OMA 2011: orthology inference among 1000 complete genomes.

OMA (Orthologous MAtrix) is a database that identifies orthologs among publicly available, complete genomes. Initiated in 2004, the project is at its 11th release. It now includes 1000 genomes, making it one of the largest resources of its kind. Here, we describe recent developments in terms of species covered; the algorithmic pipeline--in particular regarding the treatment of alternative splicing, and new features of the web (OMA Browser) and programming interface (SOAP API). In the second part, we review the various representations provided by OMA and their typical applications. The database is publicly accessible at http://omabrowser.org.

INTRODUCTION

Entire genomes are being sequenced faster than ever, yet making sense out of the resulting sequences remains a challenge. Fortunately, there is no need to start ab initio with each new genome, as much knowledge can be transferred from evolutionarily related species better characterized. In this context, a central notion is that of orthologs, pairs of genes that started diverging through speciation (1). Since by definition, orthologs were the same gene in their last common ancestor, it is commonly assumed that they have kept a similar function [e.g. (2)].

The interest for orthology has given rise to the development of several specialized databases, such as COG/KOG (3), InParanoid (4), OrthoMCL (5), YGOB (6), Roundup (7), Homologene (8), Ensembl Compara (9), HOGENOM (10), EggNog (11), MBGD (12), OrthoDB (13), PhyloDB (14) and PHOG (15).

Since 2004, we have been developing the orthology database OMA (Orthologous MAtrix), with the goal of analyzing all genomes that are publicly available (16). OMA is based on an algorithm that compares genes on the basis of evolutionary distances, considers distance inference uncertainty and accounts for differential gene losses (17). In an extensive assessment of 11 databases and methods, we showed that the orthologs inferred by OMA show high accuracy in terms of Fitch’s phylogeny-based definition and high conservation in terms of functional annotations (18). Results can be downloaded as raw data, consulted interactively using a web interface or accessed through the programming interfaces SOAP and DAS (19).

Recently, we have released the 11th revision of OMA, which includes ortholog predictions among 1000 genomes. This new milestone is an opportunity to inform the community of OMA’s latest developments. In the first part of this article, we reflect on the growth of OMA, describe algorithmic refinements and introduce new features of the web and programming interface. In the second part, we discuss the various types of representations and typical use cases. Finally, we conclude with thoughts on the future of OMA and of orthology databases in general.

RECENT DEVELOPMENTS AND NEW FUNCTIONS

Species analyzed

Between 2005 and 2010, OMA was updated 11 times, steadily increasing the number of genomes under analysis from 150 to 1000 genomes (Figure 1). This linear growth is noteworthy, because most orthology inference methods have a computational cost at least quadratic in the number of species. In OMA, we could compensate this computational burden through a combination of hardware and software improvements, and especially the 10-fold speed-up obtained from vectorizing the computation of Smith–Waterman sequence alignments (20).

Figure 1.

Growth of the OMA database since its first release.

The 11th release includes 827 bacteria, 103 eukaryotes and 70 archaea. The distribution of species among the main taxonomic ranks is depicted in Figure 2. Our primary sources for complete and annotated genomes included into OMA are GenomeReviews (21), Ensembl (22), EnsemblGenomes (23) and JGI (http://www.jgi.doe.gov). Thus, we rely on the quality and completeness standards of these databases. In addition, we also update genomes that have significantly changed since they were added to OMA. For instance, in the 10th release, 88 genomes (8.8%) were updated. The priority order of new and updated genomes is influenced by the needs of our users, whom we encourage to give us feedback.

Figure 2.

Visualization of the 1000 genomes included in the 10th release of OMA. Lineage assignments are based on NCBI Taxonomy database (24). Note that the radial scale (mean number of genes/genome) is not cumulative, i.e. it refers to the height of individual “band sectors”.

Algorithmic refinements

Since publication of the algorithm of OMA (17), our main algorithmic improvement has been in how we handle splice variants. In eukaryotic genomes, genes often have many splice variants, also called alternative splicings. In the version of the human genome currently in OMA (Ensembl v.55), genes have up to 44 annotated splice variants. This poses a challenge for ortholog prediction algorithms based on protein sequences, because orthology is defined at gene level. Thus, although all proteins produced from a particular gene should reflect its evolutionary history, problems arise when inconsistent splice variants are compared across species.

In previous works, alternative splicings have been handled in mainly three ways. Most commonly, a reference splice variant is selected, usually the longest one, and used exclusively in all computations (4,13). In Ensembl Compara, the reference (‘canonical’) variant is further required to be a bona fide transcript, and not a processed pseudogene, the result of non-sense mediated decay, or other such aberration (A. Vilella, personal communication). A potential problem with this first approach is that the reference variant might not necessarily match across all species. This problem is addressed in the second approach, which consists in keeping all splicing variants for the first part of the analysis, explicitly identifying the corresponding variants across species and choosing a representative one on this basis (25). But this idea entails markedly higher time complexity, and to our knowledge has only been applied to genome pairs. Finally, the third approach consists in considering for each gene the concatenation of all exons. This notion (‘metascript’), proposed in the context of a study on the selective pressure of protein-coding genes (26), has yet to be adopted by orthology databases (whose authors are perhaps reluctant to base all computations on artificial constructs).

