Unresolved orthology and peculiar coding sequence properties of lamprey genes: the KCNA gene family as test case
© Qiu et al; licensee BioMed Central Ltd. 2011
Received: 28 October 2010
Accepted: 23 June 2011
Published: 23 June 2011
In understanding the evolutionary process of vertebrates, cyclostomes (hagfishes and lamprey) occupy crucial positions. Resolving molecular phylogenetic relationships of cyclostome genes with gnathostomes (jawed vertebrates) genes is indispensable in deciphering both the species tree and gene trees. However, molecular phylogenetic analyses, especially those including lamprey genes, have produced highly discordant results between gene families. To efficiently scrutinize this problem using partial genome assemblies of early vertebrates, we focused on the potassium voltage-gated channel, shaker-related (KCNA) family, whose members are mostly single-exon.
Seven sea lamprey KCNA genes as well as six elephant shark genes were identified, and their orthologies to bony vertebrate subgroups were assessed. In contrast to robustly supported orthology of the elephant shark genes to gnathostome subgroups, clear orthology of any sea lamprey gene could not be established. Notably, sea lamprey KCNA sequences displayed unique codon usage pattern and amino acid composition, probably associated with exceptionally high GC-content in their coding regions. This lamprey-specific property of coding sequences was also observed generally for genes outside this gene family.
Our results suggest that secondary modifications of sequence properties unique to the lamprey lineage may be one of the factors preventing robust orthology assessments of lamprey genes, which deserves further genome-wide validation. The lamprey lineage-specific alteration of protein-coding sequence properties needs to be taken into consideration in tackling the key questions about early vertebrate evolution.
For a complete understanding of the evolution of vertebrates, jawless fishes (cyclostomes; hagfishes and lampreys) occupy crucial positions as the most early-branching lineages, which diverged more than 500 million years ago from the gnathostome (jawed vertebrate) lineage . Their phylogenetic relationships with gnathostomes serve as a crucial scaffold on which one can map phenotypic and genotypic changes [2, 3]. More importantly, genome expansions, known as 'two-round whole genome duplications (2R-WGDs)', took place around the divergences of these lineages [4, 5].
In this study, we identified KCNA genes from partial genome sequences of the sea lamprey and the elephant shark, and investigated their phylogeny and sequence properties. We observed exclusive clustering of lamprey sequences with long branches as in Figure 1A. The supported tree topology did not fit any of possible scenarios supported by the evolutionary pattern of the KCNA gene family documented previously. Notably, our analyses on KCNA and other genes revealed peculiar codon usage bias and amino acid composition unique to the sea lamprey.
Identification of sea lamprey and elephant shark KCNA genes
Seven full-length or nearly full-length KCNA protein-coding sequences were identified in the sea lamprey (Petromyzon marinus) whole genome assembly. We also identified six in the elephant shark (Callorhinchus milii), one in Ciona savignyi and one in purple urchin (Strongylocentrotus purpuratus). For Ciona intestinalis, in addition to one previously reported KCNA homolog (XP_002125274.1), one more KCNA protein sequence was found in Genbank (Additional file 1, Figure S1). Apart from the seven aforementioned KCNA genes, six and three fragments of KCNA genes (encoding < 150 amino acids peptides) were also discovered in the sea lamprey and elephant shark genome, respectively (data not shown). These remain partial probably because of incomplete genome sequencing, and they were therefore excluded from the subsequent analyses. Our search in NCBI dbEST, an expressed sequence tag (EST) archive, identified no sequences encoding KCNA proteins for species in Petromyzontiformes (lampreys), Myxiniformes (hagfishes) and Chondrichthyes (cartilaginous fishes).
Molecular phylogenetic analysis: an overview
Phylogenetic trees were constructed with the maximum-likelihood (ML) method and Bayesian inference for 32 KCNA sequences, including all of the newly identified putative KCNA sequences mentioned above (Additional file 1, Figure S1). We used human homologs of closely related potassium channel subfamilies as an outgroup. The sea lamprey PmKCNAβ gene was not included because it was partial and thus largely reduced the number of aligned sites available for tree construction. Although the best tree topologies produced by these two methods differed to some extent, all the identified sequences appeared to be genuine KCNA homologs as they formed a cluster with already reported KCNA genes with high statistical support [bootstrap probability (BP): 89; posterior probability (PP): 1.00; Additional file 2, Figure S2].
