Sequencing, assembly and annotation of an anaerobic ammonium oxidizing (anammox) enrichment culture dominated by candidatus Brocadia fulgida.

Candidatus Brocadia fulgida is a bacterium capable of anaerobic oxidation of ammonium. We have sequenced an enrichment culture obtained in a membrane bioreactor (Van der Star, 2008) consisting for over 90% of candidatus Brocadia fulgida. Sequencing was done using an IonTorrent PGM with a 200bp protocol (life technologies). The 5250695 reads were trimmed and assembled using the CLC genomics workbench (CLCbio) and 411 contigs (>500bp) were extracted based on coverage. These 411 contigs were annotated using prokka v1.7.2 (VBC) and curated manually --- van der Star, Wouter RL, et al. "The membrane bioreactor: a novel tool to grow anammox bacteria as free cells." Biotechnology and bioengineering 101.2 (2008): 286-294. --- Prokka: Prokaryotic Genome Annotation System - http://vicbioinformatics.com/

闪式念珠菌属富氏菌（Candidatus Brocadia fulgida）是一种具备厌氧氨氧化（anaerobic ammonium oxidation, anammox）能力的细菌。本研究对一株分离自膜生物反应器（membrane bioreactor，Van der Star, 2008）的富集培养物完成测序，该培养物中闪式念珠菌属富氏菌的占比超过90%。测序采用IonTorrent PGM平台，搭配200bp测序方案（Life Technologies）。本次测序共获得5250695条原始测序读段（reads），经CLC基因组工作站（CLC genomics workbench, CLCbio）完成序列修剪与组装后，基于覆盖度提取得到411条长度大于500bp的重叠群（contigs）。随后利用Prokka v1.7.2（VBC）对这411条重叠群进行基因注释，并开展人工手动审核校正。—— 参考文献：Van der Star Wouter RL, 等. 膜生物反应器：一种用于游离态厌氧氨氧化菌培养的新型工具[J]. 生物技术与生物工程, 2008, 101(2): 286-294. —— Prokka：原核生物基因组注释系统（Prokaryotic Genome Annotation System），详见 http://vicbioinformatics.com/