Linear chromosomes in bacteria: no straight edge advantage?

Galperin, Michael Y.

doi:10.1111/j.1462-2920.2007.01328.x

Cited by 5 publications

(3 citation statements)

References 42 publications

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“…The genome is either circular or there is solid evidence that it is linear. While rare, linear bacterial genomes exist [ 31 ]. To represent a circular genome, a contig must have an exact overlap of the ends that is longer than any repeat in the genome.…”

Section: Resultsmentioning

confidence: 99%

A method for achieving complete microbial genomes and improving bins from metagenomics data

2021

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Metagenomics facilitates the study of the genetic information from uncultured microbes and complex microbial communities. Assembling complete genomes from metagenomics data is difficult because most samples have high organismal complexity and strain diversity. Some studies have attempted to extract complete bacterial, archaeal, and viral genomes and often focus on species with circular genomes so they can help confirm completeness with circularity. However, less than 100 circularized bacterial and archaeal genomes have been assembled and published from metagenomics data despite the thousands of datasets that are available. Circularized genomes are important for (1) building a reference collection as scaffolds for future assemblies, (2) providing complete gene content of a genome, (3) confirming little or no contamination of a genome, (4) studying the genomic context and synteny of genes, and (5) linking protein coding genes to ribosomal RNA genes to aid metabolic inference in 16S rRNA gene sequencing studies. We developed a semi-automated method called Jorg to help circularize small bacterial, archaeal, and viral genomes using iterative assembly, binning, and read mapping. In addition, this method exposes potential misassemblies from k-mer based assemblies. We chose species of the Candidate Phyla Radiation (CPR) to focus our initial efforts because they have small genomes and are only known to have one ribosomal RNA operon. In addition to 34 circular CPR genomes, we present one circular Margulisbacteria genome, one circular Chloroflexi genome, and two circular megaphage genomes from 19 public and published datasets. We demonstrate findings that would likely be difficult without circularizing genomes, including that ribosomal genes are likely not operonic in the majority of CPR, and that some CPR harbor diverged forms of RNase P RNA. Code and a tutorial for this method is available at https://github.com/lmlui/Jorg and is available on the DOE Systems Biology KnowledgeBase as a beta app.

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Section: Resultsmentioning

confidence: 99%

A method for achieving complete microbial genomes and improving bins from metagenomics data

2021

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“…The genome is either circular or there is solid evidence that it is linear. While rare, linear bacterial genomes exist [25].…”

Section: Circularization Methodsmentioning

confidence: 99%

A method for achieving complete microbial genomes and improving bins from metagenomics data

Lui

Nielsen

Arkin

2020

Preprint

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Metagenomics facilitates the study of the genetic information from uncultured microbes and complex microbial communities. Assembling complete microbial genomes (i.e., circular with no misassemblies) from metagenomics data is difficult because most samples have high organismal complexity and strain diversity. Only 63 circularized bacterial and archaeal genomes have been assembled from metagenomics data despite the thousands of datasets that are available. Circularized genomes are important for (1) building a reference collection as scaffolds for future assemblies, (2) providing complete gene content of a genome, (3) confirming little or no contamination of a genome, (4) studying the genomic context and synteny of genes, and (5) linking protein coding genes to ribosomal RNA genes to aid metabolic inference in 16S rRNA gene sequencing studies. We developed a method to achieve circularized genomes using iterative assembly, binning, and read mapping. In addition, this method exposes potential misassemblies from k-mer based assemblies. We chose species of the Candidate Phyla Radiation (CPR) to focus our initial efforts because they have small genomes and are only known to have one copy of ribosomal RNA genes. We present 34 circular CPR genomes, one circular Margulisbacteria genome, and two circular megaphage genomes from 19 public and published datasets. We demonstrate findings that would likely be difficult without circularizing genomes, including that ribosomal genes are likely not operonic in the majority of CPR, and that some CPR harbor diverged forms of RNase P RNA.

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“…In other words, Ori and Ter were not inferred for the species presenting additional local maxima or minima. Species with known linear chromosomes or multiple chromosomes were identified from 57 and excluded from the analyses of recombination symmetry. Using the 102 species with a single circular chromosome and clearly defined Ori and Ter locations, the recombination rate of each core gene was plotted relative to the absolute distance from Ori and Ter to determine whether recombination rate varied on both replichores of each species.…”

Section: Identification Of Ori and Termentioning

confidence: 99%

Homologous Recombination Shapes the Architecture and Evolution of Bacterial Genomes

Torrance,

Diop,

Bobay

2024

Preprint

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Homologous recombination is a key evolutionary force that varies considerably across bacterial species. However, how the landscape of homologous recombination varies across genes and within individual genomes has only been studied in a few species. Here, we used Approximate Bayesian Computation to estimate the recombination rate along the genomes of 145 bacterial species. Our results show that homologous recombination varies greatly along bacterial genomes and shapes many aspects of genome architecture and evolution. The genomic landscape of recombination presents several key signatures: rates are highest near the origin of replication in most species, patterns of recombination generally appear symmetrical in both replichores (i.e.replicational halves of circular chromosomes) and most species have genomic hotpots of recombination. Furthermore, many closely related species share conserved landscapes of recombination across orthologs indicating that recombination landscapes are conserved over significant evolutionary distances. We show evidence that recombination drives the evolution of GC-content through increasing the effectiveness of selection and not through biased gene conversion, thereby contributing to an ongoing debate. Finally, we demonstrate that the rate of recombination varies across gene function and that many hotspots of recombination are associated with adaptive and mobile regions often encoding genes involved in pathogenicity.

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Linear chromosomes in bacteria: no straight edge advantage?

Cited by 5 publications

References 42 publications

A method for achieving complete microbial genomes and improving bins from metagenomics data

A method for achieving complete microbial genomes and improving bins from metagenomics data

A method for achieving complete microbial genomes and improving bins from metagenomics data

Homologous Recombination Shapes the Architecture and Evolution of Bacterial Genomes

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