Origins of bacterial diversity through horizontal genetic transfer and adaptation to new ecological niches

J Wiedenbeck, FM Cohan - FEMS microbiology reviews, 2011 - academic.oup.com
Horizontal genetic transfer (HGT) has played an important role in bacterial evolution at least
since the origins of the bacterial divisions, and HGT still facilitates the origins of bacterial …

Fungal secondary metabolism—from biochemistry to genomics

NP Keller, G Turner, JW Bennett - Nature reviews microbiology, 2005 - nature.com
Much of natural product chemistry concerns a group of compounds known as secondary
metabolites. These low-molecular-weight metabolites often have potent physiological …

Evolutionary origin of insect–Wolbachia nutritional mutualism

N Nikoh, T Hosokawa, M Moriyama… - Proceedings of the …, 2014 - National Acad Sciences
Obligate insect–bacterium nutritional mutualism is among the most sophisticated forms of
symbiosis, wherein the host and the symbiont are integrated into a coherent biological entity …

Phages and the evolution of bacterial pathogens: from genomic rearrangements to lysogenic conversion

H Brüssow, C Canchaya… - … and molecular biology …, 2004 - Am Soc Microbiol
Comparative genomics demonstrated that the chromosomes from bacteria and their viruses
(bacteriophages) are coevolving. This process is most evident for bacterial pathogens where …

GeneMark. hmm: new solutions for gene finding

AV Lukashin, M Borodovsky - Nucleic acids research, 1998 - academic.oup.com
The number of completely sequenced bacterial genomes has been growing fast. There are
computer methods available for finding genes but yet there is a need for more accurate …

RNA regulons: coordination of post-transcriptional events

JD Keene - Nature Reviews Genetics, 2007 - nature.com
Recent findings demonstrate that multiple mRNAs are co-regulated by one or more
sequence-specific RNA-binding proteins that orchestrate their splicing, export, stability …

Horizontal gene transfer in prokaryotes: quantification and classification

EV Koonin, KS Makarova… - Annual Reviews in …, 2001 - annualreviews.org
▪ Abstract Comparative analysis of bacterial, archaeal, and eukaryotic genomes indicates
that a significant fraction of the genes in the prokaryotic genomes have been subject to …

Thinking about bacterial populations as multicellular organisms

JA Shapiro - Annual review of microbiology, 1998 - annualreviews.org
▪ Abstract It has been a decade since multicellularity was proposed as a general bacterial
trait. Intercellular communication and multicellular coordination are now known to be …

The use of gene clusters to infer functional coupling

R Overbeek, M Fonstein, M D'souza… - Proceedings of the …, 1999 - National Acad Sciences
Previously, we presented evidence that it is possible to predict functional coupling between
genes based on conservation of gene clusters between genomes. With the rapid increase in …

The Phage Proteomic Tree: a genome-based taxonomy for phage

F Rohwer, R Edwards - Journal of bacteriology, 2002 - Am Soc Microbiol
There are∼ 1031 phage in the biosphere, making them the most abundant biological
entities on the planet. Despite their great numbers and ubiquitous presence, very little is …