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Abstract
We analyzed evolutionary rates of conserved, duplicated myosin V (myo5) genes in nine teleost species to examine the outcomes of duplication events. Syntenic analysis and ancestral chromosome mapping suggest one tandem gene duplication event leading to the appearance of myo5a and myo5c, two rounds of whole genome duplication for vertebrates, and an additional round of whole genome duplication for teleosts account for the presence and location of the myo5 genes and their duplicates in teleosts and other vertebrates and the timing of the duplication events. Phylogenetic analyses reveal a previously unidentified myo5 clade that we refer to now as myo5bb. Analysis using dN/dS rate comparisons revealed large regions within duplicated myo5 genes that are highly conserved. Codons identified in other studies as encoding functionally important portions of the Myo5a and Myo5b proteins are shown to be highly conserved within the newly identified myo5bb clade and in other myo5 duplicates. As much as 30% of 319 codons encoding the cargo-binding domain in the myo5aa genes are conserved in all three codon positions in nine teleost species. For the myo5bb cargo-binding domain, 6.6% of 336 codons have zero substitutions in all nine teleost species. Using molecular evolution assays, we identify the myo5bb branch as being subject to evolutionary rate variation with the cargo-binding domain, having 20% of the sites under positive selection and the motor domain having 8% of its sites under positive selection. The high number of invariant codons coupled with relatively high dN/dS values in the region of the myo5 genes encoding the ATP-binding domain suggests the encoded proteins retain function and may have acquired novel functions associated with changes to the cargo-binding domain.
Introduction
In 1970, Ohno proposed that two rounds (2R) of genome duplication had occurred in the evolutionary history of vertebrates and suggested such duplication events could have contributed to the sudden radiation and diversity of vertebrates (Ohno 1970). Since then support has grown for the 2R hypothesis such that it is currently widely accepted. An additional genome duplication event is thought to have occurred in the teleost lineage around 300 Ma (Taylor et al. 2001) since many genes that are found in single copy in other vertebrates have duplicated orthologs in teleosts. A common fate for duplicated genes is that they become lost in evolutionary time as missing ohnologs (Catchen et al. 2009), although alternative outcomes include becoming pseudogenes (Li 1980), acting as a backup copy of the original gene or evolving new or modified functions (Ohno 1970; Force et al. 1999). In teleosts, numerous genes related to pigmentation provide us with a model to study these gene duplication events (Braasch et al. 2007).
It has been suggested that pigmentation-related genes retain their duplicates in fish at a higher rate than other genes (Braasch, Brunet, et al. 2009). Although the total number of genes in fish is not much different from tetrapods, Braasch, Brunet, et al. (2009) found that there are approximately 30% more pigmentation-related genes comparted with tetrapods. Duplicated genes related to pigmentation have provided new opportunities for phenotypic diversity among fishes (Braasch, Liedtke, et al. 2009) in addition to opening the evolutionary door for neofunctionalization for one of the duplicated genes to acquire a nonpigmentation-related function over time. For example, Mills et al. (2007) showed that the kita gene is expressed in specific populations of pigment cells, whereas Mellgren and Johnson (2005) observed the kitb gene to be expressed in nonpigment-related cell types including neurons. Together, the expression patterns of these two duplicated genes approximate the expression pattern of the nonduplicated Kit gene in mouse.
Among the pigmentation-related genes that seem to have retained functionality after duplication, the myosin genes are particularly interesting. Myosins are a diverse superfamily of proteins found in all lineages of eukaryotes and include more than 20 families (myosins I-XX) of motor proteins that travel along tracks formed from actin, including some unconventional myosins (see reviews by Trybus 2008; Hammer and Wagner 2013). Myosin proteins form homodimers and contain an N-terminal motor domain (head), a neck region, and, in some subfamilies of myosin, a C-terminal cargo-binding domain (CBD). The motor domain contains sites for ATP- and actin-binding. The neck shows the least amount of conservation at the nucleotide and amino acid levels. For the myosin V subfamily, different accessory proteins associate with the myosin proteins, enabling them to interact with cargo (see reviews by Trybus 2008; Hammer and Wagner 2013).
Within the myosin V (myo5) gene family, the gene products have been shown to be involved in numerous cellular motor functions, including organelle transport and membrane trafficking in several cell types such as epidermal pigment cells, intestinal epithelial cells, and neural cells (Rodriguez and Cheney 2002; Swiatecka-Urban et al. 2007; Hammer and Wagner 2013). In mammals, there are three types of myosin V proteins (a, b, and c). Myosin Va is involved in transporting organelles, including melanosomes, along actin tracks and is expressed in much of the central nervous system (Hammer and Wagner 2013). Myosin Vb is involved in endosome recycling in epithelial cells (Swiatecka-Urban et al. 2007), and it is expressed in the central nervous system (Hammer and Wagner 2013). Myosin Vc is primarily expressed in epithelial cells (Rodriguez and Cheney 2002). With the many roles that myosins play along with the many types of tissues where these proteins are active, there have been abundant opportunities for duplicated versions of these genes to take on new or specialized roles.
Acquisition of new roles is associated with differential evolutionary rates. Muse and Gaut (1994) devised a model that determined an evolutionary rate (ω) based on a ratio of nonsynonymous and synonymous substitutions in an alignment, and this rate could vary from one branch to another in a phylogeny. Nielsen and Yang (1998) developed a codon substitution model that allowed rates at each codon to vary but kept the rate among the branches constant. With an increase in computational power, newer refined codon substitution models were developed to allow for different rates of codon site evolution to occur among codons and among branches (Yang and Nielson 2002; Bielawski and Yang 2003, 2004; Zhang et al. 2005; Anisimova and Yang 2007; Smith et al. 2015). The quantification of evolutionary rates using these methods can provide insight into the fates of duplicated gene and elucidate the mechanisms by which novel functions might evolve.
