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Microsatellite markers from expressed sequence tags (ESTs) of seaweeds in differentiating various Gracilaria species

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Abstract

Gracilaria is a red seaweed that has been cultivated worldwide and is commercially used for food, fertilizers, animal fodder, and phycocolloids. However, the high morphological plasticity of seaweeds often leads to the misidentification in the traditional identification of Gracilaria species. Molecular markers are important especially in the correct identification of Gracilaria species with high economic value. Microsatellite markers were developed from the expressed sequence tags of seaweeds deposited at the National Center for Biotechnology Information database and used for differentiating Gracilaria changii collected at various localities and two other Gracilaria species. Out of 33 primer pairs, only one primer pair gave significant results that can distinguish between three different Gracilaria species as well as G. changii from various localities based on the variation in repeated nucleotides. The unweighted pair group method using arithmetic mean dendrogram analysis grouped Gracilaria species into five main clades: (a) G. changii from Batu Besar (Malacca), Sandakan (Sabah), Bintulu (Sarawak), Batu Tengah (Malacca), Gua Tanah (Malacca), Middle Banks (Penang), Sungai (Sg.) Merbok (Kedah), Teluk Pelandok (Negeri Sembilan), Pantai Dickson (Negeri Sembilan), Sg. Kong-Kong (Johore), and Sg. Pulai (Johore); (b) Gracilaria manilaensis from Cebu, Philippines; (c) G. changii from Morib (Selangor); (d) Gracilaria fisheri from Pattani, Thailand; and (e) G. changii from Pantai Dickson (Negeri Sembilan), Gua Tanah (Malacca), Sg. Merbok (Kedah), Sg. Kong-Kong (Johore), and Sg. Pulai (Johore). This result shows that this primer pair was able to distinguish between three different species, which are G. changii from Morib (Malaysia), G. fisheri from Pattani (Thailand), and G. manilaensis from Cebu (Philippines), and also between different genotypes of G. changii. This suggested that the simple sequence repeat primer we developed was suitable for differentiating between different Gracilaria species due to the polymorphisms caused by the variability in the number of tandem repeats.

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Acknowledgments

This work was supported by the University of Malaya Research Grant Scheme: Development of Simple Sequence Repeats (SSRs) from Expressed Sequence Tags (ESTs) of Seaweeds (RG025-09SUS) and Postgraduate Research Fund (PS304/2009B and PS269/2010B), University of Malaya. We would like to thank Yow Yoon-Yen in providing the Gracilaria samples.

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Authors and Affiliations

  1. Institute of Ocean and Earth Sciences (IOES), University of Malaya, 50603, Kuala Lumpur, Malaysia

    Sze-Looi Song, Phaik-Eem Lim & Siew-Moi Phang

  2. Institute of Biological Sciences, University of Malaya, 50603, Kuala Lumpur, Malaysia

    Sze-Looi Song, Phaik-Eem Lim & Siew-Moi Phang

  3. ACGT Laboratories, Lot L3-I-1, Enterprise 4, Technology Park Malaysia, Bukit Jalil, 57000, Kuala Lumpur, Malaysia

    Weng-Wah Lee

  4. Department of Fishery Biology, Faculty of Fisheries, Kasetsart University, Chatuchak, Bangkok, 10900, Thailand

    Khanjanapaj Lewmanomont

  5. Department of Biology, University San Carlos, Talamban, Cebu City, 6000, Philippines

    Danilo B. Largo

  6. Institute of Fisheries Research Sarawak, Jalan Perbadanan, Bintawa, 93744, Kuching, Sarawak, Malaysia

    Nurridan Abdul Han

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  1. Sze-Looi Song
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Correspondence to Phaik-Eem Lim.

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This paper was presented at the 8th Asia-Pacific Conference on Algal Biotechnology, Adelaide, Australia, 2012.

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Song, SL., Lim, PE., Phang, SM. et al. Microsatellite markers from expressed sequence tags (ESTs) of seaweeds in differentiating various Gracilaria species. J Appl Phycol 25, 839–846 (2013). https://doi.org/10.1007/s10811-012-9943-9

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