Fish Comparative Genomics: Difference between revisions
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| <br> | | <br> | ||
| <br> | | <br> | ||
| <br> | | Labeotropheus fuelleborni<br> | ||
| <br> | | Blue mbuna<br> | ||
| <br> | | <br> | ||
|- | |- | ||
| <br> | | <br> | ||
| <br> | | <br> | ||
| <br> | | Maylandia zebra<br> | ||
| <br> | | Zebra mbuna<br> | ||
| <br> | | Ecological model species, aquarium fish<br> | ||
|- | |- | ||
| <br> | | <br> | ||
| <br> | | <br> | ||
| <br> | | Mchenga conophoros<br> | ||
| <br> | | <br> | ||
| <br> | | <br> | ||
| Line 89: | Line 89: | ||
| <br> | | <br> | ||
| <br> | | <br> | ||
| <br> | | Melanochromis auratus<br> | ||
| <br> | | Auratus cichlid<br> | ||
| <br> | | Phenotypic and ecological diversity<br> | ||
|- | |- | ||
| <br> | | <br> | ||
| <br> | | <br> | ||
| <br> | | Neolamprologus brichardi<br> | ||
| <br> | | Princess cichlid<br> | ||
| <br> | | Aquarium fish<br> | ||
|- | |- | ||
| <br> | | <br> | ||
| <br> | | <br> | ||
| <br> | | Oreochromis niloticus<br> | ||
| | | Nile tilapia | ||
| <br> | | Industrial species<br> | ||
|- | |- | ||
| <br> | | <br> | ||
| <br> | | <br> | ||
| <br> | | Pundamilia nyererei<br> | ||
| <br> | | <br> | ||
| <br> | | <br> | ||
|- | |- | ||
| <br> | | <br> | ||
| <br> | | Cypriniformes<br> | ||
| <br> | | Danio rerio<br> | ||
| <br> | | Zebrafish<br> | ||
| <br> | | Model species<br> | ||
|- | |- | ||
| <br> | | <br> | ||
| <br> | | <br> | ||
| <br> | | Pimephales promelas<br> | ||
| <br> | | Fathead minnow<br> | ||
| <br> | | Industrial baitfish<br> | ||
|- | |- | ||
| <br> | | <br> | ||
| <br> | | Cyprinodontiformes<br> | ||
| <br> | | Cyprinodon variegatus<br> | ||
| <br> | | Sheepshead minnow<br> | ||
| <br> | | Toxicology model<br> | ||
|- | |- | ||
| <br> | | <br> | ||
| <br> | | <br> | ||
| <br> | | Nothobranchius furzeri<br> | ||
| <br> | | Turquoise killifish<br> | ||
| <br> | | Short life span model species, metabolic diapause<br> | ||
|- | |- | ||
| <br> | | <br> | ||
| <br> | | <br> | ||
| <br> | | Nothobranchius kuhntae<br> | ||
| <br> | | Beira killifish<br> | ||
| <br> | | Short life model species<br> | ||
|- | |- | ||
| <br> | | <br> | ||
| <br> | | <br> | ||
| <br> | | Poecilia formosa<br> | ||
| <br> | | Amazon molly<br> | ||
| <br> | | Gynogenesis: all female populations<br> | ||
|- | |- | ||
| <br> | | <br> | ||
| <br> | | <br> | ||
| <br> | | Poecilia reticulata<br> | ||
| <br> | | guppy<br> | ||
| <br> | | Model species, aquarium fish<br> | ||
|- | |- | ||
| <br> | | <br> | ||
Revision as of 18:28, 4 December 2014
Summary/Abstract
Introduction
Data
- Phylogeny of genomes with polyploidy events marked
- Table of fish genomes used in this tutorial
| Class | Order |
Genus species |
Common name |
Notes |
| Cephalaspidomorphi |
Petromyzontiformes |
Lethenteron camtschaticum |
Artic lamprey |
One of few extant jawless fish |
| Petromyzon marinus |
Sea lamprey |
One of few extant jawless fish | ||
| Chondrichthyes |
Chimaeriformes |
Callorhinchus milii |
Australian ghostshark |
Proposed model cartilaginous fish |
| Rajiformes |
Leucoraja erinacea |
Little skate |
Electrosensory organ | |
| Sarcopterygii |
Coelacanthiformes |
Latimeria chalumnae |
Coelacanth |
Oldest known extant Sarcopterygii |
| Actinopterygii |
Anguilliformes |
Anguilla japonica |
Japanese eel |
Ecological model, Industry species |
| Beloniformes |
Oryzias latipes |
Medaka |
Model fish, Japanese pet fish | |
| Characiformes |
Astyanax mexicanus |
Mexican tetra |
Two forms: seeing, and cave-dwelling blind | |
| Cichliformes |
Haplochromis burtoni |
Burton’s mouthbrooder |
Ecological model species, Aquarium species | |
| Labeotropheus fuelleborni |
Blue mbuna |
|||
| Maylandia zebra |
Zebra mbuna |
Ecological model species, aquarium fish | ||
| Mchenga conophoros |
||||
| Melanochromis auratus |
Auratus cichlid |
Phenotypic and ecological diversity | ||
| Neolamprologus brichardi |
Princess cichlid |
Aquarium fish | ||
| Oreochromis niloticus |
Nile tilapia | Industrial species | ||
| Pundamilia nyererei |
||||
| Cypriniformes |
Danio rerio |
Zebrafish |
Model species | |
| Pimephales promelas |
Fathead minnow |
Industrial baitfish | ||
| Cyprinodontiformes |
Cyprinodon variegatus |
Sheepshead minnow |
Toxicology model | |
| Nothobranchius furzeri |
Turquoise killifish |
Short life span model species, metabolic diapause | ||
| Nothobranchius kuhntae |
Beira killifish |
Short life model species | ||
| Poecilia formosa |
Amazon molly |
Gynogenesis: all female populations | ||
| Poecilia reticulata |
guppy |
Model species, aquarium fish | ||
- 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