Fish Comparative Genomics: Difference between revisions

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*Phylogeny of genomes with polyploidy events marked
*Phylogeny of genomes with polyploidy events marked


*Table of fish genomes used in this tutorial
*Table of fish genomes publicly available in CoGe


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{| width="594" cellspacing="1" cellpadding="1" border="1"
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| <br>  
| <br>  
| Oreochromis niloticus<br>  
| Oreochromis niloticus<br>  
| Nile tilapia
| Nile tilapia  
| Industrial species<br>
| Industrial species<br>
|-
|-
Line 155: Line 155:
| <br>  
| <br>  
| <br>  
| <br>  
| <br>  
| Xiphophorus maculatus<br>  
| <br>  
| Southern platyfish<br>  
| <br>
| Gives live birth<br>
|-
|-
| <br>  
| <br>  
| <br>  
| Esociformes<br>  
| <br>  
| Esox lucius<br>  
| <br>  
| Northern pike<br>  
| <br>
| Angling species<br>
|-
|-
| <br>  
| <br>  
| <br>  
| Gadiformes<br>  
| <br>  
| Gadus morhua<br>  
| <br>  
| Atlantic cod<br>  
| <br>
| Industrial species<br>
|-
|-
| <br>  
| <br>  
| <br>  
| Perciformes<br>  
| <br>  
| Anoplopoma fimbria<br>  
| <br>  
| Sablefish<br>  
| <br>
| Industrial species<br>
|-
|-
| <br>  
| <br>  
| <br>  
| <br>  
| <br>  
| Dicentrarchus labrax<br>  
| <br>  
| European seabass<br>  
| <br>
| Industrial species<br>
|-
|-
| <br>  
| <br>  
| <br>  
| <br>  
| <br>  
| Gasterosteus aculeatus<br>  
| <br>  
| Three-spined stickleback<br>  
| <br>
| Model species<br>
|-
|-
| <br>  
| <br>  
| <br>  
| <br>  
| <br>  
| Sebastes nigrocinctus<br>  
| <br>  
| Tiger rockfish<br>  
| <br>
| Angling species, long lived model, live bearer<br>
|-
|-
| <br>  
| <br>  
| <br>  
| <br>  
| <br>  
| Sebastes rubrivinctus<br>  
| <br>  
| Flag rockfish<br>  
| <br>
| Angling species, industrial species<br>
|-
|-
| <br>  
| <br>  
| <br>  
| <br>  
| <br>  
| Stegastes partitus<br>  
| <br>  
| Bicolor damselfish<br>  
| <br>
| Medical model species<br>
|-
|-
| <br>  
| <br>  
| <br>  
| Pleuronectiformes<br>  
| <br>  
| Cynoglossus semilaevis<br>  
| <br>  
| Tongue sole<br>  
| <br>
| Industrial species<br>
|-
|-
| <br>  
| <br>  
| <br>  
| Salmoniformes<br>  
| <br>  
| Oncorhyncus mykiss<br>  
| <br>  
| Rainbow trout<br>  
| <br>
| Angling species, Indrustrial species<br>
|-
|-
| <br>  
| <br>  
| <br>  
| <br>  
| <br>  
| Salmo salar<br>  
| <br>  
| Atlantic salmon<br>  
| <br>
| Angling and industrial species<br>
|-
|-
| <br>  
| <br>  
| <br>  
| Semionotiformes<br>  
| <br>  
| Lepisosteus oculatus<br>  
| <br>  
| Spotted gar<br>  
| <br>
| <br>
|-
|-
| <br>  
| <br>  
| <br>  
| Scombriformes<br>  
| <br>  
| Thunnus orientalis<br>  
| <br>  
| Pacific bluefin tuna<br>  
| <br>
| Industrial species<br>
|-
|-
| <br>  
| <br>  
| <br>  
| Tetraodontiformes<br>  
| <br>  
| Takifugu flavidus<br>  
| <br>  
| Sansaifugu<br>  
| <br>
| <br>
|-
|-
| <br>  
| <br>  
| <br>  
| <br>  
| <br>  
| Tetraodon nigroviridis<br>  
| <br>  
| Spotted green pufferfish<br>  
| <br>
| Model species, low amount of repetitive sequence<br>
|-
|-
| <br>  
| <br>  
| <br>  
| <br>  
| <br>  
| Takifugu rubripes<br>  
| <br>  
| ‘Fugu’ pufferfish<br>  
| <br>
| Shortest vertebrate genome<br>
|}
|}


Revision as of 18:39, 4 December 2014

Summary/Abstract

Introduction

Data

  • Phylogeny of genomes with polyploidy events marked
  • Table of fish genomes publicly available in CoGe
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
Xiphophorus maculatus
 Southern platyfish
 Gives live birth

 Esociformes
 Esox lucius
 Northern pike
 Angling species

 Gadiformes
 Gadus morhua
 Atlantic cod
 Industrial species

 Perciformes
 Anoplopoma fimbria
 Sablefish
 Industrial species
Dicentrarchus labrax
 European seabass
 Industrial species
Gasterosteus aculeatus
 Three-spined stickleback
 Model species
Sebastes nigrocinctus
 Tiger rockfish
 Angling species, long lived model, live bearer
Sebastes rubrivinctus
 Flag rockfish
 Angling species, industrial species
Stegastes partitus
 Bicolor damselfish
 Medical model species

 Pleuronectiformes
 Cynoglossus semilaevis
 Tongue sole
 Industrial species

 Salmoniformes
 Oncorhyncus mykiss
 Rainbow trout
 Angling species, Indrustrial species
Salmo salar
 Atlantic salmon
 Angling and industrial species

 Semionotiformes
 Lepisosteus oculatus
 Spotted gar

Scombriformes
 Thunnus orientalis
 Pacific bluefin tuna
 Industrial species

 Tetraodontiformes
 Takifugu flavidus
 Sansaifugu


Tetraodon nigroviridis
 Spotted green pufferfish
 Model species, low amount of repetitive sequence
Takifugu rubripes
 ‘Fugu’ pufferfish
 Shortest vertebrate genome


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

Discussion/Conclusions

Retrieved from "https://genomevolution.org/wiki/index.php?title=Fish_Comparative_Genomics&oldid=7033"