Here, we characterize the myo5 duplicates and their evolutionary history in vertebrates. We identify a branch in a phylogeny of the myosin gene family for a duplicated gene (myo5bb) in teleosts and spotted gar. We show that regions encoding the actin-binding domains are highly conserved, including third codon positions, but there is more variability in third codon positions near the 3′ end of the gene where the CBD is encoded. In addition to presenting data that supports previously described genome duplication events, namely the vertebrate R1/R2 and fish-specific genome duplications, we identify a tandem gene duplication event for the myo5a and myo5c genes, and we propose a model for the evolution of the myo5 gene family. In our proposed evolutionary model of the myo5 gene family, we provide phylogenetic and syntenic data that supports the vestiges of two different myo5b clades that likely originated from one of the ancient R1/R2 vertebrate genome duplication events. With our analysis of codons, we identify extreme purifying selection present in 96 codons out of 319 codons (30.1%). These 96 codons are invariant and have zero nucleotide substitutions in the nine teleosts examined for the myo5aa 3′ end. In contrast, 46 codons out of 742 codons (6.2%) in the myo5ab neck region of the myo5 gene are subject to extreme purifying selection for the nine teleosts examined.
Materials and Methods
Sequence Acquisition
We collected myosin 5 sequences using Ensembl’s genomic database (Ensembl Release 86), NCBI, and the Japanese Lamprey Genome Project. The following species and genomic assemblies were used for myo5 sequence downloads: nine teleost species (cavefish, Astyanax mexicanus, AstMex102; cod, Gadus morhua, gadMor1; fugu, Takifugu rubripes, FUGU 4.0; medaka, Oryzias latipes, HdrR; platyfish, Xiphophorus maculatus, Xipmac4.4.2; stickleback, Gasterosteus aculeatus, BROAD S1; tetraodon, Tetraodon nigroviridis, TETRAODON 8.0; tilapia, Oreochromis niloticus, Orenil1.0; zebrafish, Danio rerio, GRCz10), one holostean fish (spotted gar, Lepisosteus oculatus, LepOcu1), one lobe finned fish (coelacanth, Latimeria chalumnae, LatCha1), one amphibian (western clawed frog, Xenopus tropicalis, JGI 4.2), five sauropsids (chicken, Gallus gallus, Gallus_gallus-5.0; turkey, Meleagris gallopavo, Turkey_2.01; duck, Anas platyrhynchos, BGI_duck_1.0; Chinese soft shell turtle, Pelodiscus sinensis, PelSin_1.0; green anole lizard, Anolis carolinensis, AnoCar2.0), two mammals (human, Homo sapiens, GRCh38.p7; mouse, Mus musculus, GRCm38.p5), one cartilaginous fish (elephant shark, Callorhinchus milii, Genbank assembly-GCA_000165045.2) two jawless vertebrates (sea lamprey, Petromyzon marinus, Pmarinus_7.0; Japanese lamprey, Lethenteron japonicum, Japanese lamprey genome project-APJL00000000), and two urochordates (sea squirts, Ciona intestinalis, KH; Ciona savignyi, CSAV 2.0).
Syntenic Analysis
Using Biomart in the Ensembl database, genes located within 1.5 megabases of each myo5 gene were identified. Synteny maps were constructed based on conserved patterns of gene locations for each of the myo5 gene families, and results are presented in figure 1
. Construction of syntenic regions used zebrafish and tetraodon genomes as an initial source to identify genes within 1.5 megabases for each myo5 gene family. After downloading genes from BioMart within the previously specified regions, we found 39 genes from zebrafish and 125 genes from tetraodon for the myo5aa gene family, 89 genes from zebrafish and 176 genes from tetraodon for the myo5ab gene family, 117 genes from zebrafish and 70 genes from tetraodon for the myo5ba gene family, and 74 genes from zebrafish and 137 genes from tetraodon for the myo5bb gene family. For the myo5c gene family, we used the same set of genes as in the myo5ab gene family because myo5c and myo5ab are directly next to each other on the chromosome for most of the teleosts tested, and myo5a and myo5c are directly next to each other on the chromosome for other vertebrates that have those two genes. The number of genes we found within 1.5 megabases of any myo5 gene was between 39 and 176. In making a more concise syntenic map presented in figure 1 we used approximately 30 genes total and about 10 genes in each myo5 gene neighborhood. Each gene neighborhood generally contained genes within 200,000 bases of each myo5 gene.
Ancestral Chromosome Mapping
We used ancestral chromosomal reconstructions from Nakatani et al. (2007) and Bian et al. (2016) to determine the timing of the myo5 gene duplication events relative to the major genome duplication events. Nakatani et al. provide chromosomal maps for syntenic blocks of genes for the genomes of human, chicken, and medaka and relate these syntenic blocks back to one of ten ancestral chromosomes designated A-J. Bian et al. provide chromosomal maps for syntenic blocks of genes for medaka, zebrafish, arowana and spotted gar and relate these syntenic blocks back to one of thirteen ancestral chromosomes present before the teleost and nonteleost fish (including spotted gar) split. Utilizing these two sets of chromosomal mapping data, we were able to identify whether our genes of interest split after the vertebrate first or second whole genome duplication or if the genes of interest were a result of the fish-specific genome duplication (fig. 2
).
