Yeasts illustrate the molecular mechanisms of eukaryotic genome evolution

Hemiascomycetous yeasts have the greatest number of sequenced species for a single phylum, and are at the forefront of evolutionary genomics of eukaryotes. Yeast genomes show the dynamic interplay between the formation and loss of genes and help to characterize the mechanisms involved and their functional and evolutionary consequences. These mechanisms have equivalents in the genomes of multicellular organisms. Yeast genomes show extensive loss of introns and a reduced role of transposable elements, and so probably have a more limited potential to form novel genes and functions than multicellular organisms, possibly explaining their conserved biological and morphological properties despite their considerable evolutionary range.     

Bacteriophage genomics

The past three years have seen an escalation in the number of sequenced bacteriophage genomes with more than 500 now in the NCBI phage database, representing a more than threefold increase since 2005. These span at least 70 different bacterial hosts, with two-thirds of the sequenced genomes of phages representing only eight bacterial hosts. Three key features emerge from the comparative analysis of these genomes. First, they span a very high degree of genetic diversity, suggesting early evolutionary origins. Second, the genome architectures are mosaic, reflecting an unusually high degree of horizontal genetic exchange in their evolution. Third, phage genomes contain a very high proportion of novel genetic sequences of unknown function, and probably represent the largest reservoir of unexplored genes. With an estimated 10(31) bacterial and archael viruses in the biosphere, our view of the virosphere will draw into sharper focus as further bacteriophage genomes are characterized.     

Genome SEGE: A database for 'intronless' genes in eukaryotic genomes

Background  

A number of completely sequenced eukaryotic genome data are available in the public domain. Eukaryotic genes are either 'intron containing' or 'intronless'. Eukaryotic 'intronless' genes are interesting datasets for comparative genomics and evolutionary studies. The SEGE database containing a collection of eukaryotic single exon genes is available. However, SEGE is derived using GenBank. The redundant, incomplete and heterogeneous qualities of GenBank data are a bottleneck for biological investigation in comparative genomics and evolutionary studies. Such studies often require representative gene sets from each genome and this is possible only by deriving specific datasets from completely sequenced genome data. Thus Genome SEGE, a database for 'intronless' genes in completely sequenced eukaryotic genomes, has been constructed.     

Gene structure prediction in syntenic DNA segments

The accurate prediction of higher eukaryotic gene structures and regulatory elements directly from genomic sequences is an important early step in the understanding of newly assembled contigs and finished genomes. As more new genomes are sequenced, comparative approaches are becoming increasingly practical and valuable for predicting genes and regulatory elements. We demonstrate the effectiveness of a comparative method called pattern filtering; it utilizes synteny between two or more genomic segments for the annotation of genomic sequences. Pattern filtering optimally detects the signatures of conserved functional elements despite the stochastic noise inherent in evolutionary processes, allowing more accurate annotation of gene models. We anticipate that pattern filtering will facilitate sequence annotation and the discovery of new functional elements by the genetics and genomics communities.     

昆虫比较线粒体基因组学研究进展

动物线粒体基因组因其基因组成稳定、基因排列相对保守、普遍为母系遗传、极少发生重组等而被广泛应用于进化与系统发育等研究。目前,昆虫中已有356个线粒体基因组序列被测定,代表了33个目中的28个目。大量比较基因组学研究使得我们对昆虫线粒体基因组的特征与进化方式有了较为清晰的认识。本文对昆虫线粒体基因组的测序进展、基因组的结构特征、碱基组成、控制区的特征、基因重排及其机理、进化速率及其在昆虫系统发育研究中的应用等方面的研究进展进行介绍。     

How to usefully compare homologous plant genes and chromosomes as DNA sequences

There are four sequenced and publicly available plant genomes to date. With many more slated for completion, one challenge will be to use comparative genomic methods to detect novel evolutionary patterns in plant genomes. This research requires sequence alignment algorithms to detect regions of similarity within and among genomes. However, different alignment algorithms are optimized for identifying different types of homologous sequences. This review focuses on plant genome evolution and provides a tutorial for using several sequence alignment algorithms and visualization tools to detect useful patterns of conservation: conserved non-coding sequences, false positive noise, subfunctionalization, synteny, annotation errors, inversions and local duplications. Our tutorial encourages the reader to experiment online with the reviewed tools as a companion to the text.     

