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Title: Moleculo long-read sequencing facilitates assembly and resolves functionally active genomic bins from complex soil metagenomes

Soil metagenomics has been touted as the "grand challenge" for metagenomes, as the high microbial diversity, sample complexity, and spatial heterogeneity of soils makes them unamenable to current sequencing and assembly platforms. Here we aimed to improve soil metagenomic sequence assembly by applying a synthetic long read sequencing technology (i.e. Moleculo) from three locations within Konza native prairie station in Kansas. In total, we obtained 520 GB of raw sequence data; 239 GB of short read data from the Joint Genome Institute (JGI), an additional 97 GB from Moleculo sequencing, plus 184 GB of rapid mode sequence data. The Moleculo data alone yielded over 5,600 reads greater than 10 kbp in length, mapping over 95% of the total sequence data. Hybrid assembly of all data resulted in more than 10,000 contigs over 10 kbp in length. The Moleculo sub-assemblies captured much of the functional potential of the soil community, in that 92% of the functional enzyme commission numbers (EC) predicted from the metagenome were also detected in metatranscriptome data. The Moleculo sub-assembly enabled binning of more than 100 novel soil microbial genomic bins. Candidatus Pseudomonas janssonensis strain KNPRW21, was the first genome obtained from a native soil metagenome by directmore » binning. By mapping RNA-Seq (i.e. metatranscriptomic) sequence reads back to the bins, we found that several low abundance Acidobacteria bins were highly transcriptionally active, whereas the highly abundant Verruomicrobia bins were not. Using Moleculo long reads alone or combined with conventional short read metagenomic data is therefore a useful tool for resolving complex soil microbial communities.« less
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Journal Article
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Journal Name: mSystems, 1(3)
Research Org:
Pacific Northwest National Laboratory (PNNL), Richland, WA (US)
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Country of Publication:
United States
Moleculo; metagenomic assembly; metagenomic binning; soil metagenomics; De Novo assembly