All elephant shark KCNA genes were relatively robustly placed in the phylogenetic trees (Figure 3), in accordance with its phylogenetic position in the species tree. In contrast, none of the sea lamprey KCNA genes was unambiguously assigned to any of the jawed vertebrate KCNA subgroups (Figure 3). Although sister relationships between PmKCNAα/β and KCNA10 as well as between PmKCNAδ/ε/ζ and KCNA4 were recovered by both methods, statistical support for these relationships were not high (BP: 11~59; PP: 0.39~0.97). Maximum-likelihood and Bayesian inference methods with different models, e.g, JTT+Γ4, JTT+I+Γ4+F and LG+I+Γ4, LG+I+Γ4+F produced similar results (data not shown).
Timings of gene duplications in the KCNA gene family
Probabilities of scenarios I and II and probabilistic counts of gene duplications before and after the cyclostome-gnathostome split
Probabilities of hypotheses2
Total count of gene duplications2
Amino acid composition of KCNA genes
We performed the CA of amino acid compositions in genome-wide sequences data of 15 vertebrate species (Figure 5B; see Methods for details of the dataset for the sea lamprey). The identified first two axes accounted for 63.3% and 21.6% of total variance, respectively. Whereas teleost fishes were located with tetrapods along the first axis (CA1), mammals and chicken were distinguishable from the other vertebrates along the second axis (CA2) (Figure 5B). Contrary to the elephant shark signature that was similar to those of osteichthyes, the sea lamprey was located at an extremely distant position away from the cluster of other species along both axes (Figure 5B). GC-content has been shown to be the major determinant of amino acid composition and codon usage bias, for example, in bacteria  and nematodes [19, 20]. Thus, we plotted the first factor of CA of amino acid composition (CA1) against the average GC-content of third positions in protein-coding regions (GC3) of the corresponding coding nucleotide sequence data (Figure 5C). A strong correlation was observed between these two factors (Figure 5C).
Synonymous codon usage of KCNA genes
Gene repertoires in early vertebrates
Although the genome assemblies for sea lamprey and elephant shark are incomplete, the numbers of KCNA genes identified in the present study (seven for the sea lamprey and six for the elephant shark) are close to the number of KCNA paralogs in bony vertebrates (eight in non-teleost fishes). Previously, Grus and Zhang assessed the coverage of the available sea lamprey genome assembly, and suggested that at least one exon per multi-exon gene should be identifiable in the current lamprey genome assembly . However, the possibility of missing a KCNA gene cannot be ruled out given the single-exon nature of members of this gene family. Since the elephant shark genome was so far sequenced only with 1.4-fold coverage, more genes, such as KCNA4 and -7, may still remain to be discovered.
Timing of whole genome duplications
We observed the ambiguity of the phylogenetic positions of the sea lamprey KCNA genes in conventional best tree searches (Figure 3) as well as in the likelihood-based tree topology tests that resulted in multiple tree topologies with similar likelihood values (Additional file 4, Table S1). In terms of the timing of the duplication of two KCNA clusters, phylogeny-based probabilistic analysis did not provide strong evidence, although probabilistic counts of individual gene duplications slightly favored the scenario with the cluster duplication before the cyclostome-gnathostome split (Table 1). The currently available sea lamprey genome assembly does not contain any intact KCNA gene cluster, probably because of its fragmental nature. If lampreys possess two intact KCNA tri-gene clusters, that would be robust support for the cluster duplication before the split between cyclostomes and gnathostomes. Addition of more sequences for different cyclostome lineages (e.g., southern hemisphere lampreys or hagfish) might also provide more evidence.
Unique characters of sea lamprey genes: genome-wide phenomena?
