Comparative analysis on transcriptome sequencings of six <i>Sargassum</i> species in China

WANG Guoliang; SUN Jing; LIU Guiming; WANG Liang; YU Jun; LIU Tao; CHI Shan; LIU Cui; GUO Haiyan; WANG Xumin; WU Shuangxiu

doi:10.1007/s13131-014-0439-0

Comparative analysis on transcriptome sequencings of six Sargassum species in China

doi: 10.1007/s13131-014-0439-0

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

基金项目: The National Natural Science Foundation of China under contract Nos 31140070, 31271397 and 41206116; the algal transcriptome sequencing was supported by 1KP Project (www.onekp.com).

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- 收稿日期: 2013-03-25
- 修回日期: 2013-07-24

Comparative analysis on transcriptome sequencings of six Sargassum species in China

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

摘要

摘要: Species of Sargassum are distributed worldwide, and are of great ecological and economic importance in marine ecosystems and bioresources. In this study, transcriptome sequencings of six Sargassum species were performed for the first time using an Illumina platform. For each sample, a total of 2.1-2.5 Gb of nucleotides are collected and assembled into 69 871-116 790 scaffolds, with an average length of 410-550 bp and N50 length of 756-1 462 bp. A total of 20 512-28 684 unigenes of each sample were annotated and compared well with known gene sequences from nr database. Clusters of Orthologous Groups (COG), gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were also performed for further understanding of gene functions and regulation pathways. Gene expression levels were calculated based on RPKM values and compared among these species, especially for those genes related to carbohydrate metabolism. Cluster analyses indicated that the differences of global gene expression between S. fusiforme, which was nominated as Hizikia fusiformis before, and other five species were not significant. Further phylogenetic analysis of 108 orthologous genes confirmed that S. fusiforme had closer relationship with S. hemiphyllum rather than S. horneri. These transcriptome data provided valuable information for better understanding of genome and gene characteristics of Sargassum algae and benefiting comparative and phylogenetic studies of Phaeophyceae species in future studies.
- Sargassum /
- Sargassumfusiforme /
- transcriptomesequencing /
- comparativeanalysis
Abstract: Species of Sargassum are distributed worldwide, and are of great ecological and economic importance in marine ecosystems and bioresources. In this study, transcriptome sequencings of six Sargassum species were performed for the first time using an Illumina platform. For each sample, a total of 2.1-2.5 Gb of nucleotides are collected and assembled into 69 871-116 790 scaffolds, with an average length of 410-550 bp and N50 length of 756-1 462 bp. A total of 20 512-28 684 unigenes of each sample were annotated and compared well with known gene sequences from nr database. Clusters of Orthologous Groups (COG), gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were also performed for further understanding of gene functions and regulation pathways. Gene expression levels were calculated based on RPKM values and compared among these species, especially for those genes related to carbohydrate metabolism. Cluster analyses indicated that the differences of global gene expression between S. fusiforme, which was nominated as Hizikia fusiformis before, and other five species were not significant. Further phylogenetic analysis of 108 orthologous genes confirmed that S. fusiforme had closer relationship with S. hemiphyllum rather than S. horneri. These transcriptome data provided valuable information for better understanding of genome and gene characteristics of Sargassum algae and benefiting comparative and phylogenetic studies of Phaeophyceae species in future studies.
- Sargassum /
- Sargassum fusiforme /
- transcriptome sequencing /
- comparative analysis

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参考文献(32)

Ale M T, Maruyama H, Tamauchi H, et al. 2011. Fucose-containing sulfated polysaccharides from brown seaweeds inhibit proliferation of melanoma cells and induce apoptosis by activation of caspase-3 in vitro. Mar Drugs, 9: 2605-2621

Carpenter E J, Cox J L. 1974. Production of pelagic Sargassum and a blue-green epiphyte in the Western Sargasso Sea. Limnol Oceanogr, 19: 429-436

Cho G Y, Rousseau F, de Reviers B, et al. 2006. Phylogenetic relationships within the Fucales (Phaeophyceae) assessed by the photosystem I coding psaA sequences. Phycologia, 45: 512-519

Cock J M, Sterck L, Rouze P, et al. 2010. The Ectocarpus genome and the independent evolution of multicellularity in brown algae. Nature, 465: 617-621

Conover J T, Sieburth J M. 1964. Effect of Sargassum distribution on its epibiota and antibacterial activity. Botanica Marina, 6: 147-157

Curtis B A, Tanifuji G, Burki F, et al. 2012. Algal genomes reveal evolutionary mosaicism and the fate of nucleomorphs. Nature, 492: 59?65

Deng Yunyan, Yao Jianting, Wang Xiuliang, et al. 2012. Transcriptome sequencing and comparative analysis of Saccharina japonica (Laminariales, Phaeophyceae) under blue light induction. PLoS One, 7: e39704

Dittami S M, Scornet D, Petit J L, et al. 2009. Global expression analysis of the brown alga Ectocarpus siliculosus (Phaeophyceae) reveals large-scale reprogramming of the transcriptome in response to abiotic stress. Genome Biol, 10: R66

