Figures
Abstract
Using a phylogenetic approach, the examination of 33 meiosis/meiosis-related genes in 12 Drosophila species, revealed nine independent gene duplications, involving the genes cav, mre11, meiS332, polo and mtrm. Evidence is provided that at least eight out of the nine gene duplicates are functional. Therefore, the rate at which Drosophila meiosis/meiosis-related genes are duplicated and retained is estimated to be 0.0012 per gene per million years, a value that is similar to the average for all Drosophila genes. It should be noted that by using a phylogenetic approach the confounding effect of concerted evolution, that is known to lead to overestimation of the duplication and retention rate, is avoided. This is an important issue, since even in our moderate size sample, evidence for long-term concerted evolution (lasting for more than 30 million years) was found for the meiS332 gene pair in species of the Drosophila subgenus. Most striking, in contrast to theoretical expectations, is the finding that genes that encode proteins that must follow a close stoichiometric balance, such as polo, mtrm and meiS332 have been found duplicated. The duplicated genes may be examples of gene neofunctionalization. It is speculated that meiosis duration may be a trait that is under selection in Drosophila and that it has different optimal values in different species.
Citation: Reis M, Sousa-Guimarães S, Vieira CP, Sunkel CE, Vieira J (2011) Drosophila Genes That Affect Meiosis Duration Are among the Meiosis Related Genes That Are More Often Found Duplicated. PLoS ONE 6(3): e17512. https://doi.org/10.1371/journal.pone.0017512
Editor: David Liberles, University of Wyoming, United States of America
Received: October 28, 2010; Accepted: February 4, 2011; Published: March 10, 2011
Copyright: © 2011 Reis et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Funding: This work was funded by the Fundação para a Ciência e Tecnologia (FCT) through research projects PTDC/BIA-BDE/66765/2006 and PTDC/BIA-BEC/099933/2008 and through PhD grants attributed to MR and SG, funded by Programa Operacional para a Ciência e Inovação (POCI-2010), co-funded by Fundo Europeu para o Desenvolvimento Regional (FEDER) and Programa Operacional para a Promoção da competividade (COMPETE). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Competing interests: The authors have declared that no competing interests exist.
Introduction
Gene duplication followed by the fixation of a mutation providing a different function, is one of the major sources to create genetic novelty [1]. The rate at which eukaryotic duplicated genes are retained, i.e., go to fixation, has been originally estimated to be 0.01 per gene per million years [2]. This value was obtained under the assumption that the age of the duplication events can be estimated by looking at within species synonymous divergence rates between pairs of paralogous genes. Nevertheless, this estimate is inflated due to concerted evolution [1], [3]. Concerted evolution arises due to frequent gene conversion between paralogous genes. This process leads to a severe reduction in the divergence rate between paralogous genes from the same species but not when comparing different species (see for instance [4]). Using species of the D. melanogaster subgroup, and taking into account the effect of concerted evolution, i.e, using a phylogenetic approach, Osada and Innan [1], estimated the rate of duplication to be 0.001 per gene per million years, an order of magnitude below the original estimate.
Not all gene duplicates are predicted to be equally retained. For instance, duplication of genes, that encode for proteins that are part of a complex, are likely deleterious [5], [6], [7]. Moreover, theory suggests that, duplication of genes that encode for proteins involved in regulatory networks are rarely retained, since they likely disrupt network dynamics and consequently the expression pattern of many genes [8]. Duplications of genes encoding for proteins involved in signaling networks are also expected to be rarely retained [8]. Gene duplicates that encode for proteins that participate in many reactions are, as well, less likely to be retained than genes that encode proteins that participate in a single reaction [9]. Duplicates of genes that encode for activators are also expected to be more frequently retained than genes that encode for receptors [7]. In Drosophila, developmental constraint, for instance, does appear to reduce gene duplicability, but the effect is moderate [10].
How the gene duplicates came to be also influences gene duplicate retention. For instance, in Arabidopsis, when large-scale duplication events are involved, genes that encode transcription factors, proteins with kinase activity, proteins that are involved in protein binding and modification, or in signal transduction pathways are retained at high rates, but the same categories are retained at low rates when small-scale duplications are involved [11]. As discussed by Maere et al. [11] large scale duplication events may not disrupt stoichiometric balances, while small-scale duplication events likely do. In Drosophila, however, most duplication events seem to involve less than four genes, and for the vast majority of blocks, the length of the region between the original and the duplicated block is less than 5 Kb [1]. No large scale duplications have ever been described in Drosophila.
Many meiotic pathways are highly conserved across distantly related sexually reproducing eukaryotes (for a review, see [12]). Such conservation could mean that meiotic pathways tolerate little change. Moreover, in Arabidopsis, duplicates of genes involved in DNA repair, DNA replication, DNA recombination, and cell-cycle genes are generally little retained [11]. This is not surprising since meiosis-related genes are known to participate in multiple pathways, be involved in protein complexes, and, when disrupted, affect multiple aspects of meiosis (see Table S1). Nevertheless, the time it takes to complete meiosis is known to be very variable, even among species without developmental holds. Environmental factors (temperature for instance), nuclear DNA content and genotype are among the most important factors affecting meiosis duration [13]. In Drosophila, nuclear DNA content is known to vary significantly (the C-values vary between 0.12 and 0.39; http://www.genomesize.com), but meiosis duration has been recorded so far only in D. melanogaster [13]. Unusual prophase structures such as fibrillar structures apparently coupled to the nucleolus, and multiple nucleoli are also observed in species of the virilis group [14]. These observations suggest that, even within a single genus, such as Drosophila, meiosis features are after all variable. Whether Drosophila meiosis-related neomorphs (meiosis-related genes with new functions) have evolved is also unknown. This is important, in order to infer the tolerated degree of change of an ancient machine such as the meiotic one.