Alignment and Phylogenetics
Eighty-seven sequences were aligned using ClustalW and Geneious Pro 6.0 (Biomatters Ltd). Sequences were virtually translated, verified to contain open reading frames, and then back translated. The ends of the aligned sequences were trimmed and smaller alignments from three regions (motor domain, neck, CBD) within the myo5 gene were obtained from the full-length coding sequence alignment. Model testing was performed for each of the four alignments, and the model with the best AICc value was chosen for the generation of the phylogenetic trees using Geneious 6.0. Using MrBayes 3.1 and a GTR+I+G model of evolution, trees were generated for the full-length coding sequence (6,870 bp) of myo5, the motor domain, the neck, and the CBD. The parameters used in the MrBayes-generated trees were as follows: three gamma categories were used with unconstrained branch lengths. Markov Chain Monte Carlo methods were used for 1,100,000 steps with thinning every 200 steps, four heated chains, and a preheated chain temperature of 0.2. A burn in length of 500 steps was used. Alternative models were tested using maximum likelihood and parsimony methods, and these provided similar topologies.
For the four alignments we generated, we removed sequences that did not have at least 50% coverage. For example, the duck myo5c sequence only had sequence coverage in the motor domain and in the CBD, so it was only included in those alignments and phylogenetic analyses and not in the neck or full sequence alignments. Similarly, there were other sequences that were missing sequence data for more than 50% of the alignment. These sequences were not included in those specific alignments (fig. 4).
dN/dS Rates and Identification of Invariant Codons
We determined the evolutionary rate (dN/dS) using MEGA6. “dN” is defined as the ratio of nonsynonymous substitutions per nonsynonymous site; “dS” is defined as the ratio of synonymous substitutions per synonymous site. Maximum likelihood reconstructions of ancestral states were generated using a Muse-Gaut model (Muse and Gaut 1994) of codon substitution and a general time reversible model (Nei and Kumar 2000) for nucleotide substitution. We used MEGA6 to determine the dN and dS values for each codon in our alignment for a specific clade which generally consisted of 8-10 teleost sequences for a specific myo5 duplicate. Summing the dN and dS values for all the codons in our alignment and then dividing dN by dS allowed us to determine the dN/dS ratio for each alignment. To quantify the percentage of codons that are invariant and experiencing extreme purifying selection, we counted the number of codons in each of the original four alignments (whole gene, motor domain, neck, and CBD) that had dN and dS values of zero and divided this by the total number of codons in the alignment to determine the percentage of codons that are invariant and experiencing extreme purifying selection (tables 1Teleost myo5 dN/dSValues
and [2]Percentage of Invariant Codons in Teleost myo5 Genes
).
Selection Tests
We used the Datamonkey server and the HyPhy software package (Kosakovsky Pond et al. 2005; Delport et al. 2010) to test for purifying selection, positive selection, and episodic selection at the codon level and the branch level among the phylogenies we generated. Trees that were generated as described previously using the Geneious Software package were saved as Nexus files and uploaded to the Datamonkey Server to run the selection tests. We used BUSTED (Branch site Unrestricted Statistical Test for Episodic Diversification) to assess whether episodic diversification occurs on at least one branch and at least at one site in the phylogeny. The BUSTED test allows for varying rates of evolution (ω) applied to a constrained model of selection (null model) and an unconstrained model of selection (alternative model) using a Likelihood Ratio Test. We then tested our alignments using MEME (Mixed Effects Model of Evolution), BS-REL (Branch Site-Random Effects Likelihood), aBS-REL (adaptive BS-REL), and SLAC (Single Likelihood Ancestor Counting). MEME identifies the number of sites (codons) showing episodic diversifying selection using a maximum likelihood approach. Different evolutionary rates are allowed for each codon within an alignment. The aBS-REL test determined which branches in the phylogeny showed evidence of diversifying selection using a likelihood ratio test and providing statistical support with P ≤ 0.05. Methods for the tests we used in our analyses are further described in Nielsen and Yang (1998; REL), Murrell et al. (2012; MEME), Kosakovsky Pond and Frost (2005; SLAC), Kosakovsky Pond et al. (2011; BS-REL), Murrell et al. (2015; BUSTED), Smith et al. (2015; aBS-REL). We used 8-10 teleost sequences from our alignments to test for selection among the duplicated myo5 genes using the MEME and REL selection tests. We did this for each teleost duplicated myo5 gene clade and for the smaller regions within the gene. For example, we used the 5′ end motor domain alignment of nine teleost sequences for the myo5aa teleost gene clade and ran the MEME and REL selection tests. Similarly, we tested the neck and CBD for the myo5aa teleost clade, and we ran these same selection tests using the comparable domains for the teleost clades which included myo5ab, myo5ba, and myo5bb genes (table 4).
Results
Syntenic Analysis
To determine whether myo5 duplicates arose through duplication of individual genes, chromosomes or their segments, or entire genomes, we performed syntenic analysis. We found the chromosomal locations for myo5aa and myo5ab in zebrafish on chromosomes 18 and 25, respectively, and the locus for myo5c directly downstream of myo5ab. This arrangement with myo5aa and myo5ab on separate chromosomes and myo5c on the same chromosome as myo5ab was observed in all teleosts examined; furthermore, myo5c was observed directly downstream of myo5a in nonteleost vertebrates (fig. 1). Initial phylogenetic analyses revealed a new myo5 clade (the myo5bb clade), and syntenic analyses provided further support of the presence of this gene along with neighboring genes in teleosts, spotted gar, chicken, duck, turkey, turtle, coelacanth, and shark. This gene appears to be absent in mammals, anole, and Xenopus.Figure 1 shows genes that are syntenic with myo5a as rectangles, genes syntenic with myo5ba as ovals, and genes syntenic with myo5bb as triangles.
