 437-458 ◽  
Author(s):  
Ali Masoudi-Nejad ◽  
Susumu Goto ◽  
Takashi R. Endo ◽  
Minoru Kanehisa
Keyword(s):  
Plant Genomics ◽  
Bioinformatics Resource ◽  
Genomics Research

scholarly journals Genomics of Sorghum

2008 ◽  
Vol 2008 ◽  
pp. 1-6 ◽  
Author(s):  
Andrew H. Paterson
Keyword(s):  
Cereal Crops ◽  
Plant Genomics ◽  
Noxious Weeds ◽  
Genomics Research ◽  
History Of ◽  
Complete Sequencing ◽  
Rich History ◽  
Shed Light ◽  
Size And Structure

Sorghum (Sorghum bicolor (L.) Moench) is a subject of plant genomics research based on its importance as one of the world's leading cereal crops, a biofuels crop of high and growing importance, a progenitor of one of the world's most noxious weeds, and a botanical model for many tropical grasses with complex genomes. A rich history of genome analysis, culminating in the recent complete sequencing of the genome of a leading inbred, provides a foundation for invigorating progress toward relating sorghum genes to their functions. Further characterization of the genomes other than Saccharinae cereals may shed light on mechanisms, levels, and patterns of evolution of genome size and structure, laying the foundation for further study of sugarcane and other economically important members of the group.

scholarly journals Blast2GO: A Comprehensive Suite for Functional Analysis in Plant Genomics

2008 ◽  
Vol 2008 ◽  
pp. 1-12 ◽  
Author(s):  
Ana Conesa ◽  
Stefan Götz
Keyword(s):  
Functional Annotation ◽  
Sequence Data ◽  
Enrichment Analysis ◽  
Gene Set Enrichment Analysis ◽  
Plant Genomics ◽  
Kegg Pathways ◽  
Acyclic Graphs ◽  
Genomics Research ◽  
Direct Acyclic Graphs

Functional annotation of novel sequence data is a primary requirement for the utilization of functional genomics approaches in plant research. In this paper, we describe the Blast2GO suite as a comprehensive bioinformatics tool for functional annotation of sequences and data mining on the resulting annotations, primarily based on the gene ontology (GO) vocabulary. Blast2GO optimizes function transfer from homologous sequences through an elaborate algorithm that considers similarity, the extension of the homology, the database of choice, the GO hierarchy, and the quality of the original annotations. The tool includes numerous functions for the visualization, management, and statistical analysis of annotation results, including gene set enrichment analysis. The application supports InterPro, enzyme codes, KEGG pathways, GO direct acyclic graphs (DAGs), and GOSlim. Blast2GO is a suitable tool for plant genomics research because of its versatility, easy installation, and friendly use.

scholarly journals Advances and perspectives on the use of CRISPR/Cas9 systems in plant genomics research

2016 ◽  
Vol 30 ◽  
pp. 70-77 ◽  
Author(s):  
Degao Liu ◽  
Rongbin Hu ◽  
Kaitlin J Palla ◽  
Gerald A Tuskan ◽  
Xiaohan Yang
Keyword(s):  
Plant Genomics ◽  
Genomics Research
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