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Genome Evolution: The Dynamics of Static Genomes
Current Biology, Vol. 14, R473–R474, June 22, 2004, ©2004 Elsevier Ltd. All rights reserved. DOI 10.1016/j.cub.2004.06.012
Genome Evolution: The Dynamics of Static Genomes Alexandra Stechmann
A random survey of a microsporidian genome has revealed some striking features. Although the genomes of microsporidians are among the smallest known for eukaryotes, their organisation appears to be well conserved.
Microsporidia are unicellular eukaryotes with an obligate intracellular parasitic life-style, infecting mainly animals. They were once thought to have evolved early in eukaryote evolution, because they lack mitochondria. But improvements in phylogenetic methods and the discovery that they have genes of mitochondrial origin now confidently place Microsporidia close to fungi [1,2]. Recent years have seen an increase in whole genome sequencing projects, and the genome of the microsporidian Encephalitozoon cuniculi was among the first to be completed for a unicellular eukaryote [2]. This genome is characterised by being highly compacted, possibly an adaptation to a parasitic lifestyle, and at 3.2 Mb is one of the smallest eukaryote genomes known to date. This is even smaller than many prokaryotic genomes. In E. cuniculi, many of the proteincoding genes are reduced in length compared to their homologues in other eukaryotes; intergenic regions, where present, are tiny, and genes involved in some of the biosynthetic pathways or in the tricarboxylic acid cycle are missing completely, indicating a strong dependency on the metabolism of its host. A partial genome survey of the microsporidian Antonospora locustae (formerly Nosema locustae), reported recently in Current Biology [3], reveals another astonishing aspect of these remarkable genomes. Although they branch distantly from each other in gene trees, the genomes of E. cuniculi and A. locustae are strikingly similar in their organisation, showing an unexpectedly high degree of conservation of gene order (synteny). More than a tenth of the sequences investigated from A. locustae are in the same genomic context as in E. cuniculi, and a third of the genes are separated by only a small number of short rearrangements [3]. From Genes to Genomes Molecular evolution studies in the past have been largely dominated by analyses of individual gene sequences, but the number of full genome sequencing projects and genome survey studies of diverse lineages of the tree of life is increasing at an astonishing rate. Such data allow us to study evolution at a different level, providing insights into the evolution and functional organisation of genomes. Comparative genome Department of Biochemistry and Molecular Biology, Dalhousie University, Sir Charles Tupper Building, College Street 5850, Halifax, Canada B3H 1X5. E-mail: [email protected]
Dispatch
analysis is still a relatively new field with vertebrate genomes attracting the most attention [4–6]. The total number of chromosome rearrangements between human and mouse, for example, has been estimated to be 172 [5] or even higher [6]. One would expect that the genomes of closely related organisms should display a high degree of synteny, as their genomes have not had as much time to accumulate rearrangements when compared to more distantly related organisms [7]. The data presented by Slamovits et al. [3] may not fit these predictions. The two microsporidians they compared diverged early from each other in their phylogenetic tree. The average protein distance between the two microsporidians, given as the proportion of differences in amino-acid sequence, is 0.5, roughly double the distance between the two fungi Candida albicans and Saccharomyces cerevisiae (0.29). Yet the genomes of the two microsporidians are more similar in their arrangement than the two fungal ones [3]. Such a high sequence distance either reflects the phylogenetic divergence between two organisms or could simply be caused by higher rates of sequence evolution. Are Sequence and Genome Evolution Linked? The two malaria parasites Plasmodium falciparum and P. yoelii (phylum Apicomplexa) have a higher sequence similarity to each other than Candida and Saccharomyces, and also show a high degree of synteny [8]. However, Plasmodium and another apicomplexan parasite, Cryptosporidium, which only have a slightly lower sequence divergence than the two microsporidians show no synteny [9]. Ghedin et al. [10] analysed the genomes of three trypanosomatids and detected a high degree of synteny over large chromosomal fragments (>100 kb) for all three species. Like the two microsporidia, the three trypanosomatids show a rather high level of sequence divergence — the protein distance between Leishmania and Trypanosoma is 0.55–0.6; between