Skip to main content
OSTI.GOVU.S. Department of Energy Office of Scientific and Technical Information
U.S. Department of Energy
Office of Scientific and Technical Information
 

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

Journal Article · · BMC Genomics
 [1];  [2];  [3];  [4];  [5];  [6];  [6];  [3];  [7]
  1. Univ. of South Carolina, Columbia, SC (United States). Peromyscus Genetic Stock Center, Dept. of Biological Sciences; DOE/OSTI
  2. Clemson Univ., SC (United States). Genomics Inst. Dept. of Genetics and Biochemistry
  3. Univ. of South Carolina, Columbia, SC (United States). Peromyscus Genetic Stock Center, Dept. of Biological Sciences
  4. Clemson Univ., SC (United States). Genomics Inst. and Dept. of Genetics and Biochemistry
  5. Univ. of South Carolina, Columbia, SC (United States). Peromyscus Genetic Stock Center, Dept. of Biological Sciences; Univ. of North Carolina, Chapel Hill, NC (United States). Dept. of Genetics and The Carolina Center for Genome Sciences
  6. Claflin Univ. Orangeburg, SC (United States). Dept. of Biology
  7. Savannah River Site (SRS), Aiken, SC (United States). Savannah River Ecology Lab. (SREL); Univ. of Georgia, Athens, GA (United States). Dept. of Environmental Health Science
+ Show Author Affiliations
Background: Mice of the genus Peromyscus 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 Mus/Rattus lineage and serve as an intermediary between that lineage and humans. Although Peromyscus 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 Peromyscus genome. Results: 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 Mus and Rattus, and 34 – 54% of all ESTs could be assigned to a biological process gene ontology category in either Mus or Rattus. Because the Peromyscus genome organization resembles the Rattus genome more closely than Mus we examined the distribution of the Peromyscus 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 Mus 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. Conclusion: The 2,906 Peromyscus 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.
Research Organization:
Univ. of Georgia, Athens, GA (United States)
Sponsoring Organization:
USDOE Office of Science (SC), Biological and Environmental Research (BER)
Grant/Contract Number:
AC09-08SR22470; FC09-07SR22506
OSTI ID:
1626465
Journal Information:
BMC Genomics, Journal Name: BMC Genomics Journal Issue: 1 Vol. 9; ISSN 1471-2164
Publisher:
SpringerCopyright Statement
Country of Publication:
United States
Language:
English

References (28)

Chromosomal aberrancy in white-footed mice (Peromyscus leucopus) collected on abandoned coal strip mines, Oklahoma, USA journal May 1999
Patterns and mechanisms of genome organization in the mouse
  • Graber, Joel H.; Churchill, Gary A.; Dipetrillo, Keith J.
  • Journal of Experimental Zoology Part A: Comparative Experimental Biology, Vol. 305A, Issue 9 https://doi.org/10.1002/jez.a.322
journal January 2006
Development of a deer mouse whole-genome radiation hybrid panel and comparative mapping of Mus chromosome 11 loci journal January 2006
Animal models of restricted repetitive behavior in autism journal January 2007
Estrogen receptor α and vasopressin in the paraventricular nucleus of the hypothalamus in Peromyscus journal January 2005
Rapid evolution of reproductive barriers driven by sexual conflict journal February 2000
Genetic and epigenetic incompatibilities underlie hybrid dysgenesis in Peromyscus journal May 2000
Explaining the X-linkage bias of placentally expressed genes journal January 2005
The mouse X chromosome is enriched for sex-biased genes not subject to selection by meiotic sex chromosome inactivation journal May 2004
Organization of six functional mouse alcohol dehydrogenase genes on two overlapping bacterial artificial chromosomes journal January 2002
Cross-species amplification among peromyscines of new microsatellite DNA loci from the oldfield mouse (Peromyscus polionotus subgriseus) journal June 2002
Changes in cell cycle and extracellular matrix gene expression during placental development in deer mouse (Peromyscus) hybrids journal January 2007
Positive Darwinian selection drives the evolution of several female reproductive proteins in mammals journal February 2001
Phylogeny and Divergence-Date Estimates of Rapid Radiations in Muroid Rodents Based on Multiple Nuclear Genes journal August 2004
TIGR Gene Indices clustering tools (TGICL): a software system for fast clustering of large EST datasets journal March 2003
FatiGO: a web tool for finding significant associations of Gene Ontology terms with groups of genes journal January 2004
Assessment and disease comparisons of hybrid developmental defects journal March 2007
‘Touchdown’ PCR to circumvent spurious priming during gene amplification journal January 1991
Developmental Dynamics of the Definitive Mouse Placenta Assessed by Stereology1 journal June 2004
Base-Calling of Automated Sequencer Traces Using Phred.  I. Accuracy Assessment journal March 1998
Sixty polymorphic microsatellite markers for the oldfield mouse developed in Peromyscus polionotus and Peromyscus maniculatus journal March 2006
msatcommander: detection of microsatellite repeat arrays and automated, locus-specific primer design journal January 2008
A Single Amino Acid Mutation Contributes to Adaptive Beach Mouse Color Pattern journal July 2006
A novel hantavirus associated with an outbreak of fatal respiratory disease in the southwestern United States: evolutionary relationships to known hantaviruses journal February 1994
Evidence of a Large-Scale Functional Organization of Mammalian Chromosomes journal September 2005
The Molecular Basis of High-Altitude Adaptation in Deer Mice journal March 2007
Antibodies to Multiple Tick-Borne Pathogens of Babesiosis, Ehrlichiosis, and lyme Borreliosis in White-Footed mice journal July 1997
Duration of Borrelia Burgdorferi Infectivity in White-Footed mice for the tick Vector Ixodes Scapularis Under Laboratory and Field Conditions in Ontario journal October 1997

Cited By (4)

Signatures of Rapid Evolution in Urban and Rural Transcriptomes of White-Footed Mice (Peromyscus leucopus) in the New York Metropolitan Area journal August 2013
Inbreeding and selection shape genomic diversity in captive populations: Implications for the conservation of endangered species journal April 2017
Signatures of rapid evolution in urban and rural transcriptomes of white-footed mice (Peromyscus leucopus) in the New York metropolitan area posted_content April 2013
Signatures of rapid evolution in urban and rural transcriptomes of white-footed mice (Peromyscus leucopus) in the New York metropolitan area posted_content August 2013

Similar Records

Complete genome sequence of Meiothermus silvanus type strain (VI-R2T)
Journal Article · Sun Aug 29 20:00:00 EDT 2010 · Standards in Genomic Sciences · OSTI ID:1630539
Genome sequence of the brown Norway rat yields insights into mammalian evolution
Journal Article · Sun Feb 01 23:00:00 EST 2004 · Nature · OSTI ID:825470
The Eucalyptus grandis Genome Project: Genome and transcriptome resources for comparative analysis of woody plant biology
Journal Article · Mon Sep 12 20:00:00 EDT 2011 · BMC Proceedings · OSTI ID:1629478

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
Biotechnology & Applied Microbiology
Gene Ontology
Genetics & Heredity
Hanta Virus Pulmonary Syndrome
Interspecific Backcross
Mapping Panel
Testis ESTs