Microsatellite Analysis of Patinopecten yessoensis Using Next-Generation Sequencing Method

Abstract:

Microsatellite has become an important molecular marker for genetic diversity analysis and marker-assisted breeding as its unique advantages, such as high stability and repeatability, strong specificity and codominance. To understand the distribution and frequency of microsatellite of P. yessoensis genome, the current study analyzed the microsatellite sequences of P. yessoensis genome by establishing and sequencing a RAD library. The sequences were assembled, and SSRs were detected by bioinformatics method. The total length of the DNA sequences of P. yessoensis genome is 92,551,435 bp and 3,618 contigs from all filtered 259,535 contigs containing SSR sequences. The 3460 potential SSR loci were identified with the number of repeat motif from 2 to 6 using appropriate amplifying primers. A total of 1587 trinucleotide SSRs (45.87%) were the most common motif, and ATA (11.41% of whole trinucleotide motifs) was the richest motif. The dinucleotide and the tetranucleotide types ranked the second and the third with a proportion of 37.05%(1282) and 14.48%(501), respectively, while the pentanucleotide type accounted for 2.02%(70), and the hexanucleotide type was the least amount with a proportion of 0.58%(20). Interestingly, the abundance of microsatellites of the same repeat type decreased with the increase of copy number, and the abundance of microsatellites of the same copy number decreased with the increase of the repeat unit length. The variation of length distribution frequency, copy numbers and the abundance of the microsatellite suggested that the mutation rate of shorter repeats was larger than that of the longer repeats. These results provide basic information of microsatellite of P. yessoensis, which would be useful to study the genome and population genetics of P. yessoensis.