Abstract
Genome-wide characterization of the Pohlia nutans transcriptome is essential for clarifying the role of stress-relevant genes in Antarctic moss adapting to the extreme polar environment. High-throughput Illumina sequencing was used to analyze the gene expression profile of P. nutans after cold treatment. A total of 93,488 unigenes, with an average length of 405 bp, were obtained. Gene annotation showed that 16,781 unigenes had significant similarity to known functional protein-coding genes, most of which were annotated using the GO, KOG and KEGG pathway databases. Global profiling of the differentially expressed genes revealed that 3,796 unigenes were significantly upregulated after cold treatment, while 1,405 unigenes were significantly downregulated. In addition, 816 receptor-like kinases and 1,309 transcription factors were identified from P. nutans. This overall survey of transcripts and stress-relevant genes can contribute to understanding the stress-resistance mechanism of Antarctic moss and will accelerate the practical exploitation of the genetic resources for this organism.
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Acknowledgments
We thank the Chinese National Human Genome Center (Shanghai) for their collaboration and support in the de novo assembly and annotation of the P. nutans transcriptome. We are very grateful for the critical comments and suggestions from the anonymous reviewers. This work was financially supported by the China National Natural Science Foundation (40906103 and 41206176) and Basic Scientific Research Foundation of The First Institute of Oceanography (SOA).
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Communicated by H. Atomi.
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Liu, S., Wang, N., Zhang, P. et al. Next-generation sequencing-based transcriptome profiling analysis of Pohlia nutans reveals insight into the stress-relevant genes in Antarctic moss. Extremophiles 17, 391–403 (2013). https://doi.org/10.1007/s00792-013-0528-6
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DOI: https://doi.org/10.1007/s00792-013-0528-6