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High Incidence of Cryptic Repeated Elements in Microsatellite Flanking Regions of Galatheid Genomes and its Practical Implications for Molecular Marker Development

High Incidence of Cryptic Repeated Elements in Microsatellite Flanking Regions of Galatheid... AbstractDuring the development of PCR primer sets for microsatellite marker loci from enriched genomic libraries for three squat lobster species from Galatheidae (Decapoda: Anomura); Munida rugosa (Fabricius, 1775), M. sarsi (Huus, 1935), and Galathea strigosa (Linnaeus, 1761) (collectively known as squat lobsters), a number of unforeseen problems were encountered. These included PCR amplification failure, lack of amplification consistency, and the amplification of multiple fragments. Careful examination of microsatellite containing sequences revealed the existence of cryptic repeated elements on presumed unique flanking regions. BLAST analysis of these and other VNTR containing sequences (N = 252) indicates that these cryptic elements can be grouped into families based upon sequence similarities. The unique features characterising these families suggest that different molecular mechanisms are involved. Of particular relevance is the association of microsatellites with mobile elements. This is the first reported observation of this phenomenon in crustaceans, and it also helps to explain why microsatellite primer development in galatheids has been relatively unsuccessful to date. We suggest a number of steps that can be used to identify similar problems in microsatellite marker development for other species, and also alternative approaches for both marker development and for the study of molecular evolution of species characterised by complex genome organisation. More specifically, we argue that new generation sequencing methodologies, which capitalise on parallel and multiplexed sequencing may pave the way forward for future crustacean research. http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png The Journal of Crustacean Biology Oxford University Press

High Incidence of Cryptic Repeated Elements in Microsatellite Flanking Regions of Galatheid Genomes and its Practical Implications for Molecular Marker Development

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References (56)

Publisher
Oxford University Press
Copyright
© 2010 by Koninklijke Brill NV, Leiden, The Netherlands
ISSN
0278-0372
eISSN
1937-240X
DOI
10.1651/09-3252.1
Publisher site
See Article on Publisher Site

Abstract

AbstractDuring the development of PCR primer sets for microsatellite marker loci from enriched genomic libraries for three squat lobster species from Galatheidae (Decapoda: Anomura); Munida rugosa (Fabricius, 1775), M. sarsi (Huus, 1935), and Galathea strigosa (Linnaeus, 1761) (collectively known as squat lobsters), a number of unforeseen problems were encountered. These included PCR amplification failure, lack of amplification consistency, and the amplification of multiple fragments. Careful examination of microsatellite containing sequences revealed the existence of cryptic repeated elements on presumed unique flanking regions. BLAST analysis of these and other VNTR containing sequences (N = 252) indicates that these cryptic elements can be grouped into families based upon sequence similarities. The unique features characterising these families suggest that different molecular mechanisms are involved. Of particular relevance is the association of microsatellites with mobile elements. This is the first reported observation of this phenomenon in crustaceans, and it also helps to explain why microsatellite primer development in galatheids has been relatively unsuccessful to date. We suggest a number of steps that can be used to identify similar problems in microsatellite marker development for other species, and also alternative approaches for both marker development and for the study of molecular evolution of species characterised by complex genome organisation. More specifically, we argue that new generation sequencing methodologies, which capitalise on parallel and multiplexed sequencing may pave the way forward for future crustacean research.

Journal

The Journal of Crustacean BiologyOxford University Press

Published: Oct 1, 2010

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