BACKGROUND
transfer rnas  are among the most ancient genes.
they can be traced back to the putative rna world  <cit>  before the separation of the three domains of life.
there is clear evidence, furthermore, that all trna gene are homologs, deriving from an ancestral " proto-trna"  <cit> , which in turn may have emerged from even smaller components, see e.g.
<cit> .
besides their primary ancestral function in translation, trnas appear to have acquired several additional modes of employment throughout evolution.
several recent studies, for instance, reported trna-derived small rnas in different eukaryotic clades  <cit> , which at least in part appear to be utilized in the rnai pathway.
furthermore, trna genes are a prolific source of repetitive elements   <cit> , and of trna-derived small rnas such as the small brain-specific non-messenger rna bc <dig> rna  <cit>  and other sine-derived ncrnas  <cit> .
multiple copies of functional trna genes, the existence of numerous pseudo-genes and trna-derived repeats are general characteristics of trna evolution throughout eukarya  <cit> .
in general, trna genes appear to evolve rapidly.
in e. coli, the rate of trna gene duplication/deletion events is of the order of one per million years  <cit> , and a recent analysis of schistosome genomes revealed striking differences in the trna complement between the close related platyhelminths s. mansoni and s. japonicum  <cit> .
although the trnas themselves and their sequence and structural evolution has received quite a bit of attention  <cit> , much less is known about the genomic organization of trna genes.
recent evidence, however, indicates that trna genes play a role in eukaryotic genome organization  <cit>  e.g.
by acting as barriers that separate chromatin domains.
in trypanosomes, for example, trna genes mostly appear at the boundaries of transcriptional units and may be involved in the deposition of special nucleosome variants in these regions  <cit> .
furthermore, there is a link between trna loci, in particular clusters of trna genes, and chromosomal instability  <cit> .
a recent study showed that trna genes may act as barriers to dna replication fork progression  <cit> , providing a possible mechanism for the formation of genomic fragile sites.
the genomic evolution of trna gene thus may be linked to the evolution of genome organization.
nevertheless, reports on clade-specific features, such as the strong increase of trna introns in thermoproteales  <cit> , are rare.
a peculiar feature of trna gene organization are trna tandem repeats, which so far have been reported only in the protistan parasite entamoeba histolytica  <cit> .
micrornas derived from a precursor in which an imperfectly matched inverted repeat forms a partly double-stranded region, as observed in chlamydomonas  <cit> , furthermore, suggests that head-to-head or tail-to-tail arrangements of trna gene might form an evolutionary source of small rnas.
in this contribution, we survey the genomic distribution of trna genes and pseudogenes throughout the eukarya and provide a comprehensive comparative view of the eukaryotic trna genomics.
our study makes use of the near-perfect sensitivity and specificity of trnascan-se <cit> , which reliably determines the complete trna complement of eukaryotic genomes.
RESULTS
numbers of tdnas
for each of the  <dig> genomes included in our survey we collected summary statistics on the number of trna gene and trna pseudogenes as well as on their genomic clusters.
to simplify the language, we will use the term " tdna" to refer to both trna genes and trna pseudogenes, while " trna gene" will be reserved to loci with probably intact trna sequences.
in practise, we use trnascan-se to distinguish between trna genes and trna pseudogenes .
we define two adjacent trna gene or tdnas as " clustered" if their distance is less than  <dig> nucleotides.
this threshold is motivated by a statistical analysis of the distances between adjacent tdna loci, which shows that at this distance we have to expect very few or no tdna pairs in the genomes under investigation .
we then distinguish between homogeneous clusters, consisting of tdna with the same isoacceptor family , and heterogeneous clusters.
within clusters, we separately consider the three relative orientations → →, ← →, and → ←.
data have been analyzed for putatively functional trna gene , and for all tdnas.
fig.
<dig> shows a sample of a graphical representation of the survey results.
the full figure comprising all  <dig> genomes is provided as additional file  <dig>  complete lists of tdnas in gff format can be found at the website  <cit> .
despite an overall correlation with genome size, there does not seem to be a general trend in the number of trna genes.
although some mammals, for instance, exhibit tens or even hundreds of thousands of tdna copy numbers, other mammalian genomes harbour only a few hundred copies.
for instance, old world monkeys and great apes have about  <dig> ±  <dig> tdnas, while the related bushbaby  exhibits  <dig> tdnas.
the highest counts are reached for the cow and rat genomes with more than  <dig> tdnas.
for the  <dig> sequenced drosophila species, we find  <dig> ±  <dig> tdnas.
trichoplax adhaerans, one of the most basal animals has no more than  <dig> trna genes, while the cnidaria nematostella vectensis has more than  <dig>  within teleosts, tdnas range from about  <dig> in tetraodontiformes to  <dig> in zebrafish.
variations by about an order of magnitude are also common in other major clades.
naegleria gruberi, for example has  <dig> tdnas, while kinetoplastids .
surprisingly, the variation is very small in the " green lineage".
spermatophyta show little variation with  <dig> ±  <dig> loci, the basal land plants physcomitrella patens  and selaginella moellendorffii  and even the unicellular algae volvox carteri  and chlamydomonas reinhardtii  have similar numbers.
despite the often large variation among even closely related lineages, we observe the expected correlation between the number of tdnas with genome size, fig.
