The need for speed

DNA sequence data are being produced at an ever-increasing rate. The Bowtie sequence-alignment algorithm uses advanced data structures to help data analysis keep pace with data generation.     

Nucleotide sequence of the genome of the filamentous bacteriophage I2-2: Module evolution of the filamentous phage genome

Summary The nucleotide sequence of the circular single-stranded genome of the filamentous Escherichia coli phage I2-2 has been determined and compared with those of the filamentous E. coli phages Ff(M13, fl, or fd) and IKe. The I2-2 DNA sequence comprises 6744 nucleotides; 139 nucleotides less than that of the N- and I2-plasmid-specific phage IKe, and 337 (336) nucleotides more than that of the F-plasmid-specific phage Ff. Nucleotide sequence comparisons have indicated that I2-2, IKe, and Ff have a similar genetic organization, and that the genomes of I2-2 and IKe are evolutionarily more closely related than those of I2-2 and Ff. The studies have further demonstrated that the I2-2 genome is a composite replicon, composed of only two-thirds of the ancestral genome of IKe. Only a contiguous I2-2 DNA sequence of 4615 nucleotides encompassing not only the coat protein and phage assembly genes, but also the signal required for efficient phage morphogenesis, was found to be significantly homologous to sequences in the genomes of IKe and Ff. No homology was observed between the consecutive DNA sequence that contains the origins for viral and complementary strand replication and the replication genes. Although other explanations cannot be ruled out, our data strongly suggest that the ancestor filamentous phage genome of phages I2-2 and IKe has exchanged its replication module during evolution with that of another replicon, e.g., a plasmid that also replicates via the so-called rolling circle mechanism. Offprint requests to: R.N.H. Konings     

Design of a compartmentalized shotgun assembler for the human genome

Two different strategies for determining the human genome are currently being pursued: one is the "clone-by-clone" approach, employed by the publicly funded project, and the other is the "whole genome shotgun assembler" approach, favored by researchers at Celera Genomics. An interim strategy employed at Celera, called compartmentalized shotgun assembly, makes use of preliminary data produced by both approaches. In this paper we describe the design, implementation and operation of the "compartmentalized shotgun assembler".     

Chloroplast genome phylogenetics: why we need independent approaches to plant molecular evolution

The traditional approach to plant molecular phylogenetics involves amplifying, sequencing and analyzing one or a few genes from many species and is conducive to broad taxon sampling. An independent approach involves chloroplast genome sequencing, providing much larger amounts of data per taxon but for a smaller number of species. In principle, the two strategies can inform each other but in practice their results sometimes conflict for reasons that are currently debated. An Opinion article published in the October 2004 issue of Trends in Plant Science cautioned against the pursuit of genome-based phylogenies. Here, we provide a different perspective on issues at the heart of the current debate and defend the use of chloroplast genome phylogenetics for crucial species because it provides an independent test of hypotheses generated by the traditional approach.     

The need for speed: informed land acquisitions for conservation in a dynamic property market

Land acquisition is a common approach to biodiversity conservation but is typically subject to property availability on the public market. Consequently, conservation plans are often unable to be implemented as intended. When properties come on the market, conservation agencies must make a choice: purchase immediately, often without a detailed knowledge of its biodiversity value; survey the parcel and accept the risk that it may be removed from the market during this process; or not purchase and hope a better parcel comes on the market at a later date. We describe both an optimal method, using stochastic dynamic programming, and a simple rule of thumb for making such decisions. The solutions to this problem illustrate how optimal conservation is necessarily dynamic and requires explicit consideration of both the time period allowed for implementation and the availability of properties.     

The need for speed. II. Myelin in calanoid copepods

Speed of nerve impulse conduction is greatly increased by myelin, a multi-layered membranous sheath surrounding axons. Myelinated axons are ubiquitous among the vertebrates, but relatively rare among invertebrates. Electron microscopy of calanoid copepods using rapid cryofixation techniques revealed the widespread presence of myelinated axons. Myelin sheaths of up to 60 layers were found around both sensory and motor axons of the first antenna and interneurons of the ventral nerve cord. Except at nodes, individual lamellae appeared to be continuous and circular, without seams, as opposed to the spiral structure of vertebrate and annelid myelin. The highly organized myelin was characterized by the complete exclusion of cytoplasm from the intracellular spaces of the cell generating it. In regions of compaction, extracytoplasmic space was also eliminated. Focal or fenestration nodes, rather than circumferential ones, were locally common. Myelin lamellae terminated in stepwise fashion at these nodes, appearing to fuse with the axolemma or adjacent myelin lamellae. As with vertebrate myelin, copepod sheaths are designed to minimize both resistive and capacitive current flow through the internodal membrane, greatly speeding nerve impulse conduction. Copepod myelin differs from that of any other group described, while sharing features of every group. Accepted: 8 January 2000     

The need for speed: testing acceleration for estimating animal travel rates in terrestrial dead-reckoning systems