In OMA, the way splicing variants are treated uses a combination of the first and second approaches above. First, not all splicing variants are integrated into the OMA sequence database. The longest variant is always retained, but shorter variants are only kept if they differ at least in 10% of their sequence from all longer variants retained. This way, most exons of a given gene will be part of some OMA sequence, while at the same time the total numbers of sequences is kept low. During the all-against-all pairwise alignment phase of OMA, these splicing variants are treated independently and are aligned against all other sequences (and splicing variants) in all other genomes. Later, for the formation of stable pairs, the pairs of putative orthologs, and all subsequent steps of the algorithm, only one splicing variant is used to represent a given gene. This is particularly important in OMA because such variants would be indistinguishable from paralogs, and paralogs are used as potential witnesses of non-orthology in the verification phase (27). At this stage, ideally, one would have to find the optimal combination of variants to keep for each gene, such that a maximal number of orthologs can be found. But as alluded above, the testing of the many combinations is excessively costly and thus a heuristic has to be employed. Thus, for each gene with alternative splicings, we select the variant for which the highest number of significant matches in all other genomes has been recorded in the all-against-all step. This is based on the assumption that a protein involved in more significant matches is also likely to form a higher number of orthologous pairs. For instance, with gene T22D3_HUMAN, the algorithm selects as reference splicing variant the same one as SwissProt’s canonical sequence, which happens not to be the longest transcript. In total, out of the 36 603 genes with alternate splicings, a non-longest transcript was selected 12 752 cases (34%). This proportion varies among the different genomes and is lowest for human (19%) and mouse (21%) and is highest for the pufferfish (54%). The impact on orthology inference is more difficult to assess, but we observe that the new procedure leads to more orthologous pairs inferred, and to larger OMA groups on average.

Hierarchical groups of orthologs

Starting with the 11th release (November 2010), we are adding a new type of orthologous grouping in OMA. Previously, our main type of groups were ‘OMA groups’, which are constructed with the objective that every pair of genes be orthologous. As we discuss in the next section, however, there are inherent limitations to this type of grouping strategy. As alternative to OMA groups, we now offer ‘hierarchical groups of orthologs’, groups of genes that descend from a single common ancestral gene within a given taxonomic range. This type of groups are at the core of several other orthology databases, most notably COG/KOG (3), OrthoDB (13) and EggNOG (11). We infer such groups from our pairwise orthology predictions and the NCBI taxonomy database (24) using the following idea. It can be easily shown that, with correct and complete pairwise orthology relations, hierarchical groups correspond to connected components in the orthology graph of the relevant species (the graph consists of genes as vertices, and orthology relations as edges). In practice, however, orthology graphs are rarely correct and complete. Missing edges are often not problematic, because the connected components tend to be strongly connected. Spurious edges, however, can lead to erroneous merging of distinct groups. To limit this problem, we identify and remove weak connections between clusters using a min-cut algorithm (28). We discuss applications of hierarchical groups in the last part of the article.

Web interface and API

We added new functionalities to the web and programming interfaces of OMA. First, given that one of the main interests in orthology is to determine the function of sequences, we have substantially improved the integration of Gene Ontology (GO) annotations to OMA. With each new OMA release, we retrieve the latest annotations from the GO consortium (29) and from the GOA database (30), and map them to all relevant sequences in OMA. The annotations are displayed on both protein-centric and OMA group views of the web interface. For all annotations, we now provide evidence codes and references/links to relevant PubMed articles or inference methods.

Second, whenever a gene has several splicing variants, all of them are listed under the ‘Information’ section. For variants other than the reference one, there is a link under ‘Ortholog’ to the splicing variant from which the orthology relationships have been computed.

Third, we have developed a new representation, which we call ‘genome pair view’, to provide a list of all orthologs between any two species. The function is accessible from the ‘Download’ section and the landing page of the OMA Browser. We discuss typical uses of this format in the next section.

Fourth, protein sequence search has been extended to support approximate sequence matching. The search algorithm is based on a seed-and-extend approach, with seeds of nine residues. Hence, at least nine consecutive characters need to match exactly for a sequence to be found. As a result, our system finds approximate queries almost instantaneously.

And fifth, we have added new functions to the SOAP programming interface to list the various identifiers supported in OMA (e.g. Swiss-Prot, Ensembl and GenBank) and perform conversions among them. For instance, it is now possible to retrieve the OMA identifiers corresponding to a list of Swiss-Prot gene names in a single function call. Using the same mechanism, it is also possible to retrieve Gene Ontology functional annotations corresponding to a list of proteins identified by any unique identifier supported in OMA. To help users getting started, we provide example clients in Python and Perl programming language (linked from http://omabrowser.org/API.html).

TYPES OF GROUPS AND THEIR APPLICATIONS

The primary product of the OMA pipeline is a list of high-confidence pairs of orthologous genes. This list is available for download, but is for most users too cumbersome to process and too general for typical applications. Thus, we also combine these pairwise relations into four types of groups. The existence of these different representations—and in general of multiple and at times conflicting definitions of orthologous groups—can be confusing for many users. In this section, we review the four types of groups provided in OMA, and discuss their advantages, limitations and applications (Figure 3).

