A 1463 Gene Cattle–Human Comparative Map With Anchor Points Defined by Human Genome Sequence Coordinates

Abstract

A second-generation 5000 rad radiation hybrid (RH) map of the cattle genome was constructed primarily using cattle ESTs that were targeted to gaps in the existing cattle–human comparative map, as well as to sparsely populated map intervals. A total of 870 targeted markers were added, bringing the number of markers mapped on the RH5000 panel to 1913. Of these, 1463 have significant BLASTN hits (E < e–5) against the human genome sequence. A cattle–human comparative map was created using human genome sequence coordinates of the paired orthologs. One-hundred and ninety-five conserved segments (defined by two or more genes) were identified between the cattle and human genomes, of which 31 are newly discovered and 34 were extended singletons on the first-generation map. The new map represents an improvement of 20% genome-wide comparative coverage compared with the first-generation map. Analysis of gene content within human genome regions where there are gaps in the comparative map revealed gaps with both significantly greater and significantly lower gene content. The new, more detailed cattle–human comparative map provides an improved resource for the analysis of mammalian chromosome evolution, the identification of candidate genes for economically important traits, and for proper alignment of sequence contigs on cattle chromosomes.

Cattle genomics and its implications for future nutritional strategies for dairy cattle

“…Whereas somatic cell hybrid maps and cross-species chromosome painting with the human and other species DNA probes have provided an important but patched correspondence between the cattle, human, mouse and pig genomes (Womack and Moll, 1986;Hayes, 1995;Chowdhary et al, 1996;Schmitz et al, 1998), the real breakthrough in cattle comparative studies began with the introduction of high-resolution ordered radiation hybrid maps (Band et al, 2000;Everts-van der Wind et al, 2004 and. The cattle genome was assembled to chromosomes using IL-TX RH map at Baylor College of Medicine (Btau_4.0) and BCCRC (British Columbia Cancer Research Center)-integrated fingerprint map at the University of Maryland (UMD 3.1).…”

“…Indeed, analysis of the cattle and other amniote genomes provides support for the hypothesis of adaptive value of EBRs. For example, Everts-van der Wind et al (2004) reported that evolutionary breakpoints between the cattle and human genomes are significantly enriched for genes. Recently, this observation was confirmed by multi-species genome comparisons (Murphy et al, 2005;Larkin et al, 2009).…”

An Evolutionary Biology Approach to Understanding Neurological Disorders

“…The fragile-site model leads to various testable hypotheses as to the nature of these hot spots, and factors such as DNA sequence and chromosome structure were proposed. Since then, evolutionary breakpoints have been shown, for example, to be gene-rich regions with significantly more segmental duplications and/or repetitive elements than expected, which may facilitate homologous recombination (Bailey et al, 2004;Bulazel et al, 2007;Everts-van der Wind et al, 2004Kehrer-Sawatzki & Cooper, 2008;Murphy et al, 2005;Schibler et al, 2006). These regions also encompass genes with higher densities of copy number variation and SNPs (Larkin et al, 2009).…”

Breakpoint graphs and ancestral genome reconstructions

“…Supplement L compares MGRA and inferCARs on simulated data and illustrates that MGRA generates more accurate ancestral reconstructions for all choices of parameters. However, analyzing all these tools on simulated data may generate over-optimistic results since RBM does not reflect the realities of mammalian evolution (Bailey et al 2004;van der Wind et al 2004;Zhao et al 2004;Murphy et al 2005;Webber and Kikuta et al 2007;Mehan et al 2007). We therefore decided to analyze the differences between MGRA and inferCARs reconstructions and to further track evidence for each such difference in a case-by-case fashion.…”