Abstract
Background
Streptomycetes are filamentous soil-dwelling bacteria. They are best known as the
producers of a great variety of natural products such as antibiotics, antifungals,
antiparasitics, and anticancer agents and the decomposers of organic substances
for carbon recycling. They are also model organisms for the studies of gene
regulatory networks, morphological differentiation, and stress response. The
availability of sets of genomes from closely related Streptomyces strains
makes it possible to assess the mechanisms underlying genome plasticity and
systems adaptation.
Results
We present the results of a comprehensive analysis of the genomes of five
Streptomyces species with distinct phenotypes. These streptomycetes
have a pan-genome comprised of 17,362 orthologous families which includes 3,096
components in the core genome, 5,066 components in the dispensable genome, and
9,200 components that are uniquely present in only one species. The core genome
makes up about 33%-45% of each genome repertoire. It contains important genes for
Streptomyces biology including those involved in gene regulation,
secretion, secondary metabolism and morphological differentiation. Abundant
duplicate genes have been identified, with 4%-11% of the whole genomes composed of
lineage-specific expansions (LSEs), suggesting that frequent gene duplication or
lateral gene transfer events play a role in shaping the genome diversification
within this genus. Two patterns of expansion, single gene expansion and chromosome
block expansion are observed, representing different scales of duplication.
Conclusions
Our results provide a catalog of genome components and their potential functional
roles in gene regulatory networks and metabolic networks. The core genome
components reveal the minimum requirement for streptomycetes to sustain a
successful lifecycle in the soil environment, reflecting the effects of both
genome evolution and environmental stress acting upon the expressed phenotypes. A
better understanding of the LSE gene families will, on the other hand, bring a
wealth of new insights into the mechanisms underlying strain-specific phenotypes,
such as the production of novel antibiotics, pathogenesis, and adaptive response
to environmental challenges.
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