Trypanosoma cruzi and T. brucei it is <0.45 — and a high degree of synteny. Within vertebrates and insects, a high degree of gene order conservation has been reported [6,11,12]. The plant genomes sequenced so far lack any apparent conservation in gene order, although they display some degree of local small-scale conservation (microsynteny), despite their relatively recent evolutionary origins [13,14]. These examples show that sequence and genome diversity evolve as independent processes, and that the evolutionary rates of sequences do not reflect the evolutionary rate of the genomes in which they are embedded. Re-Arranging a Genome So what is it that keeps genes in the same order over evolutionary time? It makes sense to keep functionally related genes in close physical proximity as they are often co-regulated. One well known example is the set
Dispatch R474
of Hox genes that show remarkable conservation of gene order across animal phyla and are exquisitely coordinated in their expression during development [15]. In trypanosomatids, genes are transcribed as large polycistronic precursor mRNAs before being cleaved into monocistronic messengers and it is suggested that both the direction of replication and transcription are coordinated [10]. Rearrangements could disrupt these directional processes and thus may be selected against [10]. To study further what other factors might influence gene order, Pal and Hurst [16] closely analysed the Candida and Saccharomyces genomes. They observed that essential (or vital) genes are highly clustered, and that these clusters are in regions with low recombination rates. Essentially, recombination rates are lower, and hence the gene order is more conserved, around genes that provide essential functions. The mechanisms behind gene rearrangements could be transpositions — as is most likely the case in trypanosomatids, where retrotransposon-like elements have been found in regions associated with rearrangements [10] — or inversions, which are proposed to play a major role for small-scale changes in gene order between Candida and Saccharomyces [17]. Stasis in Small Genomes? It does not seem too surprising that a high degree of synteny and small genome size go hand in hand. Changing the gene order in a genome requires breakpoints, which cause the physical disruption of a given stretch of sequence. The chances of disrupting a functional gene are much higher in compact genomes with few and small intergenic regions. Still, the question of whether the frequency of rearrangements is lower in small genomes remains open. Trypanosomatids have genomes roughly ten times larger than E. cuniculi, yet their gene order seems highly conserved [10]. Prokaryote genomes are smaller than eukaryote genomes and Huynen et al. [17] compared rearrangement rates between the genomes of Candida and Saccharomyces with those between two prokaryotes, Haemophilus influenzae and Escherichia coli. They show that the overall rate of rearrangements is lower in the prokaryotes; however, this can be explained by the operon structure of prokaryote genomes. With only 3.2 Mb, the E. cuniculi genome is even smaller than many prokaryote genomes [2], which may explain why its gene order is so conserved; however data from the entire genome of A. locustae are not available (although its genome size has been estimated to be 5.4 Mb [18]). It will be interesting to see if other microsporidians have a similarly high degree of genome compaction and synteny as that observed between E. cuniculi and A. locustae. At the moment, everything points to Microsporidia having rapidly changing gene sequences within a slow evolving genome. Perhaps this should not be too surprising — after all, the mutational mechanisms and the selective forces acting on gene sequences are very different from those affecting genome organisation. As more eukaryotic genomes become available, commonalities and differences in the process of genome evolution across the tree of life should become much clearer. It has already become
clear that the metaphor of a constant evolutionary molecular clock applies neither to genomes nor the genes they encode. References 1. Embley, T.M., and Hirt, R.P. (1998). Early branching eukaryotes? Curr. Opin. Genet. Dev. 8, 624-629. 2. Katinka, M.D., Duprat, S., Cornillot, E., Metenier, G., Thomarat, F., Prensier, G., Barbe, V., Peyretaillade, E. et al. (2001). Genome sequence and gene compaction of the eukaryote parasite Encephalitozoon cuniculi. Nature 414, 450-453. 3. Slamovits, C.H., Fast, N.M., Law, J.S., and Keeling, P.J. (2004). Genome compaction and stability in microsporidian intracellular parasites. Curr. Biol. May 25 issue. 4. Andersson, L., Archibald, A., Ashburner, M., Audun, S., Barendse, W., Bitgood, J., Bottema, C., Broad, T., et al. (1997). Comparative genome organisation of vertebrates. Mamm. Gen. 7, 717-734. 