We traced the origin of extant myo5 sequences to ancestral vertebrate and teleost chromosomes to further test the findings from our syntenic analysis (fig. 2). All myo5 sequences traced back to an ancestral vertebrate chromosome A. Nakatani et al. (2007) identified six chromosomes or linkage groups numbered A0-A5 resulting from two whole genome duplication events (R1 and R2) and a fission event. The myo5a and myo5c tandem duplicated genes are linked with the A4 fragment (fig. 2A). The myo5ba genes are linked with the A0 fragment and the myo5bb genes are linked with the A1 fragment (fig. 2A). Coduplicated genes exist, for example, mbd1 near myo5ba and mbd3 near myo5bb. Additional coduplicated genes were identified with mapk4 found near myo5ba and mapk6 found near myo5a-myo5c. The onecut3 gene was found near myo5bb, and onecut6 was found near myo5a-myo5c. Teleost myo5 genes were traced back to three of thirteen ancestral teleost chromosomes. myo5ba was traced back to ancestral teleost chromosome i, myo5aa and myo5ab-myo5c were traced back to ancestral teleost chromosome j, and myo5bb was traced back to ancestral teleost chromosome m (fig. 2B).
We identified two partial myo5 sequences for each lamprey species tested. Figure 1 shows the syntenic arrangement of genes around the myo5 sequences in both lamprey species and figure 4A and B shows the alignment of lamprey sequences in relation to the whole myo5 genes and the smaller regions of the genes used in this study. Using BLAST to compare 400,000 bases of Japanese lamprey DNA around the Japanese lamprey myo5 sequence against the sea lamprey genomic database in Ensembl, we found the pigo and ensab genes on one side of the myo5 genes, and we found mapk4, cfap53, and atp8b on the other side of the myo5 genes.
Phylogenetic and dN/dS Analyses
To understand the molecular evolution of the myo5 gene family, phylogenetic analysis was performed using 87 genes from 24 different species (see supplementary table S1, Supplementary Material online for names and genomic database identifiers). Using ClustalW, we produced a final alignment of 6,468 base pairs per gene. Four phylogenetic trees were generated, representing the full-length coding sequence (fig. 3A), the portion encoding the CBD at the 3′ end of the myo5 gene (fig. 3B), the 5′ end of the gene which encodes the motor domain with its highly conserved ATP-binding domain (fig. 3C), and the more variable portion of the myo5 gene which encodes the neck and tail regions (fig. 3D). Figure 4A shows where the smaller alignments fit within our full-length alignment. The myo5aa teleost sequences form a monophyletic clade, and the myo5ab teleost sequences form a monophyletic clade (fig. 3A, B, and D). Separate clades form for the myo5ba teleost sequences, the myo5bb sequences, and the myo5c sequences (fig. 3A, B, and D). Nonteleost myo5a sequences formed a clade sister to a clade which included spotted gar and teleost myo5aa and myo5ab sequences (fig. 3A and D). Nonteleost and teleost myo5c sequences formed a monophyletic clade (fig. 3A-D); however, tetrapod myo5b was for the most part monophyletic with teleost myo5ba, but not with teleost myo5bb (fig. 3A, B, and D). These topologies were less evident in the phylogenetic trees generated for the sequences encoding the motor domain due to the higher degree of conservation (see “Codon-specific analysis” below and fig. 4).
We determined dN/dS values for each clade and each region of the myo5 gene family (see fig. 5
and table 1). The dN/dS ratios for the myo5ba and myo5bb were higher than the dN/dS ratios for myo5aa and myo5ab (fig. 5). For the myo5a duplicates (myo5aa and myo5ab), the percentage increase is higher for the dN/dS values for the motor domain and the CBD with the largest amount of dN/dS change taking place in the CBD for the myo5ab clade. For the myo5bb clade we see a much smaller increase in the dN/dS rates for the CBD with a 68% increase compared with the 250% increase seen in the myo5ab clade. The dN/dS for the motor domain also increased a relatively small amount (33%) for the myo5bb clade compared with the motor domain of the myo5ab clade (140%).
In addition to calculating the dN/dS ratios for each of the whole genes and for specific regions within the myo5 genes, codon-specific values for dN and dS for each alignment tested were calculated. For a given region of a myo5 gene, for example the 5′ end, dN and dS were calculated by comparing sequences from at least 8 teleost species. The 3′ end where the CBD is encoded evinced far fewer invariant sites in the myo5ab clades compared with the myo5aa clades. We identified 30.1% of the codons for the teleost myo5aa clade subject to extreme purifying selection but only 7.5% of codons in the myo5ab clade showed extreme purifying selection (dN = dS = 0). No substitutions were identified in any of the three positions for codons in these invariant sites among the 8-9 teleosts analyzed. The myo5ba clade has 23.8% of codons invariant in the diverse teleost sequences tested, but only 6.6% of the codons for the myo5bb clade are invariant. The myo5ab neck region also showed fewer invariant sites than the myo5aa neck region (table 2). For other regions of the myo5 genes, the percentages of invariant codons were similar among the different paralogs. For example, the 5′ end of the myo5 genes, where the actin- and ATP-binding domains are encoded, shows similar percentages for each clade ranging from 11.5% to 13.4%, suggesting the motor domain is similarly conserved between homologous clades and may be functional for all the myo5 duplicates in teleosts.
Codon-Specific Analysis
After identifying an unexpectedly high percentage of invariant codons, we compared the dN/dS ratios of codons that encode amino acids that are known to play a functional role in MYO5 proteins in mammals. Amino acids linked with functionality in mammals are highly conserved in teleosts in the 5′ region for myo5a and myo5b duplicates (supplementary tables S2 and S3, Supplementary Material online), suggesting these duplicates retain the motor functions related to ATP- and actin-binding. However, there is a significant difference in the CBD when looking at the codon sites linked with functionally important amino acids for MYO5 proteins (supplementary tables S4 and S5, Supplementary Material online). We examined the 10 sites that are linked with RAB11a binding to MYO5b in mammals (Pylypenko 2013), and we found that the dN/dS values for these ten sites are 0 or mathematically undefined, meaning the value of the denominator (dS) equaled 0, highlighting the high conservation for these sites in myo5ba in teleosts (supplementary table S5, Supplementary Material online). These same sites are not as well conserved in the myo5bb duplicates.