Figure 3.

The four types of ortholog grouping provided in OMA. (a) protein-centric view reports orthologs to a gene of reference; (b) genome pair view lists all orthologs between two species; (c) OMA group view displays sets of genes in which all pairs of genes are orthologs and (d) hierarchical groups, groups of genes that descend from a single common ancestral gene within a given taxonomic range.

The most straightforward type of groups is the ‘protein-centric view’. In this representation, the OMA Browser provides the user with a list of genes orthologous to a specific gene. This view is appropriate for analyses centered on a single or only few genes of interest, e.g. to predict their function. More typical uses are provided in Table 1.

Table 1.

Typical applications of orthologs and their most suitable representation of orthology

Application	Appropriate orthology type	Comments
Propagate functional annotations between two genomes	Genome pair view, filtered to 1:1 orthologs	According to current models, 1:1 orthologs are likely to have a similar function.
Identify all orthologs of a gene in a given set of organisms	Protein-centric view	This includes in-paralogs in the target genomes lineages with respect to the speciation event with the query genome
Allign two whole genomes	Genome pair view	Orthologous genes are anchor points.
Align protein–protein interaction networks between two genomes	Genome pair view	Orthologs can be used to restrict the alignment search space. Thus, only conserved parts are used as anchors.
Identify all genes in vertebrates that descended from the ancestral β-hemoglobin	Hierarchical group of human β-hemoglobin with ‘Vertebrata’ as taxonomic range	This also retrieves γ-hemoglobin and ε-hemoglobin, which are thought to have diverged within the vertebrates (31).
Identify orthologs to infer a species tree	OMA groups with high-coverage of the species of interest	Since, barring classification error, all sequence pairs within an OMA group are orthologs, the corresponding gene tree is expected to follow the species tree.

For analyses involving mainly pairs of genomes, the ‘genome pair view’ accessible in the ‘Download’ section of the OMA Browser is the most appropriate: it provides a list of all pairs of orthologs between any two genomes specified by the user.

The third type of groups, ‘OMA groups’, consists in groups of genes in which all pairs are orthologs. In a graph representation with genes as nodes and orthology relations as edge, OMA groups correspond to fully connected subgraphs. Due to this definition, each OMA group includes at most one sequence per species, and, save for inference errors, the gene trees obtained from them should be congruent to the tree of the corresponding species. Indeed, the primary application of OMA groups is to provide input data for phylogenetic inference. In other applications, OMA group are often less appropriate. For example, evolutionary histories involving a duplication will, by definition, require at least two groups. Similarly, spuriously missed (i.e. false negative) orthologous predictions will also result in group fragmentation. And finally, because each protein belongs to one group at most, this representation only captures a subset of all inferred pairs of orthologs.

The last type of groups, ‘hierarchical groups’, consists in groups of genes that have descended from a common ancestral gene within a specific taxonomic range. Thus, by definition, hierarchical groups include both orthologs and in-paralogs with respect to the last common ancestor of the taxonomic range. In term of the underlying gene trees, hierarchical groups correspond to the leaves of subtrees rooted in the speciation events that define the taxonomic clade in question. By exploring groups across several levels, it is (at least in principle) possible to pinpoint the timing of particular duplication events. Hence, hierarchical groups can convey phylogenetic signal in ways that pairwise orthology/paralogy relations cannot.

CONCLUSIONS AND OUTLOOK

After 7 years of existence and trillions of alignments using over 5 million CPU hours, the OMA database now identifies orthologs among 1000 complete genomes. Recently, we have improved the way we handle alternative splicings, extended our integration of Gene Ontology functional annotations on the web interface, and added new functions to the SOAP programming interface. Furthermore, we have reviewed here how the four grouping strategies provided by OMA can be used for various typical analyses.

As for future developments, we see three areas of high potential for improvement. First, the orthology/paralogy dichotomy only considers speciation and gene duplication events. Thus, this leaves out other important evolutionary mechanisms, such as gene fusion and fission, domain shuffling, hybridization or lateral gene transfer. This latter phenomenon is particularly relevant in prokaryotes, where lateral gene transfer has long been recognized as a major evolutionary force. Second, orthology and paralogy are pairwise relations, and are thus ill-suited to expressing the evolutionary relationship of more than two genes at a time. Instead, gene trees labeled with relevant evolutionary events (speciation, duplication, LGT, etc.) constitute a better representation of the evolutionary relationships. As was suggested previously (32), we believe that in the medium term, gene trees will supersede pairwise orthology/paralogy predictions in most databases. And third, the growth in newly sequenced genomes will further accelerate in the foreseeable future. To cope with this increase, orthology inference algorithms will have to become more efficient. We are currently looking at ways to bypass part of the all-against-all phase by propagating orthology predictions across related organisms, but other approaches will need to be explored as well if we are to someday predict orthology among 10 000 genomes.

FUNDING

Funding for open access charge: The publication charges are funded through the lab’s ordinary budget.

Conflict of interest statement. None declared.