2015
DOI: 10.4014/jmb.1504.04008
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Comparative Genomics Reveals the Core and Accessory Genomes of Streptomyces Species

Abstract: The development of rapid and efficient genome sequencing methods has enabled us to study the evolutionary background of bacterial genetic information. Here, we present comparative genomic analysis of 17 Streptomyces species, for which the genome has been completely sequenced, using the pan-genome approach. The analysis revealed that 34,592 ortholog clusters constituted the pan-genome of these Streptomyces species, including 2,018 in the core genome, 11,743 in the dispensable genome, and 20,831 in the unique ge… Show more

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Cited by 65 publications
(69 citation statements)
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References 31 publications
(41 reference statements)
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“…In contrast to the vast majority of bacteria, Streptomyces possess a linear chromosome whose size is ranging from 5.96 to 11.94 Mb 1 with a central replication origin and terminally inverted repeats that are covalently bound to specific telomere proteins (Lin et al, 1993). The Streptomyces genome presents a high plasticity and their chromosome is highly compartmented, with a conserved central region including mostly housekeeping genes whereas the dispensable genes are predominantly located in the chromosomal arms (Bentley et al, 2002; Ikeda et al, 2003; Kim et al, 2015). The loss of synteny at the ends of the chromosome results from horizontally acquired DNA insertion or deletion events (Choulet et al, 2006; Thibessard and Leblond, 2014).…”
Section: Introductionmentioning
confidence: 99%
“…In contrast to the vast majority of bacteria, Streptomyces possess a linear chromosome whose size is ranging from 5.96 to 11.94 Mb 1 with a central replication origin and terminally inverted repeats that are covalently bound to specific telomere proteins (Lin et al, 1993). The Streptomyces genome presents a high plasticity and their chromosome is highly compartmented, with a conserved central region including mostly housekeeping genes whereas the dispensable genes are predominantly located in the chromosomal arms (Bentley et al, 2002; Ikeda et al, 2003; Kim et al, 2015). The loss of synteny at the ends of the chromosome results from horizontally acquired DNA insertion or deletion events (Choulet et al, 2006; Thibessard and Leblond, 2014).…”
Section: Introductionmentioning
confidence: 99%
“…Early deductions about the core and accessory genes of streptomycetes have been refined 42 : the genomes of 17 diverse strains (ranging from 6.7 to 12.3 Mb) contained from 5,382 to 10,022 CDSs, of which 2,018 were universally present (the core genome, which occupies most of the central region of Streptomyces linear chromosomes), with most of the remaining genes being present in only one or a few genomes. This accessory genome totalled 32,574 genes, so the Streptomyces pan-genome comprises at least 34,592 genes.…”
Section: Ecology and Evolutionmentioning
confidence: 99%
“…Indeed, many bacterial species show patterns consistent with this rapid turn-over of genes, where strains from a single niche contain a relatively small set of genes, while the set of genes found by sampling strains from various niches (i.e. the pan-genome) is much richer (Welch et al, 2002;Lefébure and Stanhope, 2007;Kim et al, 2015). Hence, genes appear to be rapidly lost from any individual lineage, but are retained in a much larger gene pool through HGT.…”
Section: Introductionmentioning
confidence: 99%