Antonie van Leeuwenhoek

, Volume 101, Issue 1, pp 21–34 | Cite as

Prokaryotic systematics in the genomics era

  • Xiao-Yang Zhi
  • Wei Zhao
  • Wen-Jun Li
  • Guo-Ping Zhao
Perspective

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.

Keywords

Taxonomy Genomics Prokaryotic systematics Molecular phylogeny 

Notes

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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© Springer Science+Business Media B.V. 2011

Authors and Affiliations

  • Xiao-Yang Zhi
    • 1
  • Wei Zhao
    • 2
    • 3
    • 4
  • Wen-Jun Li
    • 1
  • Guo-Ping Zhao
    • 2
    • 3
    • 5
    • 6
  1. 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 MicrobiologyYunnan UniversityKunmingChina
  2. 2.Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological SciencesChinese Academy of SciencesShanghaiChina
  3. 3.State Key Laboratory of Genetic Engineering, Department of Microbiology, School of Life Sciences and Institute of Biomedical SciencesFudan UniversityShanghaiChina
  4. 4.China HYK Gene Technology Company Ltd., ShenzhenGuangdongChina
  5. 5.Shanghai-MOST Key Laboratory of Disease and Health GenomicsChinese National Human Genome Center at ShanghaiShanghaiChina
  6. 6.Department of Microbiology and Li Ka Shing Institute of Health SciencesThe Chinese University of Hong KongHong KongChina

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