基于转录组西施舌微卫星标记开发及隐种鉴定

doi:10.16378/j.cnki.1003-1111.20119

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Abstract In the past decade genetic analyses have shown that surf clam Coelomactra antiquata consists of two cryptic species, a northern lineage and a southern lineage. In order to accurately distinguish the two cryptic species of surf clam and evaluate its germplasm resources by molecular makers, microsatellite (SSR) sequences in both transcriptomes of the two cryptic species were explored and analyzed based on transcriptome data. SSRs in orthologous genes were also explored, and SSRs on 4 groups of orthologous genes were randomly selected for experimental validation. The resulted showed that an average of one SSR was found per 16.6 unigenes and the appearance frequency was 6.0% in northern lineage, involving 63 repeating motifs. In southern lineage an average of one SSR was found per 10.5 unigenes and the occurrence frequency was 8.2%, involving 89 repeating motifs. Besides the mononucleotide repeats, in both transcriptomes of the two cryptic species the trinucleotide repeats appeared to be the most abundant SSRs. In the transcriptome of northern and southern C. antiquata AAC/GTT and ATC/ATG was the dominant repeating motif of trinucleotide repeats respectively, and the most common SSR length was 15 bp. In both transcriptomes of the two cryptic species the repeat copy numbers of SSR were mainly distributed from 5 to 10 times. A total of 409 groups of orthologous genes showing SSR polymorphism between the two cryptic species were screened, which could be used as potential molecular markers.Validation experiments showed that the PCR products with clear and no impurity peak were amplified by the 4 pairs of fluorescence-labeled SSR primers, and that the combination of the 2 pairs of primers could preliminarily distinguish the two cryptic species.

Key words： Coelomactra antiquata microsatellite marker transcriptome orthologous gene species identification

Received: 11 June 2020

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	WANG Yuji
	MENG Xueping
	YI Lefei

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WANG Yuji,MENG Xueping,YI Lefei. Isolation of Microsatellite Markers in Transcriptome of Surf Clam Coelomactra antiquata and Their Application in Cryptic Species Identification[J]. Fisheries Science, 2022, 41(2): 289-295.

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https://www.shchkx.com/EN/10.16378/j.cnki.1003-1111.20119 OR https://www.shchkx.com/EN/Y2022/V41/I2/289

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