Genomic evolution of 11 type strains within family Planctomycetaceae

PLoS One. 2014 Jan 29;9(1):e86752. doi: 10.1371/journal.pone.0086752. eCollection 2014.

Abstract

The species in family Planctomycetaceae are ideal groups for investigating the origin of eukaryotes. Their cells are divided by a lipidic intracytoplasmic membrane and they share a number of eukaryote-like molecular characteristics. However, their genomic structures, potential abilities, and evolutionary status are still unknown. In this study, we searched for common protein families and a core genome/pan genome based on 11 sequenced species in family Planctomycetaceae. Then, we constructed phylogenetic tree based on their 832 common protein families. We also annotated the 11 genomes using the Clusters of Orthologous Groups database. Moreover, we predicted and reconstructed their core/pan metabolic pathways using the KEGG (Kyoto Encyclopedia of Genes and Genomes) orthology system. Subsequently, we identified genomic islands (GIs) and structural variations (SVs) among the five complete genomes and we specifically investigated the integration of two Planctomycetaceae plasmids in all 11 genomes. The results indicate that Planctomycetaceae species share diverse genomic variations and unique genomic characteristics, as well as have huge potential for human applications.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Biological Evolution*
  • Genome, Bacterial*
  • Genomic Islands
  • Metabolic Networks and Pathways
  • Multigene Family
  • Phylogeny*
  • Planctomycetales / classification*
  • Planctomycetales / genetics*
  • Planctomycetales / metabolism
  • Planctomycetales / ultrastructure
  • Plasmids

Grants and funding

This work was supported by Shenzhen Key Laboratory of Bioenergy (grant CXB201005240001A), Shenzhen Key Laboratory of Environmental Microbial Genomics and Application(grant CXB201108250097A) and by grants from the State Key Development Program for Basic Research of China (2009CB522600), the National Natural Science Foundation of China (Contract 30930001). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.