EST data suggest that poplar is an ancient polyploid

Authors

  • Lieven Sterck,

    1. Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology (VIB), Ghent University, Technologiepark 927, B-9052 Ghent, Belgium;
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  • Stephane Rombauts,

    1. Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology (VIB), Ghent University, Technologiepark 927, B-9052 Ghent, Belgium;
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  • Stefan Jansson,

    1. Department of Biotechnology, Kungliga Tekniska Hogskolan Royal Institute of Technology, AlbaNova University Center, SE-106 91 Stockholm, Sweden;
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  • Fredrik Sterky,

    1. Department of Biotechnology, Kungliga Tekniska Hogskolan Royal Institute of Technology, AlbaNova University Center, SE-106 91 Stockholm, Sweden;
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  • Pierre Rouzé,

    1. Laboratoire Associé de l’Institut National de la Recherche Agronomique (France), Ghent University, Technologiepark 927, B-9052 Ghent, Belgium
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  • Yves Van de Peer

    Corresponding author
    1. Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology (VIB), Ghent University, Technologiepark 927, B-9052 Ghent, Belgium;
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Author for correspondence: Yves Van de Peer Tel: +32 9 331 3807 Fax: +32 9 331 3809 Email: Yves.VandePeer@psb.ugent.be

Summary

  • We analysed the publicly available expressed sequence tag (EST) collections for the genus Populus to examine whether evidence can be found for large-scale gene-duplication events in the evolutionary past of this genus.
  • The ESTs were clustered into unigenes for each poplar species examined. Gene families were constructed for all proteins deduced from these unigenes, and KS dating was performed on all paralogs within a gene family. The fraction of paralogs was then plotted against the KS values, which resulted in a distribution reflecting the age of duplicated genes in poplar.
  • Sufficient EST data were available for seven different poplar species spanning four of the six sections of the genus Populus. For all these species, there was evidence that a large-scale gene-duplication event had occurred.
  • From our analysis it is clear that all poplar species have shared the same large-scale gene-duplication event, suggesting that this event must have occurred in the ancestor of poplar, or at least very early in the evolution of the Populus genus.

Introduction

The genus Populus consists of some 30 species of woody plants including poplars, cottonwoods and aspens, all of which are found in the Northern hemisphere (Taylor, 2002). The genus is further subdivided into six distinct sections: Abaso, Turanga, Leucoides, Aigeiros, Tacamahaca and Populus (Eckenwalder, 1996 and references therein). The latter two sections each contain about a dozen species. Poplar trees have been used all over the world to produce a large variety of wood-based products including timber, pulp, and paper. In addition to their great economical value, poplars are also rapidly becoming the model organism for forest biology and tree biotechnology. They can be easily transformed and vegetatively propagated, and have rapid growth. Another major advantage of the poplars is that they have a modest genome size (≈ 500 Mbp; J. Tuskan, personal communication) organised in 19 chromosomes. It is therefore not surprising that, in 2001, poplar was selected as the first woody plant to have its genome sequenced. Because of its successful use as a model organism for trees, much genomic information and many resources are already available for poplar (for review see Brunner et al., 2004), including several expressed sequence tag (EST) collections. Public EST libraries generally form an unbiased sampling of genes that are expressed in a wide variety of conditions and have proven to be an invaluable source of information (Rudd, 2003).