Out of the 217 codons in the 5′ region of the myo5 genes, we specifically selected 21 codons that code for amino acids linked with the functional myosin motor activity for further analysis. The dN/dS rate for these 21 codons was lower compared with the dN/dS rate of the entire 5′ region. The average dN/dS for codons in the 5′ regions for teleost myo5 genes was 0.08 (table 1), but the average dN/dS value for the 21 codons linked with functionality was only 0.02. The increase in conservation for these 21 codons was seen for all five myo5 genes in teleosts for the 5′ region which included the part encoding the ATP-binding domain for the Myo5 proteins (table 1).
In the myosin head, the aspartate at position 134, D134, is an example of an amino acid that was conserved in all myo5 sequences analyzed, with the following exceptions: The inferred amino acid sequence from the single myo5 gene in Ciona manifests a D→E change. In Tetraodon, there is a D→E change for myo5ab. Cavefish and platyfish show sequence variation in the 5′ end of the myo5aa gene such that the D134 amino acid is not present. The cavefish myo5aa gene has a premature stop codon which truncates the protein before the CBD is translated, so cavefish may not have a functional myo5aa gene.
Another feature of the myosin head’s ATP-binding domain is the p-loop, a region of the protein that interacts with the terminal phosphate on ATP (Coureux et al. 2003). Among the highly conserved amino acid residues in the p-loop, which comprises amino acids 163-170 (GESGAGKT), the only variation that we see in this region is for the whole myo5bb teleost clade, in which the alanine at position 167 has been substituted with a serine, yielding the consensus sequence GESGSGKT.
The 742 codons in the neck region show the largest amount of molecular variation with dN/dS rates ranging from 0.23 for myo5aa to 0.41 for myo5ab (table 1). When comparing the duplicates for this region, myo5ab has a larger dN/dS value (0.41) than the paralogous myo5aa genes (0.23). The 23 codons that code for amino acids linked with actin binding have much more conserved sequences compared with the neck domain except for myo5aa (table 1 and supplementary table S3, Supplementary Material online). For myo5aa, the dN/dS value for the 23 codons associated with actin binding is 0.23 but for the other four teleost genes the dN/dS range is 0.04-0.14.
For the 319 codons in the 3′ end of the myo5 genes, which include the CBD, the myo5ab and myo5bb genes have the highest dN/dS values at 0.35 and 0.32, respectively. The myo5aa and myo5ba genes are much more conserved in this region with dN/dS rates of 0.10 and 0.19, respectively. When looking at the 10 codons linked with cargo binding, myo5ba has a dN/dS rate of 0 and myo5aa has a dN/dS rate of 0.13 (table 1 and supplementary tables S4 and S5, Supplementary Material online).
Selection Test Results
We carried out several selection tests (table 3Branch Site-Random Effects Likelihood (BS-REL) Test Results
Results from MEME (Mixed Effects Model of Evolution) and REL (Random Effects Likelihood)
) accessed from the Datamonkey server and utilizing the HyPhy software package. We used BUSTED to test for selection across our phylogeny and this test revealed that episodic diversifying selection was occurring somewhere in our full-length phylogeny (P < 0.05). We specifically selected myo5b branches to test as foreground branches, and the remaining branches were considered background branches. Three rate classes (ω, ωω) were determined for the test branches and background branches for a constrained model (null model) and an unconstrained model of selection. For the myo5b test branches, episodic diversifying selection was occurring on at least one site with a ω = 0.01 for 74.5% of the sites, ω = 0.60 for 23.63% of the sites, and ω = 248.95 for 1.87% of the sites. To more specifically address on which branch(es) and at which sites selection was taking place we used MEME (Mixed Effects Model of Evolution). The results from the MEME test showed many sites with episodic diversifying selection in the neck region of the myo5 gene, which is the least conserved region of the myo5 genes. The functional domains are in the motor domain and in the CBD. In the CBD, we see more episodic diversifying selection in the myo5bb clade of teleosts versus the myo5ba clade of teleosts. We also see large variations between these two clades when comparing the number of codons experiencing positive selection versus purifying selection using REL (Random Effects Likelihood). The REL test shows the number of sites (codons) experiencing positive (REL +) or negative/purifying (REL −) selection. The REL test computes two Bayes factors such that one will test for dN < dS, suggesting purifying selection, and the other Bayes factor will test for dN > dS, suggesting positive selection at specific codons (Nielsen and Yang 1998; Kosakovsky Pond and Frost 2005). The results from the REL test showed that five sites in the CBD of myo5bb were subject to positive selection and 247 sites were subject to purifying selection. For the myo5ba duplicate there were zero sites subject to positive selection and 78 sites subject to purifying selection. For the myo5aa clade and the CBD there were two sites under positive selection and 132 sites subject to purifying selection. For the myo5ab duplicate, there was one site subject to positive selection for the CBD and 103 sites subject to purifying selection (table 3).
A BS-REL (Branch Site-Random Effects Likelihood) test was used on the phylogenies we generated to test for episodic or diversifying selection along branches. We identified episodic selection taking place along the myo5bb branch leading up to the ray-finned fish lineage (table 4). On this branch, 20% of the sites in the CBD are under positive selection, 26% of the sites are under neutral selection, and 54% of the sites are under purifying selection. Two other branches that showed signs of episodic diversifying selection in the CBD were branches that led to the myo5ba teleost clade and the myo5b clade as a whole. However, both of those branches had a much higher percentage of sites under purifying selection and many fewer sites subject to positive selection.
