Comparative chloroplast genomes of Ulva prolifera and U. linza (Ulvophyceae) provide genetic resources for the development of interspecific markers

The green seaweeds Ulva linza and U. prolifera are closely related species. They usually co-occur widely and have important ecological significance as primary producers thriving in the intertidal zone. In the Yellow Sea, a genetically unique floating ecotype of U. prolifera even bloomed to cause serious green tides. However, there is still a lack of appropriate molecular markers to distinguish these two species, partially due to limited evaluations on the intraspecific variations in U. prolifera among different ecotypes. Since organelle genomes could provide rich genetic resources for phylogenetic analysis and development of genetic markers, in this study, the chloroplast genome from one attached population of U. prolifera was completely sequenced, and comparative genomic analyses were performed with other existing chloroplast genomes from U. linza and the floating ecotype of U. prolifera. The results showed that in spite of the high level of collinearity among three genomes, there were plenty of genetic variations especially within the non-coding regions, including introns and gene spacer regions. A strategy was proposed that only those signals of variation, which were identical between two ecotypes of U. prolifera but divergent between U. linza and U. prolifera , were selected to develop the interspecific markers for U. linza and U. prolifera. Two candidate markers, psa B and pet B, were shown to be able to distinguish these two closely related species and were applicable to more attached populations of U. prolifera from a wide range of geographical sources. In addition to the interspecific marker, this study would also provide resources for the development of intraspecific markers for U. prolifera . These markers might contribute to the surveys for Ulva species composition and green tide monitoring especially in the Yellow Sea region.