Recently, Anderson et al. [15] studied 33 genes involved in meiosis or meiosis-related tasks, such as, chromosome segregation, achiasmate segregation, crossover regulation, double-strand-break formation, heterochromatin binding, recombination and/or repair, sister-chromatid cohesion, spindle assembly, and telomere maintenance. That study revealed that, in Drosophila, variability patterns compatible with adaptive protein divergence and polymorphism can be found at four meiosis (Klp3A, Ku80, mtrm, and ord) and two telomere maintenance genes (mre11 and rad50). Nevertheless, as argued by Anderson et al. [15], the observed patterns can also be explained as a consequence of the fixation/persistence in Drosophila populations, of meiotic drive elements (elements that in females influence the preferential sorting of a chromosome to the pronucleus, and thus to the ovule; [15]). If meiotic drive elements are common (about 18% of the meiotic genes surveyed by Anderson et al. [15] could show evidence for meiotic drive elements), then such elements could conceivably also increase the probability of fixation, and thus the retention of meiosis gene duplicates. It should be noted, however, that the extent to which the observed within and between species amino acid variation at meiosis genes is adaptive is unknown.
In this work, in order to avoid the confounding effect of concerted evolution (see above), a phylogenetic approach is used for the estimation of the rate at which meiosis-related genes are duplicated and retained. A segmental duplication may lead to the simultaneous duplication of many neighboring genes. When segmental duplications are not taken into account, the gene duplication rate is overestimated. Therefore, in this work, the time of origin, as well as the lineage where the gene duplication occurred, is also taken into account, when inferring the number of independent gene duplication events. Due to the methodological approach used, only gene duplications that occurred after the separation of the Drosophila and Sophophora sub-genera are counted. Recent gene duplicates are expected to be found in tandem, unless they are the result of a segmental duplication, or retrotransposition is involved. Nevertheless, the separation of the two Drosophila subgenera occurred about 40 million years ago [16]. Therefore, a fraction of the inferred gene duplications may be old. Because gene order can be shuffled due to inversions and translocations, those duplications are no longer expected to be in tandem. Moreover, we infer whether the gene duplicates are functional, since such genes are potential meiosis-related neomorphs. We speculate on whether variation in meiosis gene copy numbers, as well as the appearance of putative neomorphs, can account for the variability in Drosophila meiosis features, although these findings must be corroborated by detailed functional studies.
Materials and Methods
Strains
D. virilis 1051.49 (Chaco, Argentina); D. persimilis 14011-0111.48 (California, USA); D. willistoni 14030-0811.16 (Rocha, Uruguay) and D. mojavensis 15081-1352.00 (California, USA) were used to address the expression profile of the different genes found to be duplicated and their respective duplicates. Furthermore, in order to determine the age of the mtrm gene duplication (mtrm-dup) the following species from the virilis group of Drosophila were used: D. novamexicana 15010-1031.00 (Colorado, USA), D. lummei 200 (Russia), D. littoralis BP41 (Bragança, Portugal), D. kanekoi 15010-1061.00 (Sapporo, Japan), D. ezoana E20 (Kemi, Finland), D. montana Mo1 (Kemi, Finland), D. flavomontana 15010-0981-00 (Idaho, USA), D. lacicola 15010-0991-00 (New York, USA), D. borealis 15010-0961-00 (Minnesota, USA) and D. borealis 15010-0961-03 (Idaho, USA). To test the hypothesis of preferential transmission of chromosomes having one of the variants at mtrm-dup gene, the following strains were used: D. a. americana NN97.4, NN97.8 (Nebraska, USA), W11, W23 (Lake Wappapelo, USA) and D. a. texana W29 (Lake Wappapelo, USA), LP97.7 (Louisiana, USA), ML97.5; ML97.4.2 (Louisiana, USA).
Genomic DNA extraction
Genomic DNA from single males was extracted using the QIAamp DNA Mini Kit from QIAGEN (Izasa Portugal, Lda.) according to the manufacturer's instructions.
PCR amplification
Specific primers were developed for each of the genes found to be duplicated and their respective duplicates (Table S2). To test the hypothesis of preferential transmission of chromosomes having one of the variants at mtrm-dup this gene was amplified in the species from the virilis group of Drosophila using primers 543F690 and 543R43 as described in Vieira et al. [17]. Standard amplification conditions were 35 cycles of denaturation at 94°C for 30s, primer annealing according to Table S2, for 45s, and primer extension at 72°C for 3min.
RT-PCR
Ovaries and testes were dissected from D. virilis (1051.49), D. willistoni (14030-0811.16), D. mojavensis (15081-1350.00) and D. persimilis (14011-0111.48). Total RNA was isolated from the dissected tissues using TRIzol Reagent (Invitrogen) according to the manufacturer's instructions and treated with DNase I (RNase-Free) (Ambion). cDNA was synthesized by reverse transcription with SuperScript III First-Strand Synthesis SuperMix for qRT-PCR (Invitrogen). cDNAs were amplified using the PCR conditions described above and the specific primers shown on Table S2. Specific primers were also used for the endogenous ribosomal protein L32 (RpL32) as a control for cDNA quality. No-template controls and reactions with RNA that was not reverse transcribed were performed in order to confirm the absence of genomic DNA contamination. Moreover, when possible, primers were designed in order to encompass a region of the gene with one intron. Therefore, the cDNA amplification product is expected to have a shorter size than the amplification product from genomic DNA. The results were analyzed by agarose gel electrophoresis. It should be noted that expression levels of different genes should not be compared since, for instance, amplification product sizes are different, and primer features (such as GC content, or melting temperatures) are different. Direct sequencing was performed using all the PCR products obtained from cDNA amplification as template to confirm the specificity of the primers developed for all the genes found to be duplicated and their respective duplicates. Moreover, for a given gene and its duplicates, when using cDNA, most PCR amplification products have different sizes.
