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Codon Usage Heterogeneity in the Multipartite Prokaryote Genome. Selection-Based[...]
DISCUSSION
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
Aufsatz in einer Zeitschrift
Codon Usage Heterogeneity in the Multipartite Prokaryote Genome. Selection-Based Coding Bias Associated with Gene Location, Expression Level, and Ancestry
Entstehung
2019
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