This article is part of the supplement: Proceedings of the Avian Genomics Conference and Gene Ontology Annotation Workshop

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The value of avian genomics to the conservation of wildlife

Michael N Romanov18*, Elaina M Tuttle2, Marlys L Houck1, William S Modi1, Leona G Chemnick1, Marisa L Korody2, Emily M Stremel Mork1, Christie A Otten1, Tanya Renner1, Kenneth C Jones3, Sugandha Dandekar4, Jeanette C Papp4, Yang Da5, NISC Comparative Sequencing Program6, Eric D Green6, Vincent Magrini7, Matthew T Hickenbotham7, Jarret Glasscock7, Sean McGrath7, Elaine R Mardis7 and Oliver A Ryder1

Author Affiliations

1 Genetics Division, San Diego Zoo's Institute for Conservation Research, Zoological Society of San Diego, Arnold and Mabel Beckman Center for Conservation Research, 15600 San Pasqual Valley Rd., Escondido, CA 92027, USA

2 Dept. of Biology, Indiana State University, Science 285E, 403-25 North 6th St., Terre Haute, IN 47809, USA

3 Genetic Identification Services, 9552 Topanga Canyon Blvd., Chatsworth, CA 91311, USA

4 UCLA Sequencing and Genotyping Core, Dept. of Human Genetics, 5309 Gonda, 695 Charles E. Young Dr. South, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA

5 Dept. of Animal Science, 265D Haecker Hall, University of Minnesota, 1364 Eckles Ave., St. Paul, MN 55108, USA

6 Genome Technology Branch and NIH Intramural Sequencing Center (NISC), National Human Genome Research Institute, National Institutes of Health, 50 South Dr., Bldg. 50, Rm. 5222, Bethesda, MD 20892, USA

7 Washington University Genome Sequencing Center, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Ave., St. Louis, MO 63108, USA

8 BACPAC Resources, Children's Hospital Oakland Research Institute, 747 52nd St., Oakland, CA 94609, USA

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BMC Genomics 2009, 10(Suppl 2):S10  doi:10.1186/1471-2164-10-S2-S10

Published: 14 July 2009

Additional files

Additional file 1:

Pedigree of a condor resource population chosen for microsatellite and linkage analyses, with 121 individuals.

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Additional file 2:

List of overgo probes used for the second screening of the condor BAC library.

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Additional file 3:

Chicken chromosome map (in Mb) showing location of the 199 loci aligned with the California condor BAC clones (numbers in parentheses). Created with MapChart [83] and GenomePixelizer [84] software. With the colored symbols, chicken loci are given that were anchored to condor BACs using California condor (red), New World vulture (gold) and zebra finch (green) sequence derived OVERGOs or Uprobes (blue) followed up by direct sequencing. GGAUn_random, an unknown virtual chicken chromosome sequence generated by the International Chicken Genome Sequencing Consortium [19] that is yet to be assigned to a named chromosome. LOC770630 (multiple GGAUn_random?), the probe for this locus may also align with the chicken sequence at additional unresolved locations. *, the CRES0014 and GAPR1 sequences align with several chicken chromosomes, GGA1 and GGA2 being the best matches, respectively.

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Additional file 4:

Database of condor BACs positive for known avian genes, markers and other sequences

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Additional file 5:

Chicken-condor comparative cytogenetic map showing a considerable degree of conserved synteny.

GGA, Gallus gallus (chicken) chromosomes; GCA, Gymnogyps californianus (California condor) chromosomes.

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Additional file 6:

A condor-human comparative physical map for HSA7q31

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Additional file 7:

Distribution of the condor 454 transcripts homologous to chicken genes. The histogram illustrates how the condor reads fall into the chicken gene bins where the '0' bin represents all the genes with 0 to 9 members, the '10' bin genes with 10 to 19 reads and so on. There were a lot of rare transcripts (~45,000), with 0 to 20 members, vs. small numbers of other abundant and extremely abundant transcripts, with up to 55,000+ members, in this fibroblast cell line.

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Additional file 8:

Most abundant transcripts in a transformed condor fibroblast cell line. Proteins that are expected to be expressed in a fibroblast cell line are highlighted with gray, while one protein (MAD1L1) that could be involved in abnormal cell features and functions is given in bold.

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