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Identification of host-defense genes and development of microsatellite markers from ESTs of hard clam Meretrix meretrix

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Abstract

The hard clam Meretrix meretrix is an economically important shellfish in China. However, genomic research on this species is still at early stage, and few genomic resources are available. The objective of the present study was to generate expressed sequence tags (ESTs), and identify host-defense genes and microsatellite markers for M. meretrix. Three cDNA libraries for intestine, mantle and hepatopancreas were constructed using highly efficient SMART (Switching Mechanism At 5′ end of the RNA Transcript) method. A total of 3224 random clones were single-pass sequenced from 5′-ends, resulting in 3129 high-quality (>100 bp) ESTs averaging 734 bp. All the ESTs were assembled by software Cap 3, producing 1796 unigenes—1490 singletons and 306 contigs. All the unigenes were compared to the public protein database using tblastx, and 696 (38.8%) were homologues to known genes while the remaining 1100 (61.2%) appeared to be novel sequences. A total of 31 EST clusters were related to immune and defense functions. They included immune recognition receptors, proteases and protease inhibitors, and other immune-related genes. The screening of 1796 unigenes identified 55 (3.1%) microsatellite-containing sequences, with 20 having sufficient flanking sequences for primer design. Polymerase chain reaction amplification was successful for 12 primer pairs and 7 of them showed polymorphic. The EST collection and microsatellite markers obtained in this study provide a useful resource for further gene discovery and population genetic analysis in M. meretrix.

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Acknowledgments

This work was supported by National Science Foundation of China (No. 30972246) and Liaoning Scientific Research Program of Ocean and Fisheries department (200801).

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Authors and Affiliations

  1. Liaoning Key Laboratory of Marine Fishery Molecular Biology, Liaoning Ocean and Fishery Science Institute, Dalian, 116023, China

    Hong-jun Li, Wei-dong Liu, Xiang-gang Gao, Yun-feng Li & Chong-bo He

  2. College of Life Sciences, Liaoning Normal University, Dalian, 116029, China

    Dan Zhu & Juan Wang

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  1. Hong-jun Li
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Correspondence to Chong-bo He.

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Li, Hj., Liu, Wd., Gao, Xg. et al. Identification of host-defense genes and development of microsatellite markers from ESTs of hard clam Meretrix meretrix . Mol Biol Rep 38, 769–775 (2011). https://doi.org/10.1007/s11033-010-0165-4

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