BACKGROUND
retrotransposons, which comprise a major portion of eukaryotic genomes, replicate progeny copies into new genomic loci via reverse transcription of an rna intermediate  <cit> .
as intragenomic parasites, retrotransposons have been known as a potent causative agent involved in various harmful biological processes such as insertional mutagenesis  <cit>  and ectopic recombination  <cit> .
conversely, cumulative data have evidenced that these elements play significant roles in the formation and maintenance of host chromosomes  <cit> .
the sporadic expansion of retrotransposons can also introduce genomic/phenotypic variants, which lead to speciation in the long evolutionary terms  <cit> .
retrotransposons are subdivided into two large categories, long-terminal-repeat  and non-ltr retrotransposons, according to overall structures, and the elements with ltr seem to be the most abundant type in invertebrates.
the ltr retrotransposons include multiple groups, as have been distinguished by comparing their own gene products  <cit> .
in addition to the typical ltr retrotransposons, multiple elements with unusual structural features have recently been isolated from various genomes, such as csrn <dig> of clonorchis sinensis  <cit> , xena of takifugu rubripes  <cit> , gmr <dig> of gadus morhua  <cit>  and saci- <dig> of schistosoma mansoni  <cit> .
the csrn <dig> and saci- <dig> elements were found to encode gag with unique motifs of chcc and ccch, respectively, instead of the conventional cchc.
gmr <dig> produced a pol protein, in which the functional protein domains lie in an order identical to those of ty1/copia elements .
retrotransposons of the most ancient xena group had a single open reading frame  containing a rt domain but lacking any other enzymatic domain.
taken together, these facts have suggested that the category and evolutionary episode of the diverse reverse-transcribing elements are more complex than currently understood.
paragonimus westermani is a hermaphroditic, digenetic trematode that lives as adult in the lungs of carnivorous mammals.
this parasite causes pulmonary and cerebral diseases in humans and is one of the most medically important flukes.
the natural populations of p. westermani in northeast asian countries have three different levels of polyploidy in their genomic contents, i.e., di-, tri- and tetrapolyploidy, displaying variations in morphology, allozyme patterns, and nucleotide sequences of ribosomal and mitochondrial dnas  <cit> .
the paragonimus genome contains retrotransposons, which belong to various retrotransposon groups including the csrn <dig> clade  <cit> .
csrn1-like retrotransposons have been detected largely in trematodes and insects  <cit> .
with the unique gag motif and amino acid conservation, members of the clade showed heterogeneity in their coding profiles.
furthermore, boudicca and saci- <dig> of s. mansoni contain a third orf resembling envelope protein  of errantivirus and retrovirus  <cit> .
the genomic distribution of csrn1-like elements have been well described in c. sinensis and s. mansoni, with their unique structural features  <cit> .
nevertheless, molecular information on this distinctive clade is highly limited to address their evolutionary episodes.
in this study, we isolated a novel csrn1-like ltr retrotransposon in the p. westermani genome and analyzed its intra- and inter-genomic distribution patterns among the parasite populations with different karyotes.
differential replication activity of the paragonimus element was examined by detecting the presence or absence of mrna transcripts and intergenomic polymorphism introduced by the element.
the molecular characters of multiple retrotransposons homologous to the element were also analyzed from the genomes of an african malaria mosquito anopheles gambiae, which had recently been released  <cit> , and a fruit fly drosophila melanogaster, in order to gain more detailed information on the invertebrate-specific csrn <dig> clade.
the heterogeneous expression strategies were found to be substantial within the unique clade, and the possible evolutionary relationships between elements with distinctive coding profiles were shown by phylogenetic analyses.
