Large‐scale drifting Sargassum biomass, known as golden tides, has caused considerable damage to the local environment and economy associated with the Yellow Sea of China. To understand the reoccurrence of Sargassum horneri golden tides in the Yellow Sea, large‐scale spatio‐temporal sampling was performed across nine cruises and five coastal surveys. Morphological data indicated that the floating S. horneri thalli with differing reproductive timing coexisted in the Yellow Sea. A total of 196 S. horneri samples had identical sequences of partial cox3 and rbcL‐S spacer region, revealing very low genetic diversity in the floating biomass. A total of 19 haplotypes for partial cox3 previously found in the Yellow Sea were not detected in our large‐scale sampling. Based on four novel mtDNA markers, the 196 samples could be further distinguished into two forms, which varied in proportions at various locations, but coexisted in each of the spatio‐temporal sampling. These results indicated that the floating Sargassum biomass in the Yellow Sea came from only two dominating haplotypes. The novel findings uncovered by this work will provide further insight into the underlying mechanisms of reoccurring golden tides in the Yellow Sea, and lead to the improved management of the Sargassum biomass.

To understand the evolution of Ulva chloroplast genomes at intraspecific and interspecific levels, in this study, three complete chloroplast genomes of Ulva compressa Linnaeus were sequenced and compared with the available Ulva cpDNA data. Our comparative analyses unveiled many noticeable findings. First, genome size variations of Ulva cpDNAs at intraspecific and interspecific levels were mainly caused by differences in gain or loss of group I/II introns, integration of foreign DNA fragments, and content of non-coding intergenic spacer regions. Second, chloroplast genomes of U. compressa shared the same 100 conserved genes as other Ulva cpDNA, whereas Ulva flexuosa appears to be the only Ulva species with the minD gene retained in its cpDNA. Third, five types of group I introns, most of which carry a LAGLIDADG or GIY-YIG homing endonuclease, and three of group II introns, usually encoding a reverse transcriptase/maturase, were detected at 26 insertion sites of 14 host genes in the 23 Ulva chloroplast genomes, and many intron insertion-sites have been found for the first time in Chlorophyta. Fourth, one degenerate group II intron previously ignored has been detected in the infA genes of all Ulva species, but not in the closest neighbor, Pseudoneochloris marina, and the other chlorophycean taxa, indicating that it should be the result of an independent invasion event that occurred in a common ancestor of Ulva species. Finally, the seven U. compressa cpDNAs represented a novel gene order which was different from that of other Ulva cpDNAs. The structure of Ulva chloroplast genomes is not conserved, but remarkably plastic, due to multiple rearrangement events.