Fish Comparative Genomics: Difference between revisions

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|+ Table of fish genomes publicly available in CoGe  
|+ Table of fish genomes publicly available in CoGe  
|-
|-
| '''Class  
| Class  
| Species  
| Species  
| Common name  
| Common name  
| Genome ID  
| Genome ID  
| Species notes  
| Species notes  
| CoGe Genome Links'''
| CoGe Genome Links
|-
|-
| Hyperoartia  
| Hyperoartia  
Line 42: Line 42:
| [http://www.ncbi.nlm.nih.gov/genome/16905 16905]
| [http://www.ncbi.nlm.nih.gov/genome/16905 16905]
| One of few extant jawless fish  
| One of few extant jawless fish  
|  
| [https://genomevolution.org/CoGe/GenomeInfo.pl?gid=24836 unmasked] [https://genomevolution.org/CoGe/GenomeInfo.pl?gid=24963 masked]
|-
|-
|  
|  
| '''''Petromyzon marinus'''''
| '''''Petromyzon marinus'''''
| Sea Lamprey
| Sea Lamprey
| [http://www.ncbi.nlm.nih.gov/genome/?term=Sea+lamprey 287]
| [http://www.ncbi.nlm.nih.gov/genome/287 287]
| One of few extant jawless fish
| One of few extant jawless fish
|  
| [https://genomevolution.org/CoGe/GenomeInfo.pl?gid=12390 unmasked] [https://genomevolution.org/CoGe/GenomeInfo.pl?gid=24937 masked]
|-
|-
| Chondrichthyes
| Chondrichthyes
| ''Callorhinchus milii''
| '''''Callorhinchus milii'''''
| Australian Ghostshark
| Australian Ghostshark
| [http://www.ncbi.nlm.nih.gov/genome?LinkName=bioproject_genome&from_uid=236996 689]
| [http://www.ncbi.nlm.nih.gov/genome/689 689]
| Proposed model cartilaginous fish
| Proposed model cartilaginous fish
|  
| [https://genomevolution.org/CoGe/GenomeInfo.pl?gid=25133 unmasked] [https://genomevolution.org/CoGe/GenomeInfo.pl?gid=25135 masked]
|-
|-
| Sarcopterygii
| Sarcopterygii
| ''Latimeria chalumnae''
| '''''Latimeria chalumnae'''''
| Coelacanth
| Coelacanth
| [http://www.ncbi.nlm.nih.gov/genome/?term=3262 3262]
| [http://www.ncbi.nlm.nih.gov/genome/3262 3262]
|  
| Oldest extant Sarcopterygii
|  
| [https://genomevolution.org/CoGe/GenomeInfo.pl?gid=25005 unmasked] [https://genomevolution.org/CoGe/GenomeInfo.pl?gid=25041 masked]
|-
|-
|  
| Actinopterygii
|  
| ''Anguilla japonica''
|  
| Japanese Eel
|  
| [http://www.ncbi.nlm.nih.gov/genome/13349 13349]
|  
| Ecological model, Industry species
|  
| [https://genomevolution.org/CoGe/GenomeInfo.pl?gid=24876 unmasked] [https://genomevolution.org/CoGe/GenomeInfo.pl?gid=24956]
|-
|-
|  
|  
|  
| ''Anoplopoma fimbria''
|  
| Sablefish
|  
| [http://www.ncbi.nlm.nih.gov/genome/12760 12760]
|  
| Industrial species
|  
| [https://genomevolution.org/CoGe/GenomeInfo.pl?gid=24878 unmasked]
|-
|-
|  
|  
|  
| '''''Astyanax mexicanus'''''
|  
| Mexican tetra
|  
| [http://www.ncbi.nlm.nih.gov/genome/13073 13073]
|  
| Two forms: seeing, and cave-dwelling blind
|  
| [https://genomevolution.org/CoGe/GenomeInfo.pl?gid=25134 unmasked] [https://genomevolution.org/CoGe/GenomeInfo.pl?gid=25137 masked]
|-
|-
|  
|  
|  
| '''''Cynoglossus semilaevis'''''
|  
| Tongue Sole
|  
| [http://www.ncbi.nlm.nih.gov/genome/11788 11788]
|  
| Industrial species
