Fish Comparative Genomics

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	Order	Genus species	Common name	Notes
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

• Links to CoGe Notebooks containing these genomes
  
  • All unmasked fish genomes available in CoGe
    
  • [ All masked fish genomes available in CoGe]
• Link to GenomeList for notebooks
  • [ GenomeList for all fish genomes in CoGe]

Glossary

• WGD/WGT
• Syntenic dotplot
• Microsynteny
• Ortholog
• Paralog
• Out-Paralog
• In-Paralog

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

• LoadGenome
• LoadExperiment
• Keeping data private and sharing with collaborators