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[ Cichlid Genetics ListServ| U Maryland Labs]

[ Genetic maps| BAC libraries| Physical maps| cDNA libraries ]

News and updates

October, 2010
  • Cichlid genome resources displayed in GBrowse on a new site:
  • The Broad Institute is generating a high quality draft from a Nile tilapia, Oreochromis niloticus. as well as several other East African Lake species: Astatotilapia burtoni, Metriaclima (Maylandia) zebra, Pundamila nyererei and Neolamprologus brichardi. Check on their progress here: Broad Institute
  • Kocher's lab recently published 117,000 ESTs from 19 cDNA libraries. Lee et al. 2010

    Genomic resources

    The descriptions and links below will lead you to the genome research tools already developed for studies of these fishes, including genetic linkage maps, cDNA clone libraries, and a physical map based on the restriction fingerprints of 35,000 BAC clones.

    Genetic maps

    Several genetic linkage maps of cichlid fishes have been constructed. Our latest map, based on an interspecific F2 cross between O. niloticus and O. aureus has an average spacing of 3cM between microsatellite markers (Lee et al. 2005 - PDF.

    We have also published a map for Lake Malawi cichlids, based on the F2 of an intergeneric cross of two Lake Malawi cichlids (Metriaclima zebra and Labeotropheus fuelleborni). Although this map has fewer markers, we were able to select markers from the tilapia map to fill in gaps. When we compare marker orders in these two maps, we find only two obvious rearrangements, indicating that gene order is largely conserved across this group of fishes.

    Species Family type # markers marker type Institution Reference
    Tilapia F2 550 microsatellite HCGS Lee et al., 2005
    Malawi F2 137 microsatellite HCGS Albertson et al., 2003
    Tilapia F2 229 micro/AFLP UC Davis Agresti et al., 2000
    Tilapia BC 37 microsatellite Univ Wales McConnell et al., 2000
    Tilapia haploid 162 micro/AFLP HCGS Kocher et al., 1998

    BAC Libraries

    Four tilapia BAC libraries have been produced at the Tokyo University of Fisheries (Katagiri et al. 2000) (PDF). Plates and filters for portions of libraries 3 and 4 are available. Contact Tom Kocher for more information.
    Library # primary clones Average insert size Estimated coverage Picked
    1 120k 65k 6x -
    2 800k 105k 65x -
    3 100k 145k 11x 36k
    4 40k 194k 6x 33k

  • A BAC library has been constructed for the Lake Malawi cichlid Metriaclima zebra by DiPalma et al. (2007) [PDF]. This library is also available at cost by contacting Tom Kocher (

    A library from the Lake Victoria cichlid Haplochromis chilotes (10x coverage, 128kb average insert size) has been constructed at the Tokyo Institute of Technology by Watanabe et al. (2003). [PDF]

    A third haplochromine library, from the Lake Tanganyika species Astatotilapia burtoni (12x coverage, 150kb average insert size), has been constructed by Michael Lang in Chris Amemiya's lab, in a collaboration with Axel Meyer at the University of Konstanz (Lang et al., 2006). (PDF)

    Physical maps

    With support from the US Dept. of Agriculture, we have fingerprinted more than 35,000 clones from tilapia libraries 3 and 4 (approximately 5x coverage of the genome) and produced a physical map of overlapping BAC clones Katagiri et al. (2005) [PDF]. An FPC file of the fingerprint data is available from Tom Kocher (

    cDNA resources

    There are many labs around the world working to develop cDNA resources for cichlids. Hans Hofmann (Univ Texas, Austin) is organizing a cichlid microarray collaboration.

    Laboratory Species Tissue # ESTs Online
    Okada Paralabidochromis chilotes jaw 20,701 Gene Index
    Okada Ptyochromis 'redtail sheller' jaw 13,752 Gene Index
    Okada Lipochromis 'matumbi hunter' jaw in progress
    Fernald/Hofmann/Meyer Astatotilapia burtoni several 10,212 Gene Index
    Meyer Metriaclima zebra skin in progress
    Nagahama Oreochromis niloticus developing gonad 18,186 NIBB
    Kocher Oreochromis niloticus various 116,899 BouillaBase
    Baroiller/D'Cotta Oreochromis niloticus brain and gonad in progress
    Jaso-Friedman Oreochromis niloticus nonspec. cytotoxic cells in progress
    Genomar asa Oreochromis niloticus brain/gill 2,500
    Martins Oreochromis niloticus brain/heart/muscle in progress
    Total >182,000

    University of Maryland, College Park