Phylogenomic analysis of transcriptomic sequences of mitochondria and chloroplasts for marine red algae （Rhodophyta） in China

• Published in: 海洋学报：英文版 2014, Vol.33 (2), p.86-93
• Main Author: JIA Shangang WANG Xumin QIAN Hao LI Tianyong SUN Jing WANG Liang YU Jun LI Xingang YIN Jinlong LIU Tao WU Shuangxiu
• Format: Article
• Language: English
• Subjects: RNA序列; 中国; 分类解析; 叶绿体基因; 海洋红藻; 系统发育树; 线粒体; 转录组
• ISSN: 0253-505X; 1869-1099

The chloroplast and mitochondrion of red algae （Phylum Rhodophyta） may have originated from different endosymbiosis. In this study, we carried out phylogenomic analysis to distinguish their evolutionary lin-eages by using red algal RNA-seq datasets of the 1 000 Plants （1KP） Project and publicly available complete genomes of mitochondria and chloroplasts of Rhodophyta. We have found that red algae were divided into three clades of orders, Florideophyceae, Bangiophyceae and Cyanidiophyceae. Taxonomy resolution for Class Florideophyceae showed that Order Gigartinales was close to Order Halymeniales, while Order Graci-lariales was in a clade of Order Ceramials. We confirmed Prionitis divaricata （Family Halymeniaceae） was closely related to the clade of Order Gracilariales, rather than to genus Grateloupia of Order Halymeniales as reported before. Furthermore, we found both mitochondrial and chloroplastic genes in Rhodophyta under negative selection （Ka/Ks〈1）, suggesting that red algae, as one primitive group of eukaryotic algae, might share joint evolutionary history with these two organelles for a long time, although we identified some dif-ferences in their phylogenetic trees. Our analysis provided the basic phylogenetic relationships of red algae, and demonstrated their potential ability to study endosymbiotic events.