5. Burt, D.W., Bruley, C., Dunn, I.C., Jones, C.T., Ramage, A., Law, A.S., Morrice, D.R., Paton, I.R., et al. (1999). The dynamics of chromosome evolution in birds and mammals. Nature 402, 411-413. 6. Bourque, G., Pevzner, P.A., and Tesler, G. (2004). Reconstructing the genomic architecture of ancestral mammals: lessons from human, mouse, and rat genomes. Genome Res. 14, 507-516. 7. Nadeau, J.H., and Sankoff, D. (1998). Counting on comparative maps. Trends Genet. 14, 495-501. 8. Carlton, J.M., Angiuoli, S.,V., Suh, B.B., Kooij, T.W., Pertea, M., Silva, J.C., Ermolaeva, M.D., Allen, J.E. et al. (2002). Genome sequence and comparative analysis of the model rodent malaria parasite Plasmodium yoelii yoelii. Nature 419, 512-519. 9. Bankier, A.T., Spriggs, H.F., Fartmann, B., Konfortov, B.A., Madera, M., Vogel, C., Teichmann, S.A., Ivens, A., and Dear, P.H. (2003). Integrated mapping, chromosomal sequencing and sequence analysis of Cryptosporidium parvum. Genome Res. 13, 1787-1799. 10. Ghedin, E., Bringaud, F., Peterson, J., Myler, P., Berriman, M., Ivens, A., Andersson, B., Bontempi, E. et al. (2004). Gene synteny and evolution of genome architecture in trypanosomatids. Mol. Biochem. Parasitol. 134, 183-191. 11. Zdobnov, E.M., von Mering, C., Letunic, I., Torrents, D., Suyama, M., Copley, R.R., Christophides, G.K., Thomasova, D. et al. (2002). Comparative genome and proteome analysis of Anopheles gambiae and Drosophila melanogaster. Science 298, 149-159. 12. McLysaght, A., Enright, A.J., Skrabanek, L., and Wolfe, K.H. (2000). Estimation of synteny conservation between pufferfish (Fugu) and human. Yeast 17, 22-36. 13. Bennetzen, J.L. (2000). Comparative sequence analysis of plant nuclear genomes: microlinearity and its many exceptions. Plant Cell 12, 1021-1029. 14. Delseny, M. (2004). Re-evaluating the relevance of ancestral shared synteny as a tool for crop improvement. Curr. Op. Plant Biol. 7, 126131. 15. Ferrier, D.E.K., and Minguillon, C. (2003). Evolution of the Hox/ParaHox gene clusters. Int. J. Dev. Biol. 47, 605-611. 16. Pal, C., and Hurst, L.D. (2003). Evidence for co-evolution of gene order and recombination rates. Nat. Genet. 33, 392-395. 17. Huynen, M.A., Snel, B., and Bork, P. (2001). Inversions and the dynamics of eukaryotic gene order. Trends Genet. 17, 304-306. 18. Street, D.A. (1994). Analysis of Nosema locustae (Microsporidia: Nosematidae) chromosomal DNA with pulse-field gel electrophoresis. J. Invertebr. Pathol. 63, 301-303.
Genome Evolution: The Dynamics of Static Genomes Alexandra Stechmann
A random survey of a microsporidian genome has revealed some striking features. Although the genomes of microsporidians are among the smallest known for eukaryotes, their organisation appears to be well conserved.
Microsporidia are unicellular eukaryotes with an obligate intracellular parasitic life-style, infecting mainly animals. They were once thought to have evolved early in eukaryote evolution, because they lack mitochondria. But improvements in phylogenetic methods and the discovery that they have genes of mitochondrial origin now confidently place Microsporidia close to fungi [1,2]. Recent years have seen an increase in whole genome sequencing projects, and the genome of the microsporidian Encephalitozoon cuniculi was among the first to be completed for a unicellular eukaryote [2]. This genome is characterised by being highly compacted, possibly an adaptation to a parasitic lifestyle, and at 3.2 Mb is one of the smallest eukaryote genomes known to date. This is even smaller than many prokaryotic genomes. In E. cuniculi, many of the proteincoding genes are reduced in length compared to their homologues in other eukaryotes; intergenic regions, where present, are tiny, and genes involved in some of the biosynthetic pathways or in the tricarboxylic acid cycle are missing completely, indicating a strong dependency on the metabolism of its host. A partial genome survey of the microsporidian Antonospora locustae (formerly Nosema locustae), reported recently in Current Biology [3], reveals another astonishing aspect of these remarkable genomes. Although they branch distantly from each other in gene trees, the genomes of E. cuniculi and A. locustae are strikingly similar in their organisation, showing an unexpectedly high degree of conservation of gene order (synteny). More than a tenth of the sequences investigated from A. locustae are in the same genomic context as in E. cuniculi, and a third of the genes are separated by only a small number of short rearrangements [3]. From Genes to Genomes Molecular evolution studies in the past have been largely dominated by analyses of individual gene sequences, but the number of full genome sequencing projects and genome survey studies of diverse lineages of the tree of life is increasing at an astonishing rate. Such data allow us to study evolution at a different level, providing insights into the evolution and functional organisation of genomes. Comparative genome Department of Biochemistry and Molecular Biology, Dalhousie University, Sir Charles Tupper Building, College Street 5850, Halifax, Canada B3H 1X5. E-mail: [email protected]
