High-quality bacterial genomes of a partial-nitritation/anammox system by an iterative hybrid assembly method
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RESEARCH
Open Access
High-quality bacterial genomes of a partialnitritation/anammox system by an iterative hybrid assembly method Lei Liu1,2,3, Yulin Wang1, You Che1, Yiqiang Chen1, Yu Xia1,2,3, Ruibang Luo4, Suk Hang Cheng5, Chunmiao Zheng2,3* and Tong Zhang1,3*
Abstract Background: Genome-centric approaches are widely used to investigate microbial compositions, dynamics, ecology, and interactions within various environmental systems. Hundreds or even thousands of genomes could be retrieved in a single study contributed by the cost-effective short-read sequencing and developed assembly/ binning pipelines. However, conventional binning methods usually yield highly fragmented draft genomes that limit our ability to comprehensively understand these microbial communities. Thus, to leverage advantage of both the long and short reads to retrieve more complete genomes from environmental samples is a must-do task to move this direction forward. Results: Here, we used an iterative hybrid assembly (IHA) approach to reconstruct 49 metagenome-assembled genomes (MAGs), including 27 high-quality (HQ) and high-contiguity (HC) genomes with contig number ≤ 5, eight of which were circular finished genomes from a partial-nitritation anammox (PNA) reactor. These 49 recovered MAGs (43 MAGs encoding full-length rRNA, average N50 of 2.2 Mbp), represented the majority (92.3%) of the bacterial community. Moreover, the workflow retrieved HQ and HC MAGs even with an extremely low coverage (relative abundance < 0.1%). Among them, 34 MAGs could not be assigned to the genus level, indicating the novelty of the genomes retrieved using the IHA method proposed in this study. Comparative analysis of HQ MAG pairs reconstructed using two methods, i.e., hybrid and short reads only, revealed that identical genes in the MAG pairs represented 87.5% and 95.5% of the total gene inventory of hybrid and short reads only assembled MAGs, respectively. In addition, the first finished anammox genome of the genus Ca. Brocadia reconstructed revealed that there were two identical hydrazine synthase (hzs) genes, providing the exact gene copy number of this crucial phylomarker of anammox at the genome level. (Continued on next page)
* Correspondence: [email protected]; [email protected] 1 Environmental Microbiome Engineering and Biotechnology Laboratory, The University of Hong Kong, Hong Kong SAR, China 2 State Environmental Protection Key Laboratory of Integrated Surface Water-Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, China Full list of author information is available at the end of the article © The Author(s). 2020 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made
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