Comparative analysis of four essential Gracilariaceae species in China based on whole transcriptomic sequencing

• Published in: Acta oceanologica Sinica Vol. 33; no. 2; pp. 54 - 62
• Main Authors: Xu, Jiayue, Sun, Jing, Yin, Jinlong, Wang, Liang, Wang, Xumin, Liu, Tao, Chi, Shan, Liu, Cui, Ren, Lufeng, Wu, Shuangxiu, Yu, Jun
• Format: Journal Article
• Language: English
• Published: Berlin/Heidelberg Springer Berlin Heidelberg 01.02.2014; Springer Nature B.V; 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%Changchun University of Chinese Medicine, Changchun 130117, China%College of Marine Life Science, 0cean University of China, Qingdao 266003, China
• Subjects: Algae; Amino acid sequences; Amino acids; Analysis; Annotations; Carbohydrates; Climatology; Comparative analysis; Cyanobacteria; DNA; Earth and Environmental Science; Earth Sciences; Ecology; Engineering Fluid Dynamics; Environmental Chemistry; Gene expression; Genes; Genomes; Genomics; Gracilaria; Gracilaria blodgettii; Gracilaria lemaneiformis; Gracilariaceae; Gracilariopsis lemaneiformis; Indigenous species; Marine; Marine & Freshwater Sciences; Native organisms; Next-generation sequencing; Oceanography; Phycobilisomes; Phycocyanin; Phylogenetics; Phylogeny; Sequencing; Transcriptomes; Transcriptomics; 中国; 别藻蓝蛋白; 品种; 差异表达基因; 江蓠; 测序技术; 碳水化合物; 转录组; Beijing China; United States > US; China; China, People's Rep; transcriptome sequencing; phylogeny; phycobiliprotein; Gracilaria vermiculophylla; Gracilariopsis lemaneiformis; Gracilaria blodgettii; Gracilaria chouae
• ISSN: 0253-505X; 1869-1099
• DOI: 10.1007/s13131-014-0441-6

Three Gracilaria species, G. chouae, G. blodgettii, G. vermiculophylla and a close relative species, Gracilari-opsis lemaneiformis which is now nominated as Gracilaria lemaneiformis, are the typically indigenous spe-cies which are important resources for the production of special proteins, phycobilisomes, special carbo-hydrates, and agar in China. In this study, de novo transcriptome sequencing on these four species using the next generation sequencing technology was performed for the first time. Functional annotations on assembled sequencing reads showed that the transcriptomic profiles were quite different between G. lema-neiformis and other three Gracilaria species. Comparative analysis of differential gene expression related to carbohydrate and phycobiliprotein metabolisms also showed that the expression profiles of these essential genes were different in four species. The genes encoding allophycocyanin, phycocyanin and phycoerythrin were further examined in four species and their deduced amino acid sequences were used for phylogenetic analysis to confirm that G. lemaneiformis had close relationship to genus Gracilaria, as well as that within genus Gracilaria, G. chouae had closer relationship to G. vermiculophylla rather than to G. blodgettii. The de novo transcriptome study on four species provided a valuable genomic resource for further understanding and analysis on biological and evolutionary study among marine algae.