Sequencing
The amplification products obtained for the species from the virilis group of Drosophila using primers 543F690 and 543R43 [17] were cloned using the TOPO-TA Cloning Kit for Sequencing from Invitrogen (Barcelona, Spain). Positive colonies were picked randomly, grown in 5mL of LB with Ampicillin, and plasmids were extracted using the QIAprep Spin Miniprep Kit from QIAGEN (Izasa, Portugal, Lda.). Four colonies were sequenced in order to correct for possible nucleotide missincorporations that may have occurred during the PCR reaction. Sequencing was performed using ABI PRISM Big Dye cycle-sequencing kit version 1.1 (Perkin Elmer, CA, USA) and the primers for the M13 forward and reverse priming sites of the pCR2.1 vector. Sequencing runs were performed by STABVIDA (Lisbon, Portugal).
Restriction enzyme typing of a common polymorphism on the mtrm-dup gene
To test the hypothesis of preferential transmission of chromosomes having one of the amino acid variants at mtrm-dup gene [17] a total of 32 crosses were established corresponding to all possible combinations between D. a. americana and D. a. texana strains (F0) in both directions. After emergence of new born individuals brother-sister mating was performed (F1). All the females were heterozygous for the mtrm-dup amino acid variants. In the next generation (F2) 10 males from each of the F1 crosses established were selected in a total of 320 individuals. The genomic DNA from these individuals was extracted and they were genotyped for the presence of the amino acid variant on mtrm-dup associated with the X/4 fusion, using the restriction enzyme BstBI and the PCR amplification products obtained with primers 543F69 and 543R43 (see [17]).
Datasets, sequence alignment and phylogenetic analyses
The D. melanogaster coding sequences of the 33 meiosis-related genes listed in [15], was retrieved from FlyBase (http://flybase.org/). In order to retrieve sequences from non-melanogaster Drosophila species, the tblastn option with standard parameters, as implemented in FlyBase, was used. The D. melanogaster coding sequences were used as a query. Coding sequences with an associated expected value less than 0.05 were retrieved. When gene sequences were non-annotated, a tentative manual annotation of the putative coding region was performed. For every gene dataset, translated amino acid sequences were aligned using CLUSTALW, as implemented in DAMBE [18]. The resulting amino acid alignment was used as a guide to obtain the corresponding nucleotide alignment. Bayesian trees were obtained using MrBayes [19], and nucleotide sequences, under the GTR model of sequence evolution, thus allowing for among-site rate variation and a proportion of invariable sites. Third codon positions are allowed to have a gamma distribution shape parameter that is different from that of first and second codon positions. Two simultaneous and completely independent analyzes, starting from random trees, were run for 500,000 generations (each with one cold and three heated chains). Samples were taken every 100th generation. The first 1250 samples were discarded (burn-in). The final datasets (accession numbers for the nucleotide sequences used can be found in Table S3) were obtained after inspecting the results of the phylogenetic analyses. Because of the methodology used, only gene duplications that occurred after the separation of the Drosophila and Sophophora sub-genera are counted. Since our goal was to estimate the rate of duplication of meiosis-related genes, whether the duplicated genes were created as a result of the duplication of a segment of the genome (segmental duplications) or as the result of the duplication of a single gene was not assessed. Nevertheless, given the inferred time of origin and the lineage where gene duplications are inferred to have occurred, the detected gene duplications must be the result of independent duplication events (see Results section).
Divergence estimates
Per site non-synonymous (Ka) and synonymous (Ks) rates were estimated using DNasp [20]. Values are Jukes-Cantor corrected for multiple hits.
Tajima's relative rate tests
In order to infer whether duplicated genes evolve at the same rate as the gene that was duplicated, Tajima's relative rate tests were performed, as implemented in the MEGA software [21], using all codon positions, or third codon positions (those most likely to be neutral) only. For this test, two ingroup and one outgroup sequences are used. Under the molecular clock hypothesis, irrespective of the substitution model and whether or not the substitution rate varies with the site, the number of mutations inferred for the two ingroup branches should be similar. If this hypothesis is rejected, then the molecular clock hypothesis can be rejected for this set of sequences. When the two ingroup sequences have different amino acid constraints but are subject to a similar mutation rate, statistically significant differences are expected when using all codon positions but not when using third codon positions [22].