<dig>  the correlation is significant, with correlation coefficient ρ ∈ , but subject to a high level of variation reflecting large differences in the evolutionary history of different lineages.
while the total number of tdnas scales approximately linearly with genome size, α =  <dig>  ±  <dig> , the growth in the number of intact, probably functional trna genes is much slower, consistent with n2/ <dig>  the number of trna pseudogenes, on the other hand, grows faster than linearly, ~n <dig>  ±  <dig> .
the reasons for this difference in scaling remains unclear.
one may speculate that selective forces maintain only a limited number of functional tdna copies causing the sub-linear growth of intact trna genes with genome size, while the duplication/deletion mechanism acts towards a uniform coverage of the genome with a rate that is to a first approximation constant throughout eukaryotic genome, accounting for the linear growth of the total number of tdnas.
several selective forces could act on the trna genes and/or all tdna loci to cap their number.
the bias towards small deletions over insertions observed in  <cit>  is one potential candidate that is independent of special properties of trnas.
variations in codon usage might provide another selection-based explanation for the variation of tdna copy numbers.
in eubacteria, a correlation between trna abundance, trna gene copy number, and codon usage is well established  <cit> .
whether codon bias causes tdna copy number variation or vice versa remains topic of an intense debate, however.
a mechanistic explanation describing the coevolution of codon usage with trna gene content is given in  <cit> .
it remains unclear to what extent the correlation of trna copy numbers and codon usage carries over to eukaryotic genomes.
a detailed investigation in schistosoma mansoni and schistosoma japonicum finds no correlation between trna gene numbers and codon usage, while a statistically significant but still very weak correlation is observed in schmidtea mediterranea  <cit> .
in nasonia, the correlation of codon usage and the copy numbers of trna genes appears to be restricted to highly expressed genes.
the strength of this correlation decreases with gc-content in plant genomes  <cit> .
in any case, codon usage cannot be employed to explain the observed differences in tdna copy numbers that span several orders of magnitude.
these huge fluctuations, which are observed both within some lineages and between closely related lineages, argues against a mechanism that relies on selection on the trnas.
instead, the more than linear scaling of trna pseudogenes with genome size suggests a faster tdna turnover in larger genomes - after all, pseudogenes and gene relics are steps in the evolutionary degradation of genes.
tdna clusters
in order to investigate the propensity for the formation of tdna clusters, we consider the cumulative distribution of consecutive tdna pairs as a function of their genomic distance.
based on a statistical evaluation of the distances between adjacent tdnas , we define two tdnas to be clustered in the genome if they are located within  <dig> nt.
not surprisingly, in species with small tdna copy number, clusters typically are rare.
in trichoplax adherens, for instance, all tdnas are isolated.
there is no clear-cut relation between tdna copy number and clustering, however.
in nematostella vectensis 89% of the tdnas appear in clusters.
in mammals, which have even larger tdna copy numbers, less than a quarter of the tdnas appear in clusters.
again, there do not appear to be any large-scale phylogenetic regularities.
in teleost fishes, for example, the stickleback gasterosteus aculeatus has 87% clustered tdnas, in zebrafish this number reaches 65%.
on the other hand, pufferfishes and medaka  have predominantly isolated tdnas.
similarly, large variation appears in other clades, see fig.
<dig> and additional file  <dig>  higher primates have 17% to 36% of their tdnas in clusters, with the exception of the bushbaby otolemur garnetii, with only  <dig> % of its  <dig> tdnas located in clusters.
in plants there are also no clear regularities.
the fraction of clustered tdnas stays below 25% in spermatophyta, while the chlorophyceae volvox carteri and chlamydomonas reinhardtii have 41% and 56% of their tdnas localized in genomic clusters.
most tdna clusters are small, containing only a few co-localized trna genes.
typically, the frequency of larger clusters quickly decreases, at least approximately following an exponential distribution.
this is particularly obvious in the case of mammals and drosophilids.
in some cases, however, longer clusters are more abundant.
exceptionally large tdna gene clusters, with fifty and more members, are observed for example in nematostella and in the genomes of teleost fishes, fig.
<dig>
the internal structure of tdna clusters also differs widely between lineages.
fig.
<dig> and additional files  <dig> and  <dig> summarize the relative abundances of homogeneous and heterogeneous clusters, respectively.
more precisely, we record the fraction of adjacent tdna pairs coding for the same aminoacid.
while tetrahymena, monosiga, and the drosophilids exhibit mostly homogeneous pairs, we observe mostly heterogeneous pairs in kinetoplastids, nematostella, clawed frog, and zebrafish, see fig.
<dig> for an example.
in order to further investigate the structure of heterogeneous clusters we determined how often combinations two isoacceptor families appear in adjacent pairs.
these data are conveniently represented in triangular matrices such as those in fig.