We detected a peculiar amino acid composition in the sea lamprey KCNA genes (Figure 5A). Notably, this trend is not confined to the KCNA gene family: the peculiar protein-coding sequence properties, namely GC3, codon usage and amino acid composition seem to be genome-wide features (Figures 5B, 6D-E and 7).
In bacteria [18, 25, 26] and nematodes , the global GC-content is the major factor governing variations in amino acid composition of their genes. Based on our analysis, this appears to apply to vertebrates including the sea lamprey as well: the relative positions of species along the first factor of the correspondence analysis (CA) of amino acid composition were strongly correlated with their GC3 values rather than the evolutionary distances among them (Figure 5C). Other factors than GC-content apparently seem to contribute to the difference in amino acid compositions, since the first factor of the CA only accounted for ~63% of the total variance in amino acid composition (Figure 5B).
Sea lamprey genes show a strong correlation between codon usage bias, measured by ENc, and GC3 (Figure 6A), and its distribution suggests only weak selection on the codon usage in the sea lamprey genome (see Results). In contrast, GC3 only accounted for ~1/3 of total variance of codon usage pattern among sea lamprey genes (see Results), indicating that the codon usage patterns of sea lamprey genes are further affected by other factors. Variation of codon usage bias between vertebrate species was also mainly due to the GC-content as indicated by a strong correlation between ENc and GC3 and between the first factor of the CA of codon usage pattern and GC3 (Figure 6D and 6F). Above all, the sea lamprey exhibited an exceptionally high degree of codon usage bias among the vertebrates analyzed in the present study as it displayed the most extreme GC3 by far (Figure 6D). It is unknown whether the deviated amino acid composition and codon usage bias in the sea lamprey represents an ancient feature of the common vertebrate ancestor or is a derived feature acquired uniquely in the lamprey lineage. To address this question, it will be necessary to collect data from other lamprey species (e.g., southern hemisphere lampreys) and hagfishes.
What is the biological significance of GC partitioning between coding and non-coding regions?
The peculiarity of the codon usage in the sea lamprey relative to that of other vertebrates draws a parallel in its variation among Drosophila species. An exceptionally low level of codon usage bias was observed in Drosophila willistoni compared to eleven other Drosophila species, which is related to the exceptionally low coding GC-content in this species . Based on the estimate of the divergence time between D. willistoni and the melanogster/obscura groups, this change is estimated to have occurred within 45-30 million years . In this case, changes in population size, mutational bias and tRNA abundance have been proposed as causal factors (discussed in ). These factors might also be associated with the peculiar codon usage in the sea lamprey.
One possible discrepancy in these biases between the sea lamprey and other vertebrates is the inherent nature of GC3. In vertebrates other than the lamprey, GC3, mentioned above as a source of biases in codon usage and amino acid composition (Figures 5C and 6D), is correlated with global genomic GC-content [29–32]. In lampreys, however, genomic sequences generally exhibit moderate GC-content of 40-50% , while GC-content in protein-coding regions, measured by GC3 (or GC4), is extremely high (70-90%) . Similarly, genomic supercontigs containing sea lamprey KCNA genes identified in the present study had 41~51% of genomic GC-content (excluding repetitive elements), while GC3 of the KCNA genes ranged from 60 to 95%. The intra-genomic partitioning in GC-content between protein-coding and non-coding regions, seen also in the aforementioned Drosophila species, has not been reported before for any other vertebrate than the sea lamprey.
In principle, an employment of amino acid sequences in phylogenetic analyses is thought to buffer against the unfavorable effect caused by lineage-specific changes in GC-content and codon usage. However, our findings suggest that comparative sequence analyses with conventional methods involving lampreys at the amino acid level as well as at the nucleotide level can be misleading. The lineage-specific sequence properties that would affect most lamprey genes can cause the typically, but possibly incorrectly, recovered tree topology where lamprey sequences cluster at the basal branch of a vertebrate gene tree (Figure 1A). To accommodate the lineage-specific alteration of amino acid substitution models, we employed a phylogenetic tree inference method allowing a 'non-homogeneous' model [35, 36]. This attempt resulted in a tree topology with more inconsistent relationships even inside gnathostome KCNA subgroups and did not lead to improvement for this particular gene family (data not shown). The possible causation between the lamprey lineage-specific sequence properties and their ambiguous phylogenetic positions should be verified with more sampling of gene families based on complete genomic sequences for this group of species.
