| QU Jieqiong,WANG Xumin,CHI Shan,WU Shuangxiu,SUN Jing,LIU Cui,CHEN Shengping,YU Jun,LIU Tao. 2014. Transcriptome characterization of Ishige okamurae (Phaeophyceae) shows strong environmental acclimation. Acta Oceanologica Sinica, 33(2):20－26 |
| Transcriptome characterization of Ishige okamurae (Phaeophyceae) shows strong environmental acclimation |
| Transcriptome characterization of Ishige okamurae (Phaeophyceae) shows strong environmental acclimation |
| Received:March 27, 2013 Revised:July 17, 2013 |
| DOI：10.1007/s13131-014-0437-2 |
| Key words:Ishige okamurae transcriptome environmental acclimation Rab |
| 中文关键词: Ishige okamurae transcriptome environmental acclimation Rab |
| 基金项目:The National Natural Science Foundation of China under contract Nos 41206116, 31140070 and 31271397; Technology Project of Ocean and Fisheries of Guangdong Province under contract No. A201201E03; the Fundamental Research Funds for the Central Universities under contract No. 201262003; the algal transcriptome sequencing was supported by 1KP Project (www.onekp.com). |
| Author Name | Affiliation | E-mail | | QU Jieqiong | College of Marine Life Science, Ocean University of China, Qingdao 266003, China | | | WANG Xumin | 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
Beijing Key Laboratory of Functional Genomics for Dao-di Herbs, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China | wangxm@big.ac.cn | | CHI Shan | College of Marine Life Science, Ocean University of China, Qingdao 266003, China | | | WU Shuangxiu | 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
Beijing Key Laboratory of Functional Genomics for Dao-di Herbs, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China | | | SUN Jing | 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
Beijing Key Laboratory of Functional Genomics for Dao-di Herbs, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China | | | LIU Cui | College of Marine Life Science, Ocean University of China, Qingdao 266003, China | | | CHEN Shengping | Guangdong Province Key Laboratory of Functional Molecules in Oceanic Microorganism, Zhong Shan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, China | | | YU Jun | 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
Beijing Key Laboratory of Functional Genomics for Dao-di Herbs, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China | | | LIU Tao | College of Marine Life Science, Ocean University of China, Qingdao 266003, China | liutao@ouc.edu.cn |
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| Abstract: |
| Ishige okamurae, with leathery branched narrow fronds consisting of cylindrical hairs, is the typical species of the genus Ishige, which is considered as one of the most basal genera in the phylogeny of the Phaeophyceae. Apart from great public interest from the evolutionary respect, more attention has been brought on the abundant bioactive compounds in I. okamurae for therapeutic or economic considerations, such as diphlorethohydroxycarmalol and ishigoside. Yet little is known about related key genes or metabolic pathways involved in I. okamurae, which calls upon us to carry out global analyses of transcriptome by next generation sequencing. Altogether, we obtained 78 583 assembled scaffolds with N50 of 1 709 nucleotides, and 25 357 unigenes with significant BLAST matches (E-value cutoff of 10?5). In terms of characterization of the transcriptome of I. okamurae, we focused on anti-stress metabolic pathways and synthetic routes of bioactive compounds in an attempt to obtain a better understanding of the interactive organism-environment regulatory networks. Pathway-based analysis helped us to deepen our comprehension of the interaction between I. okamurae and its surroundings, with MAPK signal pathway as an example. Furthermore, we discovered a wide range of novel putative functional proteins that could be of wide application, such as Rab family, using sequence-based transcriptome. In conclusion, transcriptome characterization of I. okamurae (Phaeophyceae) shows strong environmental acclimation. |
| 中文摘要: |
| Ishige okamurae, with leathery branched narrow fronds consisting of cylindrical hairs, is the typical species of the genus Ishige, which is considered as one of the most basal genera in the phylogeny of the Phaeophyceae. Apart from great public interest from the evolutionary respect, more attention has been brought on the abundant bioactive compounds in I. okamurae for therapeutic or economic considerations, such as diphlorethohydroxycarmalol and ishigoside. Yet little is known about related key genes or metabolic pathways involved in I. okamurae, which calls upon us to carry out global analyses of transcriptome by next generation sequencing. Altogether, we obtained 78 583 assembled scaffolds with N50 of 1 709 nucleotides, and 25 357 unigenes with significant BLAST matches (E-value cutoff of 10?5). In terms of characterization of the transcriptome of I. okamurae, we focused on anti-stress metabolic pathways and synthetic routes of bioactive compounds in an attempt to obtain a better understanding of the interactive organism-environment regulatory networks. Pathway-based analysis helped us to deepen our comprehension of the interaction between I. okamurae and its surroundings, with MAPK signal pathway as an example. Furthermore, we discovered a wide range of novel putative functional proteins that could be of wide application, such as Rab family, using sequence-based transcriptome. In conclusion, transcriptome characterization of I. okamurae (Phaeophyceae) shows strong environmental acclimation. |
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