| Summary: | Within the complicated and controversial taxonomy of cosmopolitan genus <i>Salvia</i> L. (Lamiaceae) are valuable species <i>Salvia officinalis</i> L. and <i>Salvia sclarea</i> L., which are important for the pharmaceutical, ornamental horticulture, food, and perfume industries. Genome organization and chromosome structure of these essential oil species remain insufficiently studied. For the first time, the comparative repeatome analysis of <i>S. officinalis</i> and <i>S. sclarea</i> was performed using the obtained NGS data, RepeatExplorer/TAREAN pipelines and FISH-based chromosome mapping of the revealed satellite DNA families (satDNAs). In repeatomes of these species, LTR retrotransposons made up the majority of their repetitive DNA. Interspecific variations in genome abundance of Class I and Class II transposable elements, ribosomal DNA, and satellite DNA were revealed. Four (<i>S. sclarea</i>) and twelve (<i>S. officinalis</i>) putative satDNAs were identified. Based on patterns of chromosomal distribution of 45S rDNA; 5S rDNA and the revealed satDNAs, karyograms of <i>S. officinalis</i> and <i>S. sclarea</i> were constructed. Promising satDNAs which can be further used as chromosome markers to assess inter- and intraspecific chromosome variability in <i>Salvia</i> karyotypes were determined. The specific localization of homologous satDNA and 45S rDNA on chromosomes of the studied <i>Salvia</i> species confirmed their common origin, which is consistent with previously reported molecular phylogenetic data.
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