RESULTS
isolation of csrn1-like retrotransposons from p. westermani and a. gambiae
using the previously described degenerate primers, retrotransposon-related sequences had been isolated in p. westermani  <cit> .
these sequences represented various ltr retrotransposons belonging to the multiple clades of metavirus  including the csrn <dig> clade, of which members seemed to expand uniquely in lower animal taxa such as insecta and trematoda  <cit> .
one clone  showing the highest sequence identity with csrn <dig> was used as a probe in the screening of the genomic dna library of the parasite.
as shown in figure  <dig>  the full-unit ltr retrotransposon encompassing the probe sequence was determined and named pwrn <dig>  by comparing sequences of two positive clones .
the pwrn <dig> copy in λpw-13- <dig> was  <dig> -bp long and was bound by direct repeats of  <dig> bp  known as target site duplication .
the internal sequence was corrupted by several stop codons introduced by indels and/or base substitutions, although its flanking 5'- and 3'-ltrs had an identical size  and a high degree of sequence identity .
the internal coding regions were further retrieved from different pwrn <dig> copies  .
the coding profile of pwrn <dig> was predicted with one of these sequences , which contained the longest orf of  <dig>  bp encoding a single 1194-aa polypeptide.
the corrupted nucleotides in the 5'- and 3'-upstream regions of the orf were corrected by comparing them with the equivalent regions in a consensus sequence determined from the  <dig> sequences.
the gag-pol boundary region was further confirmed by sequencing the corresponding cdnas .
the genomic sequences of a. gambiae in the genbank database were examined by using the amino acid sequence of csrn <dig> gag protein as a query .
the nucleotide sequences of matching entries were analyzed via a series of blastn searches to determine the full-unit retrotransposons encompassing each of the gag sequences.
the integrity and identity of the elements were verified by detecting a tsd pair at the boundary regions, and by comparing lengths and nucleotide sequences of their ltrs, respectively.
these procedures isolated a total of  <dig> csrn1-like retrotransposons from the mosquito genome, which were designated agcr- <dig> – agcr- <dig>  .
the complete sequences were used as a blast query to retrieve additional copy sequences from the genome.
the overall structures and coding profiles were predicted, as described above .
one-half of the agcr elements were found to be identical to the csrn1-clade members previously reported  <cit>  .
csrn1-like elements could not be retrieved from the genomic sequences of d. melanogaster, other than the retrotransposon on ae <dig>  <cit> , named dmcr- <dig> in this study.
acontig sequence containing a representative copy is listed.
bthe lengths of orfs were estimated from each of the elements, after correcting the corrupted nucleotide sequences .
cnumber in parentheses indicates a shift in the reading frame of orf <dig> compared to that of orf <dig>
dsynonymous names, as have been designated in a previous report  <cit> .
enucleotides comprising the end of the 3'-ltr and tsd were deleted in the contig and thus, tsd sequence found at the 5'-flanking region was presented.
functional motifs and structural features of pwrn <dig> and agcrs
tsd detected in all of the csrn1-like elements were found to be  <dig> bp, although there seemed to be no specific or preferential nucleotide in selecting the insertional targets among copies of each element and among the agcr types .
the short inverted repeats of  <dig> bp, found at both ends of ltr in most retrotransposons   <cit> , were slightly modified either to 5'-tgt...aaa-3' or to 5'-tgt...ata-3' .
the ltr pairs flanking each of the agcr elements displayed >97% nucleotide identities, suggestive of their recent expansion in the mosquito genome  <cit> .
the putative primer-binding site of these elements for the synthesis of the first cdna strand  was complementary to the nucleotides at the 3'-end of bovine t-rnatrp.
an additional priming site  for the synthesis of the second cdna strand was also found in the direct upstream region of 3'-ltr.
the internal regions of these elements contained orfs with different expression strategies for their autonomous retrointegration.
pwrn <dig> had an orf similar to that of csrn <dig>  in which the gag and pol genes were fused together in a single frame .
of the  <dig> agcr elements analyzed, nine elements utilized two orfs overlapped by - <dig> frameshifting to encode the gag and pol proteins, while the other six elements contained two orfs with an identical reading frame, which were intervened by a short nucleotide sequence ranging from  <dig> to  <dig> bp .
the amino acid sequences of gag proteins in retrotransposons generally diverge very rapidly so that they display a low level of sequence identity to one another, except for the functional cys-his signature   <cit> .