Ghangal R, Raghuvanshi S, Chand Sharma P. 2009. Isolation of good quality RNA from a medicinal plant seabuckthorn, rich in secondary metabolites. Plant Physiol Biochem, 47: 1113-1115

Huynh Truonggiang, Yeh Sutuen, Lina Yongchin, et al. 2011. White shrimp Litopenaeus vannamei immersed in seawater containing Sargassum hemiphyllum var. chinense powder and its extract showed increased immunity and resistance against Vibrio alginolyticus and white spot syndrome virus. Fish Shellfish Immunol, 31(2): 286-293

Johnson M T, Carpenter E J, Tian Zhijian, et al. 2012. Evaluating methods for isolating total RNA and predicting the success of sequencing phylogenetically diverse plant transcriptomes. PLoS One, 7: e50226

Li Tianyong, Ren Lei, Zhou Guan, et al. 2012. A suitable method for extracting total RNA from red algae. Transactions of Oceanology and Limnology (in Chinese), 4: 64-71

Makinen V, Salmela L, Ylinen J. 2012. Normalized N50 assembly metric using gap-restricted co-linear chaining. BMC Bioinformatics, 13: 255

Mattio L, Payri C E. 2009. Taxonomic revision of Sargassum species (Fucales, Phaeophyceae) from New Caledonia based on morphological and molecular analyses(1). J Phycol, 45: 1374-1388

Mortazavi A, Williams B A, McCue K, et al. 2008. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods, 5: 621-628

Oak J H, Suh Y, Lee I K. 2002. Phylogenetic relationships of Sargassum subgenus Bactrophycus (Sargassaceae, Phaeophyceae) inferred from rDNA ITS Sequences. Algae, 17: 235-247

Phillips N E, Smith C M, Morden C W. 2005. Testing systematic concepts of Sargassum (Fucales，Phaeophyceae) using portions of the rbcLS operon. Phycol Res, 53: 1-10

Preeprame S, Hayashi K, Lee J B, et al. 2001. A novel antivirally active fucan sulfate derived from an edible brown alga, Sargassum horneri. Chem Pharm Bull (Tokyo), 49: 484-485

Price D C, Chan C X, Yoon H S, et al. 2012. Cyanophora paradoxa genome elucidates origin of photosynthesis in algae and plants. Science, 335: 843-847

Rivera M, Scrosati R. 2006. Population dynamics of Sargassum lapazeanum (Fucales, Phaeophyta) from the Gulf of California, Mexico. Phycologia, 45: 178-189

Southichak B, Nakano K, Nomura M, et al. 2008. Marine macroalga Sargassum horneri as biosorbent for heavy metal removal: roles of calcium in ion exchange mechanism. Water Sci Technol, 58: 697-704

Stamatakis A, Aberer A J, Goll C, et al. 2012. RAxML-Light: a tool for computing terabyte phylogenies. Bioinformatics, 28: 2064-2066

Stiger V, Horiguchi T, Yoshida T, et al. 2003. Phylogenetic relationships within the genus Sargassum (Fucales, Phaeophyceae), inferred from ITS-2 nrDNA, with an emphasis on the taxonomic subdivision of the genus. Phycol Res, 51: 1-10

Tatusov R L, Fedorova N D, Jackson J D, et al. 2003. The COG database: an updated version includes eukaryotes. BMC Bioinformatics, 4: 41

Wang Guoliang, Zhao Ge, Feng Yanbin, et al. 2010. Cloning and comparative studies of seaweed trehalose-6-phosphate synthase genes. Mar Drugs, 8: 2065-2079

Wong C K, Ooi V E, Ang P O. 2000. Protective effects of seaweeds against liver injury caused by carbon tetrachloride in rats. Chemosphere, 41: 173-176

Wong C L, Ng S M, Phang S M. 2007. Use of RAPD in differentiation of selected species of Sargassum (Sargassaceae, Phaeophyta). J Appl Phycol, 19: 771-781

Xu Jia, Aileni M, Abbagani S, et al. 2010. A reliable and efficient method for total rna isolation from various members of spurge family (Euphorbiaceae). Phytochem Anal, 21: 395-398

Yao Jianting, Fu Wandong, Wang Xiuliang, et al. 2008. Improved RNA isolation from Laminaria japonica Aresch (Laminariaceae, Phaeophyta). J Appl Phycol, 21: 233-238

Zdobnov E M, Apweiler R. 2001. InterProScan—an integration platform for the signature-recognition methods in InterPro. Bioinformatics, 17: 847-848

Zeng Chengkui. 2009. Seaweeds in Bohai Sea and Yellow Sea of China (in Chinese). Beijing: Sicence Press, 363-372

Zou Dinghui, Gao Kunshan, Luo Hanjin. 2011. Short- and long-term effects of elevated CO2 on photosynthesis and respiration in the marine macroalga Hizikia Fusiformis (Sargassaceae, Phaeophyta) grown at low and high N supplies. J Phycol, 47: 87-97

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Comparative analysis on transcriptome sequencings of six Sargassum species in China

doi: 10.1007/s13131-014-0439-0

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Comparative analysis on transcriptome sequencings of six Sargassum species in China

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