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

• 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