the proteins, however, showed a high degree of amino acid conservation over their entire lengths in these csrn1-like retrotransposons.
they had the unique chcc signature  in the c-terminal regions, while it was imperfect in  <dig> elements, agcr- <dig>  - <dig> and - <dig>  the α-helix-rich secondary structures of the gag proteins were similar to those of the other ty3/gypsy-like ltr retrotransposons .
the enzymatic domains contained in the pol proteins were also well conserved with the conventional motifs/signatures: dt/sg tripeptide of pr, f/yxdd tetrapeptide of rt, das tripeptide of rh, and hhcc and dde signatures of in .
a series of ltr retrotransposons have an additional motif in the c-terminal region of in, which is implicated in non-specific binding to the target site and/or to ltr via the best-conserved gpy/f residues  <cit> .
this motif could also be detected in the corresponding proteins of pwrn <dig> and agcrs with the exceptions of agcr- <dig> and - <dig>  neither the chromatin organization modifier domain  nor env-like protein was detected in these elements.
phylogenetic analysis of csrn1-like retrotransposons
we obtained an alignment of pol proteins from a total of  <dig> elements including the  <dig> elements isolated in this study.
amino acid positions for the three functional domains  were concatenated and used in a phylogenetic analysis with the quartet-puzzling maximum likelihood method.
the representative elements belonging to the previous eight clades of ty3/gypsy-like ltr retrotransposons  <cit> , as well as those of csrn <dig> clade  <cit> , were selected for the analysis.
as shown in figure  <dig>  each of the sequences was well separated into the corresponding clades with significant quartet puzzling frequencies.
the pwrn <dig> and agcrs were categorized into the tightly conserved csrn <dig> clade with a high level of quartet puzzling support , as was predicted by the similarities in the primary structures of the gag and pol proteins.
pwrn <dig> formed a subclade with its trematode neighbors .
the agcr elements were further segregated into four distinct clusters and those with separated orfs were monophyletically distributed in the tree, even though the supporting value was relatively low .
saci- <dig> of s. mansoni, which encodes an unusual gag protein with the ccch motif  <cit> , occupied a unique phylogenetic position.
another tree based on the gag sequences of csrn1-like elements showed a topology similar to that of the pol tree , while the phylogenetic relationships especially among the anopheles elements with different expression strategies could be resolved more evidently with the rapidly evolving gag sequences.
the tree proposed that anopheles elements with the separated orfs have evolved from an ancient form with two overlapped orfs .
genomic distribution and mobile potential of pwrn1
the copy number of pwrn <dig> was estimated over  <dig>  per haploid paragonimus genome via dot blotting .
a southern blot analysis showed that these pwrn <dig> copies are interspersed throughout the genome, rather than being tandemly arrayed or being clustered at limited loci .
however, the blotting could not distinguish the distribution patterns of pwrn <dig> between diploid and triploid genomes, mainly due to the high copy number and resulting smeared hybridization signals.
for a more detailed comparison of pwrn1-occupied loci, irap analyses were conducted with the individual genomic dnas and pwrn <dig> ltr-specific primers .
numerous bands were amplified from genomic loci intervened between two copies of pwrn <dig>  the patterns were found to be homogeneous among the triploid individuals and almost all of the triploid markers were detected in at least one of the diploid genomes, especially with the korean origin .
conversely, polymorphic markers were substantially observed among the diploid genomes at intra- and interpopulation levels.
analyses of more parasite individuals  showed similar results .
given the fact that the sporadic replication of an active retrotransposon introduces intergenomic polymorphism  <cit> , this observation may reflect a differentially preserved mobile potential of pwrn <dig> depending on the karyotype of its host genome; the element has maintained the ability to produce progeny copies in diploids, whereas it has ceased to retrointegrate into new genomic loci in the triploid populations.
in accordance with this suggestion, mrna transcripts of the element were detected in a diploid population, but not in a triploid one .
the intra-genomic expansion of retrotransposons initiates by transcribing their mrnas using host rna polymerase.
