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Prokaryotic systematics in the genomics era

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Abstract

As an essential and basic biological discipline, prokaryotic systematics is entering the era of genomics. This paradigmatic shift is significant not only for understanding molecular phylogeny at the whole genome level but also in revealing the genetic or epigenetic basis that accounts for the phenotypic criteria used to classify and identify species. These developments provide an opportunity and a challenge for systematists to reanalyze the molecular mechanisms underlying the taxonomic characteristics of prokaryotes by drawing the knowledge from studies of genomics and/or functional genomics employing platform technologies and related bioinformatics tools. It is expected that taxonomic books, such as Bergey’s Manual of Systematic Bacteriology may evolve into a systematics library indexed by phylogenomic information with an comprehensive understanding of prokaryotic speciation and associated increasing knowledge of biological phenomena.

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Acknowledgments

This research was supported by the National Basic Research Program of China (Grant 2010CB833801 and 2012CB721102), the National Natural Science Foundation of China (Grants 30830002 and 31121001) and the Research Unit Fund of Li Ka Shing Institute of Health Sciences (Grant 7103506). We thank Prof. Mike Goodfellow for his helpful comments on our manuscript. And we also appreciate the comments made by Dr. Shuhua XU of the Institute of Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences.

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Authors and Affiliations

  1. Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education and the Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Institute of Microbiology, Yunnan University, Kunming, 650091, China

    Xiao-Yang Zhi & Wen-Jun Li

  2. Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China

    Wei Zhao & Guo-Ping Zhao

  3. State Key Laboratory of Genetic Engineering, Department of Microbiology, School of Life Sciences and Institute of Biomedical Sciences, Fudan University, Shanghai, 200433, China

    Wei Zhao & Guo-Ping Zhao

  4. China HYK Gene Technology Company Ltd., Shenzhen, Guangdong, 518057, China

    Wei Zhao

  5. Shanghai-MOST Key Laboratory of Disease and Health Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, 201203, China

    Guo-Ping Zhao

  6. Department of Microbiology and Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong, SAR, China

    Guo-Ping Zhao

Authors
  1. Xiao-Yang Zhi
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  2. Wei Zhao
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  3. Wen-Jun Li
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  4. Guo-Ping Zhao
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Corresponding author

Correspondence to Guo-Ping Zhao.

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Xiao-Yang Zhi and Wei Zhao contribute equally to the article.

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Zhi, XY., Zhao, W., Li, WJ. et al. Prokaryotic systematics in the genomics era. Antonie van Leeuwenhoek 101, 21–34 (2012). https://doi.org/10.1007/s10482-011-9667-x

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