Latest updates

  • The Broad transcriptome assemblies have been aligned to their respective genome assemblies using GMAP and are available as tracks in GBrowse.
  • Genome browsers are now available for Tilapia (anchored), Astatotilapia burtoni, Pundamilia nyererei, Metriaclima zebra and Neolamprologus brichardi.
  • Assemblies of Astatotilapia burtoni, Pundamilia nyererei, Metriaclima zebra and Neolamprologus brichardi are now available from the Broad ftp site.
  • Broad Institute tilapia genome assembly v.1 The Broad Institute has released version 1 of the Tilapia genome!
  • Illumina transcriptome RNA from Tilapia testis has been analyzed via Illumina RNA-seq, assembled into transcripts and aligned to stickleback.
  • Tilapia ESTs Kocher's lab has generated 116,899 Sanger ESTs from 17 normalized and two non-normalized cDNA libraries representing 16 tissues. The ESTs were assembled into 20,190 contigs and 36,028 singletons for a total of 56,218 unique sequences and a total assembled length of 35,169,981bp. The publication describing this work can be found at PMID:20433739
  • BAC end sequences The Broad Institute has sequenced 156,216 BAC-end sequences from the VMRC-44 Tilapia BAC library using Sanger sequencing technology. The sequences have been mapped to stickleback, tetraodon and medaka and are viewable in GBrowse.
  • A. burtoni linkage map Axel Meyer's lab has constructed a genetic map of Astatotilapia burtoni consisting of 25 linkage groups spanning 1249.3 cM with an average marker spacing of 6.12 cM.

Cichlid-specific resources

  • JGI reads on Tetraodon The DOE-JGI Institute sequenced 100Mb from each of 5 species of Lake Malawi haplochromine cichlid. Here they are mapped on the Tetraodon genome.
  • U Maryland Blast server Search cichlid ESTs, BAC ends and JGI reads on the U Maryland Blast server.

FIsh genomes

General comparative tools

  • Genomicus - Navigate genomes in several dimensions: linearly along chromosome axes, transversely across different species, and chronologically along evolutionary time.
  • Synteny database Automated identification of conserved synteny after whole genome duplication.
  • PhyloVista Interactive tool for analyzing multiple DNA sequence alignments.




Adult tilapia

Adult tilapia

Astatotilapia burtoni

Haplochromis burtoni

Lake Malawi cichlids

Malawi cichlids