Abstract
The 16S rRNA gene (16S) is an accepted marker of bacterial taxonomic diversity, even though differences in copy number obscure the relationship between amplicon and organismal abundances. Ancestral state reconstruction methods can predict 16S copy numbers through comparisons with closely related reference genomes; however, the database of closed genomes is limited. Here, we extend the reference database of 16S copy numbers to de novo assembled draft genomes by developing 16Stimator, a method to estimate 16S copy numbers when these repetitive regions collapse during assembly. Using a read depth approach, we estimate 16S copy numbers for 12 endophytic isolates from Arabidopsis thaliana and confirm estimates by qPCR. We further apply this approach to draft genomes deposited in NCBI and demonstrate accurate copy number estimation regardless of sequencing platform, with an overall median deviation of 14%. The expanded database of isolates with 16S copy number estimates increases the power of phylogenetic correction methods for determining organismal abundances from 16S amplicon surveys.
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Acknowledgements
We thank John Wilmes and Stefano Allesina for helpful discussions, and the Center for Research Informatics at the University of Chicago for computational resources. MP was supported by a Department of Education GAANN fellowship and a NIH Genetics & Regulation training grant. This work was supported by grant DOE DE-AC02-06CH11357 to JAG and grants NSF MCB0603515 and James S. McDonnell Foundation 220020237 to JB.
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Perisin, M., Vetter, M., Gilbert, J. et al. 16Stimator: statistical estimation of ribosomal gene copy numbers from draft genome assemblies. ISME J 10, 1020–1024 (2016). https://doi.org/10.1038/ismej.2015.161
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DOI: https://doi.org/10.1038/ismej.2015.161
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