CROSS-SPECIES COMPARISON OF SYNTENICALLY HOMOLOGOUS SEGMENTS RELATED TO HUMAN CHROMOSOME 19 IN CHICKEN AND MOUSE

¹ Biology and Biotechnology Research Program, Lawrence Livermore National Laboratory, Livermore CA, USA

² D.O.E. Joint Genome Institute, Walnut Creek, CA, USA

³ Dept. Genomics and Bioinformatics, Roslin Institute, Roslin, UK

⁴ Dept. Animal Sciences, Wageningen Agricultural University, Wageningen, The Netherlands

Cross-species comparison of syntenically homologous genome segments provides an enormously rich resource for genome annotation and for elucidating the mechanisms that drive genome evolution and vertebrate speciation. Having previously reported comparative studies of mouse homology regions related to human chromosome 19 (HSA19, Genomics 74:129-141, 2001; Science 293:104-111, 2001), genomic regions homologous to HSA19 were mapped and sequenced in chicken to provide a third, evolutionarily more distant vertebrate with which to enhance biological insight.   To maximize investigatory benefit, we generated high quality, ordered and oriented sequence from contiguously mapped BAC clones. Overgo and PCR probes were designed from chicken ESTs, identified with conserved (65-98%), protein-translated HSA19 gene sequences, and hybridized to high density filters from three libraries (one from Gallus domesticus and two from Gallus gallus). BACs identified by hybridization were restriction digested and assembled into maps to assess clonal integrity and overlap, facilitate contig extension, identify homology breaks and generate efficient sequencing tiling paths. Clones located on chicken chromosome 28 (GGA28) representing HSA19p13.3 and p13.1 have been assembled into two mapped contigs and submitted for parallel sequencing in both species. Clones from four GGA11 contigs homologous to HSA19q12-q13.1, as well as a few additional islands of homology scattered throughout the chicken genome, have also been identified and sequenced.   The availability of high-quality sequence derived from contiguous sets of clones permitted us to identify additional orthologs, generate gene models for many previously undescribed chicken genes, recognize previously undetected non-coding regulatory elements, and detail homology segment breakpoints and rearrangements at high resolution. As anticipated, the chicken genome is much more compact than human; the 12 Mb of HSA19p reprised in the two GGA28 contigs spans a mere 4.5 Mb (750 and 3750 kb, respectively) in chicken. While linkage groups as a whole are conserved in chicken, interruptions and rearrangements in synteny at the level of gene-to-gene resolution are pervasive; based on mapping data alone the two GGA28 contigs contain at least 25 homology rearrangements compared to human. Further studies include analyses by Groenen, et al., of single nucleotide polymorphisms (SNPs) between the two chicken species. Finally, we are pursuing studies to substantiate chicken gene models and verify putative regulatory elements made apparent by cross-species sequence alignments.   This work was performed under the auspices of the U.S. Department of Energy by the University of California, Lawrence Livermore National Laboratory under Contract No. W-7405-Eng-48.