Work

scMicrobe PTA: near complete genomes from single bacterial cells

Year: 2024

Type: article

Abstract: Microbial genomes produced by single-cell amplification are largely incomplete. Here, we show that primary template 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 amplification approaches were usually <30% complete. PTA-derived genomes also included more associated viruses and biosynthetic gene clusters.

Source: ISME Communications

DOI: 10.1093/ismeco/ycae085

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

Institutions: Lawrence Berkeley National Laboratory, Joint Genome Institute, Stanford Medicine, Stanford University, Chan Zuckerberg Biohub San Francisco

Language: English

Topic: Genomics and Phylogenetic Studies

Subfield: Molecular Biology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: gold

Estimated APC paid: $2,625

Funders: U.S. Department of Energy, Joint Genome Institute, National Institutes of Health, Office of Science, National Cancer Institute

Awards: G1286236842, G3083819904, G382641700, G419881185, G42916606, G4501827968, G498139845, G7205239661, Creating a Catalog of Cancer Clonotype Drug Sensitivities with Single-CellGenome Sequencing, G834277795, G969889393

OpenAlex ID: W4400573500

FWCI: 2.172

Cites: 52

Cited by: 16

Related to: 10