<dig>  homogeneous clusters populate the main diagonal, whereas heterogeneous pairs are represented by off-diagonal entries.
as for other features of the genomic trna distribution there are neither strong common patterns among all organisms investigated, nor are there systematic phylogenetic patterns.
while monosiga, for example, has almost exclusively homogeneous pairs, other species exhibit a wide variety of heterogeneous pairs.
in danio, for instance, k-n, k-s, and r-t are most frequent.
in the cow genome, many clusters involve trna pseudogenes, which are much less prevalent in the other three examples.
in the cow, c-c pseudogenes account for more than 30% of the pairs.
a comprehensive collection of co-occurrence tables is provided as additional file  <dig>  not surprisingly, there is a general trend towards more complex co-occurrence matrices for species with larger numbers of tdnas.
most adjacent tdna pairs in both homogeneous and heterogeneous clusters have parallel orientation.
if the arrangements were random, we would expect that 50% of pairs are of this type.
in many cases, e.g.
arabidopsis, selaginella, xenopus, or danio, nearly all pairs are in parallel.
among the anti-parallel pairs, some species have a strong bias for either head-to-head  or tail-to-tail arrangements .
even within primates, the ratio of head-to-head and tail-to-tail pairs varies considerably.
in most species with very large tdna copy numbers we can expect some tdna clusters to appear by chance.
we tested this by randomizing the tdna locations .
the results for eutherian mammals are compiled in tab.
<dig>  a full list of random pair configuration is given in additional file  <dig>  in most genomes, there are significantly more tdna pairs than expected, suggesting a mode of tdna evolution of favours the formation of local clusters.
local dna duplications, also underlying the copy number variations within many populations , are of course the prime suspects.
the expectation values are computed by placing the trnas at uniformly random position in the genome.
empirical p values are computed from  <dig> to  <dig> replicates.
we observe significant under-representations of tdna pairs only in a few species with very high tdna counts: dasypus novemcinctus, felis catus, and loxodonta africana.
at present, we have no biological explanation for this observation.
clusters of tdnas have been implicated in interfering with the dna replication forks  <cit> .
the tdna clusters might thus be instrumental in orchestrating the timing of dna replication.
on the other hand, replication fork pause sites are associated with genomic instability  <cit>  and hence may contribute to the rapid evolution of these tdna clusters.
furthermore, retrotransposable elements tend to select trna genes as chromosomal integration sites  <cit> , appearently in order to avoid gene disruptions upon retrotransposition.
a recent comparison of yeast genomes associated genomic rearrengements, losses, and additions with trna genes  <cit> .
taken together, tdna clusters thus appear as highly dynamic unstable genomic regions.
synteny
transfer rnas have been reported to behave similar to repetitive elements as far as their genomic mobility is concerned.
they appear to evolve via a rapid duplication-deletion mechanism that ensures that copies of trna genes within a genome are usually more similar to each other than trna gene of different species  <cit> .
in e. coli, for example, the rate of trna gene duplication/deletion events has been estimated to be about one event every  <dig>  million years  <cit> .
we are not aware of -quantitative estimates from eukaryotes.
our analysis is consistent with this mechanism .
since trna genes with the same anticodon are typically nearly identical, the only way to estimate rates of trna gene turnover is to determine, for each trna-bearing locus, whether tdnas can be found in a syntenic locations in evolutionarily related species.
we have determined such data here for eight selected species, including six mammals, namely the catarrihni homo sapiens, pan troglodytes, pongo pygmaeus, and macaca mulatta, the rodent mus musculus, and the marsupialia monodelphis domestica.
the data set includes also more distant vertebrates gallus gallus and xenopus tropicalis to investigate whether there are tdnas with very stable genomic locations.
tab.
<dig> shows the results for the one- and two-side linkage analysis .
the number of related synteny regions based on the single-side linkage analysis is significantly higher than the region number created by the two-side linkage analysis.
since the latter analysis approach is more restrictive, the results between both analysis approaches also differ.
while synteny regions in related species are mostly assigned by the single-side linkage analysis, the results of the two-side linkage analysis are more differentiated.
therefore, we discuss only the results of two-side linkage analysis in the following.
the upper right triangle quantifies the single-sided linkage results whereas the lower left triangle represents the number of two-sided linkage analysis results.
each table entry is organized as follows: the top row lists the number of synteny associations; below, the the sizes of domain and range, i.e., the numbers of tdnas in the two species, are given.
the third line gives the corresponding coverage, i.e., the fraction of syntenically conserved tdnas in the two species.
within catarrhini, tdna locations are quite well conserved.
for instance 80%  of human tdna regions are conserved in the chimp, and there are still 63%  of the rhesus tdna locations recovered in chimp.
somewhat surprisingly, there is also a large fraction of syntenic loci between mouse and opossum .
we suspect that the large fraction is confounded by the large overall number of tdna loci and the rather larger intervals of five flanking genes used to define synteny, which taken together cover a substantial fraction of the genome.
a second group of comparisons identified only a small number of syntenically conserved loci.
asymmetric results, which large retention in one direction is observed when the tdna numbers are dramatically different.
this concerns the comparisons between catharrini, on the one hand, and opossum and mouse on the other hand.
between frog and catharrini, finally, there is only a small number of syntenically conserved tdnas.
we also analyzed the tdna mobility in two invertebrate clades, drosophilids and nematode genus caenorhabditis.
within these nematodes, we observe a rather high degree of syntenic conservation, ranging from 45% between c. elegans and c. japonica up to 84% for the most closely related pair c. remanei and c. brenneri.
in general, conservation levels are consistent to the known phylogeny of the caenorhabditis species  <cit> .
for the genus drosophila with the twelve common representatives, on the other hand, there is much less syntenic conservation.
the lowest value is 17% .
the best conserved tdna arrangements are observed between the two closely related species d. simulans and d. sechellia with 78%.
on average, the percentage of conservation is just around 50% or less.
full data are shown in tab.
