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. 2023 Jul 5;51(W1):W397-W403.
doi: 10.1093/nar/gkad313.

OrthoVenn3: an integrated platform for exploring and visualizing orthologous data across genomes

Affiliations

OrthoVenn3: an integrated platform for exploring and visualizing orthologous data across genomes

Jiahe Sun et al. Nucleic Acids Res. .

Abstract

Advancements in comparative genomics research have led to a growing interest in studying species evolution and genetic diversity. To facilitate this research, OrthoVenn3 has been developed as a powerful, web-based tool that enables users to efficiently identify and annotate orthologous clusters and infer phylogenetic relationships across a range of species. The latest upgrade of OrthoVenn includes several important new features, including enhanced orthologous cluster identification accuracy, improved visualization capabilities for numerous sets of data, and wrapped phylogenetic analysis. Furthermore, OrthoVenn3 now provides gene family contraction and expansion analysis to support researchers better understanding the evolutionary history of gene families, as well as collinearity analysis to detect conserved and variable genomic structures. With its intuitive user interface and robust functionality, OrthoVenn3 is a valuable resource for comparative genomics research. The tool is freely accessible at https://orthovenn3.bioinfotoolkits.net.

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Figures

Graphical Abstract
Graphical Abstract
OrthoVenn3 accepts genomics data and optional gene annotation information for orthologous cluster analysis, phylogenetic analysis, gene family evolution analysis and collinearity analysis.
Figure 1.
Figure 1.
Orthologous cluster analysis of seven plant species: Echinochloa crusgalli, Setaria italica, Zea mays, Sorghum bicolor, Brachypodium distachyon, Oryza sativa and Arabidopsis thaliana. (A) An UpSet table displays unique and shared orthologous clusters among the species. The left horizontal bar chart shows the number of orthologous clusters per species, while the right vertical bar chart shows the number of orthologous clusters shared among the species. The lines represent intersecting sets. (B) Classic Venn and Edwards diagrams show selected species. (C) Retrieve orthologous clusters quickly using either a Cluster ID or a protein ID. (D) Upload nucleotide or protein sequences for sequence alignment with the output cluster. (E) The bar chart shows the number of protein sequences, orthologous clusters and singletons for each species. (F) The table shows the total number of sets, clusters, single-copy gene clusters, singletons and the percentage of singletons across all species. (G) The heatmap shows the number of overlapping clusters between each pair of species.
Figure 2.
Figure 2.
(A) A phylogenetic tree based on single-copy genes illustrates the evolutionary relationships and distances among the species. (B) A pie chart shows the number of gene families that have expanded (purple) or contracted (blue) during evolution, while the phylogenetic tree shows the evolutionary timeline of the species.
Figure 3.
Figure 3.
(A) A comparison of collinearity between adjacent species supports the highlighting of positions of genes of interest on the chromosome through the search box. (B) A list of chromosomes for each species allows the color of the chromosome to be changed by clicking on the color blocks. (C) Protein phylogenetic trees and collinearity within cluster15597 are shown. When the mouse hovers over a gene, the genes that are collinear with it are highlighted in orange.

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