Role of natural transformation in the evolution of small cryptic plasmids in Synechocystis sp. PCC 6803

Two defence systems eliminate plasmids from seventh pandemic Vibrio cholerae

(2022) Milena Jaskólska et al.   NATURE

An updated classification of cyanobacterial orders and families based on phylogenomic and polyphasic analysis

(2022) Otakar Strunecký et al.   JOURNAL OF PHYCOLOGY

Outcome of Different Sequencing and Assembly Approaches on the Detection of Plasmids and Localization of Antimicrobial Resistance Genes in Commensal Escherichia coli

(2021) Katharina Juraschek et al.   Microorganisms

Comparison of alternative integration sites in the chromosome and the native plasmids of the cyanobacterium Synechocystis sp. PCC 6803 in respect to expression efficiency and copy number

(2021) Csaba Nagy et al.   Microbial Cell Factories

The activation and limitation of the bacterial natural transformation system: The function in genome evolution and stability

(2021) Mi Huang et al.   MICROBIOLOGICAL RESEARCH

Frequency and diversity of small plasmids in mesophilic Aeromonas isolates from fish, water and sediment

(2021) Daniel Pérez-García et al.   PLASMID

Staphylococcal phages and pathogenicity islands drive plasmid evolution

(2021) Suzanne Humphrey et al.   Nature Communications

IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era

(2020) Bui Quang Minh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Transcriptome analysis reveals IsiA regulatory mechanisms underlying iron depletion and oxidative stress acclimation in Synechocystis sp. PCC 6803

(2020) Yarui Cheng et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Plasmid evolution

(2020) Tanita Wein et al.   CURRENT BIOLOGY

Plasmid characteristics modulate the propensity of gene exchange in bacterial vesicles

(2019) Frances Tran et al.   JOURNAL OF BACTERIOLOGY

Don't overlook the little guy: An evaluation of the frequency of small plasmids co-conjugating with larger carbapenemase gene containing plasmids

(2019) Katie Barry et al.   PLASMID

Mechanisms of DNA Uptake by Naturally Competent Bacteria

(2019) David Dubnau et al.   Annual Review of Genetics

Small Klebsiella pneumoniae Plasmids: Neglected Contributors to Antibiotic Resistance

(2019) Maria S. Ramirez et al.   Frontiers in Microbiology

Developing a Cas9-based tool to engineer native plasmids in Synechocystis sp. PCC 6803

(2018) Yi Xiao et al.   BIOTECHNOLOGY AND BIOENGINEERING

Stress-induced, highly efficient, donor cell-dependent cell-to-cell natural transformation in Bacillus subtilis

(2018) Xiaoming Zhang et al.   JOURNAL OF BACTERIOLOGY

Exploring native genetic elements as plug-in tools for synthetic biology in the cyanobacterium Synechocystis sp. PCC 6803

(2018) Deng Liu et al.   Microbial Cell Factories

Rhizobia: from saprophytes to endosymbionts

(2018) Philip Poole et al.   NATURE REVIEWS MICROBIOLOGY

Regulation Mechanism Mediated by Trans-Encoded sRNA Nc117 in Short Chain Alcohols Tolerance in Synechocystis sp. PCC 6803

(2018) Yanqi Bi et al.   Frontiers in Microbiology

RecA Regulation by RecU and DprA During Bacillus subtilis Natural Plasmid Transformation

(2018) Ester Serrano et al.   Frontiers in Microbiology

Construction of a Shuttle Vector Using an Endogenous Plasmid From the Cyanobacterium Synechocystis sp. PCC6803

(2018) Haojie Jin et al.   Frontiers in Microbiology

Salmon provides fast and bias-aware quantification of transcript expression

(2017) Rob Patro et al.   NATURE METHODS

Phenotypic characterization of Synechocystis sp. PCC 6803 substrains reveals differences in sensitivity to abiotic stress

(2017) Tomáš Zavřel et al.   PLoS One

MultiQC: summarize analysis results for multiple tools and samples in a single report

(2016) Philip Ewels et al.   BIOINFORMATICS

Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees

(2016) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

Utilising the native plasmid, pCA2.4, from the cyanobacterium Synechocystis sp. strain PCC6803 as a cloning site for enhanced product production

(2015) Patricia Armshaw et al.   Biotechnology for Biofuels

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Bacterial transformation: distribution, shared mechanisms and divergent control

(2014) Calum Johnston et al.   NATURE REVIEWS MICROBIOLOGY

RNA-Seq Analysis Provides Insights for Understanding Photoautotrophic Polyhydroxyalkanoate Production in Recombinant Synechocystis Sp.

(2014) Nyok-Sean Lau et al.   PLoS One

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

BLAST: a more efficient report with usability improvements

(2013) Grzegorz M. Boratyn et al.   NUCLEIC ACIDS RESEARCH

Small Plasmids HarboringqnrB19: a Model for Plasmid Evolution Mediated by Site-Specific Recombination atoriTand Xer Sites

(2012) Tung Tran et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Upregulation of Plasmid Genes during Stationary Phase in Synechocystis sp. Strain PCC 6803, a Cyanobacterium

(2012) Bertram M. Berla et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Microevolution in Cyanobacteria: Re-sequencing a Motile Substrain of Synechocystis sp. PCC 6803

(2012) D. Trautmann et al.   DNA RESEARCH

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Selection of Suitable Reference Genes for RT-qPCR Analyses in Cyanobacteria

(2012) Filipe Pinto et al.   PLoS One

Identification of Substrain-Specific Mutations by Massively Parallel Whole-Genome Resequencing of Synechocystis sp. PCC 6803

(2011) Y. Kanesaki et al.   DNA RESEARCH

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

The Sequence Read Archive

(2010) R. Leinonen et al.   NUCLEIC ACIDS RESEARCH

Introducing the bacterial ‘chromid’: not a chromosome, not a plasmid

(2010) Peter W. Harrison et al.   TRENDS IN MICROBIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS