Characterization of microsatellites and polymorphic marker development in ragworm (Tylorrhynchus heterochaetus) based on genome survey data

In order to understand the genomic information of Tylorrhynchus heterochaetus and efficiently develop microsatellite markers, so as to guide the conservation of its germplasm resources and genetic improvement of new varieties, we conducted a whole-genome survey by using low depth high-throughput sequencing. A total of 57.48 Gb of clean data were generated after the quality control of raw data. K-mer analysis estimates that the genome size of T. heterochaetus was 759.53 Mb; the heterozygosity rate was 1.41%; the proportion of repetitive sequences was 45.92%. Preliminary assembly obtained 2 181 621 scaffolds with a total length of 840 375 821 bp. A total of 130 216 microsatellite loci were detected with a density of 154.9 loci per Mb. The repeated number of microsatellite units largely ranged from 4 to 18. The ratio of mononucleotide loci was the highest (35.00%), followed by those of dinucleotide (32.48%) and trinucleotide (14.42%) loci. AT/AT and AAT/ATT motifs were dominant in dinucleotide and trinucleotide loci, respectively, indicating an A/T dominance. Fifteen polymorphic loci were identified from 50 randomly selected primers, and 87 alleles were amplified in a T. heterochaetus population containing 30 individuals. The number of alleles per locus ranged from 2.000 to 12.000, with an mean of 5.800. The effective allele number (N_e) and expected heterozygosity (H_e) ranged from 1.164 to 6.713 and from 0.141 to 0.789, with means of 3.328 and 0.561, respectively. The polymorphic information content (PIC) ranged from 0.136 to 0.776, with a mean of 0.511. Thirteen loci were found to be highly or moderately polymorphic, having high practical value in genetic analysis. In conclusion, T. heterochaetus genome is a complex genome, and its microsatellites have a rich variety and high polymorphic potential. The results can provide effective marker resources for germplasm resource evaluation, population genetics and molecular breeding research.