HCOP: The HGNC comparison of orthology predictions search tool

The HGNC Comparison of Orthology Predictions search tool, HCOP (), enables users to compare predicted human and mouse orthologs for a specified gene, or set of genes, from either species according to the ortholog assertions from the Ensembl, HGNC, Homologene, Inparanoid, MGI and PhIGs databases. Users can assess the reliability of the prediction from the number of these different sources that identify a particular orthologous pair. HCOP provides a useful one-stop resource to summarise, compare and access various sources of human and mouse orthology data.     

Ensembl 2002: accommodating comparative genomics

The Ensembl (http://www.ensembl.org/) database project provides a bioinformatics framework to organise biology around the sequences of large genomes. It is a comprehensive source of stable automatic annotation of human, mouse and other genome sequences, available as either an interactive web site or as flat files. Ensembl also integrates manually annotated gene structures from external sources where available. As well as being one of the leading sources of genome annotation, Ensembl is an open source software engineering project to develop a portable system able to handle very large genomes and associated requirements. These range from sequence analysis to data storage and visualisation and installations exist around the world in both companies and at academic sites. With both human and mouse genome sequences available and more vertebrate sequences to follow, many of the recent developments in Ensembl have focusing on developing automatic comparative genome analysis and visualisation.     

MultiMSOAR 2.0: an accurate tool to identify ortholog groups among multiple genomes

The identification of orthologous genes shared by multiple genomes plays an important role in evolutionary studies and gene functional analyses. Based on a recently developed accurate tool, called MSOAR 2.0, for ortholog assignment between a pair of closely related genomes based on genome rearrangement, we present a new system MultiMSOAR 2.0, to identify ortholog groups among multiple genomes in this paper. In the system, we construct gene families for all the genomes using sequence similarity search and clustering, run MSOAR 2.0 for all pairs of genomes to obtain the pairwise orthology relationship, and partition each gene family into a set of disjoint sets of orthologous genes (called super ortholog groups or SOGs) such that each SOG contains at most one gene from each genome. For each such SOG, we label the leaves of the species tree using 1 or 0 to indicate if the SOG contains a gene from the corresponding species or not. The resulting tree is called a tree of ortholog groups (or TOGs). We then label the internal nodes of each TOG based on the parsimony principle and some biological constraints. Ortholog groups are finally identified from each fully labeled TOG. In comparison with a popular tool MultiParanoid on simulated data, MultiMSOAR 2.0 shows significantly higher prediction accuracy. It also outperforms MultiParanoid, the Roundup multi-ortholog repository and the Ensembl ortholog database in real data experiments using gene symbols as a validation tool. In addition to ortholog group identification, MultiMSOAR 2.0 also provides information about gene births, duplications and losses in evolution, which may be of independent biological interest. Our experiments on simulated data demonstrate that MultiMSOAR 2.0 is able to infer these evolutionary events much more accurately than a well-known software tool Notung. The software MultiMSOAR 2.0 is available to the public for free.     

A Ruby API to query the Ensembl database for genomic features

The Ensembl database makes genomic features available via its Genome Browser. It is also possible to access the underlying data through a Perl API for advanced querying. We have developed a full-featured Ruby API to the Ensembl databases, providing the same functionality as the Perl interface with additional features. A single Ruby API is used to access different releases of the Ensembl databases and is also able to query multi-species databases. Availability and Implementation: Most functionality of the API is provided using the ActiveRecord pattern. The library depends on introspection to make it release independent. The API is available through the Rubygem system and can be installed with the command gem install ruby-ensembl-api.     

Behavior of polytene chromosomes of rhynchosciara angelae at different stages of larval development

Summary Polytene chromosomes in cells of salivary gland, Malpighian tubules and intestine of Rhynchosciara angelae are very favorable for study. The polytene chromosomes of the salivary gland are among the largest available for cytogenetics work. The ones in Malpighian tubules and in some parts of the intestine are as large and as favorable for cytological studies as the salivary chromosomes of many species of Drosophila.Two additional characteristics of Rhynchosciara make these flies excellent material for studies on the development of polytene chromosomes. 1.It is possible to observe the banding pattern of the polytene chromosomes at many stages of the larval life for at least 30 days before pupation, and 2. since the gregarious larvae develop simultaneously, one can sample the group at any stage desired. Sampling the group every day, it is possible to follow the development of the chromosomes as though one studied a single individual by observing it every day.We have followed in detail the behavior of the bands in two sections of chromosome B and in one section of chromosome C, at different stages of larval development. Some regions of the chromosomes which are represented by typical euchromatic bands at one stage of the larval development may develop in enormous bulbs, and later on may return to the banded stage again.The formation of the bulbs is not uniform in different sections of the same or of different chromosomes. In section 2 of chromosome B a certain locus swells enormously and then develops an enormous bulb, and later returns to the banded stage. At the point where the bulb was formed there is an accumulation of DNA, in amounts probably several times greater than before the bulb formation. In section 3 of chromosome B and section 3 of chromosome C the extra accumulation of DNA preceeds the formation of the bulb and is maintained during and after it. In the bulb formed in section 3 of chromosome C a single band seems to be responsible for the process.As shown by several authors, experimental evidence suggests that a gene is located within a band. The bulb formation in polytene chromosomes may then be morphological evidence of gene activities. This type of bulb formations and of return to the banded stage is a property of many chromosomes bands, during larval development. This type of behavior of many bands in polytene chromosomes is related to the process of nucleolus formation. However, this behavior may be found in almost all (if not in all) bands of the polytene chromosomes. If so, the behavior of the nucleolus organizer region is only a special case of this general process.The accumulation of DNA in different parts of the chromosome in cells of the same or of different tissues may be an argument against the theory of the constancy of the amount of DNA in all cells of a species. The bulb formations is not peculiar to R. angelae but occurs in several other Diptera.     

