Measuring genome conservation across taxa: divided strains and united kingdoms (original) (raw)
Journal Article
*To whom correspondence should be addressed. Tel: +44 1223 494653; Fax: +44 1223 494471; Email: [email protected]
Search for other works by this author on:
Search for other works by this author on:
Received:
24 September 2004
Revision received:
23 November 2004
Accepted:
20 December 2004
Published:
01 January 2005
PDF Cite
Victor Kunin, Dag Ahren, Leon Goldovsky, Paul Janssen, Christos A. Ouzounis, Measuring genome conservation across taxa: divided strains and united kingdoms, Nucleic Acids Research, Volume 33, Issue 2, 1 January 2005, Pages 616–621, https://doi.org/10.1093/nar/gki181
Close
Navbar Search Filter Mobile Enter search term Search
Abstract
Species evolutionary relationships have traditionally been defined by sequence similarities of phylogenetic marker molecules, recently followed by whole-genome phylogenies based on gene order, average ortholog similarity or gene content. Here, we introduce genome conservation—a novel metric of evolutionary distances between species that simultaneously takes into account, both gene content and sequence similarity at the whole-genome level. Genome conservation represents a robust distance measure, as demonstrated by accurate phylogenetic reconstructions. The genome conservation matrix for all presently sequenced organisms exhibits a remarkable ability to define evolutionary relationships across all taxonomic ranges. An assessment of taxonomic ranks with genome conservation shows that certain ranks are inadequately described and raises the possibility for a more precise and quantitative taxonomy in the future. All phylogenetic reconstructions are available at the genome phylogeny server: <http://maine.ebi.ac.uk:8000/cgi-bin/gps/GPS.pl>.
INTRODUCTION
Prior to the genome era, compositional signatures (1) or sequence alignments (2) were used to delineate the phylogenetic patterns across organisms. The availability of entire genome sequences has sparked a further development of methods for phylogenetic reconstructions on a genome-wide scale. Following this long tradition in molecular evolution, similar methods were expanded to encompass complete genome information, based on either compositional patterns (3,4) or concatenated alignments of orthologs (5,6).
More recently, methods that exploit the entire gene complement of completely sequenced genomes have been developed. These include phylogenies based on patterns of conservation of gene order (7), gene fusion events (8), gene content (7,9–13), protein folds (12), and average ortholog similarity (14). Only a few of these approaches were successful in resolving difficult cases, such as correctly grouping pathogens having highly reduced genomes with their free-living relatives and clustering Proteobacteria into a monophyletic group (7,9,14). In addition, most of the above mentioned methods are (i) not scalable to hundreds of species (e.g. concatenated alignments), (ii) unable to place correctly species with reduced genomes (13) and (iii) strongly affected by the number and phylogenetic proximity of species (e.g. gene order) (15).
Herein, we define a new composite measure termed ‘genome conservation’, which expresses both the conservation of sequence and gene content between two genomes. This value is derived from the sum of alignment scores between all proteins for every pair of organisms. Larger genomes tend to share more genes, irrespective of their phylogenetic distance (9). Thus, a higher conservation score can result from a higher number of shared genes, rather than from phylogenetic proximity. To counterbalance this effect, the results were normalized before tree reconstruction (see Materials and Methods).
The genome conservation method is naturally adjusted for missing genes and for gene lengths. If a gene is absent in one of the compared genomes, its contribution to the similarity is zero. However, if this absence is a direct result of reductive evolution and difference in genome sizes, absence of this gene would be calibrated by the normalization scheme described below. The gene length is taken into account in the summation of the BLAST scores: longer genes generate greater alignment scores and thus, would be more important contributors than shorter genes. Thus, the final similarity is based on both gene content and average sequence similarity of genes, with the adjustment for gene length.
MATERIALS AND METHODS
To obtain a similarity measure between any pair of genomes, we have compared all proteins using BlastP (16), with an e-value cut-off of e-10, and used the ‘bit-score’ as the measure of similarities between two sequences. The bit-score has the advantages of being independent of the searched database size. Moreover, it does not calibrate for protein length, thus, longer proteins have a greater impact than shorter ones. To eliminate noise created by paralogy in the cases when multiple hits were observed, only the best hit was used (i.e. the most significant sequence similarity). The total number of sequence similarities thus obtained exceeds 25 million pairs for 153 genomes. We will denote the sum of all best hits between genomes A and B as Σ(A,B).
