Recombination and Gene Loss Occur Simultaneously During Bacterial Horizontal Gene Transfer

Bacteria can acquire new genes by incorporating environmental DNA into their genomes, yet genome sizes stay relatively constant. In nature, gene acquisition is a rare event so it is difficult to observe. However, the Caulobacter crescentus CB2A genome contains 114 insertions of genetic material from the closely-related NA1000 strain, providing a unique opportunity to analyze the horizontal transfer of genetic material. Analyses of these insertions led to a new model that involves preferential recombination at non-homologous regions that are flanked by regions of homology and does not involve any mutational processes. The net result is the replacement of segments of the recipient genome instead of the simple addition of genetic material during horizontal gene transfer. Analyses of the genomes of closely related strains of other bacterial and archaea genera, suggested that horizontal gene transfer occurs preferentially in non-homologous regions in these organisms as well. Thus, it appears to be a general phenomenon that prokaryotic horizontal gene transfer occurs preferentially at sites where the incoming DNA contains a non-homologous region that is flanked by regions of homology. Therefore, gene replacement is a common phenomenon during horizontal gene transfer

A comparison of the Caulobacter NA1000 and K31 genomes reveals extensive genome rearrangements and differences in metabolic potential

The genus Caulobacter is found in a variety of habitats and is known for its abilityto thrive in low-nutrient conditions. K31 is a novel Caulobacter isolate that has the ability to tolerate copper and chlorophenols, and can grow at 48Cwith a doubling time of 40 h. K31 contains a 5.5 Mb chromosome that codes for more than 5500 proteins and two large plasmids (234 and 178 kb) thatcode for 438 additional proteins. A comparison of the K31 and the Caulobactercrescentus NA1000 genomes revealed extensive rearrangements of gene order,suggesting that the genomes had been randomly scrambled. However, a careful analysis revealed that the distance from the origin of replication was conserved for the majority of the genes and that many of the rearrangements involved inversions that included the origin of replication. On a finer scale, numerous small indels were observed. K31 proteins involved in essential functions shared 80-95% amino acid sequence identity with their C. crescentus homologues,while other homologue pairs tended to have lower levels of identity.In addition, the K31 chromosome contains more than 1600 genes with nohomologue in NA1000

Complex Evolution of a Highly-conserved Microsatellite Locus in Several Fish Species

The evolutionary dynamics of a highly conserved microsatellite locus (Dla 11) were studied in several fish species. The data indicated that multiple types of compound microsatellites arose through point mutations that were sometimes followed by expansion of the derived motif. Furthermore, extensive length variation was detected among species in the regions immediately flanking the repeat region

Evolution of an MHC Class La Gene Fragment in Four North American \u3cem\u3eMorone\u3c/em\u3e Species

A nucleotide sequence analysis of a fragment of a Morone MHC class Ia gene detected high levels of polymorphism in striped bass Morone saxatilis, white perch Morone americana and yellow bass Morone mississippiensis. Extremely low levels of MHC diversity, however, were detected in white bass Morone chrysops, suggesting the possibility of a severe population bottleneck for this species

Financial Innovation and Risk Management: The Cross-Guarantee Solution

The cross-guarantee concept, which is summarized below, will eliminate the regulatory moral hazard that electronic technology has greatly exacerbated in recent years. The paper concludes by outlining the many benefits cross-guarantees will bring to the financial system as well as the structural and international implications of using cross-guarantees to bring market-driven regulation to the financial services sector of the American economy.

Across Bacterial Phyla, Distantly-Related Genomes with Similar Genomic GC Content Have Similar Patterns of Amino Acid Usage

The GC content of bacterial genomes ranges from 16% to 75% and wide ranges of genomic GC content are observed within many bacterial phyla, including both Gram negative and Gram positive phyla. Thus, divergent genomic GC content has evolved repeatedly in widely separated bacterial taxa. Since genomic GC content influences codon usage, we examined codon usage patterns and predicted protein amino acid content as a function of genomic GC content within eight different phyla or classes of bacteria. We found that similar patterns of codon usage and protein amino acid content have evolved independently in all eight groups of bacteria. For example, in each group, use of amino acids encoded by GC-rich codons increased by approximately 1% for each 10% increase in genomic GC content, while the use of amino acids encoded by AT-rich codons decreased by a similar amount. This consistency within every phylum and class studied led us to conclude that GC content appears to be the primary determinant of the codon and amino acid usage patterns observed in bacterial genomes. These results also indicate that selection for translational efficiency of highly expressed genes is constrained by the genomic parameters associated with the GC content of the host genome

Effect of Harvest and Effective Population Size on Genetic Diversity in a Striped Bass Population

A major factor that contributes to loss of genetic variation in natural populations is a small effective population size. In species with a complex life history that involves overlapping generations and delayed maturity, the impact of infrequent annual reproductive bottlenecks is likely to be small because effective population size is defined by the number of individuals contributing to a generation and not to a single year-class. The striped bass Morone saxatilis is a longlived species with overlapping generations and age structure, whose recreational and commercial importance has made it a target of intense harvest.We analyzed allele frequency fluctuation among juvenile year classes of the Santee–Cooper, South Carolina, population from 1990 through 1994 with three independently segregating polymorphic nuclear DNA loci to examine genetic drift and estimate the number of breeders each year. Significant fluctuations in allele frequencies among juvenile year-classes were observed, and most of the variation was attributed to a small number of parents in 1992. The potential impact of this year-class is likely to be low because 1992 was a poor recruitment year, and striped bass have multiple opportunities to breed. However, high adult mortality due to fishing may increase the impact of the 1992 year-class by decreasing the number of adult age-classes in this population. Thus, high exploitation in species with overlapping generations can reduce the long-term effective population size by abrogating the possibility of multiple breeding opportunities

Correction: African American mitochondrial DNAs often match mtDNAs found in multiple African ethnic groups

After the publication of this work [1], we became aware that AFDIL data set used to construct our database of sub-Saharan mtDNA sequences had been mislabelled, and in fact, did not contain Sierra Leone mtDNA sequences. We have obtained the correct Sierra Leone data set from AFDIL, reconstructed the database using the new file, and reanalyzed all of the data. The size of our database was reduced from 3725 to 3717 since the new Sierra Leone data set contained 109 sequences instead of 117 in themislabelled data set. The swapping of data sets resulted in a cascade of minor corrections to Tables 2, 3, 4, 5, and 6 (see below). We also corrected an error in the entry for BAM013 in Table 7. However, the only major change was that there were a number of matches of African-American sequences to sequences in the mislabelled data set. Thus, the number of African-American matches to single ethnic groups dropped from a total of 16 to 9 (Table 3) representing just 5% of the African American sequences that we compared to the database