Gene orthogroups (family) search
Users can obtain the results of the phylogenetic tree analysis of orthogroups and the corresponding gene duplication events (support >= 0.5) between different species through the orthogroups name or gene name in this module. Users can obtain comparative information on genes between 35 species of fish through FishCODE in this module.
Users can directly input orthogroups names to obtain corresponding evolutionary trees and duplication event tables, or they can input the names of genes of interest to retrieve candidate orthogroups tables. Clicking on any column of a row in the candidate orthogroups table will allow users to obtain the corresponding evolutionary trees and duplication event tables. for details, please see "Genome analysis" section in Help Module
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Gene evolutionary tree & duplication event
Statistics Overall
FishCODE compared the 951,590 protein-conding genes across 35 fish species using OrthoFinder for comparative genomic analysis. Among them, 926,815 genes (97.4%) were located in orthogroups, while 24,775 (2.6%) lacked specific orthogroups. Within the 926,815 genes, they were distributed among 26,820 orthogroups, including 3,514 species-specific orthogroups containing 14,710 genes. Additionally, 6,502 orthogroups were present in all 35 fish species, with 48 being single-copy orthogroups. analysis results can be downloaded at here
Visualization of comparative genomic analysis
Species evolutionary tree
FishCODE includes a variety of fish species from the Actinopterygii (ray-finned fish) and Sarcopterygii (lobe-finned fish), encompassing 35 species across 15 orders. Protopterus annectens, Amia calva, Lepisosteus oculatus, and the Tibetan loach (an extreme-area fish species) are among the species that have played an important role in evolutionary studies. Oreochromis niloticus, Gasterosteus aculeatus, Coregonus clupeaformis, or Gadus morhua which are popular among the molecular ecology and evolutionary community. Danio rerio, Oryzias latipes, Nothobranchius furzeri (the currently shortest-lived vertebrate in laboratory settings), Tetraodon nigroviridis (known for having the smallest vertebrate genome), serve as important model species in various research fields such as developmental biology, environmental toxicology, injury repair, aging, and regeneration. Grass carp, Atlantic salmon, catfish and rainbow trout are economically important fish species worldwide. Puntigrus tetrazona and Xiphophorus hellerii are important aquarium ornamental fish.
The evolutionary trees for FishCODE species were generated using the evolutionary analysis module of the Orthofinder tool. The fundamental principle is to perform a multiple sequence alignment of the identified Orthogroups sequences and then employ the fasttree software (the default option) to construct the evolutionary tree.
Visualization of species evolutionary tree
Phylogenetic tree
