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7 kb. Figure?1 shows the frequency of the top-20 repeat motifs. These include all dinucleotide motif repeats (of at least six repeat units long), of which AC and AT repeats were the most abundant. Of the trinucleotide repeats (of at least four repeat units) AAT and AAC were the most frequent, followed by TTC. Excluding the dinucleotide repeats, the remaining 70 415 SSR loci were screened for the presence of sufficient forward and reverse flanking sequences suitable to design primers. This yielded 29 886 (42 %) PALs. Further filtering of these PALs by applying the most find more stringent criteria aimed at selecting single-copy loci yielded 4071 potentially amplifiable SSR loci. Figure?1. The 20 most frequent SSR motifs obtained, sorted according to frequency. Polymorphism and amplification of SSR loci A total of 136 SSR loci (117 randomly picked and 19 loci predicted to be potentially polymorphic as they appeared to have two different alleles in the sequence reads) were tested for amplification and degree of polymorphism in 10 randomly chosen individuals from different populations. Of the 117 randomly picked loci, 82 primer pairs amplified a high-quality PCR product, of which 37 (45 %) were polymorphic with a banding pattern that could be scored clearly (Table?1). Of the 19 primer pairs predicted to be polymorphic, GDC-0941 supplier 13 amplified bands of which 9 loci (69 %) were polymorphic, indicating a significantly higher rate of polymorphism (��2 test, P diglyceride SSRs successfully amplified in B. pirrotae and B. popoviana (in the latter species the amount of DNA was insufficient to test all markers). Amplification, even if it is in the same size range as the alleles in B. papyrifera, is not proof that the marker is polymorphic, but heterozygosity (two different alleles in the expected range) is. Based on that criterion at least 19 of the 46 markers are polymorphic in B. pirrotae and at least 8 of 33 tested are polymorphic in B. popoviana. Sequence assembly and annotation The Illumina reads are the first genomic resource generated in the genus Boswellia. The repeat fraction was assembled based on k-mer frequency.