Results
The vast majority (85%) of the genes involved in meiosis related tasks are not duplicated
Of the 33 meiosis-related genes studied (those listed in [15]), 31 could be found in the 12 publicly available Drosophila genomes (http://flybase.org/) although a non-negligible fraction is non-annotated or likely miss-annotated (Table S4). The c(3)G gene could not be found in D. ananassae. Nevertheless, it is found in all other species examined and thus, it is likely that the D. ananassae genomic region encompassing gene c(3)G has not been sequenced. Gene CG7676 (also known as cona; http://flybase.org/) could not be found in D.ananassae, D. willistoni, D. mojavensis, D. virilis and D. grimshawi. Therefore, the latter gene is never found in species of the Drosophila subgenus. In Fig. 1, the per site non-synonymous rate of evolution between D. melanogaster and D. virilis is shown for the 33 meiosis-related genes. For CG7676 gene this value has been extrapolated under the assumption of a molecular clock and that D. melanogaster and D. virilis have been diverging for about 40 million years while D. melanogaster and D. yakuba have been diverging for about 10 million years (see Fig. 2). CG7676 is not evolving faster than other meiosis-related genes that have a clearly recognizable orthologous copy in D. virilis (Fig. 1). Therefore, we should have been able to detect the CG7676 orthologous copy in species of the subgenus Drosophila. Given these observations it seems likely that gene CG7676 does not have an orthologous copy in the subgenus Drosophila, an unexpected observation for a gene involved in a tightly regulated process. This gene has been described as being required for the stable ‘zippering’ of transverse filaments to form the central region of the Drosophila synaptonemal complex [23].
For CG7676 gene this value has been extrapolated under the assumption of a molecular clock and that D. melanogaster and D. virilis have been diverging for about 40 million years while D. melanogaster and D. yakuba have been diverging for about 10 million years.
Adapted from http://flybase.org. Numbers are estimated divergence times in million years.
For 26 (ald, asp, Axs, c(2)M, c(3)G, Su(var)205, Klp3A, Ku70, Ku80, mei-218, mei-41, mei-P22, mei-P26, mei-9, mus304, ncd, okr, ord, rad50, smc1, spn-A, spn-B, spn-D, subito, teflon and tefu) out of the 33 genes analyzed, there is a single copy in the 12 Drosophila genomes and thus there is no evidence for gene duplications. For two genes (MeiW68 and CG7676) two copies could be found in D. sechellia and D. yakuba, respectively. It is, however, likely that these are artifacts of the genome assembly process. Indeed, the two MeiW68 gene copies are identical at the nucleotide level and the duplicated copy is located on a small scaffold that has not been anchored to any chromosome. The two proteins encoded by gene CG7676 are 194 and 190 amino acids long. Besides the indel, there is a single nucleotide difference between the two coding sequences. It should be noted that the shorter putatively duplicated gene is located on a small scaffold that has not been anchored to any chromosome. Therefore, we conclude that there is no solid evidence for MeiW68 and CG7676 gene duplications. Genus-wide, 85% of the meiosis-related genes do not have duplicates. However, nine independent gene duplications involving the genes cav, mre11, meiS332, polo and mtrm were found. The 12 Drosophila species here analyzed imply about 230 million years of independent evolution (Fig. 2). Therefore, Drosophila meiosis-related genes are duplicated at a rate of 0.0012 per gene per million years. This rate is similar to that estimated for the whole Drosophila genome [1].
In what follows, for each gene showing duplicates, their evolutionary history, as well as evidence that the gene duplicate(s) are functional is presented.
Three independent cav gene duplications
cav is a DNA-binding protein that is a component of the multiprotein Drosophila origin recognition complex [24]. Phylogenetic analyses revealed three independent cav gene duplications (Fig. 3). There is always a cav gene on Muller's element E, thus it seems reasonable to assume that this is the location of the ancestral cav gene. In the four species showing two cav copies, the duplicated gene is on three different Muller's elements, namely Muller's element A (D. virilis), element B (D. willistoni) or element E (D. persimilis, D. pseudoobscura). This finding is compatible with a scenario invoking three independent duplications, as suggested by the phylogenetic analyses. All cav gene duplicates have introns (Table S4), thus retrotransposition seems an unlikely explanation for the observed change in gene location. It should be noted that the phylogenetic tree presented in Fig. 3 implies that the cav gene duplication on Muller's element A predates the separation of the D. grimshawi and D. virilis/D. mojavensis lineages, but a duplicated copy cannot be found in either D. grimshawi or D. mojavensis. Indeed, this cav gene duplication is estimated to be as old as the split between the Sophophora and Drosophila subgenera, and thus about 40 million years old, under the assumption of a molecular clock for synonymous mutations (data not shown). It should be noted that these two cav genes are subjected to similar mutation rates but different amino acid constraints (Table 1). The accelerated rate of non-synonymous evolution of the D. virilis cav-dup gene (GJ17001) could suggest that it is a pseudogene. Nevertheless, this gene is expressed in both males and females (Fig. 4).
Numbers are posterior credibility values.
G – genomic DNA; F – female gonads; M – male gonads. The cDNA of duplicated genes were sequenced in order to assure amplification specificity. In males, for genes D. virilis cav-dup, D. persimilis cav-dup, D. mojavensis mre-11-dup and D. persimilis polo-dup1 a band with the size expected for an amplification from genomic DNA is observed. In order to rule out the possibility of contamination with genomic DNA, the PCR reactions were performed three times independently starting from different cDNA aliquots and identical results were obtained. The observation that when using the same aliquot, the duplicated gene shows two bands but the genes D. virilis cav, D. persimilis cav, D. mojavensis mre-11 and D. persimilis polo show only one band of the expected size also shows that there is no contamination with genomic DNA.
There are two cav genes in D. willistoni that are under similar amino acid constraint, and thus evolving at the same rate (Table 1). This cav gene duplication is estimated to be 10 million years old, under the assumption of a molecular clock for synonymous mutations (data not shown). There is no evidence that cav-dup is evolving faster than cav (Table 1). The duplicated gene seems to be weakly expressed and in males only (Fig. 4). There is thus no evidence that it is a pseudogene.
