Wednesday, February 4, 2015

Microbial Genomics: the State of the Art in 2015

Current Opinion in Microbiology recently published a special issue in genomics. In an excellent editorial overview, “Genomics: The era of genomically-enabled microbiology”, Neil Hall and Jay Hinton give an overview of the state of the field in microbial genomics, summarize recent contributions, and give a great synopsis of each of the reviews in this issue. Hall and Hinton’s editorial overview goes into a little more depth, but here’s a rundown of the reviews in this special issue. There’s a lot of good stuff here!
Quantitative bacterial transcriptomics with RNA-seq (James Creecy and Tyrrell Conway) discusses RNA-seq in bacteria and how transcriptome analysis adds a wealth of annotation information to the genome.
One chromosome, one contig: complete microbial genomes from long-read sequencing and assembly (Sergey Koren and Adam Phillippy) describes newer long-read sequencing technologies and their characteristics, discusses how microbial genomes can be easily and automatically finished using these methods for under $1,000, and discusses challenges for microbial and metagenome assembly.
Using comparative genomics to drive new discoveries in microbiology (Daniel Haft) describes progress using comparative genomics to make new discoveries, and takes the reader on a “bioinformatics journey” to describe a code-breaking exercise in comparative genomics that starts with weak hypotheses and uses genomics to fill in the biological picture.
Taking the pseudo out of pseudogenes (Ian Goodhead and Alistair Darby) reviews how pseudogenes are surprisingly prevalent, and discusses how problems with genome annotation can be addressed by combining multiple “omics” data.
Ten years of pan-genome analyses (George Vernikos et al.) describes how pan-genome analyses provide a framework for predicting and modling genomic diversity, where the “core genome” of many bacterial species constitutes only the minority of genes.
Lateral gene transfers and the origins of the eukaryote proteome: a view from microbial parasites (Robert Hirt et al.) reviews the dynamic nature of lateral gene transfer, its role in microbial diversity, how it contributes to eukaryotic genomes, and how once again integrating different “omics” methodologies is needed to recognize the extent to which LGT affects eukaryotes.
The application of genomics to tracing bacterial pathogen transmission (Nicholas Croucher and Xavier Didelot) reviews how bacterial whole-genome sequencing gives you the ultimate resolution for investigating direct pathogen transmission, distinguishing transmission chains, and defining outbreaks. If you haven’t kept up with this quickly growing body of literature, this review is a great place to start catching up.
The impact of genomics on population genetics of parasitic diseases (Daniel Hupalo et al.) describes the influence of genomics on parasite population genetics and how burgeoning genomic data has enabled new types of investigations, and focuses on Plasmodium population genomics as a foundation for studies of neglected parasites.

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