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	Species	Common name	Genome ID	Species notes	CoGe Genome Links
Hyperoartia	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	Callorhinchus milii	Australian Ghostshark	689	Proposed model cartilaginous fish	unmasked masked
Sarcopterygii	Latimeria chalumnae	Coelacanth	3262	Oldest extant Sarcopterygii	unmasked masked
Actinopterygii	Anguilla japonica	Japanese Eel	13349	Ecological model, Industry species	unmasked [1]
	Anoplopoma fimbria	Sablefish	12760	Industrial species	unmasked
	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
	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 [2]
	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

• 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]

All annotated unmasked fish genomes available in CoGe

All unmasked fish genomes available 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