Homology-driven assembly of a sequence-ready mouse BAC contig map spanning regions related to the 46-Mb gene-rich euchromatic segments of human chromosome 19

Joomyeong Kim, Lawrence Livermore National Laboratory
Laurie Gordon, Lawrence Livermore National Laboratory
Paramvir Dehal, Lawrence Livermore National Laboratory
Hummy Badri, Lawrence Livermore National Laboratory
Mari Christensen, Lawrence Livermore National Laboratory
Matthew Groza, Lawrence Livermore National Laboratory
Chi Ha, Lawrence Livermore National Laboratory
Sha Hammond, Lawrence Livermore National Laboratory
Michelle Vargas, Lawrence Livermore National Laboratory
Edward Wehri, Lawrence Livermore National Laboratory
Mark Wagner, Lawrence Livermore National Laboratory
Anne Olsen, Lawrence Livermore National Laboratory
Lisa Stubbs, Lawrence Livermore National Laboratory

Abstract

Draft sequence derived from the 46-Mb gene-rich euchromatic portion of human chromosome 19 (HSA19) was utilized to generate a sequence-ready physical map spanning homologous regions of mouse chromosomes. Sequence similarity searches with the human sequence identified more than 1000 individual orthologous mouse genes from which 382 overgo probes were developed for hybridization. Using human gene order and spacing as a model, these probes were used to isolate and assemble bacterial artificial chromosome (BAC) clone contigs spanning homologous mouse regions. Each contig was verified, extended, and joined to neighboring contigs by restriction enzyme fingerprinting analysis. Approximately 3000 mouse BACs were analyzed and assembled into 44 contigs with a combined length of 41.4 Mb. These BAC contigs, covering 90% of HSA19-related mouse DNA, are distributed throughout 15 homology segments derived from different regions of mouse chromosomes 7, 8, 9, 10, and 17. The alignment of the HSA19 map with the ordered mouse BAC contigs revealed a number of structural differences in several overtly conserved homologous regions and more precisely defined the borders of the known regions of HSA19-syntenic homology. Our results demonstrate that given a human draft sequence, BAC contig maps can be constructed quickly for comparative sequencing without the need for preestablished mouse-specific genetic or physical markers and indicate that similar strategies can be applied with equal success to genomes of other vertebrate species. © 2001 Academic Press.