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MICROSATELLITE DEVELOPMENT IN RHODOPHYTA USING HIGH-THROUGHPUT SEQUENCE DATA1
Article first published online: 2 NOV 2011
© 2011 Phycological Society of America
Journal of Phycology
Volume 47, Issue 6, pages 1258–1265, December 2011
How to Cite
Couceiro, L., Maneiro, I., Mauger, S., Valero, M., Ruiz, J. M. and Barreiro, R. (2011), MICROSATELLITE DEVELOPMENT IN RHODOPHYTA USING HIGH-THROUGHPUT SEQUENCE DATA. Journal of Phycology, 47: 1258–1265. doi: 10.1111/j.1529-8817.2011.01075.x
Received 29 July 2010. Accepted 20 April 2011.
- Issue published online: 1 DEC 2011
- Article first published online: 2 NOV 2011
- 454 sequencing;
- conservation genetics;
- expressed sequence tags;
- microsatellite development;
- primer design;
Shotgun genome sequencing is rapidly emerging as the method of choice for the identification of microsatellite loci in nonmodel organisms. However, to the best of our knowledge, this approach has not been applied to marine algae so far. Herein, we report the results of using the 454 next-generation sequencing (NGS) platform to randomly sample 36.0 and 40.9 Mbp (139,786 and 139,795 reads, respectively) of the genome of two red algae from the northwest Iberian Peninsula [Grateloupia lanceola (J. Agardh) J. Agardh and a still undescribed new member of the family Cruoriaceae]. Using data mining tools, we identified 4,766 and 5,174 perfect microsatellite loci in 4,344 and 4,504 sequences/contigs from G. lanceola and the Cruoriaceae, respectively. After conservative removal of potentially problematic loci (redundant sequences, mobile elements), primer design was possible for 1,371 and 1,366 loci, respectively. A survey of the literature indicates that microsatellite density in our Rhodophyta is at the low end of the values reported for other organisms investigated with the same technology (land plants and animals). A limited number of loci were successfully tested for PCR amplification and polymorphism finding that they may be suitable for population genetic studies. This study demonstrates that random genome sequencing is a rapid, effective alternative to develop useful microsatellite loci in previously unstudied red algae.