Acta Oceanol. Sin., 2014, Vol. 33, No. 2, P. 86–93 DOI: 10.1007/s13131-014-0444-3 http://www.hyxb.org.cn E-mail:
[email protected] Phylogenomic analysis of transcriptomic sequences of mitochondria and chloroplasts for marine red algae (Rhodophyta) in China JIA Shangang1,3†, WANG Xumin1,3†, QIAN Hao2, LI Tianyong2, SUN Jing1,3,4, WANG Liang1,3,4, YU Jun1,3, LI Xingang1,3, YIN Jinlong1, LIU Tao2*, WU Shuangxiu1,3* 1 CAS Key Laboratory of Genome Sciences and Information, Beijing Key Laboratory of Genome and Precision Medicine Technologies, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China 2 College of Marine Life Science, Ocean University of China, Qingdao 266003, China 3 Beijing Key Laboratory of Functional Genomics for Dao-di Herbs, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China 4 University of Chinese Academy of Sciences, Beijing 100049, China Received 22 March 2013; accepted 2013 ©The Chinese Society of Oceanography and Springer-Verlag Berlin Heidelberg 2014 Abstract 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.