| Summary: | Diatoms are responsible for approximately 40% of the global primary photosynthetic production and account for up to 20% of global carbon fixation. <i>Coscinodiscus granii</i> is a red tide forming species of the phylum Bacillariophyta that has been detected in a wide range of coastal regions, suggesting the possibility of the existence of high genetic diversity with differential adaptation. Common molecular markers including 18S rDNA, 16S rDNA, ITS, <i>cox1</i>, and <i>rbcL</i> do not provide sufficient resolution for distinguishing intra-species genetic diversity, hindering in-depth research on intra-species genetic diversity and their spatial and temporal dynamics. In this project, we aimed to develop molecular markers with high resolution and specificity for <i>C. granii</i>, attempting to identify different taxa of this species, which will set up a stage for subsequent functional assays. Comparative genomics analysis of the mtDNAs of <i>C. granii</i> strains identified a genomic region with high genomic variations, which was used to guide the development of a molecular marker with high resolution and high specificity. This new molecular marker, which was named <i>cgmt1</i> (<i>C. granii</i> mitochondrial 1), was 376 bp in size and differentiated <i>C. granii</i> samples collected in coastal regions of China into three different clades. Preliminary analysis of field samples collected in various coastal regions in China revealed that <i>C. granii</i> clades were almost exclusively found in the Bohai Sea and the north Yellow Sea. This newly developed molecular marker <i>cgmt1</i> could be used for tracking intra-species genetic diversity and biogeographic distribution of <i>C. granii</i> in different ecosystems.
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