Vom Phänotyp zum Genotyp

Forward Genomics – a comparative genomics approach to link phenotype to genotype Despite availability of several sequenced genomes, we know very little about the specific changes in the DNA that underlie phenotypic differences between species. The main reason is that species differ by both numerous genomic and phenotypic changes. A new comparative genomics method addresses this question by for phenotypes with independent evolutionary losses by searching for genomic regions that exhibit an elevated number of mutations in exactly these phenotype‐loss species. The near future sequencing of thousands of novel genomes will make it possible to use comparative genomics to systematically search for such DNA changes that are associated with phenotypic differences.     

Computational methods to detect conserved non-genic elements in phylogenetically isolated genomes: application to zebrafish

Many important model organisms for biomedical and evolutionary research have sequenced genomes, but occupy a phylogenetically isolated position, evolutionarily distant from other sequenced genomes. This phylogenetic isolation is exemplified for zebrafish, a vertebrate model for cis-regulation, development and human disease, whose evolutionary distance to all other currently sequenced fish exceeds the distance between human and chicken. Such large distances make it difficult to align genomes and use them for comparative analysis beyond gene-focused questions. In particular, detecting conserved non-genic elements (CNEs) as promising cis-regulatory elements with biological importance is challenging. Here, we develop a general comparative genomics framework to align isolated genomes and to comprehensively detect CNEs. Our approach integrates highly sensitive and quality-controlled local alignments and uses alignment transitivity and ancestral reconstruction to bridge large evolutionary distances. We apply our framework to zebrafish and demonstrate substantially improved CNE detection and quality compared with previous sets. Our zebrafish CNE set comprises 54 533 CNEs, of which 11 792 (22%) are conserved to human or mouse. Our zebrafish CNEs (http://zebrafish.stanford.edu) are highly enriched in known enhancers and extend existing experimental (ChIP-Seq) sets. The same framework can now be applied to the isolated genomes of frog, amphioxus, Caenorhabditis elegans and many others.     

Comparative genomics of yeast species: new insights into their biology

The genomes of two hemiascomycetous yeasts (Saccharomyces cerevisiae and Candida albicans) and one archiascomycete (Schizosaccharomyces pombe) have been completely sequenced and the genes have been annotated. In addition, the genomes of 13 more Hemiascomycetes have been partially sequenced. The amount of data thus obtained provides information on the evolutionary relationships between yeast species. In addition, the differential genetic characteristics of the microorganisms explain a number of distinctive biological traits. Gene order conservation is observed between phylogenetically close species and is lost in distantly related species, probably due to rearrangements of short regions of DNA. However, gene function is much more conserved along evolution. Compared to S. cerevisiae and S. pombe, C. albicans has a larger number of specific genes, i.e., genes not found in other organisms, a fact that can account for the biological characteristics of this pathogenic dimorphic yeast which is able to colonize a large variety of environments.     

Yeast genome sequencing: the power of comparative genomics

For decades, unicellular yeasts have been general models to help understand the eukaryotic cell and also our own biology. Recently, over a dozen yeast genomes have been sequenced, providing the basis to resolve several complex biological questions. Analysis of the novel sequence data has shown that the minimum number of genes from each species that need to be compared to produce a reliable phylogeny is about 20. Yeast has also become an attractive model to study speciation in eukaryotes, especially to understand molecular mechanisms behind the establishment of reproductive isolation. Comparison of closely related species helps in gene annotation and to answer how many genes there really are within the genomes. Analysis of non-coding regions among closely related species has provided an example of how to determine novel gene regulatory sequences, which were previously difficult to analyse because they are short and degenerate and occupy different positions. Comparative genomics helps to understand the origin of yeasts and points out crucial molecular events in yeast evolutionary history, such as whole-genome duplication and horizontal gene transfer(s). In addition, the accumulating sequence data provide the background to use more yeast species in model studies, to combat pathogens and for efficient manipulation of industrial strains.     

