Difference between revisions of "Fish Comparative Genomics"

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(Analyses)
(Analyses)
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*[[SynMap]]  
 
*[[SynMap]]  
 
**Identify Whole Genome Duplications  
 
**Identify Whole Genome Duplications  
***Whole genome synteny analysis of [https://genomevolution.org/r/eola ''Oncorhynchus mykiss'' (rainbow trout) compared to ''Takifugu rubripes'']. In this analysis, the [[synonymous mutation]] (Ks)
+
***Whole genome synteny analysis of [https://genomevolution.org/r/eola ''Oncorhynchus mykiss'' (rainbow trout) compared to ''Takifugu rubripes'']. In this analysis, the [[synonymous mutation]] rate (Ks) has been calculated to determine the relative age of each syntenic gene pair (represented as a dot) in the dotplot. The blue/green color indicates a newer whole genome duplication whereas the red/orange dots are noise in the dataset. The histogram below the dotplot shows the distribution of the synonymous mutation rates
  
  

Revision as of 13:05, 15 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. Bold denotes species with annotations.
Class Species Common name Genome ID Species notes CoGe Genome Links

Hyperoartia

(jawless fish)

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

(cartilaginous fish)

Callorhinchus milii Australian Ghostshark 689 Proposed model cartilaginous fish unmasked masked
Sarcopterygii

(lobe-fin fish)

Latimeria chalumnae Coelacanth 3262 Oldest extant Sarcopterygii unmasked masked

Actinopterygii

(ray-fin fish)

Anguilla japonica Japanese Eel 13349 Ecological model, Industry species unmasked masked
Anoplopoma fimbria Sablefish 12760 Industrial species unmasked masked
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 unmasked masked
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 masked
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



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
      • Whole genome synteny analysis of Oncorhynchus mykiss (rainbow trout) compared to Takifugu rubripes. In this analysis, the synonymous mutation rate (Ks) has been calculated to determine the relative age of each syntenic gene pair (represented as a dot) in the dotplot. The blue/green color indicates a newer whole genome duplication whereas the red/orange dots are noise in the dataset. The histogram below the dotplot shows the distribution of the synonymous mutation rates


    • 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