The usage of best BlastP hits, when compared with orthologs, abolishes the issue of ortholog identification, which is still an unresolved problem for datasets of this size. However, it results in non-reciprocal genomic similarities, that is Σ(A,B) ≠ Σ(B,A). To calculate the conservation between genome A and genome B, we used the minimum of the two values, i.e. min(Σ(A,B), Σ(B,A)). To normalize for differences in genome sizes, we calculated the genome conservation distance measure D in two ways (D1 and D2): D1 = 1-S/min(Σ(A,A), Σ(B,B)), or D2 = −ln(S/(√2 * Σ(A,A) * Σ(B,B)/√((Σ(A,A))2 + (Σ(B,B))2))). D1 (9) and D2 (7) correspond to strategies for the transformation and normalization of self-similarity and adjustment for genome sizes, proposed previously. The tree discussed in the text was produced using D2, for consistency with gene content trees, reported to be optimal with this normalization (7). The phylogeny generated using D1 (Supplement 4) produces equally good results.
Gene content trees were generated as described elsewhere (7), using identical data as for the genome conservation tree. Average ortholog similarity was computed as the pairwise score divided by the smallest number of hits between the genomes, divided by 1000 as a scaling factor, or Σ(A,B)/(min(N(A,B), N(B,A)) * 1000), where N(A,B) is the number of hits between genomes A and B. These values were also normalized between 0 and 100, for comparison with other measures (Figure 2).
The values of pairwise distances were used to construct a distance matrix; trees were calculated using QuickTree (17). Bootstrap values were generated by resampling the pool of alignment scores between pairs of genomes for 1000 times. This procedure was not applied to the gene content tree, as it requires a jack knife approach rather than genuine bootstrapping (7).
In order to evaluate the conservation within taxonomic units, we computed an average of the conservation values, while eliminating taxonomic over-representation. Within each species, we averaged the pairwise conservation values of its strains. For higher taxonomic ranks (e.g. genus, family), the conservation between each pair of its sub-ranking taxa was averaged, thereby avoiding bias of unequal taxonomic sampling of sequenced species.
RESULTS AND DISCUSSION
Ideally, a species distance metric should enable the reliable inference of phylogeny across variable evolutionary time scales and taxonomic ranges. To assess the performance of genome conservation, we used standard neighbor-joining procedures (17,18) and produced a phylogenetic tree for 153 species with known genomes (19). The obtained tree (Supplement 1) clusters all the major clades consistently with current taxonomic knowledge (20) and is similar to the gene content-based tree (7,9), with a number of important exceptions, described below. Overall, compared to gene content phylogeny (7), a previously proposed and widely accepted method for whole-genome-based phylogenetic reconstruction, genome conservation produces significantly improved results (Supplement 2).
In the genome conservation tree, the alpha-, gamma-, delta- and epsilon proteobacteria form highly supported clades and consistently form a monophyletic proteobacterial clade (Figure 1A). Beta proteobacteria form a clade inside gamma proteobacteria, and there are two inconsistencies with the accepted taxonomy. First, Aquifex aeolicus is placed within Proteobacteria. This placement of Aquifex is also suggested by an independent study (21). Second, the Pseudomonas clade and Nitrosomonas europaea seem to be flipped with respect to each other. Both are coupled to tree nodes with low bootstrap values (686 and 585 out of 1000, respectively). In comparison, the gene content method fails to produce a plausible phylogenetic reconstruction of Proteobacteria (Figure 1B), or other taxa (Supplement 2). Furthermore, the average ortholog similarity approach generates a plausible scenario for evolution of Proteobacteria in the shallow branches of the tree, but fails to group both delta and epsilon subdivisions with other Proteobacteria, defining them as separate deeply branching groups (data not shown).
The recognition of abundance of horizontal gene transfer (HGT) among Archaea and Bacteria led to the questioning whether a reliable bacterial phylogeny can possibly be reconstructed (22). Yet, the overall agreement of whole-genome based methods, such as genome conservation, average pairwise sequence similarity, gene content and 16S rRNA phylogenies clearly demonstrates the existence of a consistent bacterial phylogeny (23).
