Analysis of <i>Saccharina japonica</i> transcriptome using the high-throughput DNA sequencing technique and its vanadium-dependent haloperoxidase gene

LIANG Xiayuan; WANG Xumin; CHI Shan; WU Shuangxiu; SUN Jing; LIU Cui; CHEN Shengping; YU Jun; LIU Tao

doi:10.1007/s13131-014-0438-1

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Article Navigation > Acta Oceanologica Sinica > 2014 > 33(2): 27-36

LIANG Xiayuan, WANG Xumin, CHI Shan, WU Shuangxiu, SUN Jing, LIU Cui, CHEN Shengping, YU Jun, LIU Tao. Analysis of Saccharina japonica transcriptome using the high-throughput DNA sequencing technique and its vanadium-dependent haloperoxidase gene[J]. Acta Oceanologica Sinica, 2014, 33(2): 27-36. doi: 10.1007/s13131-014-0438-1

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LIANG Xiayuan, WANG Xumin, CHI Shan, WU Shuangxiu, SUN Jing, LIU Cui, CHEN Shengping, YU Jun, LIU Tao. Analysis of Saccharina japonica transcriptome using the high-throughput DNA sequencing technique and its vanadium-dependent haloperoxidase gene[J]. Acta Oceanologica Sinica, 2014, 33(2): 27-36. doi: 10.1007/s13131-014-0438-1

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Analysis of Saccharina japonica transcriptome using the high-throughput DNA sequencing technique and its vanadium-dependent haloperoxidase gene

doi: 10.1007/s13131-014-0438-1

1.
College of Marine Life Science, Ocean University of China, Qingdao 266003, China
2.
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
3.
Guangdong Province Key Laboratory of Functional Molecules in Oceanic Microorganism, Zhong Shan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, China

Received Date: 2013-03-28
Rev Recd Date: 2013-08-06

Abstract

Abstract

Saccharina is one of the most important cold-water living marine brown algal genera. In this study we analyzed the transcriptome of S. japonica, which belongs to the 1 000 Plants (OneKP) Project, by using a nextgeneration high-throughput DNA sequencing technique. About 5.16 GB of raw data were generated, and 65 536 scaffolds with an average length of 454 bp were assembled with SOAP de novo assembly method. In total, 19 040 unigenes were identified by BLAST; 25 734 scaffolds were clustered into 37 Gene ontology functional groups; 6 760 scaffolds were classified into 25 COG categories, as well as 2 665 scaffolds that were assigned to 306 KEGG pathways. Majority of the unigenes exhibited more similarities to algae including brown algae and diatom than other cyanobacteria, marine diatom, and plant. Saccharina japonica has the outstanding capability to accumulate halogen such as Br and I via halogenation processes from seawater. We acquired 42 different vanadium-dependent haloperoxidases (vHPO) in S. japonica transcriptome data, including 5 segments of vanadium-dependent iodoperoxidase (vIPO) and 37 segments of vanadium-dependent bromoperoxidase (vBPO). Complicated analyses of identified fulllength S. japonica vBPO1 and S. japonica vBPO2 revealed the importance of vBPO among species of brown algae and the strong relationship between marine algal vBPOs and vIPOs. This study will enhance our understanding of the biological characteristics and economic values of S. japonica species.
- Saccharina japonica,
- transcriptomic sequencing,
- vanadium-dependent haloperoxidase,
- phylogenic analysis

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References(48)

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