Blanc & Wolfe (2004) have proposed an elegant method to study the duplication past of genes in an organism's genome based on EST data when a complete genome annotation is not (yet) available. Within the EST data collections of different plant species, they identified paralogous sequences after which the time of duplication was inferred by estimating the number of synonymous substitutions (KS) between two duplicates. Because synonymous substitutions do not alter the amino acid sequence, they are assumed to be under no or minimal selection, and to accumulate substitutions at a neutral and steady rate. When the number of duplicated pairs of genes is plotted against their age, inferred from the number of synonymous substitutions per synonymous site (KS), the resulting age distributions exhibit a typical L-shape, with many recently duplicated genes and much fewer older duplicates. Based on these age distributions, Lynch & Conery (2000, 2003) suggested a steady-state stochastic birth–death model for the dynamics of duplicated gene populations, from which they inferred the overall rate of both gene duplication and gene loss. However, large-scale gene or entire genome duplication events cause a sharp increase in the number of paralogs over a short period, and are visible as peaks in the L-shaped age distributions (Vandepoele et al., 2003; Blanc & Wolfe, 2004; Van de Peer, 2004). Here we have analysed age distributions based on the EST data collections publicly available for poplar, to investigate whether evidence can be found for large-scale gene duplications in its evolutionary past.

Materials and Methods

Construction of the unigene sets

As no ‘unigene’ data sets are available for poplar (a unigene is the consensus sequence of a cluster of transcripts that represents a unique gene in a genome), we have assembled our own as follows. First, we selected all poplar species for which >10 000 entries exist in the dbEST database (Boguski et al., 1993). Seven different Populus species meet this criterion: Populus alba × Populus tremula; Populus balsamifera ssp. trichocarpa; P. balsamifera ssp. trichocarpa × Populus deltoides; P. tremula; P. tremula × Populus tremuloides; P. tremuloides; and Populus euphratica. ESTs for these species were downloaded from the dbEST database. At a later stage we also included nonpublic ESTs from P. balsamifera ssp. trichocarpa, P. tremula and P. tremula × P. tremuloides to confirm our results (Sterky et al., 2004). Next, the different data sets were screened for low complexity and vector contamination with the program seqclean (using the UniVec-Core database, ftp://ftp.ncbi.nih.gov/pub/UniVec), after which the cleaned ESTs are assembled into unigenes using the program tgicl. The program was run with default parameters except for the minimal overlap, which we set at 40 bases instead of the default 30. Both programs are available at http://www.tigr.org/tdb/tgi/software.

Defining paralogous relationships

The coding frame and putative coding sequence on our unigenes were determined with framed (Schiex et al., 2003), which uses a hidden Markov model (HMM) to search for the coding potential and has the ability to correct frameshifts. Because no HMM exists to recognize coding sequences in poplar, we used the Arabidopsis model provided by the framed program. From all proteins predicted by framed, we discarded all proteins that were shorter than 150 amino acids. Next, for each set of unigenes we performed an all-against-all blastP (Altschul et al., 1997). Based on the blast results, we defined gene families for each Populus species. Two sequences were regarded as paralogs if the aligned region is longer then 150 amino acids and when the sequences showed more than 30% similarity.

KS-based dating

For each gene family, all members were aligned with each other at the protein level with clustalW (Thompson et al., 1994), after which these alignments were used as a guide to align the corresponding nucleotide sequences. Then all N-containing codons and gaps were removed. Starting from these cleaned alignments, KS was estimated using a maximum-likelihood approach as implemented in the program codeml (Goldman & Yang, 1994) which is part of the paml package (Yang, 1997). Because the program can become trapped in suboptimal optima and therefore produce incorrect KS estimations, it was run five times and only the KS with the best likelihood was used for each pair of sequences.

Corrections on number of KS values

In order to exclude redundant sequences in our initial data sets, we identified all paralogous gene pairs that had both a synonymous and a nonsynonymous substitution rate equal to zero. Next, one of both sequences, preferably a singleton EST, was chosen from each of these pairs and all KS estimations involving this sequence were discarded for further analysis. The elimination of these pairs will not influence our results concerning the large-scale duplication event, because the fraction of pairs discarded this way is very small, and because such pairs are randomly spread over all KS bins.