An aBS-REL (adaptive Branch Site-Random Effects Likelihood) test was used on all the branches in the CBD. Out of 147 branches tested in the CBD, 78 branches were subject to a single rate class, ω (dN/dS). The remaining 69 branches were modeled using two rate classes ω and ω. Of these 69 branches that were subject to two rate classes, five branches showed evidence of diversifying selection with statistical significance (P < 0.004). Four of the five branches were for single genes for a single species (myo5ba-spotted gar, myo5bb-spotted gar, myo5-sea lamprey, myo5bb-coelacanth). The fifth branch that showed evidence of diversifying selection was the branch at the base of teleost myo5bb (P = 0.0003). On this branch leading to the CBD for the myo5bb teleost clade, there were two rate classes identified ω (dN/dS) = 0.316 for 76% of the sites and ω = 80.1 for 24% of the sites.
Discussion
We investigated gene duplications in the myo5 family to provide insight into the mechanisms that constrain and promote the evolution of novel gene functions. In fish, myo5 and other myosin genes have been examined but an analysis of the duplicated genes has not been done. Sonal et al. (2014) described myo5b expression in fish but did not identify or examine myo5bb. Similarly, Sittaramane and Chandrasekhar (2008) described myo5a expression along with other myosin genes in zebrafish but did not examine the duplicated versions. Hodel et al. (2014) looked at Myo7a in fish and mentioned that the antibody used is likely recognizing both Myo7a1 and Myo7a2. Here, we highlight the usefulness of analyzing genes duplicated in teleosts to provide insight into molecular evolutionary processes.
Syntenic Analysis
Our syntenic analysis supports a model in which numerous events in the evolutionary history of teleosts and nonteleost chordates contributed to myo5 gene duplications and gene losses. Four gene or genome duplication events could account for the five myo5 genes present in teleosts, four myo5 genes present in spotted gar, and three to four myo5 genes present in the lobe finned fish lineage. Three of these duplicated myo5 genes (myo5a, myo5ba, and myo5bb) appear to result from the vertebrate genome duplication events, R1 and R2 (fig. 1). One of these myo5 duplications may be the result of a tandem gene duplication event (TGD) which preceded the divergence of jawed vertebrates; the resulting paralogs are currently referred to as myo5a and myo5c. The fourth duplication event we identified is specific to teleosts and is likely the result of the teleost- or fish-specific genome duplication event (R3) and this event led to the myo5aa and myo5ab genes in fish. As four genes would be expected from the two genome duplication events (R1 and R2), we suspect a gene loss took place after the R2 duplication event. Our examination of the syntenic data and our ancestral chromosome mapping support these predictions on the placement of duplication events in the evolutionary history of the myo5 gene family. The newly identified myo5bb clade present in birds, turtle, shark, coelacanth, spotted gar, and teleosts seems to represent a case of hidden paralogy. In the Ensembl genomic database, several of these genes are identified as myo5b for nonteleosts or not identified at all for teleosts. These myo5bb genes are more closely related to teleost myo5bb than they are to human or mouse myo5b. For example, chicken myo5b should not be assumed to be more closely related to human myo5b even though they have the same name. Our results show that the chicken myo5b gene is a myo5bb gene, and it should be seen as more closely related to fish and other vertebrate myo5bb genes (see Kuraku 2010, 2013; Qiu et al. 2011 for more details about hidden paralogy).
For each lamprey species, we found a gene that aligns with the 5′ end of our alignments and a second gene that aligns with the 3′ end of our alignments. However, we suspect that one of three scenarios accounts for this finding. One possibility is that there is an error in the assembly of the contigs in Ensembl for the sea lamprey. For the sea lamprey, there are approximately 80,000 “N” nucleotides in between the ensab gene and the myo5 CBD where the myo5 motor domain should be located. We identified the myo5 motor domain on an independent small scaffold without any genes around it. We suspect that this scaffold, which includes the sea lamprey myo5 motor domain, is misplaced and that it should be part of the 80,000 “N” nucleotides which occur between the ensab gene and the myo5 CBD. Although two separate Japanese lamprey contigs were identified (one with the motor domain and a second with the CBD), both of these contigs are on the same scaffold, and results from using the surrounding sequences as query sequences for BLAST searches and comparing syntenic regions suggest that the two Japanese lamprey sequences are part of the same, contiguous myo5 gene. In addition, the sizes of the exons and introns for Japanese lamprey sequences are comparable with those of sea lamprey.
A second possibility is that the presence of two genes for each species reflects a fracturing event. A fracturing event could have occurred early in the lamprey’s evolutionary history such that one of the duplicated genes fragmented into two genes. If fragmentation took place before the divergence of the sea lamprey and Japanese lamprey, then these events would have only happened once in the ancestral lamprey. A third possibility is that two ancestral myo5 genes in lamprey could have gradually lost part of each gene and over time these became shortened. If this were the case then our phylogenetic analysis should have placed the CBD for lamprey in a different myo5 clade than the lamprey myo5 motor domains. Interestingly, we see a couple of other examples in our study where there are truncated myo5 genes. One of the cavefish genes, myo5aa, seems to have only a short sequence covering the motor domain. We identified a short tetraodon myo5c sequence that contains the first 3,000 bp in the 5′ region of the myo5 gene and is missing the CBD. We also identify the C. intestinalis sequence to be a short sequence of 2,982 bp, missing the CBD.
In addition to providing a model for the evolutionary history of the myo5 genes, our syntenic analysis (along with the phylogenetic analysis) has clarified the orthology of the myo5bb genes and has helped validate the nomenclature of the duplicated teleost genes because in some cases (namely the myo5bb genes) a myo5 name had not been assigned to all of the myo5 genes in Ensembl or other genomic data depositories (supplementary table S1, Supplementary Material online). Although we have chosen to retain the gene names used in previous studies, we recognize the potential confusion due to unevenness in the nomenclature, for example myo5ba and myo5bb representing paralogs that arose prior to the divergence of all jawed vertebrates whereas myo5aa and myo5ab represent duplicates consequent to the fish-specific genome duplication. In the latter case, myo5aaa and myo5aab would be names that better reflect the evolutionary history and relationships among the genes, but perhaps introduce unwarranted cumbersomeness.