|  
| [https://genomevolution.org/CoGe/GenomeInfo.pl?gid=25000 unmasked] [https://genomevolution.org/CoGe/GenomeInfo.pl?gid=25036 masked]
|-
|-
|  
|  
|  
| ''Cyprinodon variegatus''
|  
| Sheepshead minnow
|  
| [http://www.ncbi.nlm.nih.gov/genome/13078 13078]
|  
| Toxicology model
|  
| [https://genomevolution.org/CoGe/GenomeInfo.pl?gid=24911 unmasked] [https://genomevolution.org/CoGe/GenomeInfo.pl?gid=24958 masked]
|-
|-
|  
|  
|  
| '''''Danio rerio'''''
|  
| Zebrafish
|  
| [http://www.ncbi.nlm.nih.gov/genome/50 50]
|  
| Model species
|  
| [https://genomevolution.org/CoGe/GenomeInfo.pl?gid=25050 unmasked] [https://genomevolution.org/CoGe/GenomeInfo.pl?gid=25064 masked]
|-
|-
|  
|  
|  
| ''Dicentrarchus labrax''
|  
| European Seabass
|  
| [http://www.ncbi.nlm.nih.gov/genome/2659 2659]
|  
| Industrial species
|  
| [https://genomevolution.org/CoGe/GenomeInfo.pl?gid=24873 unmasked] [https://genomevolution.org/CoGe/GenomeInfo.pl?gid=25159 masked]
|-
|-
|  
|  
|  
| ''Esox lucius''
|  
| Northern Pike
|  
| [http://www.ncbi.nlm.nih.gov/genome/22932 22932]
|  
| Angling species
|  
|  
|-
|-
|  
|  
|  
| ''Gadus morhua''
|  
| Atlantic cod
|  
| [http://www.ncbi.nlm.nih.gov/genome/2661 2661]
|  
| Industrial species
|  
| [https://genomevolution.org/CoGe/GenomeInfo.pl?gid=14730 unmasked] [https://genomevolution.org/CoGe/GenomeInfo.pl?gid=24957 masked]
|-
|-
|  
|  
|  
| '''''Gasterosteus aculeatus'''''
|  
| Three-spined stickleback
|  
| [http://www.ncbi.nlm.nih.gov/genome/146 146]
|  
| Model species
|  
| [https://genomevolution.org/CoGe/GenomeInfo.pl?gid=23854 unmasked]
|-
|-
|  
|  
|  
| '''''Haplochromis burtoni'''''
|  
| Burton’s mouthbrooder
|  
| [http://www.ncbi.nlm.nih.gov/genome/3328 3328]
|  
| Ecological model species, Aquarium species
|  
| [https://genomevolution.org/CoGe/GenomeInfo.pl?gid=25002 unmasked] [https://genomevolution.org/CoGe/GenomeInfo.pl?gid=25062 masked]
|-
|-
|  
|  
| ''Labeotropheus fuelleborni''
| Blue mbuna
| [http://www.ncbi.nlm.nih.gov/genome/2638 2638]
|  
|  
|  
| [https://genomevolution.org/CoGe/GenomeInfo.pl?gid=24912 unmasked] [https://genomevolution.org/CoGe/GenomeInfo.pl?gid=24961 masked]
|
|
|
|-
|-
|  
|  
|  
| '''''Lepisosteus oculatus'''''
|  
| Spotted Gar
|  
| [http://www.ncbi.nlm.nih.gov/genome/10597 10597]
|  
| Lineage before Teleost whole genome duplication
|  
| [https://genomevolution.org/CoGe/GenomeInfo.pl?gid=25003 unmasked] [https://genomevolution.org/CoGe/GenomeInfo.pl?gid=25032 masked]
|-
|-
|  
|  
|  
| '''''Maylandia zebra'''''
|  
| Zebra Mbuna
|  
| [http://www.ncbi.nlm.nih.gov/genome/2640 2640]
|  
| Ecological model species, aquarium fish
|  
| [https://genomevolution.org/CoGe/GenomeInfo.pl?gid=25004 unmasked] [https://genomevolution.org/CoGe/GenomeInfo.pl?gid=25046 masked]
|-
|-
|  
|  
| ''Mchenga conophoros''
|  
|  
| [http://www.ncbi.nlm.nih.gov/genome/2585 2585]
|  
|  
|  
| [https://genomevolution.org/CoGe/GenomeInfo.pl?gid=24914 unmasked] [https://genomevolution.org/CoGe/GenomeInfo.pl?gid=24919 masked]
