Fish Comparative Genomics: Difference between revisions

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*Table of fish genomes used in this tutorial
*Table of fish genomes used in this tutorial


{| width="594" height="904" cellspacing="1" cellpadding="1" border="1"
{| width="594" cellspacing="1" cellpadding="1" border="1"
|-
|-
| Class
| Class  
| Order<br>
| Order<br>  
| Genus species<br>
| Genus species<br>  
| Common name<br>
| Common name<br>  
| Notes<br>
| Notes<br>
|-
|-
| Cephalaspidomorphi<br>
| Cephalaspidomorphi<br>  
| Petromyzontiformes<br>
| Petromyzontiformes<br>  
| Lethenteron camtschaticum<br>
| Lethenteron camtschaticum<br>  
| Artic lamprey<br>
| Artic lamprey<br>  
| One of few extant jawless fish<br>
| One of few extant jawless fish<br>
|-
|-
| <br>
| <br>  
| <br>
| <br>  
| <br>
| Petromyzon marinus<br>  
| <br>
| Sea lamprey<br>  
| <br>
| One of few extant jawless fish<br>
|-
|-
| <br>
| Chondrichthyes<br>  
| <br>
| Chimaeriformes<br>  
| <br>
| Callorhinchus milii<br>  
| <br>
| Australian ghostshark<br>  
| <br>
| Proposed model cartilaginous fish<br>
|-
|-
| <br>
| <br>  
| <br>
| Rajiformes<br>  
| <br>
| Leucoraja erinacea<br>  
| <br>
| Little skate<br>  
| <br>
| Electrosensory organ<br>
|-
|-
| <br>
| Sarcopterygii<br>  
| <br>
| Coelacanthiformes<br>  
| <br>
| Latimeria chalumnae<br>  
| <br>
| Coelacanth<br>  
| <br>
| Oldest known extant Sarcopterygii<br>
|-
|-
| <br>
| Actinopterygii<br>  
| <br>
| Anguilliformes<br>  
| <br>
| Anguilla japonica<br>  
| <br>
| Japanese eel<br>  
| <br>
| Ecological model, Industry species<br>
|-
|-
| <br>
| <br>  
| <br>
| Beloniformes<br>  
| <br>
| Oryzias latipes<br>  
| <br>
| Medaka<br>  
| <br>
| Model fish, Japanese pet fish<br>
|-
|-
| <br>
| <br>  
| <br>
| Characiformes<br>  
| <br>
| Astyanax mexicanus<br>  
| <br>
| Mexican tetra<br>  
| <br>
| Two forms: seeing, and cave-dwelling blind<br>
|-
|-
| <br>
| <br>  
| <br>
| Cichliformes<br>  
| <br>
| Haplochromis burtoni<br>  
| <br>
| Burton’s mouthbrooder<br>  
| <br>
| Ecological model species, Aquarium species<br>
|-
|-
| <br>
| <br>  
| <br>
| <br>  
| <br>
| <br>  
| <br>
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Revision as of 18:16, 4 December 2014

Summary/Abstract

Introduction

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


























































































































































Glossary

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

Discussion/Conclusions

Retrieved from "https://genomevolution.org/wiki/index.php?title=Fish_Comparative_Genomics&oldid=7031"