Our molecular phylogenetic analysis on the KCNA gene family resulted in low resolution of lamprey gene phylogeny. We identified lamprey's deviated amino acid composition and codon usage pattern from those of jawed vertebrates. It is possible that these are associated with the exceptionally high GC-content in protein-coding regions and frequently observed ambiguous molecular phylogeny of lamprey genes.
Protein-coding nucleotide and amino acid sequences of human (Homo sapiens), mouse (Mus musculus), dog (Canis familiaris), opossum (Monodelphis domestica), platypus (Ornithorhynchus anatinus), chicken (Gallus gallus), anole lizard (Anolis carolinensis), western clawed frog (Xenopus tropicalis), zebrafish (Danio rerio), fugu (Takifugu rubripes), green spotted pufferfish (Tetraodon nigroviridis), medaka (Oryzias latipes) and three spine stickleback (Gasterosteus aculeatus) were downloaded from Ensembl version 53  via BioMart. Nucleotide and amino acid sequences of the sea lamprey were downloaded from NCBI as GenBank flat files, and their protein-coding nucleotide sequences were extracted. Sequences that are derived from mitochondrial DNA or shorter than 100 amino acids were discarded. Partial genome assembly of the elephant shark was downloaded from http://esharkgenome.imcb.a-star.edu.sg/. Protein-coding sequences and their deduced amino acid sequences for this species were obtained by gene prediction using Genscan  with the organism setting 'Vertebrate'. Repetitive elements in the elephant shark genome were identified using RepeatModeler http://www.repeatmasker.org/RepeatModeler.html.
KCNA sequence set
Sea lamprey genome assembly (PMAR3.0) was downloaded from the Genome Institute at Washington University ftp://genome.wustl.edu/pub/organism/Other_Vertebrates/Petromyzon_marinus/. We performed tBlastn using human KCNA protein sequences as queries against the sea lamprey genome assembly. All genomic segments with similarity (sequence alignment ≥ 25 amino acids, identity ≥ 30%) to the queries were retrieved and subjected to gene prediction with GeneWise  to extract coding nucleotide and amino acid sequences of KCNA and closely related genes outside the KCNA subfamily. To search KCNA genes of other species, amino acid sequences of human KCNA genes were used as queries to run Blastp searches against Ensembl peptides as well as the NCBI GenPept database. All hits with similarity (sequence alignment ≥ 25 amino acids, identity ≥ 30%) to human KCNA sequences were retrieved. To remove closely related homologs outside KCNA, all retrieved sequences were subjected to Blastp searches against human Ensembl peptide database (version 53), and only those with best hit to a KCNA were retained.
Multiple sequence alignments were constructed using MAFFT  with poorly aligned regions manually removed. The best models of amino acid substitutions were selected using ProtTest verstion 2.4 . The LG+Γ4 model was selected as most suitable to the dataset for Figure S3, while the JTT+I+Γ4 was selected with the dataset for Figure 3. Maximum-likelihood trees were inferred using PhyML version 2.4.4  under the selected substitution model. Support values for individual nodes were estimated with 1000 bootstrap replicates. Bayesian inference was performed using MrBayes.3.1.2  under the selected model with four million generations (Additional file 2, Figure S2) and two million generations (Additional file 3, Figure S3) of two parallel runs. Consensus trees were generated after 'burn-in' for 25% sampled trees.