Two cav genes were also found in the two closely related species D. persimilis and D. pseudoobscura. This cav gene duplication is estimated to be 14 million years old, under the assumption of a molecular clock for synonymous mutations (data not shown). There is no evidence that cav-dup is evolving faster than cav (Table 1). The duplicated gene is expressed in both males and females (Fig. 4).
A recent mre11 gene duplication in the D. mojavensis lineage
Two mre11 copies (both on Muller's element B) are found in D. mojavensis (Fig. 5). The protein encoded by this gene is involved in telomere maintenance [25]. The mre11 gene duplication is estimated to be about 15 million years old, under the assumption of a molecular clock for synonymous mutations (data not shown). This duplication occurred in the D. mojavensis lineage after the separation from the sister group D. virilis lineage. It should be noted that the two D. mojavensis mre11 genes are subjected to similar mutation rates but different amino acid constraints (Table 1). The accelerated rate of amino acid evolution of the D. mojavensis mre11-dup gene (GI20694) could suggest that it is a pseudogene. Nevertheless, the mre11-dup gene is expressed. mre11-dup expression levels are higher in males than in females, a pattern also observed for the mre11 gene (Fig. 4).
Numbers are posterior credibility values.
Two polo gene duplications in the obscura group
Polo is a protein kinase that, in Drosophila female meiosis promotes nuclear envelope breakdown [26]. Three polo genes are found in the two closely related species D. pseudoobscura and D. persimilis (Fig. 6). The D. persimilis GL25129 and the D. pseudoobscura GA11545 genes that are on Muller's element D (where the D. melanogaster polo gene is also located) are orthologous. The D. persimilis GL25881 and the D. pseudoobscura GA25172 genes that are on Muller's element B are also orthologous, and are here named polo-dup1. The D. persimilis GL19429 and the D. pseudoobscura GA25958 genes that are on Muller's element B are also orthologous and are here named polo-dup2.
Numbers are posterior credibility values.
There are three predicted introns in polo-dup1. Therefore, retrotransposition seems an unlikely explanation for the observed change in gene location (from Muller's element D to element B). This polo gene duplication is about 6.5 million years old (under the assumption of a molecular clock for synonymous mutations; data not shown), and is thus expected to be found in species of the obscura group only. It should be noted that the two polo genes are subjected to similar mutation rates but different amino acid constraints (Table 1). This observation could suggest that polo-dup1 is a pseudogene. Nevertheless, polo-dup1 is expressed in males (Fig. 4).
polo-dup2 is about 12 million years old (under the assumption of a molecular clock for synonymous mutations; data not shown), and thus is also expected to be found in species of the obscura group only. There are no introns in polo-dup2. Therefore, in this case, retrotransposition could be an explanation for the origin of this duplication. It should be noted that such an hypothesis relies on the quality of the annotation of the D. pseudoobscura and D. persimilis genomes. polo and polo-dup2 are subjected to similar mutation rates but different amino acid constraints (Table 1). Nevertheless, polo-dup2 is expressed in males (Fig. 4), and thus, is unlikely to be a pseudogene.
There is one, three, and one fixed amino acid changes between the two polo-dup1 gene sequences and the other polo sequences here analyzed, at the first, second and third Polo boxes, respectively. In general, it is difficult to infer how important these changes might be. It should be noted, however, that the amino acid change observed in Polo box 1 (a change of a V to a I) changes an amino acid that is conserved in polo sequences from fungi to humans (see Fig. 1 in [27]). The polo-dup2 gene is a truncated version of polo where the last one third of the coding region of the gene is missing. Therefore the protein encoded by polo-dup2 does not show any POLO boxes.
Two independent mtrm gene duplications
The D. melanogaster Mtrm protein is a meiosis-specific 1∶1 stoichiometric inhibitor of the Polo kinase protein [28]. This gene is not annotated in most Drosophila genomes (Table S3) but can be always found within one intron of the exo70 gene.
In D. willistoni there are two mtrm-like genes, (Fig. 7), one on Muller's element B (that codes for a 186 amino acids long protein) and another one on Muller's element D (that codes for a 196 amino acids long protein). Since the D. melanogaster mtrm gene is located on Muller's element D, it seems likely that the duplicated gene copy is that on Muller's element B, and thus this D. willistoni copy is here named mtrm-dup. Although the two copies are on different Muller's elements, at the nucleotide level, the two sequences are 94% identical. Since mtrm gene does not have introns the possible involvement of retrotransposition in the translocation of the gene cannot be assessed. This is a recent gene duplication event, estimated to be 1.6 million years old, under the assumption of a molecular clock for synonymous sites. The two genes seem to be under similar amino acid constraint (Table 1). In D. melanogaster, phosphorylation sites (including one Polo-box domain binding motif and one Plk-phosphorylation motif, that differs at one amino acid site from the canonical sequence D/E-X-S/T-Ø-X-D/E where Ø is an hydrophobic amino acid), have been reported [28]. Both D. willistoni mtrm genes show a Polo-box domain binding motif and a typical Plk-phosphorylation motif in the same protein region as in D. melanogaster (Table 2). Moreover, most of the other phosphorylation sites reported for the D. melanogaster Mtrm protein are also present in the D. willistoni Mtrm and Mtrm-dup proteins. The only phosphorylation site that is not present is also not conserved in Mtrm proteins from other Drosophila species. Nevertheless, we could not find any evidence that the D. willistoni mtrm-dup is expressed (Fig. 4). Therefore, the hypothesis that this gene is a recent pseudogene that did not have yet time to degenerate cannot be ruled out.