A gene family of n members can be created by at most n −1 gene-duplication events. However, the number of possible pairwise comparisons within a gene family is n(n − 1)/2 and, in particular for large gene families, can thus be considerably larger than the number of gene duplications. Therefore, in order to eliminate redundant KS values when building the age distribution for duplicated genes, phylogenetic trees were constructed for each gene family using an average linkage clustering algorithm. Starting from each gene as a separate cluster, the clusters with the lowest mean intercluster KS value were iteratively merged. The splits in the average linkage tree represent the n − 1 retained duplication events. For each split, the m KS measurements between the two merged gene clusters were added to the KS distribution with a weight 1/m (Blanc & Wolfe, 2004).

A final cleaning step was performed by excluding all pairs that had a KS larger than 3.5.

Results

For four out of the six sections of the genus Populus there is a representative in our data set (Table 1). The initial number of downloaded transcripts for each species ranged from ≈ 10 000 for the smallest set to 66 000 for the largest. These sequences were clustered into unigenes for each species separately. The final unigene set consists of the assembled transcripts (contigs) and the singleton transcripts (singlets). For a substantial part of each set we were able to extract a protein longer than 150 amino acids (Table 1). Gene families were defined at the protein level using blastP.

Table 1.  Numbers of sequences for all poplar species used in this analysis
SpeciesSection in genus PopulusNo. initial ESTsNo. unigenesNo. proteinsNo. paralogsNo. familiesNo. paralogs per familyNo. used KS values
Populus alba × Populus tremulaPopulus10 446 1 565 1 166  543  1803.02  351
Populus balsamifera ssp. trichocarpaTacamahaca26 825 8 306 4 7221 701  5653.011 069
Populus balsamifera ssp. trichocarpa × Populus deltoidesTacamahaca × Aigeiros16 480 2 453 1 738  731  2452.98  463
Populus euphraticaTuranga13 903 2 162 1 587  528  1852.85  318
Populus tremulaPopulus31 28815 737 6 6302 536  8303.061 546
Populus tremula × Populus tremuloidesPopulus65 98124 15910 7324 8221 4793.263 155
Populus tremuloidesPopulus12 813 2 228 1 479  454  1582.87  265

Figure 1 shows age distributions for ESTs for the seven different poplar species obtained by plotting the number of paralogs against their KS values (see Materials and Methods). The high number of paralogs with very low KS values refers to sequence pairs that result from recent small-scale gene duplications, an ongoing process in most species (Lynch & Conery, 2000; Blanc & Wolfe, 2004). However, as can be clearly observed, for all species there is a sharp increase in the number of sequence pairs with a KS between 0.20 and 0.30, which means that a large number of gene duplicates must have been created at about the same time. The most plausible explanation for such an observation is a large-scale gene- or even entire genome-duplication event (Van de Peer, 2004). The sudden increase in the number of paralogs is even more evident when we plot the cumulative percentage of paralogs (grey line, Fig. 1). It is clearly seen that there is a sudden increase in the number of KS values in the lowest KS bins (KS < 0.45) indicating that, for all Populus species, more than half the duplicated genes originated through very recent small-scale gene duplications and one relatively recent large-scale duplication event (Fig. 1). The KS distribution for higher KS values (KS > 0.90) again shows a small increase in the number of duplicates. It should be noted that the error on the KS estimations rises quickly for KS values > 1 (Li, 1997), and that these values therefore should be interpreted with caution. Nevertheless, we believe that this increase probably reflects older large-scale gene-duplication events early in the evolution of the angiosperms (Simillion et al., 2002; Bowers et al., 2003).

Figure 1.

Age distribution of paralogous EST sequences from seven different poplar species: (a) Populus alba × Populus tremula; (b) Populus balsamifera ssp. trichocarpa; (c) Populus tremula; (d) Populus tremula × Populus tremuloides; (e) Populus tremuloides; (f) Populus balsamifera ssp. trichocarpa × Populus deltoides; (g) Populus euphratica. Left axis, percentage of paralogs; grey line, cumulative number of paralogs (right axis). One bin corresponds with a KS of 0.05.

