The molecular markers to distinguish different larval stages have various applications in ecological studies. Using the differential display RT-PCR technique, we isolated and characterized four genes, which are expressed predominantly in the megalopa stage of Eriocheir sinensis. The four genes include two cuticular proteins with different domain organization (Ers-CP15 and Ers-CP34) and two skeletal-muscle-specific genes (Ers-SCP and Ers-ActinSK1). The two cuticular protein genes were expressed predominantly in the epidermis and their expression level was significantly higher in the megalopa stage (about 7.0-folds) than it was in the zoea stage. However, their high transcriptional level in zoea IV suggested that these two cuticular protein genes may not be a useful target to discriminate megalopa from zoea. Ers-SCP encoded the invertebratespecific sarcoplasmic calcium binding protein and Ers-ActinSK1 gene encoded the crustacean skeletal muscle actin. Expressions of these two genes were detected only in muscular tissues; leg muscle, claw muscle and thoracic muscle. This suggests that the increased transcription levels of two muscle-specific genes during the megalopa stage are mainly due to increased muscular tissues. Among its three isoforms, Ers-SCPa displayed the highest difference (22.4-folds) between megalopa and zoea suggesting Ers-SCPa is the most reliable marker to distinguish megalopa from zoea. Although Ers-SCPc and Ers-ActinSK1 also showed similar expression profiles to Ers-SCPa and Ers-SCPb, differences in their expression levels were not as high as Ers-SCPa and Ers-SCPb.
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