|
|
|-
|-
|  
|  
| ''Melanochromis auratus''
| Auratus Cichlid
| [http://www.ncbi.nlm.nih.gov/genome/2639 2639]
|  
|  
|  
| [https://genomevolution.org/CoGe/GenomeInfo.pl?gid=24913 unmasked] [https://genomevolution.org/CoGe/GenomeInfo.pl?gid=24964 masked]
|
|
|
|-
|-
|  
|  
|  
| '''''Neolamprologus brichardi'''''
|  
| Princess Cichlid
|  
| [http://www.ncbi.nlm.nih.gov/genome/3329 3329]
|  
| Aquarium fish
|  
|[https://genomevolution.org/CoGe/GenomeInfo.pl?gid=25006 unmasked] [https://genomevolution.org/CoGe/GenomeInfo.pl?gid=25044 masked]
|-
|-
|  
|  
|  
| ''Nothobranchius furzeri''
|  
| Turquoise Killifish
|  
| [http://www.ncbi.nlm.nih.gov/genome/2642 2642]
|  
| Short life span model species, metabolic diapause
|  
| [https://genomevolution.org/CoGe/GenomeInfo.pl?gid=15571 unmasked] [https://genomevolution.org/CoGe/GenomeInfo.pl?gid=24920 masked]
|-
|-
|  
|  
|  
| ''Nothobranchius kuhntae''
|  
| Beira Killifish
|  
| [http://www.ncbi.nlm.nih.gov/genome/2643 2643]
|  
| Short life model species
|  
| [https://genomevolution.org/CoGe/GenomeInfo.pl?gid=15184 unmasked] [https://genomevolution.org/CoGe/GenomeInfo.pl?gid=24921 masked]
|-
|-
|  
|  
|  
| ''Oncorhynchus mykiss''
|  
| Rainbow Trout
|  
| [http://www.genoscope.cns.fr/trout-ggb/data/ Genoscope Salmon Database]
|  
| Angling and industrial species
|  
| [https://genomevolution.org/CoGe/GenomeInfo.pl?gid=24831 unmasked] [https://genomevolution.org/CoGe/GenomeInfo.pl?gid=24950 masked]
|-
|-
|  
|  
|  
| '''''Oreochromis niloticus'''''
|  
| Nile Tilapia
|  
| [http://www.ncbi.nlm.nih.gov/genome/197 197]
|  
| Industrial species
|  
| [https://genomevolution.org/CoGe/GenomeInfo.pl?gid=25007 unmasked] [https://genomevolution.org/CoGe/GenomeInfo.pl?gid=25033]
|-
|-
|  
|  
|  
| '''''Oryzias latipes'''''
|  
| Japanese Medaka
|  
| [http://www.ncbi.nlm.nih.gov/genome/542 542]
|  
| Model fish, Aquarium species
|  
| [https://genomevolution.org/CoGe/GenomeInfo.pl?gid=25008 unmasked] [https://genomevolution.org/CoGe/GenomeInfo.pl?gid=25031 masked]
|-
|-
|  
|  
|  
| ''Pimephales promelas''
|  
| Fathead Minnow
|  
| [http://www.ncbi.nlm.nih.gov/genome/13167 13167]
|  
| Industrial baitfish
|  
| [https://genomevolution.org/CoGe/GenomeInfo.pl?gid=24916 unmasked] [https://genomevolution.org/CoGe/GenomeInfo.pl?gid=24947 masked]
|-
|-
|  
|  
|  
| '''''Poecilia formosa'''''
|  
| Amazon Molly
|  
| [http://www.ncbi.nlm.nih.gov/genome/13072 13072]
|  
| Gynogenesis: all female populations
|  
| [https://genomevolution.org/CoGe/GenomeInfo.pl?gid=25009 unmasked] [https://genomevolution.org/CoGe/GenomeInfo.pl?gid=25063 masked]
|-
|-
|  
|  
|  
| '''''Poecilia reticulata'''''
|  
| Guppy
|  
| [http://www.ncbi.nlm.nih.gov/genome/23338 23338]
|  
| Model species, Aquarium fish
|  
| [https://genomevolution.org/CoGe/GenomeInfo.pl?gid=25010 unmasked] [https://genomevolution.org/CoGe/GenomeInfo.pl?gid=25047 masked]
|-
|-
|  
|  
| '''''Pundamilia nyererei'''''
|  
|  
| [http://www.ncbi.nlm.nih.gov/genome/3330 3330]
