scMicrobe PTA: near complete genomes from single bacterial cells

Bowers, Robert M.; Gonzalez-Pena, Veronica; Wardhani, Kartika; Goudeau, Danielle; Blow, Matthew James; Udwary, Daniel; Klein, David; Vill, Albert C.; Brito, Ilana L.; Woyke, Tanja; Malmstrom, Rex R.; Gawad, Charles

doi:10.1093/ismeco/ycae085

DOE OSTI · 2315613

scMicrobe PTA: near complete genomes from single bacterial cells

Bowers, Robert M.·Gonzalez-Pena, Veronica·Wardhani, Kartika·Goudeau, Danielle·Blow, Matthew James·Udwary, Daniel·Klein, David·Vill, Albert C.·Brito, Ilana L.·Woyke, Tanja·Malmstrom, Rex R.·Gawad, Charles

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Abstract

Microbial genomes produced by standard single-cell amplification methods are largely incomplete. Here, we show that primary template-directed amplification (PTA), a novel single-cell amplification technique, generated nearly complete genomes from three bacterial isolate species. Furthermore, taxonomically diverse genomes recovered from aquatic and soil microbiomes using PTA had a median completeness of 81%, whereas genomes from standard multiple displacement amplification-based approaches were usually <30% complete. PTA-derived genomes also included more associated viruses and biosynthetic gene clusters.

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59 BASIC BIOLOGICAL SCIENCES biological Science biosynthetic gene clusters microbial ecology microbiome microbiome sequencing mobile genetic elements multiple displacement amplification primary template-directed amplification single cell genomics unculturable bacteria whole genome amplification

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Bowers, Robert M., Gonzalez-Pena, Veronica, Wardhani, Kartika, Goudeau, Danielle, Blow, Matthew James, Udwary, Daniel, Klein, David, Vill, Albert C., Brito, Ilana L., Woyke, Tanja, Malmstrom, Rex R., Gawad, Charles. 2024-07-12. scMicrobe PTA: near complete genomes from single bacterial cells. https://doi.org/10.1093/ismeco%2Fycae085

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