Draft genome sequences of Arabidopsis thaliana-associated micro-organisms from Reijerscamp soil, the Netherlands

Methodological summary and relevant references

Compressed tar archive containing 447 draft bacterial genomes and their annotations used in several studies including Fourie et al. (2024; in review) and Selten et al. (2024; in prep). Genome sequences are obtained by Illumina-only sequencing of microbial cultures. Illumina reads were demultiplexed and cleaned with cutadapt (version 2.8) (Martin, 2011) and assembled into genomes using A5 (A5-miseq version 20160825) (Coil et al., 2014). Genome contamination and heterogeneity was checked with CheckM (version 1.1.3) (Parks et al., 2015) and any genomes with multiple single copy gene occurrences were subjected to MaxBin (version 2.2.7) (Wu et al., 2014) to separate the genomes from contaminated bacterial cultures. Any non-bacterial contigs in the genome assemblies were removed using MMSeqs2 (version 13.45111) (Steineigger & Schöding, 2017). Open reading frames were found and annotated by PROKKA (version 1.14.6) (Seemann, 2014) and EggNOG (version 2.1.4-2) (Cantalapiedra et al., 2021) respectively. Microbial cultures were derived from Arabidopsis thaliana roots grown in Reijerscamp soil, described in Stringlis et al., 2018 https://doi.org/10.1073/pnas.1722335115.

The uploaded files are

1. Genome assemblies
2. Prokka gene predictions in GFF3 format
3. Predicted transcripts from genes in (2)
4. Predicted proteins from genes in (2), and
5. EggNOG annotations for the proteins in (4)

Genomes and annotations pending upload om NCBI GenBank (April 2024)