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Characterization, development and exploitation of EST-derived microsatellites in Porphyra haitanensis Chang et Zheng (Bangiales, Rhodophyta)

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Abstract

The frequency, type and distribution of simple sequence repeats (SSRs) in Porphyra haitanensis genomes was investigated using expressed sequence tag (EST) data deposited in public databases. A total of 3,489 non-redundant P. haitanensis ESTs were screened for SSRs using SSRhunter software. From those, 224 SSRs in 210 ESTs were identified; trinucleotides were the most common type of SSR (64.29%), followed by dinucleotides (33.48%). Tetranucleotides, pentanucleotides, and hexanucleotides were not common. Among all identified motif types, CGG/CCG had the highest frequency (33.9%), followed by TC/AG (24.6%). From these EST-SSRs, 37 SSR primer-pairs were designed and tested using common SSR reaction conditions with 15 P. haitanensis DNAs as templates. The results showed that 28 SSR primer-pairs gave good amplification patterns. These were used to conduct SSR analyses of genetic variations of the 15 germplasm strains of P. haitanensis. A total of 224 alleles were detected, with the number of alleles ranging from 4 to 15. The effective number of alleles, expected heterozygosity, and polymorphism information content of the 15 germplasm strains of P. haitanensis were 2.81, 0.64, and 0.57, respectively. All of these parameters indicate that the 15 germplasm strains of P. haitanensis harbor rich genetic variation.

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Abbreviations

SSRs:

Simple sequence repeats

EST:

Expressed sequence tags

Ne :

Effective number of alleles

He :

Expected heterozygosity

Ho :

Observed heterozygosity

PIC :

Polymorphism information contents

UPGMA:

Unweighted pair-group method with arithmetic average

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Acknowledgments

This research was supported in part by the National High Technology Research & Development Program of China (“863” Program) (Grant No.2006AA10A413), the National Natural Science Foundation of China (Grant No.40676077), the National Natural Science Foundation of Fujian Province, China (Grant No. 2007J0064), the Construction Program of Science and Technological Platform of Fujian Province, China (Grant No. 2007N2011), and the Foundation for Young Professors of Jimei University, China (Grant No. 2007C002).

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  1. College of Fisheries, Jimei University, Xiamen, 361021, China

    Chao-Tian Xie, Chang-Sheng Chen, De-Hua Ji & Yan Xu

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  1. Chao-Tian Xie
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  2. Chang-Sheng Chen
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  3. De-Hua Ji
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  4. Yan Xu
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Correspondence to Chang-Sheng Chen.

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Xie, CT., Chen, CS., Ji, DH. et al. Characterization, development and exploitation of EST-derived microsatellites in Porphyra haitanensis Chang et Zheng (Bangiales, Rhodophyta). J Appl Phycol 21, 367–374 (2009). https://doi.org/10.1007/s10811-008-9379-4

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  • DOI: https://doi.org/10.1007/s10811-008-9379-4

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