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...

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Autores principales:	Iria Fernandez-Silva, Jonathan Whitney, Benjamin Wainwright, Kimberly R Andrews, Heather Ylitalo-Ward, Brian W Bowen, Robert J Toonen, Erica Goetze, Stephen A Karl
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2013
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/c36a8e3e5f6f4f379de19dc78dbc3490
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spelling	oai:doaj.org-article:c36a8e3e5f6f4f379de19dc78dbc34902021-11-18T07:57:57ZMicrosatellites for next-generation ecologists: a post-sequencing bioinformatics pipeline.1932-620310.1371/journal.pone.0055990https://doaj.org/article/c36a8e3e5f6f4f379de19dc78dbc34902013-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23424642/?tool=EBIhttps://doaj.org/toc/1932-6203Microsatellites 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.Iria Fernandez-SilvaJonathan WhitneyBenjamin WainwrightKimberly R AndrewsHeather Ylitalo-WardBrian W BowenRobert J ToonenErica GoetzeStephen A KarlPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 8, Iss 2, p e55990 (2013)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q 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.
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.
format	article
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
title	Microsatellites for next-generation ecologists: a post-sequencing bioinformatics pipeline.
title_short	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_sort	microsatellites for next-generation ecologists: a post-sequencing bioinformatics pipeline.
publisher	Public Library of Science (PLoS)
publishDate	2013
url	https://doaj.org/article/c36a8e3e5f6f4f379de19dc78dbc3490
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Microsatellites for next-generation ecologists: a post-sequencing bioinformatics pipeline.

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