With respect to the orthology of the myo5bb genes, we introduce the idea of the myo5b gene family having been duplicated as a result of the R1 genome duplication, an inference supported by the observation that the myo5bb gene family is found not only in teleosts but also in spotted gar, coelacanth, shark, turtle, chicken, and turkey.
There are a couple of instances where a duplicated clade might be expected but it appears that those duplicated regions have gone missing over evolutionary time. For example, in figure 2A on fragment A5, we would expect there to be a duplicated region structurally similar to what we found on fragment A4. If this were the case, then we would have a myo5ab/myo5cb on fragment A5, and the duplicated genes on fragment A4 would be named myo5aa/myo5ca.
Phylogenetic Analyses
Our phylogenetic trees presented in figure 3A and D show similar topologies that are consistent with the results presented in figures 1 and [2]. For the trees in figure 3A and D, teleost myo5aa genes group in one clade and myo5ab genes group in a sister clade consistent with the teleost genome duplication. The divergence of spotted gar myo5a prior to the genesis of the two teleost myo5a clades is expected and compatible with the current understanding of evolutionary relationships among these taxa. These two phylogenetic trees also support the divergence of a clade including a lobe finned fish along with tetrapods, which is what one would expect. Surprisingly, shark myo5a also segregates to this branch. Based on current understandings of the phylogenetic relationships among sharks and other chordates, one would have expected shark myo5a to segregate in a branch basal to the teleost and tetrapod groups.
Figure 3
D indicates the divergence of the myo5a gene family and the myo5c gene family from a (relatively recent) common ancestor. We believe this tree best represents the actual evolutionary history since the sequences for the neck regions have the most genetic diversity, and therefore analyses of these domains has the greatest power to resolve evolutionary events over geologic time frames. The other trees were based on alignments of the highly conserved motor domain (fig. 3B) and the CBD (fig. 3C), which led to poorer resolution for the branches in those phylogenies. Figure 3A showed a vastly different topology regarding the divergence of the myo5c gene family. If the tree in figure 3A was the true tree, this would suggest that the myo5a/myo5c duplication took place before R1; whereas, if figure 3D is the true tree, then it suggests that the myo5a/myo5c duplication took place after R2 and before R3.
In figure 3D, we also present support for the newly named myo5ba clade which includes an expected divergence pattern of shark, followed by bony fish which break up into two sister clades of lobe finned fish and ray finned fish with spotted gar diverging before other teleosts in the ray finned fish lineage. For the newly identified myo5bb clade we first see the divergence of coelacanth and shark myo5bb genes. These genes do not show the expected pattern of divergence because coelacanth myo5bb diverges before shark myo5bb. However, after that, we see the divergence of tetrapod myo5bb genes and ray-finned fish including spotted gar and teleost myo5bb genes.
dN/dS Analyses
As branch lengths represent the number of substitutions per site, we thought the long branches evident in the myo5bb lineage might reflect a large amount of substitutions resulting in amino acid changes (fig. 3A-D). Were that the case, our examination of the amino acid sequences encoded by the myo5bb genes would be expected to reveal an increase in the dN/dS ratio, reflecting a faster rate of evolution. A faster rate of evolution, in turn, could reflect a release from selective constraints, perhaps consequent to the duplicate becoming a pseudogene. However, we observed strong purifying selection in the region of the gene encoding the myosin head, reflected in a surprising amount of invariance in select codons (table 2).
Some of the invariant codon sites in teleosts code for amino acids that have been shown to be functionally important in the orthologous MYO5a and MYO5b proteins in mammals (Pylypenko et al. 2013). The myo5 codons orthologous to those in human MYO5A or MYO5B linked with a functional role in the Myo5 protein such as motor activity, ATP-binding, actin-binding, or cargo-binding (Pylypenko et al. 2013) had smaller dN/dS values than other codons in the myo5 genes, indicating these codons were among the most conserved codons in all 9 teleost species and among the duplicated genes (supplementary tables S2-S5, Supplementary Material online). For many of the sites in the myo5 genes (supplementary tables S2-S5, Supplementary Material online), dN/dS values equal zero as a result of having zero nonsynonymous nucleotide changes at that codon.
The more functionally constrained and therefore more conserved parts of myosin 5 proteins include the motor domain or ATP-binding region, the actin-binding domain, and the CBD (fig. 5). The largest percentage difference of invariant codons between two paralogous clades exists between the CBD of the myo5aa (30.1%) and myo5ab (7.5%) clades and between the CBDs of the myo5ba (23.8%) and myo5bb (6.6%) clades (table 2). The CBD has previously been characterized as playing a role in lightly or nonpigmented (dilute) phenotypes (Nascimento et al.1997), and in this domain sequence conservation mostly persists. The serine residue at position 1,650 has been shown to be a site for phosphorylation by which disassociation of melanosomes from the myosin motor is regulated (Karcher et al. 2001; Pylypenko et al. 2013). It is present in all of Myo5 sequences analyzed with the exception of Myo5ab from T. nigroviridis. The basic residues K1706 and K1779 were identified in Li and Nebenführ (2008) as having an important role in regulating motor activity by binding to the acidic motor domain sites D134 and D136. With few exceptions, these four residues are conserved in all sequences analyzed.
