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September 12, 2013

Fifteen years of microbial genomics: meeting the challenges and fulfilling the dream

As we approach the completed sequencing of 1,000 microbial genomes, the field of microbial genomics is poised at a crossroads. The future holds great promise for far-reaching advancements in microbiology as well as in diverse, related sciences. But realizing that potential will require meeting the challenges that have accompanied the rapid development of the underlying… [Read More]

September 12, 2013

Complete genome sequence of Anaerococcus prevotii type strain (PC1)

Anaerococcus prevotii (Foubert and Douglas 1948) Ezaki et al. 2001 is the type species of the genus, and is of phylogenetic interest because of its arguable assignment to the provisionally arranged family ‘Peptostreptococcaceae’. A. prevotii is an obligate anaerobic coccus, usually arranged in clumps or tetrads. The strain, whose genome is described here, was originally… [Read More]

September 12, 2013

Complete genome sequence of Actinosynnema mirum type strain (101(T))

Actinosynnema mirum Hasegawa et al. 1978 is the type species of the genus, and is of phylogenetic interest because of its central phylogenetic location in the Actino-synnemataceae, a rapidly growing family within the actinobacterial suborder Pseudonocardineae. A. mirum is characterized by its motile spores borne on synnemata and as a producer of nocardicin antibiotics. It… [Read More]

September 12, 2013

Complete genome sequence of Beutenbergia cavernae type strain (HKI 0122)

Beutenbergia cavernae (Groth et al. 1999) is the type species of the genus and is of phylogenetic interest because of its isolated location in the actinobacterial suborder Micrococcineae. B. cavernae HKI 0122(T) is a Gram-positive, non-motile, non-spore-forming bacterium isolated from a cave in Guangxi (China). B. cavernae grows best under aerobic conditions and shows a… [Read More]

September 12, 2013

Experimental factors affecting PCR-based estimates of microbial species richness and evenness

Pyrosequencing of 16S rRNA gene amplicons for microbial community profiling can, for equivalent costs, yield more than two orders of magnitude more sensitivity than traditional PCR cloning and Sanger sequencing. With this increased sensitivity and the ability to analyze multiple samples in parallel, it has become possible to evaluate several technical aspects of PCR-based community… [Read More]

September 12, 2013

Meeting Report from the Genomic Standards Consortium (GSC) Workshops 6 and 7

This report summarizes the proceedings of the 6th and 7th workshops of the Genomic Standards Consortium (GSC), held back-to-back in 2008. GSC 6 focused on furthering the activities of GSC working groups, GSC 7 focused on outreach to the wider community. GSC 6 was held October 10-14, 2008 at the European Bioinformatics Institute, Cambridge, United… [Read More]

September 12, 2013

Whole-genome-based phylogeny and divergence of the genus Brucella

Brucellae are worldwide bacterial pathogens of livestock and wildlife, but phylogenetic reconstructions have been challenging due to limited genetic diversity. We assessed the taxonomic and evolutionary relationships of five Brucella species-Brucella abortus, B. melitensis, B. suis, B. canis, and B. ovis-using whole-genome comparisons. We developed a phylogeny using single nucleotide polymorphisms (SNPs) from 13 genomes… [Read More]

September 12, 2013

Analysis of saccharification in Brachypodium distachyon stems under mild conditions of hydrolysis

BACKGROUND: Brachypodium distachyon constitutes an excellent model species for grasses. It is a small, easily propagated, temperate grass with a rapid life cycle and a small genome. It is a self-fertile plant that can be transformed with high efficiency using Agrobacteria and callus derived from immature embryos. In addition, considerable genetic and genomic resources are… [Read More]

September 12, 2013

A recommendation for naming transcription factor proteins in the grasses

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September 12, 2013

Early origins and evolution of microRNAs and Piwi-interacting RNAs in animals

In bilaterian animals, such as humans, flies and worms, hundreds of microRNAs (miRNAs), some conserved throughout bilaterian evolution, collectively regulate a substantial fraction of the transcriptome. In addition to miRNAs, other bilaterian small RNAs, known as Piwi-interacting RNAs (piRNAs), protect the genome from transposons. Here we identify small RNAs from animal phyla that diverged before… [Read More]
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