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="1075" cellspacing="1" cellpadding="1" border="1" height="1387" |- | &lt;b&gt;Class&lt;/b&gt; | &lt;b&gt;Order&lt;/b&gt; | &lt;b&gt;Genus species &lt;/b&gt; | &lt;b&gt;Common name&lt;/b&gt; | &lt;b&gt;Notes&lt;/b&gt; | &lt;b&gt;CoGe Genome Links&lt;/b&gt; |- | 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 | |} <br>  
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*Links to CoGe [[Notebooks]] containing these genomes<br>  
*Links to CoGe [[Notebooks]] containing these genomes<br>  

Revision as of 22:17, 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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