Microsatellite discovery by deep sequencing of enriched genomic libraries

Robust molecular markers such as microsatellites are important tools used to understand the dynamics of natural populations, but their identification and development are typically time consuming and labor intensive. The recent emergence of so-called next-generation sequencing raised the question as...
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Autor*in:	Quentin C. Santana [verfasserIn] Martin P. A. Coetzee [verfasserIn] Emma T. Steenkamp [verfasserIn] Osmond X. Mlonyeni [verfasserIn] Gifty N. A. Hammond [verfasserIn] Michael J. Wingfield [verfasserIn] Brenda D. Wingfield [verfasserIn]

Format:	E-Artikel
Sprache:	Englisch

Erschienen:	2009

Schlagwörter:	microsatellites 454 sequencing simple sequence repeats FIASCO ISSR-PCR

Übergeordnetes Werk:	In: BioTechniques - Future Science Ltd, 2019, 46(2009), 3, Seite 217-223
Übergeordnetes Werk:	volume:46 ; year:2009 ; number:3 ; pages:217-223

Links:	Link aufrufen Link aufrufen Link aufrufen Journal toc Journal toc

DOI / URN:	10.2144/000113085

Katalog-ID:	DOAJ018151361

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allfieldsSound	10.2144/000113085 doi (DE-627)DOAJ018151361 (DE-599)DOAJ58ef955838ec4859ad605d4c6badf749 DE-627 ger DE-627 rakwb eng QH301-705.5 Quentin C. Santana verfasserin aut Microsatellite discovery by deep sequencing of enriched genomic libraries 2009 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Robust molecular markers such as microsatellites are important tools used to understand the dynamics of natural populations, but their identification and development are typically time consuming and labor intensive. The recent emergence of so-called next-generation sequencing raised the question as to whether this new technology might be applied to microsatellite development. Following this view, we considered whether deep sequencing using the 454 Life Sciences/Roche GS-FLX genome sequencing system could lead to a rapid protocol to develop microsatellite primers as markers for genetic studies. For this purpose, genomic DNA was sourced from three unrelated organisms: a fungus (the pine pathogen Fusarium circinatum), an insect (the pine-damaging wasp Sirex noctilio), and the wasp's associated nematode parasite (Deladenus siricidicola). Two methods, FIASCO (fast isolation by AFLP of sequences containing repeats) and ISSR-PCR (inter-simple sequence repeat PCR), were used to generate microsatellite-enriched DNA for the 454 libraries. From the resulting 1.2–1.7 megabases of DNA sequence data, we were able to identify 873 microsatellites that have sufficient flanking sequence available for primer design and potential amplification. This approach to microsatellite discovery was substantially more rapid, effective, and economical than other methods, and this study has shown that pyrosequencing provides an outstanding new technology that can be applied to this purpose. microsatellites 454 sequencing simple sequence repeats FIASCO ISSR-PCR Biology (General) Martin P. A. Coetzee verfasserin aut Emma T. Steenkamp verfasserin aut Osmond X. Mlonyeni verfasserin aut Gifty N. A. Hammond verfasserin aut Michael J. Wingfield verfasserin aut Brenda D. Wingfield verfasserin aut In BioTechniques Future Science Ltd, 2019 46(2009), 3, Seite 217-223 (DE-627)306320746 (DE-600)1496354-1 19409818 nnns volume:46 year:2009 number:3 pages:217-223 https://doi.org/10.2144/000113085 kostenfrei https://doaj.org/article/58ef955838ec4859ad605d4c6badf749 kostenfrei https://www.future-science.com/doi/10.2144/000113085 kostenfrei https://doaj.org/toc/0736-6205 Journal toc kostenfrei https://doaj.org/toc/1940-9818 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_370 GBV_ILN_602 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 46 2009 3 217-223
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callnumber-first	Q - Science
author	Quentin C. Santana
spellingShingle	Quentin C. Santana misc QH301-705.5 misc microsatellites misc 454 sequencing misc simple sequence repeats misc FIASCO misc ISSR-PCR misc Biology (General) Microsatellite discovery by deep sequencing of enriched genomic libraries
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topic_title	QH301-705.5 Microsatellite discovery by deep sequencing of enriched genomic libraries microsatellites 454 sequencing simple sequence repeats FIASCO ISSR-PCR
topic	misc QH301-705.5 misc microsatellites misc 454 sequencing misc simple sequence repeats misc FIASCO misc ISSR-PCR misc Biology (General)
topic_unstemmed	misc QH301-705.5 misc microsatellites misc 454 sequencing misc simple sequence repeats misc FIASCO misc ISSR-PCR misc Biology (General)
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title	Microsatellite discovery by deep sequencing of enriched genomic libraries
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title_full	Microsatellite discovery by deep sequencing of enriched genomic libraries
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title_sort	microsatellite discovery by deep sequencing of enriched genomic libraries