Why Genes Evolve Faster on Secondary Chromosomes in Bacteria

In bacterial genomes composed of more than one chromosome, one replicon is typically larger, harbors more essential genes than the others, and is considered primary. The greater variability of secondary chromosomes among related taxa has led to the theory that they serve as an accessory genome for specific niches or conditions. By this rationale, purifying selection should be weaker on genes on secondary chromosomes because of their reduced necessity or usage. To test this hypothesis we selected bacterial genomes composed of multiple chromosomes from two genera, Burkholderia and Vibrio, and quantified the evolutionary rates (dN and dS) of all orthologs within each genus. Both evolutionary rate parameters were faster among orthologs found on secondary chromosomes than those on the primary chromosome. Further, in every bacterial genome with multiple chromosomes that we studied, genes on secondary chromosomes exhibited significantly weaker codon usage bias than those on primary chromosomes. Faster evolution and reduced codon bias could in turn result from global effects of chromosome position, as genes on secondary chromosomes experience reduced dosage and expression due to their delayed replication, or selection on specific gene attributes. These alternatives were evaluated using orthologs common to genomes with multiple chromosomes and genomes with single chromosomes. Analysis of these ortholog sets suggested that inherently fast-evolving genes tend to be sorted to secondary chromosomes when they arise; however, prolonged evolution on a secondary chromosome further accelerated substitution rates. In summary, secondary chromosomes in bacteria are evolutionary test beds where genes are weakly preserved and evolve more rapidly, likely because they are used less frequently.     

A genome-wide, end-sequenced 129Sv BAC library resource for targeting vector construction

The majority of gene-targeting experiments in mice are performed in 129Sv-derived embryonic stem (ES) cell lines, which are generally considered to be more reliable at colonizing the germ line than ES cells derived from other strains. Gene targeting is reliant on homologous recombination of a targeting vector with the host ES cell genome. The efficiency of recombination is affected by many factors, including the isogenicity (H. te Riele et al., 1992, Proc. Natl. Acad. Sci. USA 89, 5128-5132) and the length of homologous sequence of the targeting vector and the location of the target locus. Here we describe the double-end sequencing and mapping of 84,507 bacterial artificial chromosomes (BACs) generated from AB2.2 ES cell DNA (129S7/SvEvBrd-Hprtb-m2). We have aligned these BACs against the mouse genome and displayed them on the Ensembl genome browser, DAS: 129S7/AB2.2. This library has an average insert size of 110.68 kb and average depth of genome coverage of 3.63- and 1.24-fold across the autosomes and sex chromosomes, respectively. Over 97% of the mouse genome and 99.1% of Ensembl genes are covered by clones from this library. This publicly available BAC resource can be used for the rapid construction of targeting vectors via recombineering. Furthermore, we show that targeting vectors containing DNA recombineered from this BAC library can be used to target genes efficiently in several 129-derived ES cell lines.     

GenOrigin: A comprehensive protein-coding gene origination database on the evolutionary timescale of life

The origination of new genes contributes to the biological diversity of life. New genes may quickly build their network, exert important functions, and generate novel phenotypes. Dating gene age and inferring the origination mechanisms of new genes, like primate-specific genes, is the basis for the functional study of the genes. However, no comprehensive resource of gene age estimates across species is available. Here, we systematically date the age of 9,102,113 protein-coding genes from 565 species in the Ensembl and Ensembl Genomes databases, including 82 bacteria, 57 protists, 134 fungi, 58 plants, 56 metazoa, and 178 vertebrates, using a protein-family-based pipeline with Wagner parsimony algorithm. We also collect gene age estimate data from other studies and uniformly distribute the gene age estimates to time ranges in a million years for comparison across studies. All the data are cataloged into GenOrigin (http://genorigin.chenzxlab.cn/), a user-friendly new database of gene age estimates, where users can browse gene age estimates by species, age, and gene ontology. In GenOrigin, the information such as gene age estimates, annotation, gene ontology, ortholog, and paralog, as well as detailed gene presence/absence views for gene age inference based on the species tree with evolutionary timescale, is provided to researchers for exploring gene functions.     

