The human genome holds an extraordinary trove of information about human development, physiology, medicine and evolution. Here we report the results of an international collaboration to produce and make freely available a draft sequence of the human genome. We also present an initial analysis of the data, describing some of the insights that can be gleaned from the sequence.

Almost all aphid species (Homoptera, Insecta) have 60-80 huge cells called bacteriocytes, within which are round-shaped bacteria that are designated Buchnera. These bacteria are maternally transmitted to eggs and embryos through host generations, and the mutualism between the host and the bacteria is so obligate that neither can reproduce independently. Buchnera is a close relative of Escherichia coli, but it contains more than 100 genomic copies per cell, and its genome size is only a seventh of that of E. coli. Here we report the complete genome sequence of Buchnera sp. strain APS, which is composed of one 640,681-base-pair chromosome and two small plasmids. There are genes for the biosyntheses of amino acids essential for the hosts in the genome, but those for non-essential amino acids are missing, indicating complementarity and syntrophy between the host and the symbiont. In addition, Buchnera lacks genes for the biosynthesis of cell-surface components, including lipopolysaccharides and phospholipids, regulator genes and genes involved in defence of the cell. These results indicate that Buchnera is completely symbiotic and viable only in its limited niche, the bacteriocyte.

Many insects that rely on a single food source throughout their developmental cycle harbor beneficial microbes that provide nutrients absent from their restricted diet. Tsetse flies, the vectors of African trypanosomes, feed exclusively on blood and rely on one such intracellular microbe for nutritional provisioning and fecundity. As a result of co-evolution with hosts over millions of years, these mutualists have lost the ability to survive outside the sheltered environment of their host insect cells. We present the complete annotated genome of Wigglesworthia glossinidia brevipalpis, which is composed of one chromosome of 697,724 base pairs (bp) and one small plasmid, called pWig1, of 5,200 bp. Genes involved in the biosynthesis of vitamin metabolites, apparently essential for host nutrition and fecundity, have been retained. Unexpectedly, this obligate's genome bears hallmarks of both parasitic and free-living microbes, and the gene encoding the important regulatory protein DnaA is absent.Many arthropods with restricted diets, such as vertebrate blood, plant juice or wood, rely on symbiotic microorganisms to supply nutrients required for viability and fertility 1 . Among insects harboring such symbionts is the tsetse fly (Diptera: Glossinidae)-the vector of African trypanosomes, agents of deadly diseases in humans and animals in sub-Saharan Africa 2 . Tsetse flies harbor two symbiotic microorganisms in gut tissue: the obligate primary-symbiont Wigglesworthia glossinidia and the commensal secondarysymbiont Sodalis glossinidius. Whereas S. glossinidius may be found in various host tissue types, W. glossinidia is housed in differentiated host epithelial cells (bacteriocytes) that form the bacteriome organ 2 . The functional role of obligate symbionts in tsetses has been difficult to study, as their elimination results in retarded growth and a decrease in egg production and fecundity in the aposymbiotic host 3,4 . The ability to reproduce could be partially restored, however, when aposymbiotic flies received supplementation with B-complex vitamins, suggesting that the endosymbionts might have a metabolic role involving these compounds 5 .The phylogenetic characterization of W. glossinidia from distant tsetse species has shown that they form a distinct clade in the Enterobacteriaceae 6 and display concordant evolution with their host species 7 . This finding implies that a tsetse ancestor was infected with a bacterium some 50-100 million years ago, and extant species of tsetse and associated W. glossinidia strains radiated without horizontal transfer of genetic material between species.As a result of their intracellular lifestyle, the genomes of obligate symbionts have undergone massive reductions in comparison with their free-living relatives. The genome size of W. glossinidia has been estimated as 740-770 kilobases 8 (kb), and that of Buchnera sp., the obligate symbiont of the pea aphid (Homoptera:Aphidoidea), as 640,681 bp 9,10 . Both genomes approach the size of the smallest genome reported thus far, that of My...

By comparing 4,344 protein sequences from fission yeast Schizosaccharomyces pombe with all available eukaryotic sequences, we identified those genes that are conserved in S. pombe and nonfungal eukaryotes but are missing or highly diverged in the baker's yeast Saccharomyces cerevisiae. Since the radiation from the common ancestor with S. pombe, S. cerevisiae appears to have lost about 300 genes, and about 300 more genes have diverged by far beyond expectation. The most notable feature of the set of genes lost in S. cerevisiae is the coelimination of functionally connected groups of proteins, such as the signalosome and the spliceosome components. We predict similar coelimination of the components of the posttranscriptional gene-silencing system that includes the recently identified RNA-dependent RNA polymerase. Because one of the functions of posttranscriptional silencing appears to be ''taming'' of retrotransposons, the loss of this system in yeast could have triggered massive retrotransposition, resulting in elimination of introns and subsequent loss of spliceosome components that become dispensable. As the genome database grows, systematic analysis of coordinated gene loss may become a general approach for predicting new components of functional systems or even defining previously unknown functional complexes.A major outcome of the recent advances in comparative genomics is the realization of the major role of horizontal gene transfer and lineage-specific gene loss in the evolution of prokaryotes (1-4). These phenomena appear to account largely for the remarkable diversity of the prokaryotic gene repertoires. The likelihood of horizontal gene transfer between eukaryotes, at least multicellular ones, is low because, for a gene to be laterally transferred, it must enter the germ line. In contrast, there is no such restriction for gene loss. The dramatic variation in the number of genes among eukaryotes, in some cases even between rather closely related species-yeast Saccharomyces cerevisiae, for example, has about 6,000 genes compared with at least 8,000-9,000 in multicellular ascomycetes such as Aspergillus (5)-suggests that, along with proliferation of gene families (6), lineage-specific gene loss could have been important in eukaryotic evolution.The two yeasts, S. cerevisiae and Schizosaccharomyces pombe, are probably the optimal current choice of genomes to compare with the aim of estimating the number of lost genes. The genome of S. cerevisiae, arguably the best-studied eukaryote in terms of gene functions (6), has been completed (7), and for S. pombe, up to 70% of the genome sequence is available. For estimating gene loss, it is critical to have assurance that (nearly) all genes in the analyzed genome have been identified; S. cerevisiae is the only eukaryotic genome for which such confidence exists, particularly because of the paucity of introns, which facilitates gene detection. The two yeast species are close enough so that direct counterparts among their genes [orthologs (8)] are readily identifiable b...