<dig> for nematodes and in additional file  <dig> for drosophila.
the table shows the fraction of trna loci between pairs of species.
every field contains the fraction of tdnas of the species in the column, for which we could find a syntenic position in the row species.
the sequence conservation of syntenically conserved trnas is consistent with the duplication/deletion mechanisms.
additional file  <dig> shows a neighbor-joining tree of the trna-ala sequences of nematodes, which includes also a few additional species that are not part of the genome-wide survey.
we find that syntenically conserved trnas genes are typically conserved with an identical sequence across species, even though some trnas with the same anticodon located elsewhere in the genome show small sequence variations.
the fraction of syntenically conserved tdnas correlates with the divergence of the genomes at sequence level, fig.
<dig> and tab.
<dig>  the correlation is significant even though the data is rather noisy, a fact that can be explained at least in part by the unavoidable artifacts resulting from our approach.
utilizing annotation data directly to determine local synteny is problematic, for instance, near members of very large recently duplicated gene families.
in principle, syntenic conservation could be inferred more accurately from genome-wide alignments.
since tdnas are treated like repetitive elements in the currently available pipelines, this strategy cannot be employed in practice.
nevertheless, the method provides at least a crude estimate of the tdna turnover rate, indicating the tdnas are relocated at time-scales only 2- <dig> times slower than background mutation rate, i.e., at an evolutionary distance of  <dig> mutation per site, 20% to 60% of the tdnas have been deleted or relocated in one lineage.
these values should be regarded as upper bounds of syntenic conservation, i.e., tdna turnover is probably even faster.
for example, the identity of the tdna  was not used in the analysis.
despite of the high mobility of tdnas there are some ancient conserved loci.
we further investigated two of the  <dig> syntenic loci conserved between xenopus and human in which tdnas with the same anticodon were retained.
manual inspection of the flanking protein coding genes confirmed synteny.
neither locus is syntenically conserved in stickleback, lamprey or lancet, however.
CONCLUSIONS
we have developed a pipeline based on trnascan-se <cit>  to extract and analyze the locations of trna genes and pseudogenes of eukaryotic genomes.
in our analysis, we focus not only on the number of trna genes, but also on their relative genomic locations, and in particular on the formation of tdna clusters.
surprisingly, we found no distinctive clade-specific features or large scale trends, with the exception of the rather straightforward observation that the larger metazoan genomes typically tend to harbour large numbers of tdnas.
in some species, large clusters of tdnas occur.
this effect has first been reported in entamoeba histolytica.
the origin of this gene organization in the genus entamoeba clearly predates the common ancestor of the species investigated to date.
their function of the array-like structure remains unclear  <cit> .
we report here that this phenomenon is not restricted to a particular clade of protists but rather appears independently in many times throughout eukaryotes.
in most eukaryotes, trnas are multi-copy genes with little or no distinction between paralogs so that orthology is hard to establish, in particular in the presence of trna gene clusters.
as a consequence, the evolution of genomic trna arrangements is non-trivial to study over larger time-scales.
upper bounds on syntenic conservation can be estimated, however, by considering small sets of flanking protein coding genes for which homology information can be retrieved from existing annotation.
we found that trnas change their genomic location at time-scales comparable to mutation rates: syntenic conservation fades at roughly the same evolutionary distances as sequence conservation in unconstrained regions.
the absence of large numbers of partially degraded trna copies in many of the investigated genomes provides a hint at the mechanisms of trna mobility: at least in part the relocation events appear to be linked to chromosomal rearrangements rather than mere duplication-deletion of the trna genes themselves.
the latter mechanism, which appears to be prevalent e.g.
in mitochondrial genomes  <cit> , certainly also plays a role, since trna pseudogenes are readily observed in many species, as do trna retrogenes  <cit> .
a link between trna loci, and in particular trna clusters, and chromosomal instability has been pointed out repeatedly in the literature, showing that trna genes can interfere with the replication forks  <cit> .
the data collected here provide a basis to investigate this connection more systematically in the future.
overall, the trna complement of eukaryotes is highly dynamic part of the genomes whose organization evolves rapidly and in a highly lineage specific manner - a behavior that is in striking contrast to the extreme conservation of sequence and function of the trnas themselves.

