A cattle-human comparative map built with cattle BAC-ends and human genome sequence

Abstract

As a step toward the goal of adding the cattle genome to those available for multispecies comparative genome analysis, 40,224 cattle BAC clones were end-sequenced, yielding 60,547 sequences (BAC end sequences, BESs) after trimming with an average read length of 515 bp. Cattle BACs were anchored to the human and mouse genome sequences by BLASTN search, revealing 29.4% and 10.1% significant hits (E < e-5), respectively. More than 60% of all cattle BES hits in both the human and mouse genomes are located within known genes. In order to confirm in silico predictions of orthologyand their relative position on cattle chromosomes, 84 cattle BESs with similarity to sequences on HSA11 were mapped using a cattle-hamster radiation hybrid (RH) panel. Resulting RH maps of BTA15 and BTA29 cover approximately 85% of HSA11 sequence, revealing a complex patchwork shuffling of segments not explained by a simple translocation followed by internal rearrangements. Overlay of the mouse conserved syntenies onto HSA11 revealed that segmental boundaries appear to be conserved in all three species. The BAC clone-based comparative map provides a foundation for the evolutionary analysis of mammalian karyotypes and for sequencing of the cattle genome.

Figure 1

High-resolution cattle- and mouse-on-human comparative map of HSA11 created with current RH maps of BTA15 and BTA29 and 84 new cattle BESs. Comparative coverage on the current cattle RH₅₀₀₀ map is shown in solid red or blue blocks on the right half of the HSA11 drawing, with comparative segments indicated in Roman numerals. Mouse-on-human segments and mouse chromosome number are shown within the left half of the HSA11 drawing, with the sequence coordinates of the corresponding positions in the mouse genome indicated to the left. The distribution of BACs predicted to conserved segments of BTA15 and BTA29 is shown between the RH maps and human chromosome segments. Mapped conserved BAC ends (CASTS) increased the total comparative coverage and enabled merging of linkage groups for both cattle chromosomes. The CASTS are identified by GenBank accession number and are colored blue or red on chromosome maps. The human centromere is indicated by black ovals, and the 3.37-Mbp pericentric region on HSA11 with no BLAST hits is shaded. Black and gray circles indicate the location of centromeres on cattle and mouse chromosomes, respectively. Placement of markers appearing in boxes is defined by two-point linkage, because their order could not be determined with certainty. Framework markers are in bold text. Underlined markers are those with no hit against the human genome (microsatellites, and novel ESTs). Markers with two asterisks (^**) are not predicted by COMPASS to be in the observed segment on the basis of the available comparative map. Comparative maps were drawn using NCBI Build 29 (April 2002) of the human genome.