We made use of 9. 01 G raw data for K mer analysis and heterozygous simula tion. For your 17 mer frequency distribution, the peak on the depth distribution was about 22. The estimated genome dimension was 323 Mb, applying the formula. genome size k mer count peak on the kmer distribu tion. The minor peak at 1 two altitude with the major peak indicates the high level of heterozygosity in this genome, A total of 739,969 contigs have been assembled which has a total sequence length of 255. 7 Mb. The length of N50 was 295 bp in our assembly, as well as longest contig and scaffold seven,593 and 127,008 bp, respectively. Frequency distribution of different types of SSR markers A total of 17,172 from 273,161 scaffolds retrieved in the genome survey sequence contained 28,602 SSRs, of which five,401 contained over 1 SSR, and 1,444 SSRs have been present in compound format.
Among the derived SSR repeats, the di nucleotide was just about the most abundant repeat, accounting for 84. 72% of total SSRs, followed by tri, tetra, penta, and hexa nucleotides, There was a big proportion of both dinucleotides and trinucleotides while the rest amounted to significantly less 2%. The common frequency of happen rence was about ten. 47%, The SSR frequency of every motif is presented selleck chemical in Extra file one. The SSR motif consists of 69 forms. Among the repeat motifs in the dinucleotide, the AG CT repeat was the most common, representing 53. 72%, followed by 39. 20% AT repeats, as well as predominant motifs of trinucleotide repeats accounted for 37. 15% and 32. 56%, respectively, Polymorphism of SSR markers We very first developed and synthesised 600 SSR primer pairs from individuals scaffolds greater than 2Kb extended.
The vast majority of SSR loci had been dinucleotide repeats, and special info the remainder trinucleotide. At first, the effectiveness of these primer pairs was detected in two cultivars and M. cerifera via denaturing Web page, and 581 of those have been amplified successfully in Biqi and Dongkui, and 400 in M. cerifera. The SSR loci have been identified as heterozygous loci both in Biqi or in Dongkui. Subsequently, they had been utilised to display 32 accessions, and detected an average of eight. 25 alleles and from 3 to 15 alleles per locus, The PIC at every locus ranged from 0. 256 to 0. 883 with an typical of 0. 67 loci. The PCR item size ranged from 110 to 274 bp. All the primers generated amplicons in agreement with the anticipated sizes. The majority of the SSR primers showed vital deviation from HW equilibrium, Partial correlation ana lysis showed that substantial good correlations existed among the repeat unit length and PIC, This showed that these SSRs had high charges of transferability for M. adenophora and M. nana and reduced costs for M. cerifera, indicating that these markers are appropriate for genetic diversity analyses in other Myrica species.