Bioinformatics analysis of microsatellite sites in the RNA-sequencing of <italic>Meretrix meretrix</italic>

Abstract

<italic>Meretrix meretrix</italic> is one of the most important economic shellfish species in China due to rich nutrition, delicious meat and high economic value. In this study, <italic>Meretrix meretrix</italic> DNA was transcribed and sequenced by using the second generation high-throughput sequencing technique. Through the statistical analysis of different types of microsatellites in <italic>Meretrix meretrix</italic>, the distribution frequency and number of microsatellites were understood, and the SSR composition characteristics of <italic>Meretrix meretrix</italic> were clarified at the transcriptome level. It is beneficial to the research of individual identification, germplasm resource identification, biological genetic mapping and so on, and has important reference value for further using microsatellite marker technology to carry out genetic marker-assisted breeding and population genetics research. The bioinformatics method was used to analyze the distribution of microsatellite sequences in the transcriptome of <italic>Meretrix meretrix</italic>. After searching the SSR loci of <italic>Meretrix meretrix</italic>, 8 856 complete SSR loci were found. The total length of SSR was 162 416 bp, with an average length of 18.34 bp, accounting for about 0.15% of the total sequence size, including 3 001 single-base repeat sequences, 2 254 three-base repeat sequences, 2 200 four-base repeats sequence, 1 052 two-base repeats sequences, 332 five-base repeat sequences and 13 six-base repeat sequences. The SSR of <italic>Meretrix meretrix</italic> transcriptome contained 26 types of repeats, among which the most was single-base repeat sequence A / T (2 809). The second most was triple-base repeat sequence AAC / TTG (907). Four-base repeat sequence AAAC / TTTG and two-base repeat sequence AT / TA was 588 and 561, respectively, indicating that the distribution of microsatellites in the RNA-sequencing of <italic>Meretrix meretrix</italic> had a preference for A / T. The average length of SSR (integrity) of <italic>Meretrix meretrix</italic> was 18.34 bp, and the main length of microsatellite was 12-20 bp, accounting for 41%. Most of the 8 856 SSR loci in the transcriptome had moderate polymorphism potential, which meant certain value for the future development of microsatellite molecular markers. The results of this study will provide a theoretical basis for the development of microsatellite markers, population genetic diversity, genetic linkage map, identification of germplasm resources and molecular genetics and breeding of shellfish. It also has important reference value for further study of genetic marker-assisted breeding and population genetics by using microsatellite marker technology.