Back to Search
Start Over
The complete replicons of 16 Ensifer meliloti strains offer insights into intra- and inter-replicon gene transfer, transposon-associated loci, and repeat elements
- Source :
- Microbial Genomics
- Publication Year :
- 2018
-
Abstract
- Ensifer meliloti (formerly Rhizobium meliloti and Sinorhizobium meliloti) is a model bacterium for understanding legume–rhizobial symbioses. The tripartite genome of E. meliloti consists of a chromosome, pSymA and pSymB, and in some instances strain-specific accessory plasmids. The majority of previous sequencing studies have relied on the use of assemblies generated from short read sequencing, which leads to gaps and assembly errors. Here we used PacBio-based, long-read assemblies and were able to assemble, de novo, complete circular replicons. In this study, we sequenced, de novo-assembled and analysed 10 E. meliloti strains. Sequence comparisons were also done with data from six previously published genomes. We identified genome differences between the replicons, including mol% G+C and gene content, nucleotide repeats, and transposon-associated loci. Additionally, genomic rearrangements both within and between replicons were identified, providing insight into evolutionary processes at the structural level. There were few cases of inter-replicon gene transfer of core genes between the main replicons. Accessory plasmids were more similar to pSymA than to either pSymB or the chromosome, with respect to gene content, transposon content and G+C content. In our population, the accessory plasmids appeared to share an open genome with pSymA, which contains many nodulation- and nitrogen fixation-related genes. This may explain previous observations that horizontal gene transfer has a greater effect on the content of pSymA than pSymB, or the chromosome, and why some rhizobia show unstable nodulation phenotypes on legume hosts.
- Subjects :
- 0301 basic medicine
Transposable element
Genome evolution
Gene Transfer, Horizontal
030106 microbiology
Population
comparative genomics
Biology
genome evolution
rhizobia
Genome
Plant Root Nodulation
repeat and IS elements
accessory plasmids
Evolution, Molecular
03 medical and health sciences
Bacterial Proteins
Nitrogen Fixation
Animals
education
Gene
Genetics
Comparative genomics
education.field_of_study
Sinorhizobium meliloti
Base Composition
structural variation
food and beverages
Fabaceae
General Medicine
Genomics
Sequence Analysis, DNA
Systems Microbiology: Large-scale Comparative Genomics
biochemical phenomena, metabolism, and nutrition
Chromosomes, Bacterial
biology.organism_classification
030104 developmental biology
Genetic Loci
Horizontal gene transfer
DNA Transposable Elements
bacteria
Replicon
Genome, Bacterial
Plasmids
Rhizobium
Research Article
Subjects
Details
- ISSN :
- 20575858
- Volume :
- 4
- Issue :
- 5
- Database :
- OpenAIRE
- Journal :
- Microbial genomics
- Accession number :
- edsair.doi.dedup.....757d4f06a4061e5607f46ec52f86dd12