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title_auth	Microsatellite discovery by deep sequencing of enriched genomic libraries
abstract	Robust molecular markers such as microsatellites are important tools used to understand the dynamics of natural populations, but their identification and development are typically time consuming and labor intensive. The recent emergence of so-called next-generation sequencing raised the question as to whether this new technology might be applied to microsatellite development. Following this view, we considered whether deep sequencing using the 454 Life Sciences/Roche GS-FLX genome sequencing system could lead to a rapid protocol to develop microsatellite primers as markers for genetic studies. For this purpose, genomic DNA was sourced from three unrelated organisms: a fungus (the pine pathogen Fusarium circinatum), an insect (the pine-damaging wasp Sirex noctilio), and the wasp's associated nematode parasite (Deladenus siricidicola). Two methods, FIASCO (fast isolation by AFLP of sequences containing repeats) and ISSR-PCR (inter-simple sequence repeat PCR), were used to generate microsatellite-enriched DNA for the 454 libraries. From the resulting 1.2–1.7 megabases of DNA sequence data, we were able to identify 873 microsatellites that have sufficient flanking sequence available for primer design and potential amplification. This approach to microsatellite discovery was substantially more rapid, effective, and economical than other methods, and this study has shown that pyrosequencing provides an outstanding new technology that can be applied to this purpose.
abstractGer	Robust molecular markers such as microsatellites are important tools used to understand the dynamics of natural populations, but their identification and development are typically time consuming and labor intensive. The recent emergence of so-called next-generation sequencing raised the question as to whether this new technology might be applied to microsatellite development. Following this view, we considered whether deep sequencing using the 454 Life Sciences/Roche GS-FLX genome sequencing system could lead to a rapid protocol to develop microsatellite primers as markers for genetic studies. For this purpose, genomic DNA was sourced from three unrelated organisms: a fungus (the pine pathogen Fusarium circinatum), an insect (the pine-damaging wasp Sirex noctilio), and the wasp's associated nematode parasite (Deladenus siricidicola). Two methods, FIASCO (fast isolation by AFLP of sequences containing repeats) and ISSR-PCR (inter-simple sequence repeat PCR), were used to generate microsatellite-enriched DNA for the 454 libraries. From the resulting 1.2–1.7 megabases of DNA sequence data, we were able to identify 873 microsatellites that have sufficient flanking sequence available for primer design and potential amplification. This approach to microsatellite discovery was substantially more rapid, effective, and economical than other methods, and this study has shown that pyrosequencing provides an outstanding new technology that can be applied to this purpose.
abstract_unstemmed	Robust molecular markers such as microsatellites are important tools used to understand the dynamics of natural populations, but their identification and development are typically time consuming and labor intensive. The recent emergence of so-called next-generation sequencing raised the question as to whether this new technology might be applied to microsatellite development. Following this view, we considered whether deep sequencing using the 454 Life Sciences/Roche GS-FLX genome sequencing system could lead to a rapid protocol to develop microsatellite primers as markers for genetic studies. For this purpose, genomic DNA was sourced from three unrelated organisms: a fungus (the pine pathogen Fusarium circinatum), an insect (the pine-damaging wasp Sirex noctilio), and the wasp's associated nematode parasite (Deladenus siricidicola). Two methods, FIASCO (fast isolation by AFLP of sequences containing repeats) and ISSR-PCR (inter-simple sequence repeat PCR), were used to generate microsatellite-enriched DNA for the 454 libraries. From the resulting 1.2–1.7 megabases of DNA sequence data, we were able to identify 873 microsatellites that have sufficient flanking sequence available for primer design and potential amplification. This approach to microsatellite discovery was substantially more rapid, effective, and economical than other methods, and this study has shown that pyrosequencing provides an outstanding new technology that can be applied to this purpose.
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title_short	Microsatellite discovery by deep sequencing of enriched genomic libraries
url	https://doi.org/10.2144/000113085 https://doaj.org/article/58ef955838ec4859ad605d4c6badf749 https://www.future-science.com/doi/10.2144/000113085 https://doaj.org/toc/0736-6205 https://doaj.org/toc/1940-9818
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up_date	2024-07-03T16:14:18.058Z
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Microsatellite discovery by deep sequencing of enriched genomic libraries

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