Munich information center for protein sequences plant genome resources: a framework for integrative and comparative analyses 1(W)

With several plant genomes sequenced, the power of comparative genome analysis can now be applied. However, genome-scale cross-species analyses are limited by the effort for data integration. To develop an integrated cross-species plant genome resource, we maintain comprehensive databases for model plant genomes, including Arabidopsis (Arabidopsis thaliana), maize (Zea mays), Medicago truncatula, and rice (Oryza sativa). Integration of data and resources is emphasized, both in house as well as with external partners and databases. Manual curation and state-of-the-art bioinformatic analysis are combined to achieve quality data. Easy access to the data is provided through Web interfaces and visualization tools, bulk downloads, and Web services for application-level access. This allows a consistent view of the model plant genomes for comparative and evolutionary studies, the transfer of knowledge between species, and the integration with functional genomics data.     

Transproteomic evidence of a loop-deletion mechanism for enhancing protein thermostability.

Understanding the molecular determinants of protein thermostability is of theoretical and practical importance. While numerous determinants have been suggested, no molecular feature has been judged of paramount importance, with the possible exception of ion-pair networks. The difficulty in identifying the main determinants may have been the limited structural information available on the thermostable proteins. Recently the complete genomes for mesophilic, thermophilic and hyperthermophilic organisms have been sequenced, vastly improving the potential for uncovering general trends in sequence and structure evolution related to thermostability and, thus, for isolating the more important determinants. From a comparative analysis of 20 complete genomes, we find a trend towards shortened thermophilic proteins relative to their mesophilic homologs. Moreover, sequence alignments to proteins of known structure indicate that thermophilic sequences are more likely than their mesophilic homologs to have deletions in exposed loop regions. The new genomes offer enough comparable sequences to compute meaningful statistics that point to loop deletion as a general evolutionary strategy for increasing thermostability.     

Phylogenetic taxonomy in Drosophila: Problems and prospects

The genus Drosophila is one of the best-studied model systems in modern biology, with twelve fully sequenced genomes available. In spite of the large number of genetic and genomic resources, little is known concerning the phylogenetic relationships, ecology, and evolutionary history of all but a few species. Recent molecular systematic studies have shown that this genus is comprised of at least three independent lineages and that several other genera are actually embedded within Drosophila. This genus accounts for over 2000 described, and many more undescribed, species. While some Drosophila researchers are advocating dividing this genus into three or more separate genera, others favor maintaining Drosophila as a single large genus. With the recent sequencing of the genomes of multiple Drosophila species and their expanding use in comparative biology, it is critical that the Drosophila research community understands the taxonomic framework underlying the naming and relationships of these species. The subdivision of this genus has significant biological implications, ranging from the accurate annotation of single genes to understanding how ecological adaptations have occurred over the history of the group.     

Yeasty clocks: dating genomic changes in yeasts

Calibration of clocks to date evolutionary changes is of primary importance for comparative genomics. In the absence of fossil records, the dating of changes during yeast genome evolution can only rely on the properties of the genomes themselves, given the uncertainty of extrapolations using clocks from other organisms. In this work, we use the experimentally determined mutational rate of Saccharomyces cerevisiae to calculate the numbers of successive generations corresponding to observed sequence polymorphism between strains or species of other yeasts. We then examine synteny conservation across the entire subphylum of Saccharomycotina yeasts, and compare this second clock based on chromosomal rearrangements with the first one based on sequence divergence. A non-linear relationship is observed, that interestingly also applies to insects although, for equivalent sequence divergence, their rate of chromosomal rearrangements is higher than that of yeasts.     

Comparative genomics in teleost species: Knowledge transfer by linking the genomes of model and non-model fish species

Comparative genomics is a powerful tool to transfer knowledge coming from model fish species to non-model fish species of economic or/and evolutionary interest. Such transfer is of importance as functional studies either are difficult to perform with most non-model species. The first comparative map constructed using the human and the chimpanzee genome allowed the identification of putative orthologues. Although comparative mapping in teleosts is still in its infancy, five model teleost genomes from different orders have been fully sequenced to date and the sequencing of several commercially important species are also underway or near completion. The accessibility of these whole genome sequences and rapid developments in genomics of fish species are paving the way towards new and valuable research in comparative genetics and genomics. With the accumulation of information in model species, the genetic and genomic characterization of non-model, but economically, physiologically or evolutionary important species is now feasible. Furthermore, comparison of low coverage gene maps of non-model fish species against fully sequenced fish species will enhance the efficiency of candidate gene identification projected for quantitative trait loci (QTL) scans for traits of special interest.     