by adapting to this unique replication mode, host defense mechanisms have diversely evolved by focusing on the protection of transcription and/or destruction of mrna transcripts, including chromatin modification and rna interference.
therefore, pwrn <dig> was likely to be suppressed at the initial transcription stage in the triploid population, although no relevant mechanism could be addressed in this study.
discussion
since the first detection of ltr retrotransposons with an unusual capsid protein in a trematode and insect species  <cit> , a series of similar elements have been isolated from genomes of the other trematodes and insects.
they share unique properties such as pbs for t-rnatrp,  <dig> bp of tsd and tight amino acid conservation in the encoded proteins.
the most conspicuous feature, nevertheless, can be found in the amino acid sequences of gag proteins.
in general, the first orf contained in various retrotransposons diverge rapidly so that they display low levels of sequence identity to one another, except for the active cys-his motif   <cit> .
however, the proteins of csrn1-like elements have been known to conserve a novel sequence motif of cx2hx9cx3c , instead of the conventional cchc motif.
these facts have suggested that members of this clade are originated from an intermediate form of reverse-transcribing elements, which have emerged in the common ancestor of the monophylyl ecdysozoan and lophotrochozoan animals.
retrotransposons characterized from the lung fluke and mosquito possessed all of these features and thus, further supported the notion that these elements are selectively expanded in the lower animal taxa.
the gag protein of retrotransposons functions as a nucleocapsid protein during the assembly of virus-like particle , which is thought to be an important intermediate in retrotransposition  <cit> .
the origin and functional relevance of gag found in the csrn1-like elements could not be properly addressed, because neither cellular nor the other retrotransposon-related protein was detected during homolog searches based on the blast algorithm and hidden markov models.
considering the well-conserved, α-helix-rich secondary structure  and the active replication of these elements including csrn <dig>  <cit> , the proteins seem to have nucleic acid-binding capacity to form vlps.
malik and eickbush  <cit>  have proposed the chimeric origin of ltr retrotransposons and retroviruses, between a preexisting element and non-ltr element/host gene.
this may reflect the genetic flexibility endogenous in the mobile elements to generate novel functional/structural variants.
a gag gene equipped in the preexisting element is likely to have been substituted by a presently unidentified host gene with the unusual motif during the evolutionary start point of csrn1-like elements.
different expression strategies were observed among the csrn1-like elements .
a single primary transcript is responsible for the production of multiple retrotransposon proteins, which are essential for the autonomous replication of the corresponding element, and is subjected to ribosomal frameshifting to maintain a proper ratio between the gag and pol proteins  <cit> .
genetic events including insertion/deletion of single nucleotide around the frameshifting region are occasionally attributable to the generation of retrotransposons with a single fused orf.
the gag and pol proteins are produced by proteolytic cleavage of a single translation product in the cases of single-orf variants  <cit> .
the variant form will replace the previous one in the host genome, via the highly efficient vlp formation  <cit> .
the structural variation was not detected with the multiple pwrn <dig> copies retrieved by pcr.
the ancient copies with two overlapped orfs might have decayed in the paragonimus genome, mainly due to the low propagation rate.
otherwise, diagnostic base substitutions in priming regions of the variant copies might lead to a failure in the amplification of the corresponding dna segments.
retrotransposons generally show very low retrotransposition and excision rates, and their expansion is largely restricted to germ cells and/or an early developmental stage  <cit> .
these elements, however, become unstable under specific circumstances and can rapidly expand in the host genomes by increasing their replication frequency.
the mobile potential of pwrn <dig> seemed to be differentially preserved among p. westermani populations; the element maintained its activity in diploids, while a majority of the activity had been suppressed in triploid individuals .
in association with the origin of the triploid worms, an allopolyploidic hybridization occurred in ancestral diploids at the intra- or interspecies level has been suggested as a relevant genomic event .
irap markers shared in the diploid and triploid worms are likely to represent genomic loci flanked by pwrn <dig> copies in the putative ancestral diploids, and may provide further genomic evidence supporting the proposed mechanism.
