De novo sequencing and comparative analysis of three red algal species of Family Solieriaceae to discover putative genes associated with carrageenan biosysthesis  

作　　者：SONG Lipu WU Shuangxiu SUN Jing WANG Liang LIU Tao CHI Shan LIU Cui LI Xingang YIN Jinlong WANG Xumin YU Jun 

机构地区：[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 [2]Beijing Key Laboratory of Functional Genomics for Dao-di Herbs,Beijing Institute of Genomics,Chinese Academy of Sciences [3]University of Chinese Academy of Sciences [4]College of Marine Life Science,Ocean University of China

出　　处：《Acta Oceanologica Sinica》2014年第2期45-53,共9页海洋学报（英文版）

基　　金：The National Natural Science Foundation of China under contract Nos 31140070,31271397 and 41206116;the algal transcrip-tome sequencing was supported by 1KP Project(www.onekp.com)

摘　　要：Betaphycus gelatinus, Kappaphycus alvarezii and Eucheuma denticulatum of Family Solieriaceae, Order Gi-gartinales, Class Rhodophyceae are three important carrageenan-producing red algal species, which pro-duce 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 So-lieriaceae 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 biosynthe-sis. 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 me-tabolism. We also found 8 different expressed KEGG orthologs for sulfur metabolism which might be impor-tantly 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.Betaphycus gelatinus, Kappaphycus alvarezii and Eucheuma denticulatum of Family Solieriaceae, Order Gi-gartinales, Class Rhodophyceae are three important carrageenan-producing red algal species, which pro-duce 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 So-lieriaceae 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 biosynthe-sis. 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 me-tabolism. We also found 8 different expressed KEGG orthologs for sulfur metabolism which might be impor-tantly 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.

关 键 词：Betaphycus gelatinus Kappaphycus alvarezii Eucheuma denticulatum SOLIERIACEAE de novo transcriptome sequencing CARRAGEENAN 

分 类 号：Q943.2[生物学—植物学]