 transfer rnas are among the most ancient genes. they can be traced back to the putative rna world before the separation of the three domains of life. there is clear evidence, furthermore, that all trna gene are homologs, deriving from an ancestral " proto-trna", which in turn may have emerged from even smaller components, see e.g.. besides their primary ancestral function in translation, trnas appear to have acquired several additional modes of employment throughout evolution. several recent studies, for instance, reported trna-derived small rnas in different eukaryotic clades, which at least in part appear to be utilized in the rnai pathway. furthermore, trna genes are a prolific source of repetitive elements, and of trna-derived small rnas such as the small brain-specific non-messenger rna bc rna and other sine-derived ncrnas. multiple copies of functional trna genes, the existence of numerous pseudo-genes and trna-derived repeats are general characteristics of trna evolution throughout eukarya. in general, trna genes appear to evolve rapidly. in e. coli, the rate of trna gene duplication/deletion events is of the order of one per million years, and a recent analysis of schistosome genomes revealed striking differences in the trna complement between the close related platyhelminths s. mansoni and s. japonicum. although the trnas themselves and their sequence and structural evolution has received quite a bit of attention, much less is known about the genomic organization of trna genes. recent evidence, however, indicates that trna genes play a role in eukaryotic genome organization e.g. by acting as barriers that separate chromatin domains. in trypanosomes, for example, trna genes mostly appear at the boundaries of transcriptional units and may be involved in the deposition of special nucleosome variants in these regions. furthermore, there is a link between trna loci, in particular clusters of trna genes, and chromosomal instability. a recent study showed that trna genes may act as barriers to dna replication fork progression, providing a possible mechanism for the formation of genomic fragile sites. the genomic evolution of trna gene thus may be linked to the evolution of genome organization. nevertheless, reports on clade-specific features, such as the strong increase of trna introns in thermoproteales, are rare. a peculiar feature of trna gene organization are trna tandem repeats, which so far have been reported only in the protistan parasite entamoeba histolytica. micrornas derived from a precursor in which an imperfectly matched inverted repeat forms a partly double-stranded region, as observed in chlamydomonas, furthermore, suggests that head-to-head or tail-to-tail arrangements of trna gene might form an evolutionary source of small rnas. in this contribution, we survey the genomic distribution of trna genes and pseudogenes throughout the eukarya and provide a comprehensive comparative view of the eukaryotic trna genomics. our study makes use of the near-perfect sensitivity and specificity of trnascan-se, which reliably determines the complete trna complement of eukaryotic genomes.  numbers of tdnas for each of the genomes included in our survey we collected summary statistics on the number of trna gene and trna pseudogenes as well as on their genomic clusters. to simplify the language, we will use the term " tdna" to refer to both trna genes and trna pseudogenes, while " trna gene" will be reserved to loci with probably intact trna sequences. in practise, we use trnascan-se to distinguish between trna genes and trna pseudogenes. we define two adjacent trna gene or tdnas as " clustered" if their distance is less than nucleotides. this threshold is motivated by a statistical analysis of the distances between adjacent tdna loci, which shows that at this distance we have to expect very few or no tdna pairs in the genomes under investigation. we then distinguish between homogeneous clusters, consisting of tdna with the same isoacceptor family, and heterogeneous clusters. within clusters, we separately consider the three relative orientations → →, ← →, and → ←. data have been analyzed for putatively functional trna gene, and for all tdnas. fig. shows a sample of a graphical representation of the survey results. the full figure comprising all genomes is provided as additional file complete lists of tdnas in gff format can be found at the website. despite an overall correlation with genome size, there does not seem to be a general trend in the number of trna genes. although some mammals, for instance, exhibit tens or even hundreds of thousands of tdna copy numbers, other mammalian genomes harbour only a few hundred copies. for instance, old world monkeys and great apes have about ± tdnas, while the related bushbaby exhibits tdnas. the highest counts are reached for the cow and rat genomes with more than tdnas. for the sequenced drosophila species, we find ± tdnas. trichoplax adhaerans, one of the most basal animals has no more than trna genes, while the cnidaria nematostella vectensis has more than within teleosts, tdnas range from about in tetraodontiformes to in zebrafish. variations by about an order of magnitude are also common in other major clades. naegleria gruberi, for example has tdnas, while kinetoplastids. surprisingly, the variation is very small in the " green lineage". spermatophyta show little variation with ± loci, the basal land plants physcomitrella patens and selaginella moellendorffii and even the unicellular algae volvox carteri and chlamydomonas reinhardtii have similar numbers. despite the often large variation among even closely related lineages, we observe the expected correlation between the number of tdnas with genome size, fig. the correlation is significant, with correlation coefficient ρ ∈, but subject to a high level of variation reflecting large differences in the evolutionary history of different lineages. while the total number of tdnas scales approximately linearly with genome size, α = ±, the growth in the number of intact, probably functional trna genes is much slower, consistent with n2/ the number of trna pseudogenes, on the other hand, grows faster than linearly, ~n ±. the reasons for this difference in scaling remains unclear. one may speculate that selective forces maintain only a limited number of functional tdna copies causing the sub-linear growth of intact trna genes with genome size, while the duplication/deletion mechanism acts towards a uniform coverage of the genome with a rate that is to a first approximation constant throughout eukaryotic genome, accounting for the linear growth of the total number of tdnas. several selective forces could act on the trna genes and/or all tdna loci to cap their number. the bias towards small deletions over insertions observed in is one potential candidate that is independent of special properties of trnas. variations in codon usage might provide another selection-based explanation for the variation of tdna copy numbers. in eubacteria, a correlation between trna abundance, trna gene copy number, and codon usage is well established. whether codon bias causes tdna copy number variation or vice versa remains topic of an intense debate, however. a mechanistic explanation describing the coevolution of codon usage with trna gene content is given in. it remains unclear to what extent the correlation of trna copy numbers and codon usage carries over to eukaryotic genomes. a detailed investigation in schistosoma mansoni and schistosoma japonicum finds no correlation between trna gene numbers and codon usage, while a statistically significant but still very weak correlation is observed in schmidtea mediterranea. in nasonia, the correlation of codon usage and the copy numbers of trna genes appears