Numbers are posterior credibility values.
In D. virilis there are also two mtrm-like genes, namely, one on Muller's element A and another one on Muller's element D, being the latter the orthologous of the D. melanogaster mtrm gene. mtrm and mtrm-dup are intronless genes. Therefore, it is not possible to infer the role of retrotransposition in the transposition of this gene from Muller's element D to A.
Bayesian phylogenetic analyses suggest that this mtrm gene duplication predates the separation of the D. grimshawi/(D. mojavensis/D. virilis) lineages (Fig. 7), and this conclusion is independent of the alignment algorithm used (data not shown). Moreover, mtrm-dup is not evolving faster than the mtrm gene (Table 1). The pair-wise synonymous divergence values suggest that, under the assumption of a molecular clock, mtrm-dup is about 35 million years old, and as such, would indeed predate the separation of the D. grimshawi/(D. mojavensis/D. virilis) lineages. Nevertheless, there is no evidence for a mtrm gene duplicate in either D. grimshawi or D. mojavensis. Therefore, taken at face value, these results imply two independent losses of the mtrm-dup gene.
The two neighbors of the D. virilis mtrm-dup gene (the D. melanogaster CG7326 and CG34401 orthologous genes) are gene neighbors in D. grimshawi and D. mojavensis. Each independent gene loss should be a unique event and thus leave a different genomic signature. Therefore, the comparison of the CG7326 - CG34401 region in D. virilis, D. grimshawi and D. mojavensis could, in principle, shed light on this issue. The intergenic regions can be confidently aligned, as revealed by the per site rates of change, namely 0.36 and 0.54 for the D. virilis – D. mojavensis and the D. virilis – D. grimshawi comparisons, respectively. The largest insertion, besides the mtrm coding region, in D. virilis relative to the other two species is only 27 bp long, and in total, there are 61 fixed gapped positions between the D. virilis sequence and the D. grimshawi/D. mojavensis sequences. Therefore, it seems that the only main difference in D. virilis relative to the other species is the insertion of the mtrm coding region. mtrm-dup is not, however, a pseudogene, since this gene is expressed in females (Fig. 4).
The mtrm-dup gene could also be amplified from 12 species of the virilis group from all major group phylads. Therefore, the mtrm-dup gene must be older than the age of the virilis group that is estimated to be 10 million years old [29]. Although 90% of the coding region of this gene was analyzed in the 12 species of the virilis group, no evidence for in-frame stop codons has been found. All mtrm-dup sequences show conservation of the T40 (a putative Cdk5 phosphorylation site), S48, S52 (putative Cdk or MAPK phosphorylation sites), S137, and S124 phosphorylation orthologous sites identified in D. melanogaster by Xiang et al. [28]. The S121 and S123 phosphorylation sites are not conserved in the mtrm-dup gene. Nevertheless, not all mtrm sequences show conservation of these sites either (Table 2).
The mtrm-dup gene does not show a Plk phosphorylation-like amino acid motif, due to a four amino acid insertion that is present in all mtrm-dup copies. It should be noted, however, that the D. virilis, D. mojavensis and D. grimshawi mtrm amino acid sequences do not have such a feature either, due to a three amino acid insertion. Therefore, in species of the Drosophila subgenus, the presence of a Plk phosphorylation-like amino acid motif is not an essential feature.
Although mtrm-dup is a functional gene, there are no data to support the assumption that this gene plays an essential role in meiosis in species of the virilis group of Drosophila. Indeed, it is conceivable that this gene represents a non-essential meiotic drive element that went to fixation in the common ancestor of species of the virilis group. Once fixed, it may be difficult to lose such an element since chromosomes carrying it are more represented in the next generation than chromosomes carrying alternative deleted copies of this element. Thus, such a gene could show most of the features expected for an essential gene. For D. melanogaster/D. simulans Anderson et al. [15] showed patterns of evolution at the mtrm gene that are compatible with both adaptive protein evolution and the sequential fixation of meiotic drive elements. Therefore, this hypothesis is here addressed in D. americana, a species of the virilis group of Drosophila.
Vieira et al. [17] reported an amino acid polymorphism for D. americana, at the gene CG18543 (mtrm-dup) that is a marker for the common polymorphic X/4 fusion. We have followed the transmission of the two types of chromosomes by looking at the male progeny of females heterozygous for the mtrm-dup amino acid variant under different genomic backgrounds (Table 3). There is no evidence that the reported amino acid polymorphism represents meiotic drivers of different strength (Chi-square test with one degree of freedom; P>0.05).
Concerted evolution at the Drosophila subgenus meiS332-like genes
meiS332 gene duplications have been found as well. The phylogeny presented in Fig. 8 suggests that this gene has been independently duplicated three times. Nevertheless, the two copies of the gene are located on Muller's element C always with opposite transcription orientations, and at about the same distance. The finding of a similar gene arrangement in D. virilis, D. mojavensis and D. grimshawi thus suggests a unique duplication event, rather than three independent recent duplications. The little divergence observed between the two copies in each species suggests that this is a case of concerted evolution. Concerted evolution has been reported at Drosophila genes other than rRNA gene loci (see for instance [4], [30], [31], [32], [33], [34]. The meiS332 gene duplication is an example of long-term (more than 30 million years) concerted evolution in the Drosophila subgenus. Similar long-term concerted evolution (also lasting for more than 30 million years) has been reported at the polyhomeotic (ph) gene duplication in the Sophophora subgenus [32].
