Comparative genome mapping of the deer mouse (Peromyscus maniculatus) reveals greater similarity to rat (Rattus norvegicus) than to the lab mouse (Mus musculus)

<p>Abstract</p> <p>Background</p> <p>Deer mice (<it>Peromyscus maniculatus</it>) and congeneric species are the most common North American mammals. They represent an emerging system for the genetic analyses of the physiological and behavioral bases of habitat adaptation. Phylogenetic evidence suggests a much more ancient divergence of <it>Peromyscus </it>from laboratory mice (<it>Mus</it>) and rats (<it>Rattus</it>) than that separating latter two. Nevertheless, early karyotypic analyses of the three groups suggest <it>Peromyscus </it>to be exhibit greater similarities with <it>Rattus </it>than with <it>Mus</it>.</p> <p>Results</p> <p>Comparative linkage mapping of an estimated 35% of the deer mouse genome was done with respect to the Rattus and Mus genomes. We particularly focused on regions that span synteny breakpoint regions between the rat and mouse genomes. The linkage analysis revealed the Peromyscus genome to have a higher degree of synteny and gene order conservation with the Rattus genome.</p> <p>Conclusion</p> <p>These data suggest that: 1. the <it>Rattus </it>and <it>Peromyscus </it>genomes more closely represent ancestral Muroid and rodent genomes than that of <it>Mus</it>. 2. the high level of genome rearrangement observed in Muroid rodents is especially pronounced in <it>Mus</it>. 3. evolution of genome organization can operate independently of more commonly assayed measures of genetic change (e.g. SNP frequency).</p

Expressed sequence tags from Peromyscus testis and placenta tissue: Analysis, annotation, and utility for mapping

<p>Abstract</p> <p>Background</p> <p>Mice of the genus <it>Peromyscus </it>are found in nearly every habitat from Alaska to Central America and from the Atlantic to the Pacific. They provide an evolutionary outgroup to the <it>Mus/Rattus </it>lineage and serve as an intermediary between that lineage and humans. Although <it>Peromyscus </it>has been studied extensively under both field and laboratory conditions, research has been limited by the lack of molecular resources. Genes associated with reproduction typically evolve rapidly and thus are excellent sources of evolutionary information. In this study we describe the generation of two cDNA libraries, one from placenta and one from testis, characterize the resulting ESTs, and describe their utility for mapping the <it>Peromyscus </it>genome.</p> <p>Results</p> <p>The 5' ends of 1,510 placenta and 4,798 testis clones were sequenced. Low quality sequences were removed and after clustering and contig assembly, 904 unique placenta and 2,002 unique testis sequences remained. Average lengths of placenta and testis ESTs were 711 bp and 826 bp, respectively. Approximately 82% of all ESTs were identified using the BLASTX algorithm to <it>Mus </it>and <it>Rattus</it>, and 34 – 54% of all ESTs could be assigned to a biological process gene ontology category in either <it>Mus </it>or <it>Rattus</it>. Because the <it>Peromyscus </it>genome organization resembles the <it>Rattus </it>genome more closely than <it>Mus </it>we examined the distribution of the <it>Peromyscus </it>ESTs across the rat genome finding markers on all rat chromosomes except the Y. Approximately 40% of all ESTs were specific to only one location in the <it>Mus </it>genome and spanned introns of an appropriate size for sequencing and SNP detection. Of the primers that were tried 54% provided useful assays for genotyping on interspecific backcross and whole-genome radiation hybrid cell panels.</p> <p>Conclusion</p> <p>The 2,906 <it>Peromyscus </it>placenta and testis ESTs described here significantly expands the molecular resources available for the genus. These ESTs allow for specific PCR amplification and broad coverage across the genome, creating an excellent genetic marker resource for the generation of a medium-density genomic map. Thus, this resource will significantly aid research of a genus that is uniquely well-suited to both laboratory and field research.</p

Comparison of the organization of genes on Chr 1, and Chrs 7, 10, 17, and 19, with the linkage of their orthologous genes in

The break in the continuity of the linkage groups indicates a lack of detectable linkage between the groups.<p><b>Copyright information:</b></p><p>Taken from "Comparative genome mapping of the deer mouse () reveals greater similarity to rat () than to the lab mouse ()"</p><p>http://www.biomedcentral.com/1471-2148/8/65</p><p>BMC Evolutionary Biology 2008;8():65-65.</p><p>Published online 26 Feb 2008</p><p>PMCID:PMC2266908.</p><p></p

Comparison of the organization of genes on Chrs 1, 6, 9, and 10, and Chr 17 with the linkage of their orthologous genes in

The break in the continuity of the linkage groups indicates a lack of detectable linkage between the groups.<p><b>Copyright information:</b></p><p>Taken from "Comparative genome mapping of the deer mouse () reveals greater similarity to rat () than to the lab mouse ()"</p><p>http://www.biomedcentral.com/1471-2148/8/65</p><p>BMC Evolutionary Biology 2008;8():65-65.</p><p>Published online 26 Feb 2008</p><p>PMCID:PMC2266908.</p><p></p

Comparison of the organization of genes on Chrs 1 and 2, and Chr 13, with the linkage of their orthologous genes in

The break in the continuity of the linkage groups indicates a lack of detectable linkage between the groups.<p><b>Copyright information:</b></p><p>Taken from "Comparative genome mapping of the deer mouse () reveals greater similarity to rat () than to the lab mouse ()"</p><p>http://www.biomedcentral.com/1471-2148/8/65</p><p>BMC Evolutionary Biology 2008;8():65-65.</p><p>Published online 26 Feb 2008</p><p>PMCID:PMC2266908.</p><p></p

Comparison of the organization of genes on Chr 6, and Chrs 5, 12, and 17, with the linkage of their orthologous genes in

The break in the continuity of the linkage groups indicates a lack of detectable linkage between the groups.<p><b>Copyright information:</b></p><p>Taken from "Comparative genome mapping of the deer mouse () reveals greater similarity to rat () than to the lab mouse ()"</p><p>http://www.biomedcentral.com/1471-2148/8/65</p><p>BMC Evolutionary Biology 2008;8():65-65.</p><p>Published online 26 Feb 2008</p><p>PMCID:PMC2266908.</p><p></p

Comparison of the organization of genes on Chrs 5, 9, and 13, and Chrs 1 and 4 with the linkage of their orthologous genes in

The break in the continuity of the linkage groups indicates a lack of detectable linkage between the groups.<p><b>Copyright information:</b></p><p>Taken from "Comparative genome mapping of the deer mouse () reveals greater similarity to rat () than to the lab mouse ()"</p><p>http://www.biomedcentral.com/1471-2148/8/65</p><p>BMC Evolutionary Biology 2008;8():65-65.</p><p>Published online 26 Feb 2008</p><p>PMCID:PMC2266908.</p><p></p

Comparison of the organization of genes on Chrs 16, 17, and 19, and Chrs 2 and 8, with the linkage of their orthologous genes in

The break in the continuity of the linkage groups indicates a lack of detectable linkage between the groups.<p><b>Copyright information:</b></p><p>Taken from "Comparative genome mapping of the deer mouse () reveals greater similarity to rat () than to the lab mouse ()"</p><p>http://www.biomedcentral.com/1471-2148/8/65</p><p>BMC Evolutionary Biology 2008;8():65-65.</p><p>Published online 26 Feb 2008</p><p>PMCID:PMC2266908.</p><p></p