Transcriptome sequencing of essential marine brown and red algal species in China and its significance in algal biology and phylogeny

WU Shuangxiu; SUN Jing; CHI Shan; WANG Liang; WANG Xumin; LIU Cui; LI Xingang; YIN Jinlong; LIU Tao; YU Jun

doi:10.1007/s13131-014-0435-4

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WU Shuangxiu, SUN Jing, CHI Shan, WANG Liang, WANG Xumin, LIU Cui, LI Xingang, YIN Jinlong, LIU Tao, YU Jun. Transcriptome sequencing of essential marine brown and red algal species in China and its significance in algal biology and phylogeny[J]. Acta Oceanologica Sinica, 2014, 33(2): 1-12. doi: 10.1007/s13131-014-0435-4

Citation:

WU Shuangxiu, SUN Jing, CHI Shan, WANG Liang, WANG Xumin, LIU Cui, LI Xingang, YIN Jinlong, LIU Tao, YU Jun. Transcriptome sequencing of essential marine brown and red algal species in China and its significance in algal biology and phylogeny[J]. Acta Oceanologica Sinica, 2014, 33(2): 1-12. doi: 10.1007/s13131-014-0435-4

Citation:

WU Shuangxiu, SUN Jing, CHI Shan, WANG Liang, WANG Xumin, LIU Cui, LI Xingang, YIN Jinlong, LIU Tao, YU Jun. Transcriptome sequencing of essential marine brown and red algal species in China and its significance in algal biology and phylogeny[J]. Acta Oceanologica Sinica, 2014, 33(2): 1-12. doi: 10.1007/s13131-014-0435-4

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Transcriptome sequencing of essential marine brown and red algal species in China and its significance in algal biology and phylogeny

doi: 10.1007/s13131-014-0435-4

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;Beijing Key Laboratory of Functional Genomics for Dao-di Herbs, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, 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;University of Chinese Academy of Sciences, Beijing 100049, China
3.
College of Marine Life Science, Ocean University of China, Qingdao 266003, China
4.
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

Received Date: 2013-04-03
Rev Recd Date: 2013-07-26

Abstract

Abstract

Most phaeophytes (brown algae) and rhodophytes (red algae) dwell exclusively in marine habitats and play important roles in marine ecology and biodiversity. Many of these brown and red algae are also important resources for industries such as food, medicine and materials due to their unique metabolisms and metabolites. However, many fundamental questions surrounding their origins, early diversification, taxonomy, and special metabolisms remain unsolved because of poor molecular bases in brown and red algal study. As part of the 1 000 Plant Project, the marine macroalgal transcriptomes of 19 Phaeophyceae species and 21 Rhodophyta species from China's coast were sequenced, covering a total of 2 phyla, 3 classes, 11 orders, and 19 families. An average of 2 Gb per sample and a total 87.3 Gb of RNA-seq raw data were generated. Approximately 15 000 to 25 000 unigenes for each brown algal sample and 5 000 to 10 000 unigenes for each red algal sample were annotated and analyzed. The annotation results showed obvious differences in gene expression and genome characteristics between red algae and brown algae; these differences could even be seen between multicellular and unicellular red algae. The results elucidate some fundamental questions about the phylogenetic taxonomy within phaeophytes and rhodophytes, and also reveal many novel metabolic pathways. These pathways include algal CO₂ fixation and particular carbohydrate metabolisms, and related gene/gene family characteristics and evolution in brown and red algae. These findings build on known algal genetic information and significantly improve our understanding of algal biology, biodiversity, evolution, and potential utilization of these marine algae.
- Phaeophyceae,
- brown algae,
- Rhodophyta,
- red algae,
- marine macroalgae,
- transcriptome sequencing,
- secondary generation sequencing

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