to be restricted to highly expressed genes. the strength of this correlation decreases with gc-content in plant genomes. in any case, codon usage cannot be employed to explain the observed differences in tdna copy numbers that span several orders of magnitude. these huge fluctuations, which are observed both within some lineages and between closely related lineages, argues against a mechanism that relies on selection on the trnas. instead, the more than linear scaling of trna pseudogenes with genome size suggests a faster tdna turnover in larger genomes - after all, pseudogenes and gene relics are steps in the evolutionary degradation of genes. tdna clusters in order to investigate the propensity for the formation of tdna clusters, we consider the cumulative distribution of consecutive tdna pairs as a function of their genomic distance. based on a statistical evaluation of the distances between adjacent tdnas, we define two tdnas to be clustered in the genome if they are located within nt. not surprisingly, in species with small tdna copy number, clusters typically are rare. in trichoplax adherens, for instance, all tdnas are isolated. there is no clear-cut relation between tdna copy number and clustering, however. in nematostella vectensis 89% of the tdnas appear in clusters. in mammals, which have even larger tdna copy numbers, less than a quarter of the tdnas appear in clusters. again, there do not appear to be any large-scale phylogenetic regularities. in teleost fishes, for example, the stickleback gasterosteus aculeatus has 87% clustered tdnas, in zebrafish this number reaches 65%. on the other hand, pufferfishes and medaka have predominantly isolated tdnas. similarly, large variation appears in other clades, see fig. and additional file higher primates have 17% to 36% of their tdnas in clusters, with the exception of the bushbaby otolemur garnetii, with only % of its tdnas located in clusters. in plants there are also no clear regularities. the fraction of clustered tdnas stays below 25% in spermatophyta, while the chlorophyceae volvox carteri and chlamydomonas reinhardtii have 41% and 56% of their tdnas localized in genomic clusters. most tdna clusters are small, containing only a few co-localized trna genes. typically, the frequency of larger clusters quickly decreases, at least approximately following an exponential distribution. this is particularly obvious in the case of mammals and drosophilids. in some cases, however, longer clusters are more abundant. exceptionally large tdna gene clusters, with fifty and more members, are observed for example in nematostella and in the genomes of teleost fishes, fig. the internal structure of tdna clusters also differs widely between lineages. fig. and additional files and summarize the relative abundances of homogeneous and heterogeneous clusters, respectively. more precisely, we record the fraction of adjacent tdna pairs coding for the same aminoacid. while tetrahymena, monosiga, and the drosophilids exhibit mostly homogeneous pairs, we observe mostly heterogeneous pairs in kinetoplastids, nematostella, clawed frog, and zebrafish, see fig. for an example. in order to further investigate the structure of heterogeneous clusters we determined how often combinations two isoacceptor families appear in adjacent pairs. these data are conveniently represented in triangular matrices such as those in fig. homogeneous clusters populate the main diagonal, whereas heterogeneous pairs are represented by off-diagonal entries. as for other features of the genomic trna distribution there are neither strong common patterns among all organisms investigated, nor are there systematic phylogenetic patterns. while monosiga, for example, has almost exclusively homogeneous pairs, other species exhibit a wide variety of heterogeneous pairs. in danio, for instance, k-n, k-s, and r-t are most frequent. in the cow genome, many clusters involve trna pseudogenes, which are much less prevalent in the other three examples. in the cow, c-c pseudogenes account for more than 30% of the pairs. a comprehensive collection of co-occurrence tables is provided as additional file not surprisingly, there is a general trend towards more complex co-occurrence matrices for species with larger numbers of tdnas. most adjacent tdna pairs in both homogeneous and heterogeneous clusters have parallel orientation. if the arrangements were random, we would expect that 50% of pairs are of this type. in many cases, e.g. arabidopsis, selaginella, xenopus, or danio, nearly all pairs are in parallel. among the anti-parallel pairs, some species have a strong bias for either head-to-head or tail-to-tail arrangements. even within primates, the ratio of head-to-head and tail-to-tail pairs varies considerably. in most species with very large tdna copy numbers we can expect some tdna clusters to appear by chance. we tested this by randomizing the tdna locations. the results for eutherian mammals are compiled in tab. a full list of random pair configuration is given in additional file in most genomes, there are significantly more tdna pairs than expected, suggesting a mode of tdna evolution of favours the formation of local clusters. local dna duplications, also underlying the copy number variations within many populations, are of course the prime suspects. the expectation values are computed by placing the trnas at uniformly random position in the genome. empirical p values are computed from to replicates. we observe significant under-representations of tdna pairs only in a few species with very high tdna counts: dasypus novemcinctus, felis catus, and loxodonta africana. at present, we have no biological explanation for this observation. clusters of tdnas have been implicated in interfering with the dna replication forks. the tdna clusters might thus be instrumental in orchestrating the timing of dna replication. on the other hand, replication fork pause sites are associated with genomic instability and hence may contribute to the rapid evolution of these tdna clusters. furthermore, retrotransposable elements tend to select trna genes as chromosomal integration sites, appearently in order to avoid gene disruptions upon retrotransposition. a recent comparison of yeast genomes associated genomic rearrengements, losses, and additions with trna genes. taken together, tdna clusters thus appear as highly dynamic unstable genomic regions. synteny transfer rnas have been reported to behave similar to repetitive elements as far as their genomic mobility is concerned. they appear to evolve via a rapid duplication-deletion mechanism that ensures that copies of trna genes within a genome are usually more similar to each other than trna gene of different species. in e. coli, for example, the rate of trna gene duplication/deletion events has been estimated to be about one event every million years. we are not aware of -quantitative estimates from eukaryotes. our analysis is consistent with this mechanism. since trna genes with the same anticodon are typically nearly identical, the only way to estimate rates of trna gene turnover is to determine, for each trna-bearing locus, whether tdnas can be found in a syntenic locations in evolutionarily related species. we have determined such data here for eight selected species, including six mammals, namely the catarrihni homo sapiens, pan troglodytes, pongo pygmaeus, and macaca mulatta, the rodent mus musculus, and the marsupialia monodelphis domestica. the data set includes also more distant vertebrates gallus gallus and xenopus tropicalis to investigate whether there are tdnas with very stable genomic locations. tab. shows the results for the one- and two-side linkage analysis. the number of related synteny regions based on the single-side linkage analysis