Microsatellite Sequencing and Primer Design for Origanum vulgare

Microsatellite sequences from O. vulgare L. ssp. hirtum were identified as a service by Ecogenics GmbH following NGS sequencing of an O. vulgare L. ssp. hirtum genomic DNA sample. The Illumina TruSeq nano DNA library was sequenced on an Illumina MiSeq sequencing platform using a nano v2 500 cycles sequencing chip. The resulting paired-end reads which passed Illumina’s chastity filter were subjected to de-multiplexing and trimming of Illumina adaptor residuals. Subsequently the quality of the surviving reads was checked with FastQC v0.11.8 [14 ]. In a next step, the paired-end reads were quality filtered and merged with USEARCH v11.0.667 [15 (link)] to in silico reform the sequenced molecules. The resulting merged reads were screened with the software Tandem Repeats Finder, v4.09 [16 (link)]. After this process, 6121 merged reads contained a microsatellite insert with a tetra- or a trinucleotide of at least six repeat units or a dinucleotide of at least ten repeat units. Primer design was performed with primer 3 [17 (link),18 (link)]. Raw NGS sequences can be accessed at the NCBI Sequence Read Archive under project number PRJNA921701.