It could be argued that the data sets of hybrid poplars should not be used for studying duplication history in the genus Populus by means of KS dating, because the hybridization event could interfere with the duplication event. However, in general the difference between two alleles is much smaller than the differences between duplicates (not shown). Moreover, we believe our results show that this is not a concern, the strongest argument being the fact that we observe the large-scale duplication peak in all species examined at the same time, regardless of whether the poplar species are hybrids (Fig. 1a,d,f) or not (Fig. 1b,c,e,g).

Discussion

Although the number of EST sequences and paralogs is quite small for some species (Table 1), some general trends can be observed for all collections. For example, for all EST sets, even the smaller ones, the large-scale duplication event can clearly be uncovered. This proves that the approach used is quite robust and suggests that general duplication trends in a genome can already be recognized, even in species for which there is a limited amount of EST data available. For all seven species, a sharp increase in the number of paralogs is observed at a KS of 0.20–0.30, which points to a large-scale duplication event that has occurred at the same time in all species. As it is most unlikely that there was a duplication event independently in all these species at the same time, we conclude that the duplication event must have occurred very early in, if not before, the evolution of the genus Populus.

When KS values are converted to time (T = KS/2λ), using a rate (λ) of 1.5 × 10−8 synonymous substitutions per synonymous site per year, as proposed by Koch et al. (2000), the polyploidy event in poplar is estimated to have occurred some 8 myr ago. Using a different rate of 9.1 × 10−9 synonymous mutations per synonymous site per year, as suggested elsewhere (Lynch & Conery, 2000), the large-scale gene-duplication event in poplar is dated at ≈ 13 myr ago. Although these dates differ considerably and should be interpreted with caution, it is clear that all the poplar species examined share the polyploidy event. This can be explained only if the genome duplication occurred in the ancestor of all these species, somewhere between 8 and 13 myr ago. This also means that the divergence of the different poplar sections must be more recent than the polyploidy event. The earliest fossils claimed as being of poplar are 58-myr-old leaves ascribed to the section Abaso, which is probably one of the earliest diverging poplar species (Fig. 2; Eckenwalder, 1996), but for which unfortunately no EST data exist. Therefore we cannot conclude for sure whether the Abaso section shares the duplication event. In this respect it would also be interesting to examine the duplication past of other members of the family Salicaceae, such as the sister genus of Populus, Salix, which is closely related (Leskinen & Alström-Rapaport, 1999; Wikström et al., 2001), to see whether they share the same duplication event. Unfortunately too few EST data are available for the other Salicaceae, so this question remains unanswered. The earliest fossil evidence ascribed to the other poplar sections is claimed to be between 18 and 40 myr old (Eckenwalder, 1996 and references therein), which predates the polyploidy event, and is thus clearly in disagreement with our data. There are two possible explanations for this incongruence. The first is that the poplar fossils are not correctly ascribed to the different poplar sections. Alternatively, it is possible that the rate of synonymous substitutions (λ) for poplar is somewhat different than the value generally used for dicots (see above). This is not unlikely considering the fact that the generation time of a species is known to affect its nucleotide-substitution rate (Gaut, 1998) and that poplar has a much longer generation time than most other plant species used in molecular research. Careful calibration of some poplar molecular markers in the future may shed further light on this.

Figure 2.

Schematic representation of the phylogeny of the genus Populus and some relevant plant species, based on Blanc & Wolfe (2004); Eckenwalder (1996); Wikström et al. (2001). Grey dots indicate large-scale duplication events proposed by Blanc & Wolfe (2004; see also Van de Peer, 2004); a black dot denotes the large-scale duplication event in poplar proposed in the current study.

Acknowledgements

We would like to thank Stefanie De Bodt, Steven Maere and Klaas Vandepoele for their help in producing and interpreting the KS estimations. We also acknowledge the support of our institution and thank all members of the biocomputing group for helpful discussions. This work was supported by a grant from the European Community, FOOD-CT-2004-506223-GRAIN LEGUMES.

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