Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes

The sequence of the human genome

A 2.91-billion base pair (bp) consensus sequence of the euchromatic portion of the human genome was generated by the whole-genome shotgun sequencing method. The 14.8-billion bp DNA sequence was generated over 9 months from 27,271,853 high-quality sequence reads (5.11-fold coverage of the genome) from both ends of plasmid clones made from the DNA of five individuals. Two assembly strategies-a whole-genome assembly and a regional chromosome assembly-were used, each combining sequence data from Celera and the publicly funded genome effort. The public data were shredded into 550-bp segments to create a 2.9-fold coverage of those genome regions that had been sequenced, without including biases inherent in the cloning and assembly procedure used by the publicly funded group. This brought the effective coverage in the assemblies to eightfold, reducing the number and size of gaps in the final assembly over what would be obtained with 5.11-fold coverage. The two assembly strategies yielded very similar results that largely agree with independent mapping data. The assemblies effectively cover the euchromatic regions of the human chromosomes. More than 90% of the genome is in scaffold assemblies of 100,000 bp or more, and 25% of the genome is in scaffolds of 10 million bp or larger. Analysis of the genome sequence revealed 26,588 protein-encoding transcripts for which there was strong corroborating evidence and an additional approximately 12,000 computationally derived genes with mouse matches or other weak supporting evidence. Although gene-dense clusters are obvious, almost half the genes are dispersed in low G+C sequence separated by large tracts of apparently noncoding sequence. Only 1.1% of the genome is spanned by exons, whereas 24% is in introns, with 75% of the genome being intergenic DNA. Duplications of segmental blocks, ranging in size up to chromosomal lengths, are abundant throughout the genome and reveal a complex evolutionary history. Comparative genomic analysis indicates vertebrate expansions of genes associated with neuronal function, with tissue-specific developmental regulation, and with the hemostasis and immune systems. DNA sequence comparisons between the consensus sequence and publicly funded genome data provided locations of 2.1 million single-nucleotide polymorphisms (SNPs). A random pair of human haploid genomes differed at a rate of 1 bp per 1250 on average, but there was marked heterogeneity in the level of polymorphism across the genome. Less than 1% of all SNPs resulted in variation in proteins, but the task of determining which SNPs have functional consequences remains an open challenge.

Genome comparisons highlight similarity and diversity within the eukaryotic kingdoms

In 2000, the number of completely sequenced eukaryotic genomes increased to four. The addition of Drosophila and Arabidopsis into this cohort permits additional insights into the processes that have shaped evolution. Analysis and comparisons of both completed genomes and partially sequenced genomes have already shed light on mechanisms such as gene duplication and gene loss that have long been hypothesized to be major forces in speciation. Indeed, duplicate gene pairs in Saccharomyces, Arabidopsis, Caenorhabditis and Drosophila are high: 30%, 60%, 48% and 40%, respectively. Evidence of horizontal gene-transfer, thought to be a major evolutionary force in bacteria, has been found in Arabidopsis. The release of the 'first draft' of the human genome sequence in 2000 heralds a new stage of biological study. Understanding the as-yet-unannotated human genome will be largely based on conclusions, techniques and tools developed during the analysis and comparison of the genome of these four model organisms.

Abundant protein domains occur in proportion to proteome size

BACKGROUND

Conserved domains in proteins have crucial roles in protein interactions, DNA binding, enzyme activity and other important cellular processes. It will be of interest to determine the proportions of genes containing such domains in the proteomes of different eukaryotes.

RESULTS

The average proportion of conserved domains in each of five eukaryote genomes was calculated. In pairwise genome comparisons, the ratio of genes containing a given conserved domain in the two genomes on average reflected the ratio of the predicted total gene numbers of the two genomes. These ratios have been verified using a repository of databases and one of its subdivisions of conserved domains.

CONCLUSIONS

Many conserved domains occur as a constant proportion of proteome size across the five sequenced eukaryotic genomes. This raises the possibility that this proportion is maintained because of functional constraints on interacting domains. The universality of the ratio in the five eukaryotic genomes attests to its potential importance.