Expressed sequence tags from <it>Peromyscus </it>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>lin...
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| Format: | Article |
| Language: | English |
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BMC
2008-06-01
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| Series: | BMC Genomics |
| Online Access: | http://www.biomedcentral.com/1471-2164/9/300 |
| _version_ | 1818661658027884544 |
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| author | Bullard-Dillard Rebecca Ramsdell Clifton M Cheng Chun-Huai Lewandowski Adrienne Chen Chin-Fu Glenn Julie Chen Jianguo Dewey Michael J Glenn Travis C |
| author_facet | Bullard-Dillard Rebecca Ramsdell Clifton M Cheng Chun-Huai Lewandowski Adrienne Chen Chin-Fu Glenn Julie Chen Jianguo Dewey Michael J Glenn Travis C |
| author_sort | Bullard-Dillard Rebecca |
| collection | DOAJ |
| description | <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> |
| first_indexed | 2024-12-17T04:48:33Z |
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| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-17T04:48:33Z |
| publishDate | 2008-06-01 |
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| spelling | doaj.art-72195a62b1d649c48ee34661f8cc02842022-12-21T22:02:59ZengBMCBMC Genomics1471-21642008-06-019130010.1186/1471-2164-9-300Expressed sequence tags from <it>Peromyscus </it>testis and placenta tissue: Analysis, annotation, and utility for mappingBullard-Dillard RebeccaRamsdell Clifton MCheng Chun-HuaiLewandowski AdrienneChen Chin-FuGlenn JulieChen JianguoDewey Michael JGlenn Travis C<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>http://www.biomedcentral.com/1471-2164/9/300 |
| spellingShingle | Bullard-Dillard Rebecca Ramsdell Clifton M Cheng Chun-Huai Lewandowski Adrienne Chen Chin-Fu Glenn Julie Chen Jianguo Dewey Michael J Glenn Travis C Expressed sequence tags from <it>Peromyscus </it>testis and placenta tissue: Analysis, annotation, and utility for mapping BMC Genomics |
| title | Expressed sequence tags from <it>Peromyscus </it>testis and placenta tissue: Analysis, annotation, and utility for mapping |
| title_full | Expressed sequence tags from <it>Peromyscus </it>testis and placenta tissue: Analysis, annotation, and utility for mapping |
| title_fullStr | Expressed sequence tags from <it>Peromyscus </it>testis and placenta tissue: Analysis, annotation, and utility for mapping |
| title_full_unstemmed | Expressed sequence tags from <it>Peromyscus </it>testis and placenta tissue: Analysis, annotation, and utility for mapping |
| title_short | Expressed sequence tags from <it>Peromyscus </it>testis and placenta tissue: Analysis, annotation, and utility for mapping |
| title_sort | expressed sequence tags from it peromyscus it testis and placenta tissue analysis annotation and utility for mapping |
| url | http://www.biomedcentral.com/1471-2164/9/300 |
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