Fish Comparative Genomics

Introduction

• Phylogeny of genomes with polyploidy events marked
  

Sample Datasets

To access sample datasets

• Takifugu rubripes genome (http://de.iplantcollaborative.org/dl/d/05199A88-82ED-4D09-94AA-99CF3D8B64FE/Takifugu_rubripes_genome_NCBIv1.faa)

• Takifugu rubripes genome annotation (http://de.iplantcollaborative.org/dl/d/989C12FD-D62C-48B5-8FB8-80706BCB028D/T_rubripes_annotation_GCF_000180615.1.gff.gz)

Setting the hook: getting data loaded into CoGe

• Loading new genomes into CoGe
  • Loading genomes into the Bio.ci (iPlant Data Store) for the first time
    • Sign up for an account or log in
    • Access the Data Store
    • Direct upload from your computer
      • Press the upload tab on the top left and select 'Simple upload from Desktop'
      • Find the genome(s) FASTA file and select
      • Enjoy a picnic outside while they upload
    • Using FTP/HTTP links for uploading genomes in the Data Store
      • 1) In the top left of the screen click on the 'Upload' button
        • a) Select 'Import using URL'
        • b) This will create several spaces to paste URLs into so that the Data Store will retrieve files (in this case genome FASTA files/.fa files). Once the blank areas come up, open a new tab in your browser
      • 2) copy the link location of the genome FASTA file from an FTP site or webpage
      • 3) paste the URL into a blank on the Data Store page
      • Enjoy some tea or coffee while they upload
  • Once the genomes have been uploaded into the Data Store
    • Select them and move them into the folder names 'coge_data'
    • The genome should now be visible in the CoGe platform

• • Direct upload

• • CoGe NCBI Loader
    

• OR Use genomes already available in CoGe
  • Select your favorite fish genome from the table below
  • Or search CoGe for other organisms using OrganismView

Sequenced fish genomes

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 masked
	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
	Salmo salar	Atlantic salmon	[ NCBI Bioproject]	Angling species, Industrial species	unmasked masked
	Sebastes aleutianus	Rougheye Rockfish	NCBI Bioproject	Angling species, Industrial species, Does not age/senesce	soft masked
	Sebastes nigrocinctus	Tiger Rockfish	14568	Angling species, long lived model, live bearer	masked
	Sebastes rubrivinctus	Flag Rockfish	11458	Angling species, Industrial species	unmasked masked
	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 fish 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

Casting the Line: analyses for comparing genomes

Whole genome syntenic analysis

• SynMap (tutorial)
  • Identify Whole Genome Duplications
    • Example 1: 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
    • Non-synonymous mutation rates for syntenic gene pairs between O. mykiss and T. rubripes
    • Ka/Ks rates for syntenic gene pairs between O. mykiss and T. rubripes

Microsyntenic analysis

• GEvo
  • Validate microsynteny
    • Example 1: Microsynteny analysis using GeVo to compare T. rubripes to O. mykiss. This analysis shows evidence of whole genome duplication in O. mykiss (the Salmonid WGD) when compared to another Teleost fish that does not have a WGD after the Teleost WGDfff.

• • Identify Conserved non-coding sequences (regulatory function)

Ortholog/paralog finding with synteny

• SynFind
  • Identify orthologous regions across many species

Sinkers to Cast Further and Deeper: adding weight to genomes with additional data types

Adding new data (genomes, RNASeq, SNPs) to CoGe

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

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