Summary auto-generated
This article introduces a monthly column tracking newly sequenced prokaryotic genomes and genome comparison methods. As of December 2003, 161 prokaryotic genomes had been sequenced, with bacterial genomes published almost weekly. The article highlights four recently sequenced genomes: Vibrio vulnificus (marine pathogen with two chromosomes and a plasmid totaling >5 Mbp), Gloeobacter violaceus (cyanobacterium lacking thylakoid membranes, 4.7 Mbp), Geobacter sulfurreducens (first delta-Proteobacteria genome, 3.8 Mbp, useful for bioremediation), and Phytoplasma asteris (plant pathogen, 860 kb, showing reductive evolution). The article discusses basic genome comparison methods using tabular data including genome length, AT content, gene counts, and rRNA operons. Notably, differences in rRNA operon numbers reflect organismal growth rates: V. vulnificus has nine rRNA operons supporting rapid 45-minute doubling time, while slow-growing Gloeobacter violaceus has only one. The article notes 144 bacterial and 17 archaeal genomes were publicly available at the time, with approximately 50 published during 2003. A significant lag exists between genome sequencing and full annotation/publication.
Key findings
- Four prokaryotic genomes were sequenced in early December 2003: V. vulnificus, G. violaceus, G. sulfurreducens, and P. asteris, each revealing unique evolutionary adaptations
- G. violaceus lacks thylakoid membranes and possesses genes with inteins and transposases, indicating distinct evolutionary history among cyanobacteria
- G. sulfurreducens contains unprecedented diversity of c-type cytochromes and may be more mobile and aerotolerant than previously thought
- P. asteris exhibits reductive evolution with a minimal 860 kb genome lacking genes considered essential for life, informing minimal genome concepts
- rRNA operon number correlates with doubling time: V. vulnificus (nine operons, ~45 min doubling) versus G. violaceus (one operon, ~72 hr doubling)
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Abstract
Bacterial genomes are now being published almost every week. The purpose of this new column is to provide monthly updates on new genomes which have been published, as well as to discuss methods for genome comparison of the more than 100 bacterial genomes which are already publicly available. Thus, each column will be divided into two parts, with the first part devoted to a brief description of highlights of the recently sequenced genomes and the second part devoted to a discussion of relevant methods currently being used to compare sequenced genomes to each other. Each month a table will be presented, as shown in Table 1, with the name, length, AT content, number of rRNAs, tRNAs, CDS regions annotated and accession numbers for each new genome. The genome sequences of four species have been published in the first half of December 2003: Vibrio vulnificus, a marine pathogen, the cyanobacterium Gloeobacter violaceus, the soil bacterium Geobacter sulfurreducens and the plant pathogen Phytoplasma asteris.