is significantly higher than the region number created by the two-side linkage analysis. since the latter analysis approach is more restrictive, the results between both analysis approaches also differ. while synteny regions in related species are mostly assigned by the single-side linkage analysis, the results of the two-side linkage analysis are more differentiated. therefore, we discuss only the results of two-side linkage analysis in the following. the upper right triangle quantifies the single-sided linkage results whereas the lower left triangle represents the number of two-sided linkage analysis results. each table entry is organized as follows: the top row lists the number of synteny associations; below, the the sizes of domain and range, i.e., the numbers of tdnas in the two species, are given. the third line gives the corresponding coverage, i.e., the fraction of syntenically conserved tdnas in the two species. within catarrhini, tdna locations are quite well conserved. for instance 80% of human tdna regions are conserved in the chimp, and there are still 63% of the rhesus tdna locations recovered in chimp. somewhat surprisingly, there is also a large fraction of syntenic loci between mouse and opossum. we suspect that the large fraction is confounded by the large overall number of tdna loci and the rather larger intervals of five flanking genes used to define synteny, which taken together cover a substantial fraction of the genome. a second group of comparisons identified only a small number of syntenically conserved loci. asymmetric results, which large retention in one direction is observed when the tdna numbers are dramatically different. this concerns the comparisons between catharrini, on the one hand, and opossum and mouse on the other hand. between frog and catharrini, finally, there is only a small number of syntenically conserved tdnas. we also analyzed the tdna mobility in two invertebrate clades, drosophilids and nematode genus caenorhabditis. within these nematodes, we observe a rather high degree of syntenic conservation, ranging from 45% between c. elegans and c. japonica up to 84% for the most closely related pair c. remanei and c. brenneri. in general, conservation levels are consistent to the known phylogeny of the caenorhabditis species. for the genus drosophila with the twelve common representatives, on the other hand, there is much less syntenic conservation. the lowest value is 17%. the best conserved tdna arrangements are observed between the two closely related species d. simulans and d. sechellia with 78%. on average, the percentage of conservation is just around 50% or less. full data are shown in tab. for nematodes and in additional file for drosophila. the table shows the fraction of trna loci between pairs of species. every field contains the fraction of tdnas of the species in the column, for which we could find a syntenic position in the row species. the sequence conservation of syntenically conserved trnas is consistent with the duplication/deletion mechanisms. additional file shows a neighbor-joining tree of the trna-ala sequences of nematodes, which includes also a few additional species that are not part of the genome-wide survey. we find that syntenically conserved trnas genes are typically conserved with an identical sequence across species, even though some trnas with the same anticodon located elsewhere in the genome show small sequence variations. the fraction of syntenically conserved tdnas correlates with the divergence of the genomes at sequence level, fig. and tab. the correlation is significant even though the data is rather noisy, a fact that can be explained at least in part by the unavoidable artifacts resulting from our approach. utilizing annotation data directly to determine local synteny is problematic, for instance, near members of very large recently duplicated gene families. in principle, syntenic conservation could be inferred more accurately from genome-wide alignments. since tdnas are treated like repetitive elements in the currently available pipelines, this strategy cannot be employed in practice. nevertheless, the method provides at least a crude estimate of the tdna turnover rate, indicating the tdnas are relocated at time-scales only 2- times slower than background mutation rate, i.e., at an evolutionary distance of mutation per site, 20% to 60% of the tdnas have been deleted or relocated in one lineage. these values should be regarded as upper bounds of syntenic conservation, i.e., tdna turnover is probably even faster. for example, the identity of the tdna was not used in the analysis. despite of the high mobility of tdnas there are some ancient conserved loci. we further investigated two of the syntenic loci conserved between xenopus and human in which tdnas with the same anticodon were retained. manual inspection of the flanking protein coding genes confirmed synteny. neither locus is syntenically conserved in stickleback, lamprey or lancet, however.  we have developed a pipeline based on trnascan-se to extract and analyze the locations of trna genes and pseudogenes of eukaryotic genomes. in our analysis, we focus not only on the number of trna genes, but also on their relative genomic locations, and in particular on the formation of tdna clusters. surprisingly, we found no distinctive clade-specific features or large scale trends, with the exception of the rather straightforward observation that the larger metazoan genomes typically tend to harbour large numbers of tdnas. in some species, large clusters of tdnas occur. this effect has first been reported in entamoeba histolytica. the origin of this gene organization in the genus entamoeba clearly predates the common ancestor of the species investigated to date. their function of the array-like structure remains unclear. we report here that this phenomenon is not restricted to a particular clade of protists but rather appears independently in many times throughout eukaryotes. in most eukaryotes, trnas are multi-copy genes with little or no distinction between paralogs so that orthology is hard to establish, in particular in the presence of trna gene clusters. as a consequence, the evolution of genomic trna arrangements is non-trivial to study over larger time-scales. upper bounds on syntenic conservation can be estimated, however, by considering small sets of flanking protein coding genes for which homology information can be retrieved from existing annotation. we found that trnas change their genomic location at time-scales comparable to mutation rates: syntenic conservation fades at roughly the same evolutionary distances as sequence conservation in unconstrained regions. the absence of large numbers of partially degraded trna copies in many of the investigated genomes provides a hint at the mechanisms of trna mobility: at least in part the relocation events appear to be linked to chromosomal rearrangements rather than mere duplication-deletion of the trna genes themselves. the latter mechanism, which appears to be prevalent e.g. in mitochondrial genomes, certainly also plays a role, since trna pseudogenes are readily observed in many species, as do trna retrogenes. a link between trna loci, and in particular trna clusters, and chromosomal instability has been pointed out repeatedly in the literature, showing that trna genes can interfere with the replication forks. the data collected here provide a basis to investigate this connection more systematically in the future. overall, the trna complement of eukaryotes is highly dynamic part of the genomes whose organization evolves rapidly and in a highly lineage specific manner - a behavior that is in striking contrast to the extreme conservation of sequence and function of the trnas themselves. 