Transmission of alien tomato chromosomes from BC1 to BC2 progenies derived from backcrossing potato (+) tomato fusion hybrids to potato: the selection of single additions for seven different tomato chromosomes

 By backcrossing three BC₁ genotypes of potato (+) tomato fusion hybrids to different tetraploid potato pollinators, BC₂ populations were produced. A combined total of 97 BC₂ plants from three BC₂ populations were analysed with chromosome-specific probes through restriction fragment length polymorphism (RFLP) for the presence of alien tomato chromosomes. The number of different alien tomato chromosomes transmitted through the female BC₁ parent ranged from 0 to 6, and the average number of different alien chromosomes transmitted per BC₂ plant varied between 1.7 and 3.4 in the different populations. This variation corresponded to the chromosome constitution of the individual BC₁ parents: parent 6739, which possessed 11 different alien chromosomes in a single condition, gave rise to progeny with a lower average number of alien chromosomes per plant than the BC₁ parent 2003 that possessed 2 of the 12 alien chromosomes in a disomic condition. In the latter case, the higher transmission rate was attributed to the more regular distribution of the two alien chromosomes in the disomic condition because of regular bivalent formation during meiosis as revealed by genomic in situ hybridisation (GISH) and fluorescent in situ hybridisation (FISH). The transmission frequencies of individual alien chromosomes were subjected to statistical analysis to test whether the maternal genotypes had an effect on alien-chromosome transmission. Among the BC₂ plants, a total of 27 single additions were detected for as many as seven different chromosomes (1, 2, 4, 6, 8, 10 and 12) out of the 12 possible types. Received: 4 March 1997 / Accepted: 28 August 1997     

Patterns of segmental duplication in the human genome

We analyzed the completed human genome for recent segmental duplications (size > or = 1 kb and sequence similarity > or = 90%). We found that approximately 4% of the genome is covered by duplications and that the extent of segmental duplication varies from 1% to 14% among the 24 chromosomes. Intrachromosomal duplication is more frequent than interchromosomal duplication in 15 chromosomes. The duplication frequencies in pericentromeric and subtelomeric regions are greater than the genome average by approximately threefold and fourfold. We examined factors that may affect the frequency of duplication in a region. Within individual chromosomes, the duplication frequency shows little correlation with local gene density, repeat density, recombination rate, and GC content, except chromosomes 7 and Y. For the entire genome, the duplication frequency is correlated with each of the above factors. Based on known genes and Ensembl genes, the proportion of duplications containing complete genes is 3.4% and 10.7%, respectively. The proportion of duplications containing genes is higher in intrachromosomal than in interchromosomal duplications, and duplications containing genes have a higher sequence similarity and tend to be longer than duplications containing no genes. Our simulation suggests that many duplications containing genes have been selectively maintained in the genome.     

Microdissection and molecular manipulation of single chromosomes in woody fruit trees with small chromosomes using pomelo (<Emphasis Type="Italic">Citrus grandis</Emphasis>) as a model. II. Cloning of resistance gene analogs from single chromosomes

Amplification of resistance gene analogs (RGAs) is both a useful method for acquiring DNA markers closely linked to disease resistance (R) genes and a potential approach for the rapid cloning of R genes in plants. However, the screening of target sequences from among the numerous amplified RGAs can be very laborious. The amplification of RGAs from specific chromosomes could greatly reduce the number of RGAs to be screened and, consequently, speed up the identification of target RGAs. We have developed two methods for amplifying RGAs from single chromosomes. Method 1 uses products of Sau3A linker adaptor-mediated PCR (LAM-PCR) from a single chromosome as the templates for RGA amplification, while Method 2 directly uses a single chromosomal DNA molecule as the template. Using a pair of degenerate primers designed on the basis of the conserved nucleotide-binding-site motifs in many R genes, RGAs were successfully amplified from single chromosomes of pomelo using both these methods. Sequencing and cluster analysis of RGA clones obtained from single chromosomes revealed the number, type and organization of R-gene clusters on the chromosomes. We suggest that Method 1 is suitable for analyzing chromosomes that are unidentifiable under a microscope, while Method 2 is more appropriate when chromosomes can be clearly identified.Communicated by P. Langridge     

HCOP: a searchable database of human orthology predictions

The HUGO Gene Nomenclature Committee (HGNC) Comparison of Orthology Predictions (HCOP) search tool combines the human, mouse, rat and chicken orthology assertions made by PhIGs, HomoloGene, Ensembl, Inparanoid, Mouse Genome Informatics (MGI) and HGNC, enabling users to identify predicted ortholog pairs for a specified gene or genes. The HCOP resource provides a useful method to integrate, compare and access a variety of disparate sources of human orthology data. The HCOP search tool, data and documentation are available at http://www.gene.ucl.ac.uk/hcop.     