Numerous methods are currently available to track animal movements. However, only one of these, dead-reckoning, has the capacity to provide continuous data for animal movements over fine scales. Dead-reckoning has been applied almost exclusively in the study of marine species, in part due to the difficulty of accurately measuring the speed of terrestrial species. In the present study we evaluate the use of accelerometers and a metric known as overall dynamic body acceleration (ODBA) as a proxy for the measurement of speed for use in dead-reckoning. Data were collated from previous studies, for 10 species locomoting on a treadmill and their ODBA measured by an attached data logger. All species except one showed a highly significant linear relationship between speed and ODBA; however, there was appreciable inter- and intra-specific variance in this relationship. ODBA was then used to estimate speed in a simple trial run of a dead-reckoning track. Estimating distance travelled using speed derived from prior calibration for ODBA resulted in appreciable errors. We describe a method by which these errors can be minimised, by periodic ground-truthing (e.g., by GPS or VHF telemetry) of the dead-reckoned track and adjusting the relationship between speed and ODBA until actual known positions and dead-reckoned positions accord.     

The animal in the genome: comparative genomics and evolution

Comparisons between completely sequenced metazoan genomes have generally emphasized how similar their encoded protein content is, even when the comparison is between phyla. Given the manifest differences between phyla and, in particular, intuitive notions that some animals are more complex than others, this creates something of a paradox. Simplistic explanations have included arguments such as increased numbers of genes; greater numbers of protein products produced through alternative splicing; increased numbers of regulatory non-coding RNAs and increased complexity of the cis-regulatory code. An obvious value of complete genome sequences lies in their ability to provide us with inventories of such components. I examine progress being made in linking genome content to the pattern of animal evolution, and argue that the gap between genomic and phenotypic complexity can only be understood through the totality of interacting components.     

GENESIS: genome evolution scenarios

Summary: We implemented a software tool called GENESIS for threedifferent genome rearrangement problems: Sorting a unichromosomalgenome by weighted reversals and transpositions (SwRT), sortinga multichromosomal genome by reversals, translocations, fusionsand fissions (SRTl), and sorting a multichromosomal genome byweighted reversals, translocations, fusions, fissions and transpositions(SwRTTl). Availability: Source code can be obtained by the authors, oruse the web interface http://www.uni-ulm.de/in/theo/research/genesis.html Contact: simon.gog{at}uni-ulm.de Associate Editor: Chris Stoeckert     

The evolution of genome size in ants

Background  

Despite the economic and ecological importance of ants, genomic tools for this family (Formicidae) remain woefully scarce. Knowledge of genome size, for example, is a useful and necessary prerequisite for the development of many genomic resources, yet it has been reported for only one ant species (Solenopsis invicta), and the two published estimates for this species differ by 146.7 Mb (0.15 pg).     

Integrons: natural tools for bacterial genome evolution

Integrons were first identified as the primary mechanism for antibiotic resistance gene capture and dissemination among Gram-negative bacteria. More recently, their role in genome evolution has been extended with the discovery of larger integron structures, the super-integrons, as genuine components of the genomes of many species throughout the gamma-proteobacterial radiation. The functional platforms of these integrons appear to be sedentary, whereas their gene cassette contents are highly variable. Nevertheless, the gene cassettes for which an activity has been experimentally demonstrated encode proteins related to simple adaptive functions and their recruitment is seen as providing the bacterial host with a selective advantage. The widespread occurrence of the integron system among Gram-negative bacteria is discussed, with special focus on the super-integrons. Some of the adaptive functions encoded by these genes are also reviewed, and implications of integron-mediated genome evolution in the emergence of novel bacterial species are highlighted.     

Directed evolution of a filamentous fungus for thermotolerance

Background  

Filamentous fungi are the most widely used eukaryotic biocatalysts in industrial and chemical applications. Consequently, there is tremendous interest in methodology that can use the power of genetics to develop strains with improved performance. For example, Metarhizium anisopliae is a broad host range entomopathogenic fungus currently under intensive investigation as a biologically based alternative to chemical pesticides. However, it use is limited by the relatively low tolerance of this species to abiotic stresses such as heat, with most strains displaying little to no growth between 35–37°C. In this study, we used a newly developed automated continuous culture method called the Evolugator™, which takes advantage of a natural selection-adaptation strategy, to select for thermotolerant variants of M. anisopliae strain 2575 displaying robust growth at 37°C.     

The tomato genome: implications for plant breeding, genomics and evolution

ABSTRACT: The genome sequence of tomato (Solanum lycopersicum), one of the most important vegetable crops, has recently been decoded. We address implications of the tomato genome for plant breeding, genomics and evolutionary studies, and its potential to fuel future crop biology research.     

The genome: an isochore ensemble and its evolution

The genomes of eukaryotes are mosaics of isochores. These are long DNA stretches that are fairly homogeneous in base composition and that belong to a small number of families characterized by different ratios of GC to AT and different short-sequence patterns (i.e., different DNA structures that interact with different proteins). This genome organization led to two discoveries: (1) the genomic code, which refers to two correlations, that of the composition of coding and contiguous noncoding sequences, and that of coding sequences and the structural properties of the encoded proteins; and (2) the genome phenotypes, which correspond to the patterns of isochore families in the genomes. These patterns indicate that genome evolution may proceed either according to a conservative mode or to a transitional (isochore shifting) mode, apparently depending upon whether the environment is constant or shifting. According to the neoselectionist theory, natural selection is responsible for both modes.