|  
|  
|  
| [https://genomevolution.org/CoGe/GenomeInfo.pl?gid=25011 unmasked] [https://genomevolution.org/CoGe/GenomeInfo.pl?gid=25055 masked]
|
|
|-
|-
|  
|  
|  
| '''''Sebastes nigrocinctus'''''
|  
| Tiger Rockfish
|  
| [http://www.ncbi.nlm.nih.gov/genome/14568 14568]
|  
| Angling species, long lived model, live bearer
|  
| [https://genomevolution.org/CoGe/GenomeInfo.pl?gid=24936 masked]
|-
|-
|  
|  
|  
| ''Sebastes rubrivinctus''
|  
| Flag Rockfish
|  
| [http://www.ncbi.nlm.nih.gov/genome/11458 11458]
|  
| Angling species, Industrial species
|  
| [https://genomevolution.org/CoGe/GenomeInfo.pl?gid=24886 unmasked]
|-
|-
|  
|  
|  
| '''''Stegastes partitus'''''
|  
| Bicolor damselfish
|  
| [http://www.ncbi.nlm.nih.gov/genome/13077 13077]
|  
| Medical model species
|  
| [https://genomevolution.org/CoGe/GenomeInfo.pl?gid=25012 unmasked] [https://genomevolution.org/CoGe/GenomeInfo.pl?gid=25054 masked]
|-
|-
|  
|  
| ''Takifugu flavidus''
| Sansaifugu
| [http://www.ncbi.nlm.nih.gov/genome/14185 14185]
|  
|  
|  
| [https://genomevolution.org/CoGe/GenomeInfo.pl?gid=24910 unmasked] [https://genomevolution.org/CoGe/GenomeInfo.pl?gid=24924 masked]
|
|
|
|-
|-
|  
|  
|  
| '''''Takifugu rubripes'''''
|  
| Torafugu
|  
| [http://www.ncbi.nlm.nih.gov/genome/63 63]
|  
| Shortest vertebrate genome known
|  
| [https://genomevolution.org/CoGe/GenomeInfo.pl?gid=25013 unmasked] [https://genomevolution.org/CoGe/GenomeInfo.pl?gid=25052 masked]
|-
|-
|  
|  
|  
| '''''Tetraodon nigroviridis'''''
|  
|Spotted Green Pufferfish
|  
| [http://www.ncbi.nlm.nih.gov/genome/191 191]
|  
| Model species, low amount of repetitive sequence
|  
| [https://genomevolution.org/CoGe/GenomeInfo.pl?gid=23254 unmasked] [https://genomevolution.org/CoGe/GenomeInfo.pl?gid=24926 masked]
|-
|-
|  
|  
|  
| ''Thunnus orientalis''
|  
| Pacific Bluefin Tuna
|  
| [http://www.ncbi.nlm.nih.gov/genome/13314 13314]
|  
| Industrial species
|  
| [https://genomevolution.org/CoGe/GenomeInfo.pl?gid=24952 unmasked] [https://genomevolution.org/CoGe/GenomeInfo.pl?gid=24968 masked]
|-
|-
|  
|  
|  
| '''''Xiphophorus maculatus'''''
|  
| Southern Platyfish
|  
| [http://www.ncbi.nlm.nih.gov/genome/10764 10764]
|  
| Live bearer
|  
| [https://genomevolution.org/CoGe/GenomeInfo.pl?gid=25014 unmasked] [https://genomevolution.org/CoGe/GenomeInfo.pl?gid=25053 masked]
|-
|-
|  
|  
| ''''
|  
|  
|  
| [http://www.ncbi.nlm.nih.gov/genome/ ]
|
|  
|  
|  
|  
|-
|-
|  
|  
| ''''
|  
|  
|  
| [http://www.ncbi.nlm.nih.gov/genome/ ]
|
|  
|  
|  
|  

Revision as of 23:12, 8 January 2015

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
Class Species Common name Genome ID Species notes CoGe Genome Links
Hyperoartia Lethenteron camtschaticum Artic lamprey 16905 One of few extant jawless fish unmasked masked
Petromyzon marinus Sea Lamprey 287 One of few extant jawless fish unmasked masked
Chondrichthyes Callorhinchus milii Australian Ghostshark 689 Proposed model cartilaginous fish unmasked masked
