Fish Comparative Genomics: Difference between revisions

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</p><p>== Setting the hook: getting data loaded into CoGe == <br /> <br /> *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 <br /> *Table of fish genomes publicly available in CoGe {| width="1075" cellspacing="1" cellpadding="1" border="1" height="1387" |- | <b>Class</b> | <b>Order</b><br /> | <b>Genus species<br /></b> | <b>Common name</b><br /> | <b>Notes</b><br /> | <b>CoGe Genome Links</b> |- | Cephalaspidomorphi<br /> | Petromyzontiformes<br /> | Lethenteron camtschaticum<br /> | Artic lamprey<br /> | One of few extant jawless fish<br /> | |- | <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<br /> | Takifugu flavidus<br /> | Sansaifugu<br /> | <br /> | |- | <br /> | <br /> | Tetraodon nigroviridis<br /> | Spotted green pufferfish<br /> | Model species, low amount of repetitive sequence<br /> | |- | <br /> | <br /> | Takifugu rubripes<br /> | ‘Fugu’ pufferfish<br /> | Shortest vertebrate genome<br /> | |} <br /> *Links to CoGe <a href="/wiki/index.php/Notebooks" title="Notebooks">Notebooks</a> containing these genomes<br /> **<a href="https://genomevolution.org/CoGe/NotebookView.pl?nid=890" class="external text" title="https://genomevolution.org/CoGe/NotebookView.pl?nid=890" rel="nofollow" target="_blank">All unmasked fish genomes available in CoGe</a><br /> **[ All masked fish genomes available in CoGe] *Link to <a href="/wiki/index.php/GenomeList" title="GenomeList">GenomeList</a> for notebooks **[ GenomeList for all fish genomes in CoGe]
</p>


== Setting the hook: getting data loaded into CoGe == <br> <br> *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 <br> *Table of fish genomes publicly available in CoGe {| width="1075" cellspacing="1" cellpadding="1" border="1" height="1387" |- | '''Class''' | '''Order'''<br> | '''Genus species<br>''' | '''Common name'''<br> | '''Notes'''<br> | '''CoGe Genome Links''' |- | Cephalaspidomorphi<br> | Petromyzontiformes<br> | Lethenteron camtschaticum<br> | Artic lamprey<br> | One of few extant jawless fish<br> | |- | <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<br> | Takifugu flavidus<br> | Sansaifugu<br> | <br> | |- | <br> | <br> | Tetraodon nigroviridis<br> | Spotted green pufferfish<br> | Model species, low amount of repetitive sequence<br> | |- | <br> | <br> | Takifugu rubripes<br> | ‘Fugu’ pufferfish<br> | Shortest vertebrate genome<br> | |} <br> *Links to CoGe [[Notebooks]] containing these genomes<br> **[https://genomevolution.org/CoGe/NotebookView.pl?nid=890 All unmasked fish genomes available in CoGe]<br> **[ All masked fish genomes available in CoGe] *Link to [[GenomeList]] for notebooks **[ GenomeList for all fish genomes in CoGe]
== 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 <br>  
 
 
*Table of fish genomes publicly available in CoGe  
 
{| width="1075" cellspacing="1" cellpadding="1" border="1" height="1387" |- | '''Class''' | '''Order'''<br> | '''Genus species<br>''' | '''Common name'''<br> | '''Notes'''<br> | '''CoGe Genome Links''' |- | Cephalaspidomorphi<br> | Petromyzontiformes<br> | Lethenteron camtschaticum<br> | Artic lamprey<br> | One of few extant jawless fish<br> | |- | <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<br> | Takifugu flavidus<br> | Sansaifugu<br> | <br> | |- | <br> | <br> | Tetraodon nigroviridis<br> | Spotted green pufferfish<br> | Model species, low amount of repetitive sequence<br> | |- | <br> | <br> | Takifugu rubripes<br> | ‘Fugu’ pufferfish<br> | Shortest vertebrate genome<br> | |} <br>  
 
 
 
*Links to CoGe [[Notebooks]] containing these genomes<br>  
**[https://genomevolution.org/CoGe/NotebookView.pl?nid=890 All unmasked fish genomes available in CoGe]<br>  
**[ All masked fish genomes available in CoGe]  
*Link to [[GenomeList]] for notebooks  
**[ GenomeList for all fish genomes in CoGe]


== Glossary ==
== Glossary ==

Revision as of 21:59, 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

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


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