Representativeness of microsatellite distributions in genomes, as revealed by 454 GS-FLX Titanium pyrosequencing
<p>Abstract</p> <p>Background</p> <p>Microsatellites are markers of choice in population genetics and genomics, as they provide useful insight into patterns and processes as diverse as genome evolutionary dynamics and demographic processes. The acquisition of microsatel...
| Main Authors: | , , , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2010-10-01
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| Series: | BMC Genomics |
| Online Access: | http://www.biomedcentral.com/1471-2164/11/560 |
| _version_ | 1818835595694178304 |
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| author | Malausa Thibaut Dubut Vincent Costedoat Caroline Ferreira Stéphanie Meglécz Emese Pech Nicolas Martin Jean-Francois Gilles André |
| author_facet | Malausa Thibaut Dubut Vincent Costedoat Caroline Ferreira Stéphanie Meglécz Emese Pech Nicolas Martin Jean-Francois Gilles André |
| author_sort | Malausa Thibaut |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>Microsatellites are markers of choice in population genetics and genomics, as they provide useful insight into patterns and processes as diverse as genome evolutionary dynamics and demographic processes. The acquisition of microsatellites through multiplex-enriched libraries and 454 GS-FLX Titanium pyrosequencing is a promising new tool for the isolation of new markers in unknown genomes. This approach can also be used to evaluate the extent to which microsatellite-enriched libraries are representative of the genome from which they were isolated. In this study, we deciphered potential discrepancies in microsatellite content recovery for two reference genomes (<it>Apis mellifera </it>and <it>Danio rerio</it>), selected on the basis of their extreme heterogeneity in terms of the proportions and distributions of microsatellites on chromosomes.</p> <p>Results</p> <p>The <it>A. mellifera </it>genome, in particular, was found to be highly heterogeneous, due to extremely high rates of recombination, with hotspots, but the only bias consistently introduced into pyrosequenced multiplex-enriched libraries concerned sequence length, with the overrepresentation of sequences 160 to 320 bp in length. Other deviations from expected proportions or distributions of motifs on chromosomes were observed, but the significance and intensity of these deviations was mostly limited. Furthermore, no consistent adverse competition between multiplexed probes was observed during the motif enrichment phase.</p> <p>Conclusions</p> <p>This approach therefore appears to be a promising strategy for improving the development of microsatellites, as it introduces no major bias in terms of the proportions and distribution of microsatellites.</p> |
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| format | Article |
| id | doaj.art-8dd2120e804249cab93e90f3d6f6de21 |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-19T02:53:13Z |
| publishDate | 2010-10-01 |
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| series | BMC Genomics |
| spelling | doaj.art-8dd2120e804249cab93e90f3d6f6de212022-12-21T20:38:29ZengBMCBMC Genomics1471-21642010-10-0111156010.1186/1471-2164-11-560Representativeness of microsatellite distributions in genomes, as revealed by 454 GS-FLX Titanium pyrosequencingMalausa ThibautDubut VincentCostedoat CarolineFerreira StéphanieMeglécz EmesePech NicolasMartin Jean-FrancoisGilles André<p>Abstract</p> <p>Background</p> <p>Microsatellites are markers of choice in population genetics and genomics, as they provide useful insight into patterns and processes as diverse as genome evolutionary dynamics and demographic processes. The acquisition of microsatellites through multiplex-enriched libraries and 454 GS-FLX Titanium pyrosequencing is a promising new tool for the isolation of new markers in unknown genomes. This approach can also be used to evaluate the extent to which microsatellite-enriched libraries are representative of the genome from which they were isolated. In this study, we deciphered potential discrepancies in microsatellite content recovery for two reference genomes (<it>Apis mellifera </it>and <it>Danio rerio</it>), selected on the basis of their extreme heterogeneity in terms of the proportions and distributions of microsatellites on chromosomes.</p> <p>Results</p> <p>The <it>A. mellifera </it>genome, in particular, was found to be highly heterogeneous, due to extremely high rates of recombination, with hotspots, but the only bias consistently introduced into pyrosequenced multiplex-enriched libraries concerned sequence length, with the overrepresentation of sequences 160 to 320 bp in length. Other deviations from expected proportions or distributions of motifs on chromosomes were observed, but the significance and intensity of these deviations was mostly limited. Furthermore, no consistent adverse competition between multiplexed probes was observed during the motif enrichment phase.</p> <p>Conclusions</p> <p>This approach therefore appears to be a promising strategy for improving the development of microsatellites, as it introduces no major bias in terms of the proportions and distribution of microsatellites.</p>http://www.biomedcentral.com/1471-2164/11/560 |
| spellingShingle | Malausa Thibaut Dubut Vincent Costedoat Caroline Ferreira Stéphanie Meglécz Emese Pech Nicolas Martin Jean-Francois Gilles André Representativeness of microsatellite distributions in genomes, as revealed by 454 GS-FLX Titanium pyrosequencing BMC Genomics |
| title | Representativeness of microsatellite distributions in genomes, as revealed by 454 GS-FLX Titanium pyrosequencing |
| title_full | Representativeness of microsatellite distributions in genomes, as revealed by 454 GS-FLX Titanium pyrosequencing |
| title_fullStr | Representativeness of microsatellite distributions in genomes, as revealed by 454 GS-FLX Titanium pyrosequencing |
| title_full_unstemmed | Representativeness of microsatellite distributions in genomes, as revealed by 454 GS-FLX Titanium pyrosequencing |
| title_short | Representativeness of microsatellite distributions in genomes, as revealed by 454 GS-FLX Titanium pyrosequencing |
| title_sort | representativeness of microsatellite distributions in genomes as revealed by 454 gs flx titanium pyrosequencing |
| url | http://www.biomedcentral.com/1471-2164/11/560 |
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