We report the complete genome sequence of Zymomonas mobilis ZM4 (ATCC31821), an ethanologenic microorganism of interest for the production of fuel ethanol. The genome consists of 2,056,416 base pairs forming a circular chromosome with 1,998 open reading frames (ORFs) and three ribosomal RNA transcription units. The genome lacks recognizable genes for 6-phosphofructokinase, an essential enzyme in the Embden-Meyerhof-Parnas pathway, and for two enzymes in the tricarboxylic acid cycle, the 2-oxoglutarate dehydrogenase complex and malate dehydrogenase, so glucose can be metabolized only by the Entner-Doudoroff pathway. Whole genome microarrays were used for genomic comparisons with the Z. mobilis type strain ZM1 (ATCC10988) revealing that 54 ORFs predicted to encode for transport and secretory proteins, transcriptional regulators and oxidoreductase in the ZM4 strain were absent from ZM1. Most of these ORFs were also found to be actively transcribed in association with ethanol production by ZM4.Growing environmental concerns over the use and depletion of nonrenewable energy resources, together with the recent price increases and instabilities in the international oil markets have stimulated an increasing interest in the use of fermentation processes for the large-scale production of alternative fuels such as ethanol. As such, ethanol-producing microorganisms, such as the Gram-negative bacterium Z. mobilis, have potential for the production of fuel ethanol.Z. mobilis, which is used in the tropics to produce pulque and alcoholic palm wines, uses the Entner-Doudoroff (ED) pathway to metabolize glucose, which results in only 1 mole of ATP being produced per mole of glucose 1 . The potential advantages of using Z. mobilis for ethanol production include: (i) its high and specific rates of sugar uptake and ethanol production, (ii) its production of ethanol at yields close to the theoretical maximum with relatively low biomass formation, (iii) its high ethanol tolerance of up to 16% (vol/vol) and (iv) its facility for genetic manipulation 2-6 . However, wild strains of Z. mobilis can use only glucose, fructose and sucrose as carbon substrates, so recent research has focused on the development of recombinant strains capable of using pentose sugars 7,8 for the conversion of cheaper lignocellulosic hydrolysates to ethanol. Improved mutants 9-11 as well as the application of metabolic flux analysis, sitedirected mutagenesis, specific gene deletion/insertion and metabolic engineering for strain developlment 12,13 have also been reported. A physical map of Z. mobilis ZM4 genome and the ribosomal transcriptional unit have been previously reported 14,15 . In the current paper, the features of the complete sequence of the Z. mobilis ZM4 genome are presented and genomic characters are compared with those of another Z. mobilis strain, ZM1.

Massively parallel sequencing technologies have identified a broad spectrum of human genome diversity. Here we deep sequenced and correlated 18 genomes and 17 transcriptomes of unrelated Korean individuals. This has allowed us to construct a genome-wide map of common and rare variants and also identify variants formed during DNA-RNA transcription. We identified 9.56 million genomic variants, 23.2% of which appear to be previously unidentified. From transcriptome sequencing, we discovered 4,414 transcripts not previously annotated. Finally, we revealed 1,809 sites of transcriptional base modification, where the transcriptional landscape is different from the corresponding genomic sequences, and 580 sites of allele-specific expression. Our findings suggest that a considerable number of unexplored genomic variants still remain to be identified in the human genome, and that the integrated analysis of genome and transcriptome sequencing is powerful for understanding the diversity and functional aspects of human genomic variants.

Supplementary data are available at Bioinformatics online.