despite this large variation in abundance in eukarya we observe a significant correlation between the number of trna genes, trna pseudogenes, and genome size. surprisingly little is known about the organization and distribution of trna genes and trna-related sequences on a genome-wide scale. while trna gene complements are usually reported in passing as part of genome annotation efforts, and peculiar features such as the tandem arrangements of trna gene in entamoeba histolytica have been described in some detail, systematic comparative studies are rare and mostly restricted to bacteria. we therefore set out to survey the genomic arrangement of trna genes and pseudogenes in a wide range of eukaryotes to identify common patterns and taxon-specific peculiarities. in line with previous reports, we find that trna complements evolve rapidly and trna gene and pseudogene locations are subject to rapid turnover. at phylum level, the distributions of the number of trna genes and pseudogenes numbers are very broad, with standard deviations on the order of the mean. for instance, 65% and 87% of the trna genes and pseudogenes are located in genomic clusters in zebrafish and stickleback, resp., while such arrangements are relatively rare in the other three sequenced teleost fish genomes. among basal metazoa, trichoplax adhaerens has hardly any duplicated trna gene, while the sea anemone nematostella vectensis boasts more than trna genes and pseudogenes. higher primates, for instance, have ± trna genes and pseudogenes of which 17% to 36% are arranged in clusters, while the genome of the bushbaby otolemur garnetti has trna genes and pseudogenes of which only % appear in clusters. consistent with this variability, syntenic conservation of trna genes and pseudogenes is also poor in general, with turn-over rates comparable to those of unconstrained sequence elements. the genomic organization of trna genes and pseudogenes shows complex lineage-specific patterns characterized by an extensive variability that is in striking contrast to the extreme levels of sequence-conservation of the trnas themselves. the comprehensive analysis of the genomic organization of trna genes and pseudogenes in eukarya provides a basis for further studies into the interplay of trna gene arrangements and genome organization in general. dramatic variations are observed even within the eutherian mammals.
 surprisingly little is known about the organization and distribution of trna genes and trna-related sequences on a genome-wide scale. while trna gene complements are usually reported in passing as part of genome annotation efforts, and peculiar features such as the tandem arrangements of trna gene in entamoeba histolytica have been described in some detail, systematic comparative studies are rare and mostly restricted to bacteria. we therefore set out to survey the genomic arrangement of trna genes and pseudogenes in a wide range of eukaryotes to identify common patterns and taxon-specific peculiarities.  in line with previous reports, we find that trna complements evolve rapidly and trna gene and pseudogene locations are subject to rapid turnover. at phylum level, the distributions of the number of trna genes and pseudogenes numbers are very broad, with standard deviations on the order of the mean. even among closely related species we observe dramatic changes in local organization. for instance, 65% and 87% of the trna genes and pseudogenes are located in genomic clusters in zebrafish and stickleback, resp., while such arrangements are relatively rare in the other three sequenced teleost fish genomes. among basal metazoa, trichoplax adhaerens has hardly any duplicated trna gene, while the sea anemone nematostella vectensis boasts more than trna genes and pseudogenes. dramatic variations are observed even within the eutherian mammals. higher primates, for instance, have ± trna genes and pseudogenes of which 17% to 36% are arranged in clusters, while the genome of the bushbaby otolemur garnetti has trna genes and pseudogenes of which only % appear in clusters. in contrast, the distribution is surprisingly uniform across plant genomes. consistent with this variability, syntenic conservation of trna genes and pseudogenes is also poor in general, with turn-over rates comparable to those of unconstrained sequence elements. despite this large variation in abundance in eukarya we observe a significant correlation between the number of trna genes, trna pseudogenes, and genome size.  the genomic organization of trna genes and pseudogenes shows complex lineage-specific patterns characterized by an extensive variability that is in striking contrast to the extreme levels of sequence-conservation of the trnas themselves. the comprehensive analysis of the genomic organization of trna genes and pseudogenes in eukarya provides a basis for further studies into the interplay of trna gene arrangements and genome organization in general. 