AI Article Synopsis
- Synteny and collinearity analysis helps researchers understand genomic conservation and evolution, but current visualization tools lack effective graphical outputs, especially for high-resolution data from 3rd generation sequencing.
- VGSC2 is a new web-based toolkit designed to address these limitations, offering multiple plot types for analyzing synteny, collinearity, and gene family evolution.
- The toolkit is user-friendly, enabling easy creation of vector graphs (like SVG, EPS, and PDF) and is available for free online as open-source software.
Article Abstract
Synteny and collinearity analysis is a standard investigative strategy done in many comparative genomic studies to understand genomic conservation and evolution. Currently, most visualization toolkits of synteny and collinearity do not emphasize the graphical representation of the results, especially the lack of extensible format on vector graphics outputs. This limitation becomes more apparent as 3rd generation sequencing brings high-throughput data, requiring relatively higher resolution for the resulting images. We developed VGSC2, the 2nd version of the web-based vector graph toolkit for genome synteny and collinearity analysis. The updated version enables four types of plots for synteny and collinearity, and three types of plots for gene family evolutionary research. Using web-based technologies, VGSC2 provides an easy-to-use user interface to display the homologous genomic result into vector graphs such as SVG, EPS, and PDF, as well as an online editor. VGSC2 is open source and freely available for use online through the web server available at http://bio.njfu.edu.cn/vgsc2.
Download full-text PDF |
Source |
|---|---|
| http://dx.doi.org/10.1016/j.ygeno.2019.02.007 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Genome-Wide Identification and Functional Characterization of Gene Family Reveal Its Involvement in Response to Stress in Cotton.
Int J Mol Sci
January 2025
Institute of Cotton, Hebei Academy of Agriculture and Forestry Sciences/Key Laboratory of Cotton Biology and Genetic Breeding in Huanghuaihai Semiarid Area, Ministry of Agriculture and Rural Affairs, Shijiazhuang 050000, China.
SKP1 constitutes the Skp1-Cullin-F-box ubiquitin E3 ligase (SCF), which plays a role in plant growth and development and biotic and abiotic stress in ubiquitination. However, the response of the gene family to abiotic and biotic stresses in cotton has not been well characterized. In this study, a total of 72 genes with the conserved domain of SKP1 were identified in four Gossypium species.
View Article and Find Full Text PDFGenome-wide identification, characterization, and functional analysis of the CHX, SOS, and RLK genes in Solanum lycopersicum under salt stress.
Sci Rep
January 2025
Department of Plant Genetic Transformation, Agricultural Genetic Engineering Research Institute (AGERI), Agricultural Research Center (ARC), Cairo, Egypt.
The cation/proton exchanger (CHX), salt overly sensitive (SOS), and receptor-like kinase (RLK) genes play significant roles in the response to salt stress in plants. This study is the first to identify the SOS gene in Solanum lycopersicum (tomato) through genome-wide analysis under salt stress conditions. Quantitative reverse transcription PCR (qRT-PCR) results indicated that the expression levels of CHX, SOS, and RLK genes were upregulated, with fold changes of 1.
View Article and Find Full Text PDFComparative genetic mapping and a consensus interspecific genetic map reveal strong synteny and collinearity within the genus.
Front Plant Sci
December 2024
Genoscope, Institut de Biologie François-Jacob, Commissariat à l'Energie Atomique (CEA), Université Paris-Saclay, Evry, France.
Introduction: Useful germplasm for citrus breeding includes all sexually compatible species of the former genera , and , now merged in the single genus. An improved knowledge on the synteny/collinearity between the genome of these different species, and on their recombination landscapes, is essential to optimize interspecific breeding schemes.
Method: We have performed a large comparative genetic mapping study including several main clades of the genus.
Identifying candidate genes for sugar accumulation in sugarcane: an integrative approach.
BMC Genomics
December 2024
Institute of Biology (IB), State University of Campinas (UNICAMP), Campinas, SP, Brazil.
Background: Elucidating the intricacies of the sugarcane genome is essential for breeding superior cultivars. This economically important crop originates from hybridizations of highly polyploid Saccharum species. However, the large size (10 Gb), high degree of polyploidy, and aneuploidy of the sugarcane genome pose significant challenges to complete genome sequencing, assembly, and annotation.
View Article and Find Full Text PDFSaltational Episodes of Reticulate Evolution in the Drosophila saltans Species Group.
Mol Biol Evol
December 2024
Department of Biology, UNESP-São Paulo State University, São José do Rio Preto, São Paulo, Brazil.
Phylogenomics reveals reticulate evolution to be widespread across taxa, but whether reticulation is due to low statistical power or it is a true evolutionary pattern remains a field of study. Here, we investigate the phylogeny and quantify reticulation in the Drosophila saltans species group, a Neotropical clade of the subgenus Sophophora comprising 23 species whose relationships have long been problematic. Phylogenetic analyses revealed conflicting topologies between the X chromosome, autosomes and the mitochondria.
View Article and Find Full Text PDFWant AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!