together with biotic/abiotic stresses such as aridity  <cit> , polyploidization can boost the mobile potential of various retrotransposons  <cit> .
therefore, it was unexpected to find that pwrn <dig> is less active in triploid genomes.
host genome surveillance for retrotransposons is likely to be reinforced in association with an increase in genomic dosage  <cit> .
alternatively, pwrn <dig> itself would give a feedback effect as a mechanism to compensate for the amplified copy number, following the hybridization process.
phylogenetic and comparative analyses with the multiple pwrn <dig> copy sequences will be informative to elucidate the evolutionary status/mode of the element among the paragonimus populations with different polyploidy.
there have been various reports on the comparison of p. westermani genomes to address the issue regarding the origin of polyploid genomes .
molecular data such as the nucleotide sequences of mitochondrial and ribosomal dnas dichotomized the genomes into the northeast  and south  asian groups, but failed in establishing more detailed relationships among the northeast populations with different polyploidy  <cit> .
the retrointegration of retrotransposons is an irreversible event and the integration site is randomly selected  <cit> .
these characteristics of mobile elements are particularly suitable for the comparative population studies at the intra- and interspecies levels  <cit> .
in this study, we provided molecular evidence demonstrating genomic conservation and/or diversification between korean diploids and triploids by analyzing intergenomic distributions of pwrn <dig> .
the data suggests that irap and locus-specific typing of active retrotransposons can be an informative genetic marker in exploring the flow of haplotypes among p. westermani populations, and in elucidating the controversial hypotheses on the origin of the triploid populations.
in plants, transposable elements are believed to be reactivated very early following polyploid formation and thus contribute to genetic diversity in the polyploidy species  <cit> .
however, understanding on the role of these elements in polyploidy evolution is just beginning to emerge.
the polyploid genomes are less common in animals than in plants.
our results on the suppressed mobile activity of pwrn <dig> in the triploid paragonimus genomes can boost research to examine the evolutionary impacts of retrotransposons in polyploid animal genomes.
CONCLUSIONS
with the completion of genome projects from numerous eukaryotic organisms, comprehensive studies on the mobile genetic elements have been conducted with the whole genomic sequences.
these studies have broadened our knowledge on the dynamics and impacts of retrotransposons in the host genomes.
despite the rapid accumulation of data, however, only limited information is currently available from a few species in the wide phylum platyhelminthes.
it is apparent that these invertebrate animal genomes contain diverse retrotransposons and that these elements are actively involved in the remodeling and diversification of their host genomes.
our results on the csrn1-like elements of p. westermani and a. gambiae, especially in association with the diversified expression strategies, can make a significant step toward a better understanding of evolutionary episode within the unique csrn <dig> clade of ltr retrotransposons, which is specifically expanded in the lower animal taxa.
the differentially preserved mobile potential of pwrn <dig> and resulting genomic polymorphism in diploid individuals will also be helpful in designing a comparative genomic study with the northeast asian populations of p. westermani.