In comparative genomics, it is crucial to accurately measure the evolutionary distance between organisms. Levels of conservation of 16S rRNA sequence may not be sufficient to estimate the evolutionary distance and guarantee species identity, especially in the case of recently divergent organisms (24). Presently, species distances are often estimated in millions of years of divergence (25–27). However, the time of divergence estimated from the ‘molecular clock’ is extremely imprecise (28) and only organisms with fossil records can be dated with some accuracy (29). Another popular form of estimating evolutionary distance is measuring the number of neutral substitutions per site. This technique is appropriate for higher eukaryotes or closely related bacteria; however, saturation in mutations hinders reliable estimations for highly divergent bacterial species (30).
We propose the use of pairwise genome conservation metric as a stable whole-genome based evolutionary measurement to assess conservation between organisms. A pictorial representation of the genome conservation matrix across all presently sequenced organisms readily demonstrates the ability of this species distance metric to define evolutionary relationships at variable taxonomic ranges, from strain variants up to the three domains of life (Figure 2A; the complete set of values is available as Supplement 3).
We have compared the similarity matrices derived from the three principal genome-based phylogeny methods, namely genome conservation, gene content and average ortholog similarity. All matrices evidently contain a strong phylogenetic signal, represented both by the diagonal (self-hits) and various groupings of related taxa (Figure 2). All matrices are also able to clearly separate the three domains of life and delineate closely related groups. These similarity matrices are transformed to distance matrices for the construction of phylogenetic trees (see Materials and Methods), which produce different results.
Massive gene loss in some intracellular parasites, such as Buchnera and Wolbachia, creates an effect where these species share their entire gene content with multiple, distantly related lineages. The similarity estimated from gene content, normalized by the size of the minimal genome, fails to accurately estimate species distances (Figure 2B). The genome conservation approach also suffers from the same effect, however on a significantly lower level (Figure 2A). Finally, average ortholog similarity (Figure 2C) is independent of genome size, and thus resistant to the problem of drastically reduced genome sizes.
However, it is evident that genome conservation allows the detection of phylogenetic groupings at variable taxonomy ranges, from stains up to entire domains of life (Figure 2A). Despite the fact that some of these patterns are also present in the gene content and average ortholog similarity matrices (Figure 2B and C, respectively), their resolution is less pronounced, reflected by a blurred distribution of color-encoded similarity across taxa.
Having demonstrated that the genome conservation metric reflects meaningful evolutionary relationships, we subsequently explored its ability to resolve long-standing arguments in defining the concept of bacterial taxa (31). Using genome conservation as a measure of evolutionary divergence, we investigated how the levels of taxonomical classification in Bacteria correspond to evolutionary distances (Figure 3). Overall, there is a clear decrease in genome conservation at the higher taxonomic ranks. However, the definition of some taxonomic units is not precise, and the ranges of genome conservation for various ranks often overlap (Figure 3). The other two measures, namely, gene content and average ortholog similarity, also exhibit a gradual reduction across increasing taxonomic distances, yet within a narrower value range, which renders them less effective in detecting taxonomic ranks (data not shown). It is worth noting that in all cases, the ranks of genus and family are the least well-defined, according to any genomic similarity measure.
In particular, we found that the broadest distribution of genome conservation scores is observed within the genus rank. The similarity between species belonging to the same genus can vary considerably. For example, Mycobacterium tuberculosis and M.bovis are 96% similar whereas Mycoplasma gallisepticum, M.pneumoniae and M.penetrans are only 16% similar. Another example of questionable classification involves Prochlorococcus marinus strains MIT9313 and MED4, which present a challenging case for rRNA-based taxonomy. These two strains are 97% similar in their 16S rRNA sequence (32), while representing distinct genetic populations, with a 2-fold difference in genome size and content (33), as well as specific phenotypic properties. Genome conservation between these strains is only 49%, which is more typical for distances between genera within a family, rather than strains within a species. The genome conservation measurement of classification provides a possibility of a precise and quantitative definition of each taxonomic unit and a guide for future taxonomic classification.
In summary, the genome conservation method uses a genomic perspective of gene content and couples it with sequence divergence at the whole-genome level. Despite the limitation that an entire genome is required in order to place a species in its taxonomic context, this approach can delineate poorly resolved taxa and potentially be coupled with local rRNA-based phylogenies. However, with the new approaches to whole-genome sequencing in environmental genomics (34), the genome conservation approach can provide an unambiguous and consistent classification system for the newly discovered species. The proposed species distance metric provides a clear measure based on sequence divergence for use in comparative genomics and taxonomy.