Approximately half of all human genes have CpG islands (CGIs)around their promoter regions. Although CGIs usually escape methylation, those on Chromosome X in females and those in the vicinity of imprinted genes are exceptions: They have both methylated and unmethylated alleles to display a “composite” pattern in methylation analysis. In addition, aberrant methylation of CGIs is known to often occur in cancer cells. Here we developed a simple HpaII-McrBC PCR method for discrimination of full, null, incomplete, and composite methylation patterns, and applied it to all computationally identified CGIs on human Chromosome 21q. This comprehensive analysis revealed that, although most CGIs (103 out of 149)escape methylation, a sizable fraction (31 out of 149)are fully methylated even in normal peripheral blood cells. Furthermore, we identified seven CGIs showing the composite methylation, and demonstrated that three of them are indeed methylated monoallelically. Further analyses using informative pedigrees revealed that two of the three are subject to maternal allele-specific methylation. Intriguingly, the other CGI is methylated in an allele-specific but parental-origin-independent manner. Thus, the cell seems to have a broader repertoire of methylating CGIs than previously thought, and our approach may contribute to uncover novel modes of allelic methylation

The recently released human genome sequences provide us with reference data to conduct comparative genomic research on primates, which will be important to understand what genetic information makes us human. Here we present a first-generation human-chimpanzee comparative genome map and its initial analysis. The map was constructed through paired alignment of 77,461 chimpanzee bacterial artificial chromosome end sequences with publicly available human genome sequences. We detected candidate positions, including two clusters on human chromosome 21 that suggest large, nonrandom regions of difference between the two genomes.

In order to identify single nucleotide polymorphisms (SNPs) and haplotype frequencies of CYP3A4 in a Japanese population, the distal enhancer and proximal promoter regions, all exons, and the surrounding introns were sequenced from genomic DNA of 416 Japanese subjects. We found 24 SNPs, including 17 novel ones: two in the distal enhancer, four in the proximal promoter, one in the 5'-untranslated region (UTR), seven in the introns, and three in the 3'-UTR. The most common SNP was c.1026+12G>A (IVS10+12G>A), with a 0.249 frequency. Four non-synonymous SNPs, c.554C>G (p.T185S, CYP3A4(*)16), c.830_831insA (p.E277fsX8, (*)6), c.878T>C (p.L293P, (*)18), and c.1088 C>T (p.T363M, (*)11) were found with frequencies of 0.014, 0.001, 0.028, and 0.002, respectively. No SNP was found in the known nuclear transcriptional factor-binding sites in the enhancer and promoter regions. Using these 24 SNPs, 16 haplotypes were unambiguously identified, and nine haplotypes were inferred by aid of an expectation-maximization-based program. In addition, using data from 186 subjects enabled a close linkage to be found between CYP3A4 and CYP3A5 SNPs, especially among the SNPs at c.1026+12 in CYP3A4 and c.219-237 (IVS3-237, a key SNP site for CYP3A5(*)3), c.865+77 (IVS9+77) and c.1523 in CYP3A5. This result suggested that CYP3A4 and CYP3A5 are within the same gene block. Haplotype analysis between CYP3A4 and CYP3A5 revealed several major haplotype combinations in the CYP3A4-CYP3A5 block. Our findings provide fundamental and useful information for genotyping CYP3A4 (and CYP3A5) in the Japanese, and probably Asian populations.

To test the hypotheses that eubacterial genomes leave evolutionarily stable structures and that the variety of genome size is brought about through genome doubling during evolution, the genome structures of Haemophilus influenzae, Mycoplasma genitalium, Escherichia coli, and Bacillus subtilis were compared using the DNA sequences of the entire genome or substantial portions of genome. In these comparisons, the locations of orthologous genes were examined among different genomes. Using orthologous genes for the comparisons guaranteed that differences revealed in physical location would reflect changes in genome structure after speciation. We found that dynamic rearrangements have so frequently occurred in eubacterial genomes as to break operon structures during evolution, even after the relatively recent divergence between E. coli and H. influenzae. Interestingly, in such eubacterial genomes of high plasticity, we could find several highly conservative regions with the longest conserved region comprising the S10, spc, and alpha operons. This suggests that such exceptional conservative regions have undergone strong structural constraints during evolution.