 retrotransposons, which comprise a major portion of eukaryotic genomes, replicate progeny copies into new genomic loci via reverse transcription of an rna intermediate. as intragenomic parasites, retrotransposons have been known as a potent causative agent involved in various harmful biological processes such as insertional mutagenesis and ectopic recombination. conversely, cumulative data have evidenced that these elements play significant roles in the formation and maintenance of host chromosomes. the sporadic expansion of retrotransposons can also introduce genomic/phenotypic variants, which lead to speciation in the long evolutionary terms. retrotransposons are subdivided into two large categories, long-terminal-repeat and non-ltr retrotransposons, according to overall structures, and the elements with ltr seem to be the most abundant type in invertebrates. the ltr retrotransposons include multiple groups, as have been distinguished by comparing their own gene products. in addition to the typical ltr retrotransposons, multiple elements with unusual structural features have recently been isolated from various genomes, such as csrn of clonorchis sinensis, xena of takifugu rubripes, gmr of gadus morhua and saci- of schistosoma mansoni. the csrn and saci- elements were found to encode gag with unique motifs of chcc and ccch, respectively, instead of the conventional cchc. gmr produced a pol protein, in which the functional protein domains lie in an order identical to those of ty1/copia elements. retrotransposons of the most ancient xena group had a single open reading frame containing a rt domain but lacking any other enzymatic domain. taken together, these facts have suggested that the category and evolutionary episode of the diverse reverse-transcribing elements are more complex than currently understood. paragonimus westermani is a hermaphroditic, digenetic trematode that lives as adult in the lungs of carnivorous mammals. this parasite causes pulmonary and cerebral diseases in humans and is one of the most medically important flukes. the natural populations of p. westermani in northeast asian countries have three different levels of polyploidy in their genomic contents, i.e., di-, tri- and tetrapolyploidy, displaying variations in morphology, allozyme patterns, and nucleotide sequences of ribosomal and mitochondrial dnas. the paragonimus genome contains retrotransposons, which belong to various retrotransposon groups including the csrn clade. csrn1-like retrotransposons have been detected largely in trematodes and insects. with the unique gag motif and amino acid conservation, members of the clade showed heterogeneity in their coding profiles. furthermore, boudicca and saci- of s. mansoni contain a third orf resembling envelope protein of errantivirus and retrovirus. the genomic distribution of csrn1-like elements have been well described in c. sinensis and s. mansoni, with their unique structural features. nevertheless, molecular information on this distinctive clade is highly limited to address their evolutionary episodes. in this study, we isolated a novel csrn1-like ltr retrotransposon in the p. westermani genome and analyzed its intra- and inter-genomic distribution patterns among the parasite populations with different karyotes. differential replication activity of the paragonimus element was examined by detecting the presence or absence of mrna transcripts and intergenomic polymorphism introduced by the element. the molecular characters of multiple retrotransposons homologous to the element were also analyzed from the genomes of an african malaria mosquito anopheles gambiae, which had recently been released, and a fruit fly drosophila melanogaster, in order to gain more detailed information on the invertebrate-specific csrn clade. the heterogeneous expression strategies were found to be substantial within the unique clade, and the possible evolutionary relationships between elements with distinctive coding profiles were shown by phylogenetic analyses.  isolation of csrn1-like retrotransposons from p. westermani and a. gambiae using the previously described degenerate primers, retrotransposon-related sequences had been isolated in p. westermani. these sequences represented various ltr retrotransposons belonging to the multiple clades of metavirus including the csrn clade, of which members seemed to expand uniquely in lower animal taxa such as insecta and trematoda. one clone showing the highest sequence identity with csrn was used as a probe in the screening of the genomic dna library of the parasite. as shown in figure the full-unit ltr retrotransposon encompassing the probe sequence was determined and named pwrn by comparing sequences of two positive clones. the pwrn copy in λpw-13- was -bp long and was bound by direct repeats of bp known as target site duplication. the internal sequence was corrupted by several stop codons introduced by indels and/or base substitutions, although its flanking 5'- and 3'-ltrs had an identical size and a high degree of sequence identity. the internal coding regions were further retrieved from different pwrn copies. the coding profile of pwrn was predicted with one of these sequences, which contained the longest orf of bp encoding a single 1194-aa polypeptide. the corrupted nucleotides in the 5'- and 3'-upstream regions of the orf were corrected by comparing them with the equivalent regions in a consensus sequence determined from the sequences. the gag-pol boundary region was