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Functional genomic analysis of Hawaii marine metagenomes

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  • Life & Medical Sciences
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Science Bulletin

Abstract

Using high-throughput sequencing on metagenome to analyze marine microbial community, it is one of current main issues in the field of environmental microbe research. In this paper, we conducted the functional analysis on seven samples of metagenomic data from different depth seawater in Hawaii. The results of gene prediction and function annotation indicate that there are large amounts of potential novel genes of which functions remain unknown at present. Based on the gene annotation, codon usage bias is studied on ribosomal protein-related genes and shows an evident influence by the marine extreme environment. Furthermore, focusing on the marine environmental differences such as light intensity, dissolved oxygen, temperature and pressure among various depths, comparative analysis is carried out on related genes and metabolic pathways. Thus, the understanding as well as new insights into the correlation between marine environment and microbes are proposed at molecular level. Therefore, the studies herein afford a clue to reveal the special living strategies of microbial community from sea surface to deep sea.

摘要

对宏基因组高通量测序数据的分析, 是当前研究海洋微生物的重要方法。作者对夏威夷海域不同深度海水的微生物群落宏基因组进行功能基因组学分析。通过基因功能注释, 发现了大量潜在的新基因, 结果也表明极端环境加强了微生物密码子使用偏好。进一步根据光强、氧含量和低温高压等环境因素, 进行代谢通路和基因序列分析, 从分子水平上对海洋微生物与环境的关联和适应性提出若干新的认识, 探讨不同深度海洋环境中微生物特有的生存机制。

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Acknowledgements

This work was supported by the National “Twelfth Five-Year” Plan for Science and Technology of China (2012BAI06B02), the National Natural Science Foundation of China (91231119, 30970667 and 11021463), and the National Basic Research Program of China (2011CB707500). We thank Prof. Zuhong Lu of Peking University for his interest to the project and valuable discussions. We also thank Dr. Yongchu Liu, Dr. Xiaobin Zheng, Longshu Yang, Feifei He, Qiuyue Wang, Fumeng Wang, and Peng Zhai for their helpful discussions.

Conflict of interest

The authors declare that they have no conflict of interest.

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Authors and Affiliations

  1. Department of Biomedical Engineering, College of Engineering, Peking University, Beijing, 100871, China

    Xiaoqi Wang, Qi Wang, Luying Liu, Jiangtao Guo & Huaiqiu Zhu

  2. Center for Quantitative Biology, Peking University, Beijing, 100871, China

    Xiaoqi Wang, Qi Wang, Xiao Guo, Luying Liu, Jiangtao Guo & Huaiqiu Zhu

  3. School of Life Sciences, Peking University, Beijing, 100871, China

    Jinxian Yao

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  1. Xiaoqi Wang
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  2. Qi Wang
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  4. Luying Liu
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Correspondence to Huaiqiu Zhu.

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Wang, X., Wang, Q., Guo, X. et al. Functional genomic analysis of Hawaii marine metagenomes. Sci. Bull. 60, 348–355 (2015). https://doi.org/10.1007/s11434-014-0658-y

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