López, J. L.; Lozano, M. J.; Lagares, A.; Fabre, M. L.; Draghi, W. O.; Del Papa, M. F.; Pistorio, M.; Becker, A.; Wibberg, Daniel; Schlüter, Andreas; Pühler, Alfred; Blom, J.; Goesmann, A.; Lagares, A.: Codon Usage Heterogeneity in the Multipartite Prokaryote Genome. Selection-Based Coding Bias Associated with Gene Location, Expression Level, and Ance [...]. In: mBio. Jg.10 H. 3. 2019
Inhalt
- RESULTS
- Deep sequencing of an S. meliloti cryptic plasmidome from a previously characterized collection of strains.
- COG class abundances and compositional variations in the S. meliloti plasmidome compared to those present in the pSyms and in the chromosome.
- Evidence for gene transfer between the S. meliloti accessory plasmidome and the other rhizobial replicons: the GC content and codon usage in different gene sets.
- A progressive analysis of codon usage in different and sequential core fractions throughout rhizobial phylogeny.
- Codon usage adaptation of core genes, tRNA abundance, and protein expression levels.
- DISCUSSION
- MATERIALS AND METHODS
- Sinorhizobium meliloti isolates used in this work.
- Plasmid purification and sequencing.
- Identification of sequence reads of plasmid origin and assembly of continuous overlapping DNA sequences (contigs).
- Multivariate analysis of the composition of ortholog clusters in the S. meliloti replicons.
- Identification of chromosome and megaplasmid core genes and singletons.
- Codon usage analysis.
- Phylogenetic analysis.
- S. meliloti modal tRNA adaptation index (m-tAI).
- Quantitative composition of the S. meliloti proteome.
- Data accessibility.
- SUPPLEMENTAL MATERIAL
- ACKNOWLEDGMENTS
- REFERENCES