One exception to D134 not being conserved is with the cavefish myo5aa gene. The cave dwelling nonpigmented cavefish have a premature stop codon in the myo5aa gene (fig. 3D), precluding translation of the CBD, and likely preventing the Myo5aa protein from transporting its melanin cargo. Because our sequence data are based on the cave dwelling cavefish, a comparison with the closely related surface dwelling form which has pigment could provide additional insight into the significance of these changes in the duplicated gene. It is possible that the surface dwelling cavefish utilize the Myo5ab protein to transport melanosomes or the surface dwellers might have a fully functional Myo5aa protein.
Slightly C-terminal of the D134 site is the p-loop of the motor domain. This highly conserved region has an alanine to serine (A→S) change in the myo5bb clade. This change could render the myo5bb’s nonfunctional by compromising ATP binding, or this could be a regulatory change as serine residues are known to be sites of phosphorylation. Ramakrishnan et al. (2002) summarized the numerous variants for this conserved sequence with a general motif of GXXXXGKT being present in 92 identified variations of this region. Although this A to S substitution has been identified in two other proteins (phosphoenolpyruvate carboxykinase and dioxygenase), it had not been previously identified in any of the myosin proteins.
Selection Tests
Our tests for selection using MEME showed that there were more evolutionary changes taking place in the neck region of the myo5 genes compared with other regions of the myo5 genes. In comparing the CBD, there were many more sites in the myo5bb clade subject to positive selection (5 with P < 0.05) than in the myo5ba clade (0 with P < 0.05). Using the BS-REL selection test, we found evidence of episodic diversifying selection along the myo5b clades, including the whole myo5b clade and the myo5ba clade, and the myo5bb clade. Most of the diversity here came along the myo5bb branch, supporting the idea that this branch and the myo5bb CBD has experienced more evolutionary changes than other clades, increasing the likelihood for the neofunctionalization or subfunctionalization of this clade. This inference may be supported by the observation that the sites associated with binding Rab11a are not as well conserved in the Myo5bb duplicates, suggesting that Myo5bb binds to something other than Rab11a or that there are different regions within the Myo5bb CBD that have not been previously identified and that are involved in binding to cargo. Also, because there is significant variation among teleosts for the myo5bb clade, there could be different cargoes or functions associated with this Myo5bb region in teleosts.
In addition to detailing the evolutionary history of the myosin V gene family, we present evolutionary rate data comparing duplicated genes. These evolutionary rate comparisons highlight a high degree of sequence conservation at codons linked with functionality for the myosin 5 proteins. Using phylogenetic and syntenic analyses along with evolutionary rate comparisons, our data imply that these duplications have persisted over evolutionary time with a high degree of conservation at specific sites and suggest that selection continues to operate on the protein products of these genes. This finding raises the question as to why sites are so highly conserved over hundreds of millions of years if these duplicated genes are nonfunctional. Although the possibility exists that one of these duplicated genes has obtained a neofunctional role over evolutionary time, an alternative explanation for our data supports a model of relaxed selective pressure likely due to the redundancy of the duplicated genes.
Using dN/dS evolutionary rate comparisons, selection tests, and the identification of a high percentage of codons subject to extreme purifying selection, we present data linking the newly identified myo5bb clade with a high degree of conservation at functionally important amino acids, suggesting myo5bb is a duplicate that has retained function. The relaxed selective pressure on this myo5bb family of genes could lead to alternative expression patterns developmentally or within the organisms and possibly leading to a new function for the Myo5bb proteins. The high degree of conservation of specific sites linked with functionality supports an evolutionary pathway leading to relaxed selective pressure at a minimum and possibly neofunctionalization for the myo5ab duplicated genes (found in teleosts only) and myo5bb duplicated genes (found in birds, turtle, shark, coelacanth, spotted gar, and teleosts).
We have utilized a family of duplicated genes with one of the duplicates known to play a role in the pigmentation process but the role of the duplicates of these genes remains to be identified. Teleosts seem to have a higher proportion of pigment-related genes in duplicate compared with nonteleosts (Braasch, Brunet, et al. 2009). It is possible that the duplicates may still be functional, and the duplicates may be expressed at a different time in development or in a different type of cell. It is also possible that a neofunctional role may have evolved in one of the duplicates. Although, we suspect that myo5aa is carrying out the melanosome shuttling role similar to myo5a in nonteleosts, the role of myo5ab remains to be determined. In addition, we suspect that myo5ba in fish are carrying out the same role as myo5b (more accurately, myo5ba) in nonteleosts but what is taking place among the newly identified myo5bb clade remains a mystery. Due to the high degree of conservation in the motor domain, we suspect that the proteins encoded by these genes still have a functional role and we suspect that the new role is related to the variability and positive selection we have identified in the CBD.
The data presented for percentage of invariant codons or codons under extreme purifying selection demonstrated this high level of purifying selection remains in fish and nonfish vertebrates in duplicated versions of the myo5 genes. As far as the first and second codon position, there seems to be high conservation at the codons linked with functionality, supporting the idea that these duplicated genes are likely functional, active and subject to selection. For a large percentage of codons, the third codon positions are highly conserved over hundreds of millions of years of evolution. We speculate that this conservation may reflect post-transcriptional regulation of gene expression by microRNAs. Conserved sequences as short as six to eight nucleotides in length may provide an opportunity for microRNA binding (Brennecke et al. 2005; Krek et al. 2005; Lewis et al. 2005) We identified invariant codons to exist throughout our alignments of duplicated genes and at times these invariant codons were clustered in groups of as many as 10 invariant codons (30 identical nucleotides) raising the possibility that some duplicates may be regulated by microRNAs. The data presented provide insights into molecular evolution and underscores the usefulness of teleosts in helping to understand the evolutionary consequences of gene duplication events.
Supplementary Material
Supplementary data are available at Genome Biology and Evolution online.
Supplementary Material
Click here for additional data file.
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