Fish Comparative Genomics

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 {| width="1075" cellspacing="1" cellpadding="1" border="1" height="1387" |- | Class | Order
| Genus species
| Common name
| Notes
| CoGe Genome Links |- | 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
| |- | 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
| |- |
| 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
| |}
*Links to CoGe Notebooks containing these genomes
**All unmasked fish genomes available in CoGe
**[ All masked fish genomes available in CoGe] *Link to GenomeList for notebooks **[ GenomeList for all fish genomes in CoGe]

Glossary

• WGD/WGT
• Syntenic dotplot
• Microsynteny
• Ortholog
• Paralog
• Out-Paralog
• In-Paralog

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