Evolutionary relatedness between glycolytic enzymes most frequently occurring in genomes

More than 100 sequenced genomes were searched for genes coding for the enzymes involved in glycolysis in an effort to find the most frequently occurring ones. Triosephosphate isomerase (TIM), glyceraldehyde-3-phosphate dehydrogenase (GAPD), phosphoglycerate kinase (PGK) and enolase (ENOL) were found to be present in 90 investigated genomes all together. The final set consisted of 80 prokaryotic and 10 eukaryotic genomes. Of the 80 prokaryotic genomes, 73 were from Bacteria, 7 from Archaea. Two microbial genomes were also from Eucarya (yeasts). Eight genomes of nonmicrobial origin were included for comparison. The amino acid sequences of TIMs, GAPDs, PGKs and ENOLs were collected and aligned, and their individual as well as concatenated evolutionary trees were constructed and discussed. The trees clearly demonstrate a closer relatedness between Eucarya and Archaea (especially the concatenated tree) but they do not support the hypothesis that eukaryotic glycolytic enzymes should be closely related to their alpha-proteobacterial counterparts. Phylogenetic analyses further reveal that although the taxonomic groups (e.g., alpha-proteobacteria, gamma-proteobacteria, firmicutes, actinobacteria, etc.) form their more or less compact clusters in the trees, the inter-clade relationships between the trees are not conserved at all. On the other hand, several examples of conservative relatedness separating some clades of the same taxonomic groups were observed, e.g., Buchnera along with Wigglesworthia and the rest of gamma-proteobacteria, or mycoplasmas and the rest of firmicutes. The results support the view that these glycolytic enzymes may have their own evolutionary history.     

A model of the statistical power of comparative genome sequence analysis

Comparative genome sequence analysis is powerful, but sequencing genomes is expensive. It is desirable to be able to predict how many genomes are needed for comparative genomics, and at what evolutionary distances. Here I describe a simple mathematical model for the common problem of identifying conserved sequences. The model leads to some useful rules of thumb. For a given evolutionary distance, the number of comparative genomes needed for a constant level of statistical stringency in identifying conserved regions scales inversely with the size of the conserved feature to be detected. At short evolutionary distances, the number of comparative genomes required also scales inversely with distance. These scaling behaviors provide some intuition for future comparative genome sequencing needs, such as the proposed use of “phylogenetic shadowing” methods using closely related comparative genomes, and the feasibility of high-resolution detection of small conserved features.     

Drosophila biology in the genomic age

Over the course of the past century, flies in the family Drosophilidae have been important models for understanding genetic, developmental, cellular, ecological, and evolutionary processes. Full genome sequences from a total of 12 species promise to extend this work by facilitating comparative studies of gene expression, of molecules such as proteins, of developmental mechanisms, and of ecological adaptation. Here we review basic biological and ecological information of the species whose genomes have recently been completely sequenced in the context of current research.     

Origin and phylogeny of chloroplasts revealed by a simple correlation analysis of complete genomes

The complete sequenced genomes of chloroplast have provided much information on the origin and evolution of this organelle. In this paper we attempt to use these sequences to test a novel approach for phylogenetic analysis of complete genomes based on correlation analysis of compositional vectors. All protein sequences from 21 complete chloroplast genomes are analyzed in comparison with selected archaea, eubacteria, and eukaryotes. The distance-based analysis shows that the chloroplast genomes are most closely related to cyanobacteria, consistent with the endosymbiotic origin of chloroplasts. The chloroplast genomes are separated to two major clades corresponding to chlorophytes (green plants) s.l. and rhodophytes (red algae) s.l. The interrelationships among the chloroplasts are largely in agreement with the current understanding on chloroplast evolution. For instance, the analysis places the chloroplasts of two chromophytes (Guillardia and Odontella) within the rhodophyte lineage, supporting secondary endosymbiosis as the source of these chloroplasts. The relationships among the green algae and land plants in our tree also agree with results from traditional phylogenetic analyses. Thus, this study establishes the value of our simple correlation analysis in elucidating the evolutionary relationships among genomes. It is hoped that this approach will provide insights on comparative genome analysis.