Expressed sequence tags from Peromyscus testis and placenta tissue: Analysis, annotation, and utility for mapping
Julie L Weston Glenn1, Chin-Fu Chen2, Adrienne Lewandowski1, Chun-Huai Cheng2, Clifton M Ramsdell1,3, Rebecca Bullard-Dillard4, Jianguo Chen4, Michael J Dewey1, and Travis C Glenn5,6
1Peromyscus
Genetic Stock Center, Department of Biological Sciences, University
of South Carolina, Columbia, SC 29208, USA
2Department of Genetics and Biochemistry, Clemson University,
and Clemson University Genomics Institute, Clemson, SC 29634, USA
3Department of Genetics and The Carolina Center for Genome
Sciences, University of North Carolina, Chapel Hill, NC 27599, USA
4Department of Biology, Claflin University, Orangeburg, SC
29115, USA
5Savannah River Ecology Laboratory, Aiken, SC 29803, USA
6Department of Environmental Health Science, University of
Georgia, Athens, GA 30602, USA
Abstract:
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.
SREL Reprint #3102
Glenn, J.
L. W., C.-F. Chen, A. Lewandowski, C.-H. Cheng, C. M. Ramsdell, R. Bullard-Dillard,
J. Chen, M. J. Dewey, and T. C. Glenn. 2008. Expressed sequence tags from
Peromyscus testis and placenta tissue: Analysis, annotation, and
utility for mapping. BMC Genomics 9:300(doi:10.1186/1471-2164-9-300)
