De novo sequencing and comparative analysis of three red algal species of Family Solieriaceae to discover putative genes
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De novo sequencing and comparative analysis of three red algal species of Family Solieriaceae to discover putative genes associated with carrageenan biosysthesis SONG Lipu1,3,4†, WU Shuangxiu1,3†, SUN Jing1,3,4†, WANG Liang1,3,4, LIU Tao2, CHI Shan2, LIU Cui2, LI Xingang1,3, YIN Jinlong1, WANG Xumin1,3*, YU Jun1,3* 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 25 March 2013; accepted 22 July 2013 ©The Chinese Society of Oceanography and Springer-Verlag Berlin Heidelberg 2014
Abstract Betaphycus gelatinus, Kappaphycus alvarezii and Eucheuma denticulatum of Family Solieriaceae, Order Gigartinales, Class Rhodophyceae are three important carrageenan-producing red algal species, which produce different types of carrageenans, beta (β)-carrageenan, kappa (κ)-carrageenan and iota (ι)-carrageenan. So far the carrageenan biosynthesis pathway is not fully understood and few information is about the Solieriaceae genome and transcriptome sequence. Here, we performed the de novo transcriptome sequencing, assembly, functional annotation and comparative analysis of these three commercial-valuable species using an Illumina short-sequencing platform Hiseq 2000 and bioinformatic software. Furthermore, we compared the different expression of some unigenes involved in some pathways relevant to carrageenan biosynthesis. We finally found 861 different expressed KEGG orthologs which contained a glycolysis/gluconeogenesis pathway (21 orthologs), carbon fixation in photosynthetic organisms (16 orthologs), galactose metabolism (5 orthologs), and fructose and mannose metabolism (9 orthologs) which are parts of the carbohydrate metabolism. We also found 8 different expressed KEGG orthologs for sulfur metabolism which might be importantly related to biosynthesis of different types of carrageenans. The results presented in this study provided valuable resources for functional genomics annotation and investigation of mechanisms underlying the biosynthesis of carrageenan in Family Solieriaceae. Key words: Betaphycus gelatinus, Kappaphycus alvarezii, Eucheuma denticulatum, Solieriaceae, de novo transcriptome sequencing, carrageenan Citation: Song Lipu, Wu Shuangxiu, Sun Jing, Wang Liang, Liu Tao, Chi Shan, Liu Cui, Li Xingang, Yin Jinlong, Wang Xumin, Yu Jun. 2014. De novo sequencing and comparative analysis of three red algal species of Family Solieriaceae to discover putative genes associated with carrageenan biosysthesis. Acta Oceanologica Sinica, 33(2): 45–53, doi: 10.1007/s13131-014-0440-7
1 Introduction Solieriaceae is a red algal family in Order Gigartinales of Class Rhodophyceae
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