The raw sequencing files of <i>Aureococcus anophagefferens</i> based on <i>trn</i>D-<i>dam</i>1

<i>Aureococcus anophagefferens</i>, a globally distributed picoplanktonic species, is an important primary producer in the ocean,and responsible for brown tides in coastal waters, exhibiting significant ecological impacts in coastal ecosystems. We hypothesized that the wide geographical distribution of<i> A. anophagefferens</i> in different marine environments (estuarine, coastal and open ocean) drives intraspecies genetic diversity, leading to different adaptations to environmental gradients. This study investigated the genetic diversity of<i> A. anophagefferens </i>in estuarine and coastal waters of China, while supplementary research involving comparative analysis of a limited number of samples from the Kuroshio Current origin and flow regions in the western Pacific (WP); and exploration of the implications for intraspecific differentiation of ecological adaptability. A high-resolution mitochondrial molecular marker (<i>trn</i>D-<i>dam</i>1) was developed to identify three distinct genotypes among field samples collected from the Bohai Sea and Yellow Sea in China, and the WP. The results revealed that Type I was predominant during brown-tide periods in China, while Type II exhibited preferences for cooler and higher-salinity conditions, potentially aligning with its dominance in the American Atlantic coast. Environmental correlations indicated that temperature, salinity, and nutrient availability significantly influence the distribution patterns of these genotypes. These findings suggest that intraspecific differentiation within <i>A. anophagefferens</i> may reflect adaptive strategies tailored to local environmental conditions. Additionally, the study highlights the potential role of ocean currents in shaping the global genetic structure of this species. This research provides critical insights into understanding the global distribution and adaptation strategies of <i>A. anophagefferens</i>.