Dispatch
analysis is still a relatively new field with vertebrate genomes attracting the most attention [4–6]. The total number of chromosome rearrangements between human and mouse, for example, has been estimated to be 172 [5] or even higher [6]. One would expect that the genomes of closely related organisms should display a high degree of synteny, as their genomes have not had as much time to accumulate rearrangements when compared to more distantly related organisms [7]. The data presented by Slamovits et al. [3] may not fit these predictions. The two microsporidians they compared diverged early from each other in their phylogenetic tree. The average protein distance between the two microsporidians, given as the proportion of differences in amino-acid sequence, is 0.5, roughly double the distance between the two fungi Candida albicans and Saccharomyces cerevisiae (0.29). Yet the genomes of the two microsporidians are more similar in their arrangement than the two fungal ones [3]. Such a high sequence distance either reflects the phylogenetic divergence between two organisms or could simply be caused by higher rates of sequence evolution. Are Sequence and Genome Evolution Linked? The two malaria parasites Plasmodium falciparum and P. yoelii (phylum Apicomplexa) have a higher sequence similarity to each other than Candida and Saccharomyces, and also show a high degree of synteny [8]. However, Plasmodium and another apicomplexan parasite, Cryptosporidium, which only have a slightly lower sequence divergence than the two microsporidians show no synteny [9]. Ghedin et al. [10] analysed the genomes of three trypanosomatids and detected a high degree of synteny over large chromosomal fragments (>100 kb) for all three species. Like the two microsporidia, the three trypanosomatids show a rather high level of sequence divergence — the protein distance between Leishmania and Trypanosoma is 0.55–0.6; between Trypanosoma cruzi and T. brucei it is <0.45 — and a high degree of synteny. Within vertebrates and insects, a high degree of gene order conservation has been reported [6,11,12]. The plant genomes sequenced so far lack any apparent conservation in gene order, although they display some degree of local small-scale conservation (microsynteny), despite their relatively recent evolutionary origins [13,14]. These examples show that sequence and genome diversity evolve as independent processes, and that the evolutionary rates of sequences do not reflect the evolutionary rate of the genomes in which they are embedded. Re-Arranging a Genome So what is it that keeps genes in the same order over evolutionary time? It makes sense to keep functionally related genes in close physical proximity as they are often co-regulated. One well known example is the set
Dispatch R474
of Hox genes that show remarkable conservation of gene order across animal phyla and are exquisitely coordinated in their expression during development [15]. In trypanosomatids, genes are transcribed as large polycistronic precursor mRNAs before being cleaved into monocistronic messengers and it is suggested that both the direction of replication and transcription are coordinated [10]. Rearrangements could disrupt these directional processes and thus may be selected against [10]. To study further what other factors might influence gene order, Pal and Hurst [16] closely analysed the Candida and Saccharomyces genomes. They observed that essential (or vital) genes are highly clustered, and that these clusters are in regions with low recombination rates. Essentially, recombination rates are lower, and hence the gene order is more conserved, around genes that provide essential functions. The mechanisms behind gene rearrangements could be transpositions — as is most likely the case in trypanosomatids, where retrotransposon-like elements have been found in regions associated with rearrangements [10] — or inversions, which are proposed to play a major role for small-scale changes in gene order between Candida and Saccharomyces [17]. Stasis in Small Genomes? It does not seem too surprising that a high degree of synteny and small genome size go hand in hand. Changing the gene order in a genome requires breakpoints, which cause the physical disruption of a given stretch of sequence. The chances of disrupting a functional gene are much higher in compact genomes with few and small intergenic regions. Still, the question of whether the frequency