Phylogenetic positions of individual sea lamprey genes were further investigated by likelihood-based statistical tests under the assumed framework of gnathostome KCNA phylogeny documented previously (Figure 4) (; also see Figure 2). The analysis was performed using Tree-Puzzle 5.2  under the JTT+I+Γ4 model by inputting all possible tree topologies for relevant taxa in the 'user-defined tree' mode. For each tree, relationships within individual gnathostome KCNA subgroups were constrained according to the generally accepted species phylogeny. Relationships among KCNA4, -7 and -1/2/3/5/6/10 were constrained according to the previously supported phylogenetic scenario . All three possible relationships between KCNA1/2, 3/6 and 5/10 were regarded as equally likely. Under these conditions, we statistically analyzed positions of all seven sea lamprey KCNA genes individually by adding each of them to the gnathostome KCNA gene set. For each sea lamprey sequence, there were 45 possible tree topologies (Figure 4B). Probabilities of the tree topologies were calculated using CONSEL .
Probabilistic counts of gene duplications before (Nbef) and after (Naft) the cyclostome-gnathostome split were performed as in a previous study . For each sea lamprey KCNA gene, we divided all of the 45 possible tree topologies into three groups supporting scenarios I or/and II (see Figure 4A for details of scenario I and II). First, 21 tree topologies support scenario I in which the tri-gene cluster duplication occurred after the cyclostome-gnathostome split. Second, 18 tree topologies support scenario II in which the tri-gene cluster duplication occurred before the cyclostome-gnathostome split. Third, six tree topologies in which sea lamprey genes grouped with KCNA4 or -7 could not statistically distinguish between scenario I or II, In the third case, we assumed that scenario I and II are equally possible (Figure 4B).
Correspondence analysis of amino acid composition
To investigate the amino acid composition, protein sequences for each species were concatenated, and frequencies of each amino acid were calculated. A correspondence analysis of amino acid composition was performed using the 'dudi.coa' function implemented in the ADE-4 package  under the R statistical computing environment. Only the longest peptide sequence per gene was used in this analysis. For the sea lamprey, to avoid biases in amino acid composition measurements caused by biased sampling of protein families, such as the abundant variable lymphocyte receptors , we removed identical or highly homologous sequences that show ≥ 60% similarity at the amino acid sequence level. Our final sequence set for the sea lamprey contained 173 genes (Additional file 5, Table S2). For the elephant shark, we used predicted peptide sequences mentioned above. To remove false positive gene predictions, all predicted peptide sequences were used as queries to run Blastp against protein sequences of human, chicken, western clawed frog, zebrafish, medaka and fugu, and only sequences with significant similarity (e-value ≤ 1e-20) were retained. The resulting sequences were further used as queries to run tBlastn against a repetitive element library built for this species (see above). All sequences with significant similarity (e-value ≤ 1e-20) to any repetitive element were discarded.
Amino acid composition of alignable regions of vertebrate KCNA proteins sequences was analyzed based on the aforementioned procedure. Partial KCNA sequences (containing < 70% of alignable region in length) were excluded. As variable regions account for substantial parts of KCNA proteins, a separate analysis was performed using the full-length protein sequences of the same set of KCNA genes.
Synonymous codon usage analysis
Effective number of codons index (ENc)  and base compositions were calculated using codonW http://codonw.sourceforge.net/. Synonymous codon usage was investigated by within-group correspondence analysis (WCA) of codon counts [22, 23] and by correspondence analysis of relative synonymous codon usage (CA-RSCU). The latter is the most widely used method for codon usage analysis, whereas the former has been recently demonstrated to produce more unbiased results because it takes into account both amino acid composition and codon degeneracy information . For each species, protein-coding sequences were concatenated and frequencies of 59 synonymous codons were calculated. Correspondence analyses were performed using the 'dudi.coa' and 'within' functions in the ADE-4 package . If a given gene had multiple alternative splicing variants, only the one with the longest coding sequence was used. Heat maps of relative synonymous codon usage were generated using CIMMiner http://discover.nci.nih.gov/cimminer.
The sea lamprey genomic data were produced by the Genome Institute at Washington University and can be obtained from ftp://genome.wustl.edu/pub/organism/Other_Vertebrates/Petromyzon_marinus/. We thank Maria Anisimova for insightful discussion. This study was supported by the Young Scholar Fund of University of Konstanz to S.K. and grants from the German Research Foundation (DFG) to S. K. (grant No. KU2669/1-1).
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