Sarcopterygii Latimeria chalumnae Coelacanth 3262 Oldest extant Sarcopterygii unmasked masked
Actinopterygii Anguilla japonica Japanese Eel 13349 Ecological model, Industry species unmasked [1]
Anoplopoma fimbria Sablefish 12760 Industrial species unmasked
Astyanax mexicanus Mexican tetra 13073 Two forms: seeing, and cave-dwelling blind unmasked masked
Cynoglossus semilaevis Tongue Sole 11788 Industrial species unmasked masked
Cyprinodon variegatus Sheepshead minnow 13078 Toxicology model unmasked masked
Danio rerio Zebrafish 50 Model species unmasked masked
Dicentrarchus labrax European Seabass 2659 Industrial species unmasked masked
Esox lucius Northern Pike 22932 Angling species
Gadus morhua Atlantic cod 2661 Industrial species unmasked masked
Gasterosteus aculeatus Three-spined stickleback 146 Model species unmasked
Haplochromis burtoni Burton’s mouthbrooder 3328 Ecological model species, Aquarium species unmasked masked
Labeotropheus fuelleborni Blue mbuna 2638 unmasked masked
Lepisosteus oculatus Spotted Gar 10597 Lineage before Teleost whole genome duplication unmasked masked
Maylandia zebra Zebra Mbuna 2640 Ecological model species, aquarium fish unmasked masked
Mchenga conophoros 2585 unmasked masked
Melanochromis auratus Auratus Cichlid 2639 unmasked masked
Neolamprologus brichardi Princess Cichlid 3329 Aquarium fish unmasked masked
Nothobranchius furzeri Turquoise Killifish 2642 Short life span model species, metabolic diapause unmasked masked
Nothobranchius kuhntae Beira Killifish 2643 Short life model species unmasked masked
Oncorhynchus mykiss Rainbow Trout Genoscope Salmon Database Angling and industrial species unmasked masked
Oreochromis niloticus Nile Tilapia 197 Industrial species unmasked [2]
Oryzias latipes Japanese Medaka 542 Model fish, Aquarium species unmasked masked
Pimephales promelas Fathead Minnow 13167 Industrial baitfish unmasked masked
Poecilia formosa Amazon Molly 13072 Gynogenesis: all female populations unmasked masked
Poecilia reticulata Guppy 23338 Model species, Aquarium fish unmasked masked
Pundamilia nyererei 3330 unmasked masked
Sebastes nigrocinctus Tiger Rockfish 14568 Angling species, long lived model, live bearer masked
Sebastes rubrivinctus Flag Rockfish 11458 Angling species, Industrial species unmasked
Stegastes partitus Bicolor damselfish 13077 Medical model species unmasked masked
Takifugu flavidus Sansaifugu 14185 unmasked masked
Takifugu rubripes Torafugu 63 Shortest vertebrate genome known unmasked masked
Tetraodon nigroviridis Spotted Green Pufferfish 191 Model species, low amount of repetitive sequence unmasked masked
Thunnus orientalis Pacific Bluefin Tuna 13314 Industrial species unmasked masked
Xiphophorus maculatus Southern Platyfish 10764 Live bearer unmasked masked
' [3]
' [4]



All annotated unmasked fish genomes available in CoGe

All unmasked fish genomes available 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

Discussion/Conclusions


Retrieved from "https://genomevolution.org/wiki/index.php?title=Fish_Comparative_Genomics&oldid=7153"