Segmented Genome: Elementary Units of Genome Structure

Numerous observations, measurements and calculations strongly indicate that both eukaryotic and prokaryotic genomes are built as linear arrays of units of rather uniform size, about 400 base pairs. The units are likely to correspond to early individual genes that existed, presumably, in form of DNA circles. Their combinatorial fusion resulted eventually in formation of the early segmented genomes. The segmented structure of the genomes is, apparently, still maintained by some structural selection pressures. Some of the units can be recognized by characteristic sequence motifs at the borders of the units. Identification and characterization of the units, their mapping on the genomes should become an important prerequisite of genome comparisons and genome evolution studies.     

人类基因组计划与后基因组时代

2003年4月14日生命科学诞生了一个新的重要里程碑,人类基因组计划完成,后基因组时代正式来临。着重介绍了人类基因组计划的提出、目标与任务、实施与进展等方面的基本情况,讨论了后基因组时代的时间界定,分析展望了后基因组时代与人类基因组计划密切相关的生物信息学、功能基因组学、蛋白质组学、药物基因组学等几个重要研究领域 。     

Genome duality

A report on 'Higher Order Genome Architecture', the third meeting of the Marie Curie Conferences and Training Courses (MC-GARD), Edinburgh, UK, 1-5 April 2009.     

Genome instability

The paper deals with the various manifestations and the role of genome changes, mainly in eukaryotes. I. Hereditary changes: 1) multiplication of genes in animals; 2) multiplication of genes in prokaryotes; 3) microsymbionts, mobile elements and supermutability; 4) extrachromosomal element delta in Drosophila; 5) hybrid dysgenesis in Drosophila; 6) mobile and unstable genes in drosophila; 7) controlling elements in planrs. II. Genome changes as a regulatory factor of genetic activity: 1) immunoglobulin genes; 2) mating types in yeast; 3) the inversion mechanism of switching gene activity in prokaryotes; 4) ribosomal and histone genes; 5) changes of DNA fractions in ontogenesis; 6) regulation of genome changes.     

Examination of Prokaryotic Multipartite Genome Evolution through Experimental Genome Reduction

Many bacteria carry two or more chromosome-like replicons. This occurs in pathogens such as Vibrio cholerea and Brucella abortis as well as in many N₂-fixing plant symbionts including all isolates of the alfalfa root-nodule bacteria Sinorhizobium meliloti. Understanding the evolution and role of this multipartite genome organization will provide significant insight into these important organisms; yet this knowledge remains incomplete, in part, because technical challenges of large-scale genome manipulations have limited experimental analyses. The distinct evolutionary histories and characteristics of the three replicons that constitute the S. meliloti genome (the chromosome (3.65 Mb), pSymA megaplasmid (1.35 Mb), and pSymB chromid (1.68 Mb)) makes this a good model to examine this topic. We transferred essential genes from pSymB into the chromosome, and constructed strains that lack pSymB as well as both pSymA and pSymB. This is the largest reduction (45.4%, 3.04 megabases, 2866 genes) of a prokaryotic genome to date and the first removal of an essential chromid. Strikingly, strains lacking pSymA and pSymB (ΔpSymAB) lost the ability to utilize 55 of 74 carbon sources and various sources of nitrogen, phosphorous and sulfur, yet the ΔpSymAB strain grew well in minimal salts media and in sterile soil. This suggests that the core chromosome is sufficient for growth in a bulk soil environment and that the pSymA and pSymB replicons carry genes with more specialized functions such as growth in the rhizosphere and interaction with the plant. These experimental data support a generalized evolutionary model, in which non-chromosomal replicons primarily carry genes with more specialized functions. These large secondary replicons increase the organism''s niche range, which offsets their metabolic burden on the cell (e.g. pSymA). Subsequent co-evolution with the chromosome then leads to the formation of a chromid through the acquisition of functions core to all niches (e.g. pSymB).     

Genome aliquoting revisited

We prove that the genome aliquoting problem, the problem of finding a recent polyploid ancestor of a genome, with breakpoint distance can be solved in polynomial time. We propose an aliquoting algorithm that is a 2-approximation for the genome aliquoting problem with double cut and join distance, improving upon the previous best solution to this problem, Feij?o and Meidanis' 4-approximation algorithm.