Assembly and features of secondary metabolite biosynthetic gene clusters in Streptomyces ansochromogenes

Xingyu Zhong,Yuqing Tian,Huarong Tan,Guoqing Niu

doi:10.1007/s11427-013-4506-0

Abstract

A draft genome sequence of Streptomyces ansochromogenes 7100 was generated using 454 sequencing technology. In combination with local BLAST searches and gap filling techniques, a comprehensive antiSMASH-based method was adopted to assemble the secondary metabolite biosynthetic gene clusters in the draft genome of S. ansochromogenes. A total of at least 35 putative gene clusters were identified and assembled. Transcriptional analysis showed that 20 of the 35 gene clusters were expressed in either or all of the three different media tested, whereas the other 15 gene clusters were silent in all three different media. This study provides a comprehensive method to identify and assemble secondary metabolite biosynthetic gene clusters in draft genomes of Streptomyces, and will significantly promote functional studies of these secondary metabolite biosynthetic gene clusters.

Highlights

A draft genome sequence of Streptomyces ansochromogenes 7100 was generated using 454 sequencing technology
The sequences of the homologous gene clusters were used to perform local BLAST searches against the nucleotide database created from S. ansochromogenes draft genome sequence
Contigs related to an individual homologous gene cluster were picked out, and the order and orientation of these contigs were determined based on the synteny between the secondary metabolites (SMs) biosynthetic gene clusters in S. ansochromogenes and homologous clusters in other organisms

Summary

Introduction

A draft genome sequence of Streptomyces ansochromogenes 7100 was generated using 454 sequencing technology. In combination with local BLAST searches and gap filling techniques, a comprehensive antiSMASH-based method was adopted to assemble the secondary metabolite biosynthetic gene clusters in the draft genome of S. ansochromogenes. This study provides a comprehensive method to identify and assemble secondary metabolite biosynthetic gene clusters in draft genomes of Streptomyces, and will significantly promote functional studies of these secondary metabolite biosynthetic gene clusters. A large number of SM biosynthetic gene clusters were found to be distributed widely in other Streptomyces genomes and the majority of them are species specific [3]. The discovery of natural SM products via genomic-based approaches is largely dependent on the identification and annotation of SM biosynthetic gene clusters through in silico analysis.

Methods

Results

Conclusion