of rearrangements is lower in small genomes remains open. Trypanosomatids have genomes roughly ten times larger than E. cuniculi, yet their gene order seems highly conserved [10]. Prokaryote genomes are smaller than eukaryote genomes and Huynen et al. [17] compared rearrangement rates between the genomes of Candida and Saccharomyces with those between two prokaryotes, Haemophilus influenzae and Escherichia coli. They show that the overall rate of rearrangements is lower in the prokaryotes; however, this can be explained by the operon structure of prokaryote genomes. With only 3.2 Mb, the E. cuniculi genome is even smaller than many prokaryote genomes [2], which may explain why its gene order is so conserved; however data from the entire genome of A. locustae are not available (although its genome size has been estimated to be 5.4 Mb [18]). It will be interesting to see if other microsporidians have a similarly high degree of genome compaction and synteny as that observed between E. cuniculi and A. locustae. At the moment, everything points to Microsporidia having rapidly changing gene sequences within a slow evolving genome. Perhaps this should not be too surprising — after all, the mutational mechanisms and the selective forces acting on gene sequences are very different from those affecting genome organisation. As more eukaryotic genomes become available, commonalities and differences in the process of genome evolution across the tree of life should become much clearer. It has already become
clear that the metaphor of a constant evolutionary molecular clock applies neither to genomes nor the genes they encode. References 1. Embley, T.M., and Hirt, R.P. (1998). Early branching eukaryotes? Curr. Opin. Genet. Dev. 8, 624-629. 2. Katinka, M.D., Duprat, S., Cornillot, E., Metenier, G., Thomarat, F., Prensier, G., Barbe, V., Peyretaillade, E. et al. (2001). Genome sequence and gene compaction of the eukaryote parasite Encephalitozoon cuniculi. Nature 414, 450-453. 3. Slamovits, C.H., Fast, N.M., Law, J.S., and Keeling, P.J. (2004). Genome compaction and stability in microsporidian intracellular parasites. Curr. Biol. May 25 issue. 4. Andersson, L., Archibald, A., Ashburner, M., Audun, S., Barendse, W., Bitgood, J., Bottema, C., Broad, T., et al. (1997). Comparative genome organisation of vertebrates. Mamm. Gen. 7, 717-734. 5. Burt, D.W., Bruley, C., Dunn, I.C., Jones, C.T., Ramage, A., Law, A.S., Morrice, D.R., Paton, I.R., et al. (1999). The dynamics of chromosome evolution in birds and mammals. Nature 402, 411-413. 6. Bourque, G., Pevzner, P.A., and Tesler, G. (2004). Reconstructing the genomic architecture of ancestral mammals: lessons from human, mouse, and rat genomes. Genome Res. 14, 507-516. 7. Nadeau, J.H., and Sankoff, D. (1998). Counting on comparative maps. Trends Genet. 14, 495-501. 8. Carlton, J.M., Angiuoli, S.,V., Suh, B.B., Kooij, T.W., Pertea, M., Silva, J.C., Ermolaeva, M.D., Allen, J.E. et al. (2002). Genome sequence and comparative analysis of the model rodent malaria parasite Plasmodium yoelii yoelii. Nature 419, 512-519. 9. Bankier, A.T., Spriggs, H.F., Fartmann, B., Konfortov, B.A., Madera, M., Vogel, C., Teichmann, S.A., Ivens, A., and Dear, P.H. (2003). Integrated mapping, chromosomal sequencing and sequence analysis of Cryptosporidium parvum. Genome Res. 13, 1787-1799. 10. Ghedin, E., Bringaud, F., Peterson, J., Myler, P., Berriman, M., Ivens, A., Andersson, B., Bontempi, E. et al. (2004). Gene synteny and evolution of genome architecture in trypanosomatids. Mol. Biochem. Parasitol. 134, 183-191. 11. Zdobnov, E.M., von Mering, C., Letunic, I., Torrents, D., Suyama, M., Copley, R.R., Christophides, G.K., Thomasova, D. et al. (2002). Comparative genome and proteome analysis of Anopheles gambiae and Drosophila melanogaster. Science 298, 149-159. 12. McLysaght, A., Enright, A.J., Skrabanek, L., and Wolfe, K.H. (2000). Estimation of synteny conservation between pufferfish (Fugu) and human. Yeast 17, 22-36. 13. Bennetzen, J.L. (2000). Comparative sequence analysis of plant nuclear genomes: microlinearity and its many exceptions. Plant Cell 12, 1021-1029. 14. Delseny, M. (2004). Re-evaluating the relevance of ancestral shared synteny as a tool for crop improvement. Curr. Op. Plant Biol. 7, 126131. 15. Ferrier, D.E.K., and Minguillon, C. (2003). Evolution of the Hox/ParaHox gene clusters. Int. J. Dev. Biol. 47, 605-611. 16. Pal, C., and Hurst, L.D. (2003). Evidence for co-evolution of gene order and recombination rates. Nat. Genet. 33, 392-395. 17. Huynen, M.A., Snel, B., and Bork, P. (2001). Inversions and the dynamics of eukaryotic gene order. Trends Genet. 17, 304-306. 18. Street, D.A. (1994). Analysis of Nosema locustae (Microsporidia: Nosematidae) chromosomal DNA with pulse-field gel electrophoresis. J. Invertebr. Pathol. 63, 301-303.