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Generation and analysis of expressed sequence tags for microsatellite marker development in Calamus simplicifolius C. F. Wei

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Abstract

Rattans serve as an important source of raw non-wood materials for furniture and handicraft industries worldwide. However, their genomic sequence information in public databases is very limited. In this study, a set of 2,528 good-quality expressed sequence tags (ESTs) were generated from a full-length cDNA library constructed previously with root, stem and male inflorescence tissues of Calamus simplicifolius C. F. Wei, a rattan species native to Hainan Island, China. The ESTs were assembled into 1,588 unigenes, including 1,221 singletons and 367 contigs. BlastX searches against the GenBank non-redundant protein database revealed that 1,248 (78.6 %) unigenes had at least one significant match (E ≤ 10−5). The gene ontology functional classification assigned 991, 669 and 977 of the unigenes to the cellular component, molecular function and biological process categories, respectively. A total of 71 simple sequence repeat (SSR) loci were developed among these ESTs, including 65 polymorphic across 19 rattan species representing three genera. High levels of cross-species/genus transferability were observed for the EST-SSRs. For the polymorphic EST-SSR markers, the number of alleles per locus and polymorphic information content ranged from 2 to 25 (mean 11.1) and from 0.135 to 0.949 (mean 0.695), respectively. The EST sequences and the EST-SSR primers have been deposited in GenBank databases of EST (IDs JK838364–40891) and Probe (IDs Pr16718978–9048, to be assigned).

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Acknowledgments

This work was financially supported by a grant from the Ministry of Science and Technology of China (2011AA100202). The authors wish to thank Dr. Rongsheng Li for kind help in plant sample collection and Changpin Zhou for technical assistance with denaturing polyacrylamide gel electrophoresis as well as Drs. Tom Wood and Jules Freeman for helpful suggestion on an earlier version of the manuscript.

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Authors and Affiliations

  1. State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Xiangshan Road, Beijing, 100091, China

    Fagen Li & Siming Gan

  2. Research Institute of Tropical Forestry, Chinese Academy of Forestry, Longdong, Guangzhou, 510520, China

    Fagen Li, Fan Yang, Qijie Weng, Guangtian Yin, Mei Li & Siming Gan

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  1. Fagen Li
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  2. Fan Yang
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  3. Qijie Weng
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  4. Guangtian Yin
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Correspondence to Siming Gan.

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Fagen Li and Fan Yang contributed equally to this work.

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Li, F., Yang, F., Weng, Q. et al. Generation and analysis of expressed sequence tags for microsatellite marker development in Calamus simplicifolius C. F. Wei. Mol Breeding 31, 867–877 (2013). https://doi.org/10.1007/s11032-013-9840-1

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