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De novo transcriptome analysis-gained insights into physiological and metabolic characteristics of Sargassum thunbergii (Fucales, Phaeophyceae)

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Abstract

Sargassum thunbergii has been studied extensively because of its particular ecology and economic value. Unfortunately, further progress has been hampered by lack of available genomic information. In this study, we sequenced and de novo assembled the transcriptome of S. thunbergii. A total of 53,490,957 clean reads were produced and were assembled into 46,269 contigs with the length from 351 nt to 21,538 nt and an average of 1,130 nt. Open reading frame (ORF) prediction in the assembled sequences showed that 30,139 (65.1 %) contigs had ORFs, and BLAST analysis indicated that 28,667 (61.96 %) sequences were annotated with putative functions. A total of 15,166 (32.8 %) putative genes were assigned at least one gene ontology term and 4,263 (10.0 %) putative proteins were classified into 25 categories by aligning against COG/KOG database. Function annotation with KEGG database assigned 11,798 (25.5 %) putative genes to 299 pathways. Out of the six enzymes that may be involved in alginate biosynthesis pathway, four have been identified from the transcriptome. Two pathways of guanosine diphosphate-mannose synthesis were identified in this alga, and the genes encoding the three putative enzymes responsible for mannitol cycle were discovered. Moreover, about 209 putative genes encoding the different kinds of heat shock proteins and a total of 119 putative genes encoding kinds of reactive oxygen species scavengers were also identified in the transcriptome, indicating that S. thunbergii may have strong resistance or tolerance to various stresses. In short, to our knowledge, this is the first data set for S. thunbergii transcriptome and will be a valuable resource for further studies on this alga.

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Acknowledgments

This research was funded by the 863 Hi-Tech Research and Development Program of China (2012AA10A413) and also supported by the Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences. The authors are grateful to the anonymous reviewers for their constructive comments on this paper.

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Authors and Affiliations

  1. Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China

    Fuli Liu, Xiutao Sun, Wenjun Wang, Zhourui Liang & Feijiu Wang

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  1. Fuli Liu
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Correspondence to Feijiu Wang.

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Supporting information file 1

Functional annotation by BLAST against different database for the assembled sequences with or without predicted ORF. (XLSX 181 kb)

Supporting information file 2

Detailed information about the 299 pathways involved 11798 genes identified from the transcriptome. (XLSX 13 kb)

Supporting information file 3

Functional annotation by BLAST against different database for the putative genes encoding the enzymes related to alginate, fucoidan and mannitol metabolisms, as well as to HSP and ROS scavenging enzymes. (XLSX 80 kb)

Supporting information file 4

The sequences of genes encoding the enzymes related to alginate, fucoidan and mannitol metabolisms, as well as to HSP and ROS scavenging enzymes. (TXT 744 kb)

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Liu, F., Sun, X., Wang, W. et al. De novo transcriptome analysis-gained insights into physiological and metabolic characteristics of Sargassum thunbergii (Fucales, Phaeophyceae). J Appl Phycol 26, 1519–1526 (2014). https://doi.org/10.1007/s10811-013-0140-2

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  • DOI: https://doi.org/10.1007/s10811-013-0140-2

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