Fish Comparative Genomics

Data

• Phylogeny of genomes with polyploidy events marked

• Table of fish genomes used in this tutorial

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
	Rajiformes	Leucoraja erinacea	Little skate	Electrosensory organ
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

• 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