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

Species	Common name	Bioproject ID	Species notes	CoGe Genome Links
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]

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