Numbers are posterior credibility values.
In D. melanogaster, there are two Polo binding sites in MEI-S332, namely SSP from residue 233 to 235, and STP from residue 330 to 332 [35]. As shown in Table 4, the SSP motif is conserved in species of the melanogaster subgroup, in the two D. grimshawi sequences and in one of the two D. virilis sequences. The STP motif is conserved in all sequences with the exception of the D. mojavensis duplicated copy. It should be noted that, in D. melanogaster, phosphorylation was unaffected by the S234A mutation but was abolished with the T331A mutation [35]. This finding fits our observation of a better conservation of the STP motif than that of the SSP motif. Most MEI-S332 sequences from species of the Drosophila subgenus show three S(S/T)P motifs. These findings suggest that, with the exception of the D. mojavensis duplicate, all other duplicated genes are functional. Nevertheless, expression was detected in D. virilis and D. mojavensis meiS332-dup gene. We could not obtain non-mutant D. grimshawi strains, and thus expression was not tested in this species.
Discussion
Nine independent gene duplications involving the genes cav, mre11, meiS332, polo and mtrm were found. The 12 Drosophila species here analyzed imply about 230 million years of independent evolution. Therefore, Drosophila meiosis-related genes are duplicated and retained at a rate of 0.0012 per gene per million years. This value is similar to that estimated for the whole Drosophila genome using species of the melanogaster subgroup [1]. The rate at which gene duplicates are created and go to fixation, i.e, are retained, depends on population genetics variables such as birth rate, mutation rate, and effective population size (see for instance, [36]). While it is unlikely that those population genetics variables have remained constant over 230 million years of independent evolution, there is no reason to believe that using all 12 Drosophila genomes and all genes would produce an estimate that is substantially different from that provided by Osada and Innan [1]. For instance, when the dataset of 33 meiosis related genes is used, the rate of gene duplication and fixation is estimated to be 0.0013 and 0.0011 for species of the Drosophila and Sophophora subgenera, respectively (the estimate becomes 0.0009 for the Sophophora subgenus if the only likely non-functional D. willistoni mtrm-dup gene is not included in the calculations; see Table 5). It should be noted that, a detailed analysis of the 33 meiosis genes, revealed that a substantial fraction is non-annotated or likely miss-annotated. Although we do not provide a human-curated annotation for the studied genes in the 12 Drosophila genomes, we did analyze in detail the gene annotation for those cases where the non-annotation or miss-annotation could lead to erroneous conclusions (see Results).
The finding that functional meiosis-related gene duplications go to fixation at the same rate as the average for all genes is surprising, especially in the light of the complex roles that the genes under study perform (see Table S1). Indeed, meiosis-related genes are known to participate in multiple pathways, be involved in protein complexes, and, when disrupted, affect multiple aspects of meiosis (see Table S1).
It remains to be shown whether the gene duplicates play an essential role in meiosis-related features in the species where they are found. Therefore, it could be argued that they are non-essential meiotic drive gene duplicates that went to fixation. Nevertheless, the segregation experiments performed with the D. americana mtrm-dup gene did not reveal evidence for meiotic drive elements. The possibility of subfunctionalization [37] cannot be, however, ruled out. In Arabidopsis, gene duplicates involved in DNA repair, replication and recombination, as well as in cell-cycle are little retained [11].
The possibility that the duplicated meiosis related genes represent cases of neofunctionalization should thus be addressed by performing additional detailed cellular and biochemical experiments that are beyond the scope of this work. Indeed, about 50% of the gene duplicates are evolving faster than the original gene, a pattern that is compatible with a short period of relaxed selection or/and acquisition of a new function. Moreover, three out of the five genes that have been found to be duplicated are known to physically interact (meiS332, polo and mtrm). There are no reasons to believe that these genes are more prone to accumulate meiotic drive elements or more prone to subfunctionalization. Indeed, given the known function of these genes, they were, a priori, unlikely to be found duplicated. The D. melanogaster Mtrm protein is a meiosis-specific 1∶1 stoichiometric inhibitor of the Polo kinase protein. In this species activation of Cdc25 by an excess of Polo protein at stage 13 triggers nuclear envelope breakdown and entry into prometaphase [28]. Therefore, any changes in protein levels in either Polo or Mtrm could result in precocious entry into prometaphase or meiotic arrest. On the other hand, Polo antagonizes MeiS332 and removes this protein from centromeres, a step required for proper chromosome segregation at the metaphase II/anaphase II transition [35]. If meiosis is not completed, no gametes will be produced. On the other hand, significant defects in achiasmate segregation (the segregation of chromosomes that did not experience recombination) are observed when there is a precocious entry into prometaphase [28]. Therefore, in what follows we speculate on the conceivable adaptive value of each gene duplicate(s).
cav is a DNA-binding protein that is a component of the multiprotein Drosophila origin recognition complex [24]. In Drosophila, the cav gene has been duplicated three times independently. All three independent duplications are old and all cav duplicates are expressed. The functional significance of having two cav gene copies in D. virilis with similar expression patterns is unclear, but it could be related to the high D. virilis heterochromatin content. Although D. melanogaster and D. virilis have similar euchromatin sizes, the C- value for these species is about 0.17 and 0.37, respectively (http://www.genomesize.com). It has been proposed that heterochromatin protein 1 (HP1), in association with the origin recognition complex, recruits underphosphorylated isoforms of HP1 to sites of heterochromatin nucleation [38]. High cav-related protein levels could be advantageous in species with high heterochromatin content such as D. virilis.
