| Phylogenic analysis based on nucleotide sequences is excellent in the studies of algal biogeography and evolution.In recent years, large-scale green tides bloomed successively in the Yellow Sea, which caused in ecological and social problems. It is necessary to carry out molecular analysis on classification and distribution of mainly green-tide-forming algae, Ulva and Enteromorpha in this sea area, in addition to the genetic diversity and phylogenetic relationship between the green-tide-forming algae in the Yellow Sea and the reported species all over the world. In the present study, based on the analysis of nuclear rDNA ITS, chloroplast rbcL, and psbA sequences, it's found that ITS sequence divergencies among all free-floating samples were very low (0.0%–2.5%), while sequence divergency between free-floating samples and attached samples were much higher, ranging from 7.6% to 24.4%. According to the phylogenetic tree, all free-floating samples were grouped to one cluster; 15 attached samples were resolved into five other clades, which demonstrated that free-floating samples were unialgal, and the attached Ulvaceae species from Qingdao coasts in summer 2007 were not the biogeographic origin of the free-floating one. In the ITS sequence, 19 out of the 21 Yellow Sea samples of 2008 were identical to those of a sample collected from Qingdao in 2007. A low divergence (0.2%) was found in two remaining samples. Similar evidence was shown by pairwise distances of rbcL and psbA gene sequence data, implying the uniformity of the Yellow Sea blooms in 2007 and 2008. Molecular phylogenetic results grouped the free-floating alga into one clade with E. procera, E. linza and E. prolifera, while the morphological character of this alga is identical to E. prolifera. Both molecular and morphological analysis revealed the free-floating samples are not Ulva species. The haplotypes of the Yellow Sea free-floating E. prolifera were closely related to those from the Japanese coast but less to European and American algae, which reflect the relationship between biogeographic distance and genetic diversity. Recent investigation showed there are at least 8 species of Ulva and Enteromorpha distribute at both side of the Yellow Sea. However, none attached population of free-floating E. prolifera was found in this sea area.Molecular analysis was also carried out on evolution of algae. Phycobiliprotein genes of two color-differing K. alvarezii were cloned in the study, but there was not any difference which indicates that color variation was independent of nucleotide composition and arrangement of phycobiliprotein genes. Phycobiliprotein sequences of K. alvarezii, other representative red macroalgae (e.g. Porphyra, Gracilaria) together with those of cyanobacteria were used to illuminate the phylogenetic position and evolution of red algae. When comparing to high-light-adapted (HL-) Prochlorococcu, the red algae have a closer relationship with low-light-adapted (LL-) Prochlorococcu in this phylogenetic tree. Forty-eight amino acid sites of PE-βin red algae were identical to LL-Prochlorococcu but different from HL-Prochlorococcu, while 4 amino acid sites of PE-βin red algae were identical to HL-Prochlorococcu but divergent with LL-Prochlorococcu. These sites were generally located at domain ofα-helix, chromophore or linker interaction, which revealed that the evolution of red algae was not only associated with low light environment but also with high light adaptation. Similar to that of Porphyra, analysis of PSII photochemical efficiency of K. alvarezii displayed a low minimum saturating irradiance of 115μmol m-2 s-1, which also proved that these representative red macroalgae belong to low-light-adapted species. However, which is also reflected by PSII photochemical parameters, K. alvarezii can adapt the high light. The low-light-adapted adaptability of red algae might be correlated with the above mentioned forty-eight amino acid sites, while 4 amino acid sites in PE correspond to high-light-adapted adaptability. APC sequences of red algae, Cryptophytes and cycanobacteria were conservative when it was compared to PC. Generally, PC sequences of red algae and brown algae were more similar to those of PE deficient Synechococcus RS9917 and WH5701 compared to PE contained Synechococcus species, which also improved that APC has likely evolved together, while PC and PE have evolved independently during the evolution of phycobiliproteins from cycanobacteria to red algae and brown algae, allowing these algae rapid adaptation to a variety of light niches.
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