Complete Genome Sequence of Amycolatopsis mediterranei S699 Based on De Novo Assembly via a Combinatorial Sequencing Strategy

Abstract

fThe genome of Amycolatopsis mediterranei S699 was resequenced and assembled de novo. By comparing the sequences of S699 previously released and that of A. mediterranei U32, about 10 kb of major indels was found to differ between the two S699 genomes, and the differences are likely attributable to their different assembly strategies.

Genetics and Genomics of the Genus Amycolatopsis

“…The original strain synthesized a mixture of rifamycins (rifamycin complex), however the addition of sodium diethylbarbiturate resulted in the production of a single fermentation product rifamycin B [11]. Subsequently, two mutant strains A. mediterranei ATCC 21789 and S699 capable of producing sole rifamycin B without the addition of sodium diethylbarbiturate in the medium were isolated [11]. The origin of these strains is very ambiguous as they have moved from one industry to another in the past 50 years.…”

“…Its ability for the production of rifamycin was recognized in the same year [12]. The original strain synthesized a mixture of rifamycins (rifamycin complex), however the addition of sodium diethylbarbiturate resulted in the production of a single fermentation product rifamycin B [11]. Subsequently, two mutant strains A. mediterranei ATCC 21789 and S699 capable of producing sole rifamycin B without the addition of sodium diethylbarbiturate in the medium were isolated [11].…”

“…Amycolatopsis mediterranei S699 was derived from the original strain A. mediterranei ATCC 13685, isolated from a soil sample at St. Raphael, France in 1957 [11]. Unlike the original strain, S699 was capable of producing solely rifamycin B without the addition of sodium barbiturate [11].…”

“…In an attempt to further analyze these strains, genomes of some of these strains have been sequenced: U32 [13], S699 [11,12], RB (unpublished), DSM 46096 [20], DSM 40773 [21] and HP-130 [5]. ND no data available…”

“…While the genomes of Streptomyces spp. have been extensively studied, Amycolatopsis genomes appear to have been sequenced only recently [11][12][13]. The information on the secondary metabolome based on genomic analysis of species belonging to the genera Streptomyces, Saccharopolyspora, Salinispora, Frankia and Rhodococcus have already been reviewed [14], the analysis of recently sequenced genomes of Amycolatopsis has not been carried out.…”