Construction of genomic marker sets based on the chloroplast genome of a green alga, Ulva pertusa (syn. Ulva australis), leads to simple detection of Ulva species.

In closed sea areas such as Tokyo Bay, a phenomenon known as a green tide often occurs, in which large amounts of Ulva seaweed grow abnormally and form mats along the coast. This is currently a serious environmental problem. Green tides are generated by the explosive growth of multiple types of Ulva algae. However, many Ulva species show similar characteristics to each other and are indistinguishable by appearance, making it difficult to identify the Ulva algae in green tides. In this study, we determined the entire nucleotide sequence of the chloroplast genome of Ulva pertusa (syn. Ulva australis) and identified two large inversions of gene order, suggesting the occurrence of genome inversions. We also detected structural polymorphisms among Ulva chloroplast genomes. Ulva pertusa was classified in a different clade from that containing U. lactuca and U. ohnoi, suggesting that U. pertusa is evolutionarily divergent from these species. Based on this knowledge, we constructed a genetic diagnosis system for Ulva algae. Using this approach, we established a simple method that can determine the species of Ulva algae by PCR using specific molecular markers, through which representative Ulva species such as U. lactuca, U. ohnoi and U. pertusa were easily distinguished.