SUPPLEMENTARY MATERIAL
Supplementary Material is available at NAR Online.
Figure 1
Part of the complete tree of life containing the Proteobacteria generated by genome conservation (A) and gene content (B) methods. Classes are color-coded, and the Spirochaetum Leptospira interrogans and deeply branching Aquifex aeolicus are shown in black. Trees were generated using D2 normalization as described in Materials and Methods; the complete tree is available in Supplement 1.
Figure 2
Similarity matrices across all completely sequenced organisms, derived from genome conservation (A), gene content (B) and average ortholog similarity (C). Each matrix element represents a pairwise comparison of the corresponding genomes. Genome conservation and gene content were computed using D1 normalization (see Materials and Methods). Species are ordered consistently across the different matrices, sorted according to their position on the genome conservation tree (Supplement 1), and major clades are indicated in (A). The conservation levels in percentages are color-coded, and the values for individual pairwise scores for genome conservation are available (Supplement 3). It is evident that there are three fields of values, seen as lighter blue sub-matrices representing Eukarya, Archaea and Bacteria, from top left to bottom right in (A). The diagonal values of 100% represent self-similarity. Highly similar groups are evident, for instance Escherichia coli strains (red or yellow) and enterobacteria (green), both within γ-proteobacteria. For the comparison of the matrices, see text.
Figure 3
Genome conservation within bacterial taxonomic ranks. Error bars mark standard deviations. See text for discussion, genome conservation computed using D1 normalization (see Materials and Methods).
We would like to thank Russell F. Doolittle (UCSD) for his comments. We also thank Lee Bofkin (EBI) and members of the Computational Genomics Group for valuable discussions. C.A.O. acknowledges additional support from IBM Research. All computations were carried out on the IBM 200-CPU cluster at the EBI. Funding to pay the Open Access publication charges for this article was provided by EMBL.
REFERENCES
1
Fox, G.E., Stackebrandt, E., Hespell, R.B., Gibson, J., Maniloff, J., Dyer, T.A., Wolfe, R.S., Balch, W.E., Tanner, R.S., Magrum, L.J., et al.
1980
The phylogeny of prokaryotes
Science
209
457
–463
2
Doolittle, R.F.
1981
Similar amino acid sequences: chance or common ancestry?
Science
214
149
–159
3
Kreil, D.P. and Ouzounis, C.A.
2001
Identification of thermophilic species by the amino acid compositions deduced from their genomes
Nucleic Acids Res.
29
1608
–1615
4
Qi, J., Wang, B., Hao, B.I.
2004
Whole proteome prokaryote phylogeny without sequence alignment: a K-string composition approach
J. Mol. Evol.
58
1
–11
5
Brown, J.R., Douady, C.J., Italia, M.J., Marshall, W.E., Stanhope, M.J.
2001
Universal trees based on large combined protein sequence data sets
Nature Genet.
28
281
–285
6
Rokas, A., Williams, B.L., King, N., Carroll, S.B.
2003
Genome-scale approaches to resolving incongruence in molecular phylogenies
Nature
425
798
–804
7
Korbel, J.O., Snel, B., Huynen, M.A., Bork, P.
2002
SHOT: a web server for the construction of genome phylogenies
Trends Genet.
18
158
–162
8
Enright, A.J. and Ouzounis, C.A.
2001
Functional associations of proteins in entire genomes by means of exhaustive detection of gene fusions
Genome Biol.
2
RESEARCH0034
9
Snel, B., Bork, P., Huynen, M.A.
1999
Genome phylogeny based on gene content
Nature Genet.
21
108
–110
10
Fitz-Gibbon, S.T. and House, C.H.
1999
Whole genome-based phylogenetic analysis of free-living microorganisms
Nucleic Acids Res.
27
4218
–4222
11
Tekaia, F., Lazcano, A., Dujon, B.
1999
The genomic tree as revealed from whole proteome comparisons
Genome Res.
9
550
–557
12
Lin, J. and Gerstein, M.
2000
Whole-genome trees based on the occurrence of folds and orthologs: implications for comparing genomes on different levels
Genome Res.
10
808
–818
13
House, C.H. and Fitz-Gibbon, S.T.
2002
Using homolog groups to create a whole-genomic tree of free-living organisms: an update
J. Mol. Evol.
54
539
–547
14
Clarke, G.D., Beiko, R.G., Ragan, M.A., Charlebois, R.L.
