Microsatellite Screening and Characterization Analysis of Sepia esculenta Based on Full-length Transcriptome Sequencing

Abstract:

To better protect the resource of Sepia esculenta, we need to understand its population genetic structure. In the field of genetics, microsatellites have become important molecular markers for genetic diversity and marker-assisted breeding, because of their unique advantages, such as abundant polymorphism, rich information, codominance, and conservation. In this study, 177,951 unigenes obtained via transcriptome sequencing of the golden cuttlefish were used to detect and analyze the simple sequence repeat (SSR) loci information using Micro Satellite (MISA) software. The results showed that 161,327 SSR loci were detected in the transcriptome of S. esculenta, which are distributed in 64,933 unigenes with a distribution frequency (of SSR loci) of 36.49%, and the frequency of occurrence was 90.66%. Among them, the main types of repeats were mononucleotide, dinucleotides, and trinucleotides, which accounted for 46.00%, 39.93%, and 9.48% of the total SSR, respectively. Among the repeat motifs contained in the SSR, A/T was the predominant repeat type of a mononucleotide, and AT/AT and AC/GT were the dominant repeat types of dinucleotides. There were 66,004 repeat motifs with a length of ≥ 20 bp, accounting for 40.91% of the total number of SSRs, and the number of SSR loci in which low-level motifs (di- and trinucleotide repeats) are dominant. The above results indicated that SSR loci in the transcriptome of golden cuttlefish had a high frequency and a rich variety, and high polymorphic potential. The results provided a powerful reference for the better development of SSR molecular markers and the protection and utilization of S. esculenta germplasm resources, genetic diversity evaluation, and future molecular marker-assisted breeding.