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
    

| Class

Table of fish genomes publicly available in CoGe

Species	Common name	Genome ID	Species notes	CoGe Genome Links
Hyperoartia	Lethenteron camtschaticum	Artic lamprey	16905	One of few extant jawless fish
| Petromyzon marinus	Sea Lamprey	287	One of few extant jawless fish
Chondrichthyes	Callorhinchus milii	Australian Ghostshark	689	Proposed model cartilaginous fish
Sarcopterygii	Latimeria chalumnae	Coelacanth	3262

• 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