2002
Inferring genome trees by using a filter to eliminate phylogenetically discordant sequences and a distance matrix based on mean normalized BLASTP scores
J. Bacteriol.
184
2072
–2080
15
Wolf, Y.I., Rogozin, I.B., Grishin, N.V., Koonin, E.V.
2002
Genome trees and the tree of life
Trends Genet.
18
472
–479
16
Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J., Zhang, Z., Miller, W., Lipman, D.J.
1997
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
Nucleic Acids Res.
25
3389
–3402
17
Howe, K., Bateman, A., Durbin, R.
2002
QuickTree: building huge Neighbour-Joining trees of protein sequences
Bioinformatics
18
1546
–1547
18
Saitou, N. and Nei, M.
1987
The neighbor-joining method: a new method for reconstructing phylogenetic trees
Mol. Biol. Evol.
4
406
–425
19
Janssen, P., Enright, A.J., Audit, B., Cases, I., Goldovsky, L., Harte, N., Kunin, V., Ouzounis, C.A.
2003
COmplete GENome Tracking (COGENT): a flexible data environment for computational genomics
Bioinformatics
19
1451
–1452
20
Wheeler, D.L., Church, D.M., Edgar, R., Federhen, S., Helmberg, W., Madden, T.L., Pontius, J.U., Schuler, G.D., Schriml, L.M., Sequeira, E., et al.
2004
Database resources of the National Center for Biotechnology Information: update
Nucleic Acids Res.
32
D35
–D40
21
Dutilh, B.E., Huynen, M.A., Bruno, W.J., Snel, B.
2004
The consistent phylogenetic signal in genome trees revealed by reducing the impact of noise
J. Mol. Evol.
58
527
–539
22
Doolittle, W.F.
1999
Phylogenetic classification and the universal tree
Science
284
2124
–2129
23
Kurland, C.G., Canback, B., Berg, O.G.
2003
Horizontal gene transfer: a critical view
Proc. Natl Acad. Sci. USA
100
9658
–9662
24
Fox, G.E., Wisotzkey, J.D., Jurtshuk, P., Jr.
1992
How close is close: 16S rRNA sequence identity may not be sufficient to guarantee species identity
Int. J. Syst. Bacteriol.
42
166
–170
25
Hedges, S.B.
2002
The origin and evolution of model organisms
Nature Rev. Genet.
3
838
–849
26
Hedges, S.B., Parker, P.H., Sibley, C.G., Kumar, S.
1996
Continental breakup and the ordinal diversification of birds and mammals
Nature
381
226
–229
27
Kumar, S. and Hedges, S.B.
1998
A molecular timescale for vertebrate evolution
Nature
392
917
–920
28
Graur, D. and Martin, W.
2004
Reading the entrails of chickens: molecular timescales of evolution and the illusion of precision
Trends Genet.
20
80
–86
29
Benton, M.J. and Ayala, F.J.
2003
Dating the tree of life
Science
300
1698
–1700
30
Gribaldo, S. and Philippe, H.
2002
Ancient phylogenetic relationships
Theor. Popul. Biol.
61
391
–408
31
Cohan, F.M.
2002
What are bacterial species?
Annu. Rev. Microbiol.
56
457
–487
32
Moore, L.R., Rocap, G., Chisholm, S.W.
1998
Physiology and molecular phylogeny of coexisting Prochlorococcus ecotypes
Nature
393
464
–467
33
Rocap, G., Larimer, F.W., Lamerdin, J., Malfatti, S., Chain, P., Ahlgren, N.A., Arellano, A., Coleman, M., Hauser, L., Hess, W.R., et al.
2003
Genome divergence in two Prochlorococcus ecotypes reflects oceanic niche differentiation
Nature
424
1042
–1047
34
Venter, J.C., Remington, K., Heidelberg, J.F., Halpern, A.L., Rusch, D., Eisen, J.A., Wu, D., Paulsen, I., Nelson, K.E., Nelson, W., et al.
2004
Environmental genome shotgun sequencing of the Sargasso Sea
Science
304
66
–74
© The Author 2005. Published by Oxford University Press. All rights reserved The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact [email protected].
I agree to the terms and conditions. You must accept the terms and conditions.
Submit a comment
Name
Affiliations
Comment title
Comment
You have entered an invalid code
Thank you for submitting a comment on this article. Your comment will be reviewed and published at the journal's discretion. Please check for further notifications by email.