Silver staining of the centromeric area of acrocentric and Robertsonian metacentric mouse chromosomes

A silver stain (Kt) technique was used to analyze the centromeric area in metacentric chromosomes originating from Robertsonian rearrangements in the mouse. The 2n=40 all-acrocentric mouse karyotype and two Robertsonian-rearranged karyotypes (2n=24 and 2n=26 from Upper Valtellina) were used. The existence was demonstrated of a single centromeric pattern common to metacentric and to acrocentric chromosomes except for the Y, and consisting of two deeply stained dots, one per chromatid. In many cells this technique stains the nucleolar organizers and resolves the paracentromeric constitutive heterochromatin in chromomeres.     

The Ensembl genome database project

The Ensembl (http://www.ensembl.org/) database project provides a bioinformatics framework to organise biology around the sequences of large genomes. It is a comprehensive source of stable automatic annotation of the human genome sequence, with confirmed gene predictions that have been integrated with external data sources, and is available as either an interactive web site or as flat files. It is also an open source software engineering project to develop a portable system able to handle very large genomes and associated requirements from sequence analysis to data storage and visualisation. The Ensembl site is one of the leading sources of human genome sequence annotation and provided much of the analysis for publication by the international human genome project of the draft genome. The Ensembl system is being installed around the world in both companies and academic sites on machines ranging from supercomputers to laptops.     

Cytogenetic and biochemical investigations on fibroblast cultures and clones with one and two active X chromosomes of a 69,XXY triploidy

Bromodeoxyuridine replication patterns showed that fibroblasts from a 69,XXY triploidy carried either one or two early replicating X chromosomes. The activity of alpha-galactosidase A measured in single cells fell into two classes with a ratio of 1:2. Dilute plating produced clones of both types with the activity of alpha-galactosidase A corresponding to the number of active X chromosomes. To our knowledge, this is the first report on clones of a triploidy with different numbers of active X chromosomes, and on a gene-dosage effect of an X-linked gene using triploid cells with one active X as control.     

Transmission analysis of mitotically unstable B chromosomes in Locusta migratoria.

Seventeen controlled crosses in which the mitotically unstable B chromosome of Locusta migratoria was carried by one parent only have provided evidence that B chromosomes are significantly eliminated during sexual transmission in males, at a mean rate that almost counteracts the premeiotic accumulation derived from mitotic instability during germ line development. On the other hand, B chromosomes are significantly accumulated in females, presumably by their preferential migration to the secondary oocyte during the first meiotic division. These results substantially change the current knowledge about this B chromosome system, because the main B accumulation occurs in females and not in males, as was hitherto thought. Furthermore, this case shows that the maintenance of a single B system in natural populations may be the result of many different forces and mechanisms acting for and against B chromosomes.     

Meiosis in haploid barley — An interpretation of non-homologous chromosome associations

Detailed meiotic studies were conducted on ten haploid plants representing six different genotypes of barley (Hordeum vulgare, 2n=14). At pachytene stages the non-homologous chromosomes were observed to pair as intimately as homologous chromosomes in many cells. Foldback pairing, involving single chromosomes, and multivalent associations were common. At diplotene, up to 4 chiasmatalike structures were observed in paired chromosomes but it is not likely that they resulted from crossing over. At diakinesis the bivalent frequency mean was from 1 to 1.3 per cell whereas by metaphase I the paired associations were rare with a single rod bivalent being observed in 3 to 5% of the cells. The frequencies of various types of secondary associations at metaphase were also recorded. — The origin and significance of bivalents and secondary associations in haploids is reviewed and discussed. Caution is urged in the interpretation that low levels of chromosome pairing in haploids is evidence of homology. It is concluded that very little chromosome duplication is likely to be found within the haploid set of barley chromosomes and that the basic chromosome number is seven.     

Chromosomal behaviour and evolutionary trends in Chlorophytum (Liliaceae)

Chlorophytum laxum R. Rr. (Liliaceae) is a common perennial herb occurring in many parts of India, Ceylon, Borneo, Tropical Africa and Australia. The earlier cytological studies report two numbers of chromosomes, viz. 2n = 14 & 16, for the species. The present study, based on meiotic behaviour, concludes that this species is a segmental allopolyploid from two closely related but still unknown species with 2n = 8 chromosomes. Further evolution proceeded in two different directions. In one, diploidization by chromosomal rearrangements resulted into species with 2n = 16 chromosomes, while in the other, elimination of a non-homologous segment gave rise to species with 2n = 14 chromosomes and several autopolyploids.