The functional significance of having in D. persimilis/D. pseudoobscura a cav gene duplicate is also unclear. Even more puzzling is the functional significance of having one cav gene duplicate in D. willistoni with an apparent male-specific expression, since the original cav gene is expressed in both females and males. It should be noted that the C-value of these species is similar to the one reported for D. melanogaster (http://www.genomesize.com). Detailed expression studies are needed in order to address this issue.
The Mre11 protein is involved in telomere maintenance by preventing telomere fusion [25], [39]. In D. mojavensis there are two mre11-like genes. mre11 is expressed both in males and females being, however, more highly expressed in males. The mre11-dup gene seems to be expressed in males only. Therefore, in principle, the effect of the gene duplication is to exacerbate even more the difference in Mre11 expression levels in males and females. It can be speculated that D. mojavensis telomeres are for some reason stickier than those of other species. This is a possibility because the telomeric and half-telomeric retrotransposons of D. mojavensis display a number of unique features when compared to other Drosophila species [40]. In D. melanogaster, as in any eukaryote, recombination-based mechanisms also help maintain chromosome termini [41]. Nevertheless, in Drosophila males, there is no recombination, and thus the higher mre11 expression levels in males than in females might have been anticipated.
Two functional polo gene duplicates are observed in D. persimilis/D. pseudoobscura. polo-dup1 and polo-dup2 are apparently exclusively expressed in males. It can thus be predicted that in the obscura group of Drosophila nuclear envelope breakdown and entry into prometaphase occurs earlier in males from these species when compared with what happens in D. melanogaster.
The D. melanogaster Mtrm protein is a meiosis-specific 1∶1 stoichiometric inhibitor of the Polo kinase protein. Two independent duplications of this gene were found, one in D. willistoni and the other in D. virilis. The D. willistoni mtrm-dup gene seems to be a recent pseudogene, whereas strong evidence is here presented supporting the fact that the D. virilis mtrm-dup is an old functional gene duplication. It is unlikely that mtrm-dup is a meiotic drive element that was duplicated just by chance. It can thus be predicted that in D. virilis nuclear envelope breakdown and entry into prometaphase occurs later than in D. melanogaster. It should be noted that the D. virilis mtrm-dup is expressed in females only.
There are functional gene duplicates of meiS332 in D. mojavensis and D. virilis. If there is more MeiS332 protein to be removed from centromeres by Polo, then meiosis would be delayed, since removal of MeiS332 from centromeres is a step required for proper chromosome segregation at the metaphase II/anaphase II transition. Interestingly, in D. virilis females the mtrm gene is also duplicated. As noted above, an increase in Mtrm protein levels is also predicted to result in a delay in meiosis. A delayed meiosis could result in more time available to deal with large genomes such as that of D. virilis. It is, however, unclear whether the high heterochromatin content found in D. virilis is the consequence of an historically advantageous long meiosis duration that allowed the accumulation of high amounts of heterochromatin without deleterious consequences, or whether the long meiosis duration is an adaptive response aiming at handling the large amount of heterochromatin found in this species, that may have accumulated due to other reasons.
In conclusion, in this work we find that, contrary to theoretical expectations, meiosis-related genes are duplicated and retained at the same rate as the average for all genes. The duplicated genes were, a priori, unlikely to be found duplicated, and may represent examples of neofunctionalization. Detailed cellular and biochemical experiments must be performed in order to address this issue. Nevertheless, given the nature of the genes that were found duplicated, it is here speculated that the duplicated genes may affect meiosis duration. D. melanogaster is the only Drosophila species where meiosis duration has been recorded (it takes about 1-2 days; [13]). The results here presented suggest that in the obscura group of species, male meiosis duration may be shorter than in D. melanogaster, while in D. virilis, where three meiosis genes are duplicated, meiosis duration may be much longer than in D. melanogaster. Interestingly, D. virilis is among the Drosophila species the one with highest nuclear DNA content, and Bennett [13] has shown a linear correlation in insects between nuclear DNA content and the duration of meiosis. If the correlation derived by Bennett holds true, then, at the same temperature, meiosis should take about twice as long in D. virilis than in D. melanogaster. Environmental factors should be taken into consideration as well, when making such predictions. Indeed, Bennett [13] shows that in insects, a decrease of 10°C in environmental temperature means a doubling in meiosis duration. Therefore, under their natural environments, Drosophila temperate species (such as species of the virilis group) should show, anyway, longer meiosis duration times than tropical species (such as D. melanogaster African populations).
Supporting Information
Table S1.
Overview of the meiosis-related genes studied.
https://doi.org/10.1371/journal.pone.0017512.s001
(PDF)
Table S3.
Accession numbers for the 33 meiosis genes studied from 12 Drosophila species.
https://doi.org/10.1371/journal.pone.0017512.s003
(PDF)
Table S4.
Coding sequence size and intron number (in brackets) of 33 meiosis genes from 12 Drosophila species.
https://doi.org/10.1371/journal.pone.0017512.s004
(PDF)
Acknowledgments
The authors want to thank R. Scott Hawley and S. Kendall Smith for critically reading the manuscript, as well as David Liberles, Fyodor Kondrashov, and two anonymous reviewers for providing useful insights into this work.
Author Contributions
Conceived and designed the experiments: MR SG CPV CS JV. Performed the experiments: MR SG CPV CS JV. Analyzed the data: MR SG CPV CS JV. Contributed reagents/materials/analysis tools: MR SG CPV CS JV. Wrote the paper: MR SG CPV CS JV.
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