scholarly journals Impact of Small Repeat Sequences on Bacterial Genome Evolution

2011 ◽  
Vol 3 ◽  
pp. 959-973 ◽  
Author(s):  
Nicholas Delihas
Keyword(s):  
Genome Evolution ◽  
Bacterial Genome ◽  
Repeat Sequences

scholarly journals An algebraic view of bacterial genome evolution

2013 ◽  
Vol 69 (6-7) ◽  
pp. 1693-1718 ◽  
Author(s):  
Andrew R. Francis
Keyword(s):  
Genome Evolution ◽  
Bacterial Genome

scholarly journals Bacterial genome evolution within a clonal population: fromin vitroinvestigations toin vivoobservations

2013 ◽  
Vol 8 (5) ◽  
pp. 661-674 ◽  
Author(s):  
Marie Beaume ◽  
Nadezda Monina ◽  
Jacques Schrenzel ◽  
Patrice François
Keyword(s):  
Genome Evolution ◽  
Bacterial Genome ◽  
Clonal Population

scholarly journals Replicon-Dependent Bacterial Genome Evolution: The Case of Sinorhizobium meliloti

2013 ◽  
Vol 5 (3) ◽  
pp. 542-558 ◽  
Author(s):  
Marco Galardini ◽  
Francesco Pini ◽  
Marco Bazzicalupo ◽  
Emanuele G. Biondi ◽  
Alessio Mengoni
Keyword(s):  
Genome Evolution ◽  
Sinorhizobium Meliloti ◽  
Bacterial Genome

scholarly journals Accurate and Complete Genomes from Metagenomes

2019 ◽  
Author(s):  
Lin-Xing Chen ◽  
Karthik Anantharaman ◽  
Alon Shaiber ◽  
A. Murat Eren ◽  
Jillian F. Banfield
Keyword(s):  
Bacterial Genome ◽  
Biological Information ◽  
Microbial Life ◽  
Repeat Sequences ◽  
Bacterial Genome Sequence ◽  
Gc Skew ◽  
Local Assembly ◽  
Bioinformatic Approaches ◽  
Reference Genomes ◽  
Very High

AbstractGenomes are an integral component of the biological information about an organism and, logically, the more complete the genome, the more informative it is. Historically, bacterial and archaeal genomes were reconstructed from pure (monoclonal) cultures and the first reported sequences were manually curated to completion. However, the bottleneck imposed by the requirement for isolates precluded genomic insights for the vast majority of microbial life. Shotgun sequencing of microbial communities, referred to initially as community genomics and subsequently as genome-resolved metagenomics, can circumvent this limitation by obtaining metagenome-assembled genomes (MAGs), but gaps, local assembly errors, chimeras and contamination by fragments from other genomes limit the value of these genomes. Here, we discuss genome curation to improve and in some cases achieve complete (circularized, no gaps) MAGs (CMAGs). To date, few CMAGs have been generated, although notably some are from very complex systems such as soil and sediment. Through analysis of ~7000 published complete bacterial isolate genomes, we verify the value of cumulative GC skew in combination with other metrics to establish bacterial genome sequence accuracy. Interestingly, analysis of cumulative GC skew identified potential mis-assemblies in some reference genomes of isolated bacteria and the repeat sequences that likely gave rise to them. We discuss methods that could be implemented in bioinformatic approaches for curation to ensure that metabolic and evolutionary analyses can be based on very high-quality genomes.

scholarly journals Polypolish: short-read polishing of long-read bacterial genome assemblies

2021 ◽  
Author(s):  
Ryan R Wick ◽  
Kathryn E Holt
Keyword(s):  
Bacterial Genome ◽  
Short Read ◽  
Read Alignment ◽  
Short Reads ◽  
Repeat Sequences ◽  
Short Read Alignment ◽  
Long Read ◽  
Genome Assemblies ◽  
Residual Errors

Long-read-only bacterial genome assemblies usually contain residual errors, most commonly homopolymer-length errors. Short-read polishing tools can use short reads to fix these errors, but most rely on short-read alignment which is unreliable in repeat regions. Errors in such regions are therefore challenging to fix and often remain after short-read polishing. Here we introduce Polypolish, a new short-read polisher which uses all-per-read alignments to repair errors in repeat sequences that other polishers cannot. In benchmarking tests using both simulated and real reads, we find that Polypolish performs well, and the best results are achieved by using Polypolish in combination with other short-read polishers.

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