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  


{| width="200" cellspacing="1" cellpadding="1" border="1" height="1000" |- | '''Class''' | '''Order''' | '''Genus species''' | '''Common name''' | '''Notes'''| '''CoGe Genome Links''' |- | Cephalaspidomorphi | Petromyzontiformes | Lethenteron camtschaticum | Artic lamprey<br> | One of few extant jawless fish | |- | <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| Takifugu flavidus | Sansaifugu |  | |- |  |  | Tetraodon nigroviridis | Spotted green pufferfish| Model species, low amount of repetitive sequence | |- |  |  | Takifugu rubripes | ‘Fugu’ pufferfish | Shortest vertebrate genome| |}
 





Revision as of 22:12, 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