Microsatellites for next-generation ecologists: a post-sequencing bioinformatics pipeline.
Microsatellites are the markers of choice for a variety of population genetic studies. The recent advent of next-generation pyrosequencing has drastically accelerated microsatellite locus discovery by providing a greater amount of DNA sequencing reads at lower costs compared to other techniques. How...
| Main Authors: | , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2013-01-01
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| Series: | PLoS ONE |
| Online Access: | https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23424642/?tool=EBI |
| _version_ | 1818573686422110208 |
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| author | Iria Fernandez-Silva Jonathan Whitney Benjamin Wainwright Kimberly R Andrews Heather Ylitalo-Ward Brian W Bowen Robert J Toonen Erica Goetze Stephen A Karl |
| author_facet | Iria Fernandez-Silva Jonathan Whitney Benjamin Wainwright Kimberly R Andrews Heather Ylitalo-Ward Brian W Bowen Robert J Toonen Erica Goetze Stephen A Karl |
| author_sort | Iria Fernandez-Silva |
| collection | DOAJ |
| description | Microsatellites are the markers of choice for a variety of population genetic studies. The recent advent of next-generation pyrosequencing has drastically accelerated microsatellite locus discovery by providing a greater amount of DNA sequencing reads at lower costs compared to other techniques. However, laboratory testing of PCR primers targeting potential microsatellite markers remains time consuming and costly. Here we show how to reduce this workload by screening microsatellite loci via bioinformatic analyses prior to primer design. Our method emphasizes the importance of sequence quality, and we avoid loci associated with repetitive elements by screening with repetitive sequence databases available for a growing number of taxa. Testing with the Yellowstripe Goatfish Mulloidichthys flavolineatus and the marine planktonic copepod Pleuromamma xiphias we show higher success rate of primers selected by our pipeline in comparison to previous in silico microsatellite detection methodologies. Following the same pipeline, we discover and select microsatellite loci in nine additional species including fishes, sea stars, copepods and octopuses. |
| first_indexed | 2024-12-15T00:14:56Z |
| format | Article |
| id | doaj.art-c36a8e3e5f6f4f379de19dc78dbc3490 |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-12-15T00:14:56Z |
| publishDate | 2013-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-c36a8e3e5f6f4f379de19dc78dbc34902022-12-21T22:42:29ZengPublic Library of Science (PLoS)PLoS ONE1932-62032013-01-0182e5599010.1371/journal.pone.0055990Microsatellites for next-generation ecologists: a post-sequencing bioinformatics pipeline.Iria Fernandez-SilvaJonathan WhitneyBenjamin WainwrightKimberly R AndrewsHeather Ylitalo-WardBrian W BowenRobert J ToonenErica GoetzeStephen A KarlMicrosatellites are the markers of choice for a variety of population genetic studies. The recent advent of next-generation pyrosequencing has drastically accelerated microsatellite locus discovery by providing a greater amount of DNA sequencing reads at lower costs compared to other techniques. However, laboratory testing of PCR primers targeting potential microsatellite markers remains time consuming and costly. Here we show how to reduce this workload by screening microsatellite loci via bioinformatic analyses prior to primer design. Our method emphasizes the importance of sequence quality, and we avoid loci associated with repetitive elements by screening with repetitive sequence databases available for a growing number of taxa. Testing with the Yellowstripe Goatfish Mulloidichthys flavolineatus and the marine planktonic copepod Pleuromamma xiphias we show higher success rate of primers selected by our pipeline in comparison to previous in silico microsatellite detection methodologies. Following the same pipeline, we discover and select microsatellite loci in nine additional species including fishes, sea stars, copepods and octopuses.https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23424642/?tool=EBI |
| spellingShingle | Iria Fernandez-Silva Jonathan Whitney Benjamin Wainwright Kimberly R Andrews Heather Ylitalo-Ward Brian W Bowen Robert J Toonen Erica Goetze Stephen A Karl Microsatellites for next-generation ecologists: a post-sequencing bioinformatics pipeline. PLoS ONE |
| title | Microsatellites for next-generation ecologists: a post-sequencing bioinformatics pipeline. |
| title_full | Microsatellites for next-generation ecologists: a post-sequencing bioinformatics pipeline. |
| title_fullStr | Microsatellites for next-generation ecologists: a post-sequencing bioinformatics pipeline. |
| title_full_unstemmed | Microsatellites for next-generation ecologists: a post-sequencing bioinformatics pipeline. |
| title_short | Microsatellites for next-generation ecologists: a post-sequencing bioinformatics pipeline. |
| title_sort | microsatellites for next generation ecologists a post sequencing bioinformatics pipeline |
| url | https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23424642/?tool=EBI |
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