Fish Comparative Genomics: Difference between revisions
Jump to navigation
Jump to search
No edit summary |
|||
| Line 25: | Line 25: | ||
*Table of fish genomes publicly available in CoGe | *Table of fish genomes publicly available in CoGe | ||
{| width=" | {| width="200" cellspacing="1" cellpadding="1" border="1" height="1000" |- | '''Class''' | '''Order''' | '''Genus species''' | '''Common name''' | '''Notes'''| '''CoGe Genome Links''' |- | Cephalaspidomorphi | Petromyzontiformes | Lethenteron camtschaticum | Artic lamprey<br> | One of few extant jawless fish | |- | <br> | <br> | Petromyzon marinus<br> | Sea lamprey<br> | One of few extant jawless fish<br> | |- | Chondrichthyes<br> | Chimaeriformes<br> | Callorhinchus milii<br> | Australian ghostshark<br> | Proposed model cartilaginous fish<br> | |- | Sarcopterygii<br> | Coelacanthiformes<br> | Latimeria chalumnae<br> | Coelacanth<br> | Oldest known extant Sarcopterygii<br> | |- | Actinopterygii<br> | Anguilliformes<br> | Anguilla japonica<br> | Japanese eel<br> | Ecological model, Industry species<br> | |- | <br> | Beloniformes<br> | Oryzias latipes<br> | Medaka<br> | Model fish, Japanese pet fish<br> | |- | <br> | Characiformes<br> | Astyanax mexicanus<br> | Mexican tetra<br> | Two forms: seeing, and cave-dwelling blind<br> | |- | <br> | Cichliformes<br> | Haplochromis burtoni<br> | Burton’s mouthbrooder<br> | Ecological model species, Aquarium species<br> | |- | <br> | <br> | Labeotropheus fuelleborni<br> | Blue mbuna<br> | <br> | |- | <br> | <br> | Maylandia zebra<br> | Zebra mbuna<br> | Ecological model species, aquarium fish<br> | |- | <br> | <br> | Mchenga conophoros<br> | <br> | <br> | |- | <br> | <br> | Melanochromis auratus<br> | Auratus cichlid<br> | Phenotypic and ecological diversity<br> | |- | <br> | <br> | Neolamprologus brichardi<br> | Princess cichlid<br> | Aquarium fish<br> | |- | <br> | <br> | Oreochromis niloticus<br> | Nile tilapia | Industrial species<br> | |- | <br> | <br> | Pundamilia nyererei<br> | <br> | <br> | |- | <br> | Cypriniformes<br> | Danio rerio<br> | Zebrafish<br> | Model species<br> | |- | <br> | <br> | Pimephales promelas<br> | Fathead minnow<br> | Industrial baitfish<br> | |- | <br> | Cyprinodontiformes<br> | Cyprinodon variegatus<br> | Sheepshead minnow<br> | Toxicology model<br> | |- | <br> | <br> | Nothobranchius furzeri<br> | Turquoise killifish<br> | Short life span model species, metabolic diapause<br> | |- | <br> | <br> | Nothobranchius kuhntae<br> | Beira killifish<br> | Short life model species<br> | |- | <br> | <br> | Poecilia formosa<br> | Amazon molly<br> | Gynogenesis: all female populations<br> | |- | <br> | <br> | Poecilia reticulata<br> | guppy<br> | Model species, aquarium fish<br> | |- | <br> | <br> | Xiphophorus maculatus<br> | Southern platyfish<br> | Gives live birth<br> | |- | <br> | Esociformes<br> | Esox lucius<br> | Northern pike<br> | Angling species<br> | |- | <br> | Gadiformes<br> | Gadus morhua<br> | Atlantic cod<br> | Industrial species<br> | |- | <br> | Perciformes<br> | Anoplopoma fimbria<br> | Sablefish<br> | Industrial species<br> | |- | <br> | <br> | Dicentrarchus labrax<br> | European seabass<br> | Industrial species<br> | |- | <br> | <br> | Gasterosteus aculeatus<br> | Three-spined stickleback<br> | Model species<br> | |- | <br> | <br> | Sebastes nigrocinctus<br> | Tiger rockfish<br> | Angling species, long lived model, live bearer<br> | |- | <br> | <br> | Sebastes rubrivinctus<br> | Flag rockfish<br> | Angling species, industrial species<br> | |- | <br> | <br> | Stegastes partitus<br> | Bicolor damselfish<br> | Medical model species<br> | |- | <br> | Pleuronectiformes<br> | Cynoglossus semilaevis<br> | Tongue sole<br> | Industrial species<br> | |- | <br> | Salmoniformes<br> | Oncorhyncus mykiss<br> | Rainbow trout<br> | Angling species, Indrustrial species<br> | |- | <br> | Semionotiformes<br> | Lepisosteus oculatus<br> | Spotted gar<br> | <br> | |- | <br> | Scombriformes<br> | Thunnus orientalis<br> | Pacific bluefin tuna<br> | Industrial species<br> | |- | <br> | Tetraodontiformes| Takifugu flavidus | Sansaifugu | | |- | | | Tetraodon nigroviridis | Spotted green pufferfish| Model species, low amount of repetitive sequence | |- | | | Takifugu rubripes | ‘Fugu’ pufferfish | Shortest vertebrate genome| |} | ||
Revision as of 22:11, 5 December 2014
Summary/Abstract
Introduction
- Phylogeny of genomes with polyploidy events marked
Setting the hook: getting data loaded into CoGe
- Loading new genomes into CoGe
- Loading from the iPlant Data Store When loading a new genome
- Using FTP/HTTP links for uploading genomes
- Direct upload
- NCBI Loader
- Table of fish genomes publicly available in CoGe
- Links to CoGe Notebooks containing these genomes
- All unmasked fish genomes available in CoGe
- [ All masked fish genomes available in CoGe]
- All unmasked fish genomes available in CoGe
- Link to GenomeList for notebooks
- [ GenomeList for all fish genomes in CoGe]
Glossary
Analyses
Whole genome syntenic analysis
- SynMap
- Identify Whole Genome Duplications
- Identify Synteny
- Synonymous/nonsynonymous gene pair evolution
Microsyntenic analysis
- GEvo
- Validate microsynteny
- Identify Conserved non-coding sequences (regulatory function)
Ortholog/paralog finding with synteny
- SynFind
- Identify orthologous regions across many species
Gene family analysis
- CoGeBlast
- Identify many gene family members within/across species
- Extract sequences (nucleotide/protein)
- Phylogenetic tree reconstruction using iPlant/iAnimal for multiple sequence alignment and tree building
Functional genomics
- Adding/visualizing RNAseq data
Adding new data (genomes, RNASeq, SNPs) to CoGe
- LoadGenome
- LoadExperiment
- Keeping data private and sharing with collaborators
Discussion/Conclusions