further confirmed by sequencing the corresponding cdnas. the genomic sequences of a. gambiae in the genbank database were examined by using the amino acid sequence of csrn gag protein as a query. the nucleotide sequences of matching entries were analyzed via a series of blastn searches to determine the full-unit retrotransposons encompassing each of the gag sequences. the integrity and identity of the elements were verified by detecting a tsd pair at the boundary regions, and by comparing lengths and nucleotide sequences of their ltrs, respectively. these procedures isolated a total of csrn1-like retrotransposons from the mosquito genome, which were designated agcr- – agcr-. the complete sequences were used as a blast query to retrieve additional copy sequences from the genome. the overall structures and coding profiles were predicted, as described above. one-half of the agcr elements were found to be identical to the csrn1-clade members previously reported. csrn1-like elements could not be retrieved from the genomic sequences of d. melanogaster, other than the retrotransposon on ae, named dmcr- in this study. acontig sequence containing a representative copy is listed. bthe lengths of orfs were estimated from each of the elements, after correcting the corrupted nucleotide sequences. cnumber in parentheses indicates a shift in the reading frame of orf compared to that of orf dsynonymous names, as have been designated in a previous report. enucleotides comprising the end of the 3'-ltr and tsd were deleted in the contig and thus, tsd sequence found at the 5'-flanking region was presented. functional motifs and structural features of pwrn and agcrs tsd detected in all of the csrn1-like elements were found to be bp, although there seemed to be no specific or preferential nucleotide in selecting the insertional targets among copies of each element and among the agcr types. the short inverted repeats of bp, found at both ends of ltr in most retrotransposons, were slightly modified either to 5'-tgt...aaa-3' or to 5'-tgt...ata-3'. the ltr pairs flanking each of the agcr elements displayed >97% nucleotide identities, suggestive of their recent expansion in the mosquito genome. the putative primer-binding site of these elements for the synthesis of the first cdna strand was complementary to the nucleotides at the 3'-end of bovine t-rnatrp. an additional priming site for the synthesis of the second cdna strand was also found in the direct upstream region of 3'-ltr. the internal regions of these elements contained orfs with different expression strategies for their autonomous retrointegration. pwrn had an orf similar to that of csrn in which the gag and pol genes were fused together in a single frame. of the agcr elements analyzed, nine elements utilized two orfs overlapped by - frameshifting to encode the gag and pol proteins, while the other six elements contained two orfs with an identical reading frame, which were intervened by a short nucleotide sequence ranging from to bp. the amino acid sequences of gag proteins in retrotransposons generally diverge very rapidly so that they display a low level of sequence identity to one another, except for the functional cys-his signature. the proteins, however, showed a high degree of amino acid conservation over their entire lengths in these csrn1-like retrotransposons. they had the unique chcc signature in the c-terminal regions, while it was imperfect in elements, agcr- - and - the α-helix-rich secondary structures of the gag proteins were similar to those of the other ty3/gypsy-like ltr retrotransposons. the enzymatic domains contained in the pol proteins were also well conserved with the conventional motifs/signatures: dt/sg tripeptide of pr, f/yxdd tetrapeptide of rt, das tripeptide of rh, and hhcc and dde signatures of in. a series of ltr retrotransposons have an additional motif in the c-terminal region of in, which is implicated in non-specific binding to the target site and/or to ltr via the best-conserved gpy/f residues. this motif could also be detected in the corresponding proteins of pwrn and agcrs with the exceptions of agcr- and - neither the chromatin organization modifier domain nor env-like protein was detected in these elements. phylogenetic analysis of csrn1-like retrotransposons we obtained an alignment of pol proteins from a total of elements including the elements isolated in this study. amino acid positions for the three functional domains were concatenated and used in a phylogenetic analysis with the quartet-puzzling maximum likelihood method. the representative elements belonging to the previous eight clades of ty3/gypsy-like ltr retrotransposons, as well as those of csrn clade, were selected for the analysis. as shown in figure each of the sequences was well separated into the corresponding clades with significant quartet puzzling frequencies. the pwrn and agcrs were categorized into the tightly conserved csrn clade with a high level of quartet puzzling support, as was predicted by the similarities in the primary structures of the gag and pol proteins. pwrn formed a subclade with its trematode neighbors. the agcr elements were further segregated into four distinct clusters and those with separated orfs were monophyletically distributed in the tree, even though the supporting value was relatively low. saci- of s. mansoni, which encodes an unusual gag protein with the ccch motif, occupied a unique phylogenetic position. another tree based on the gag sequences of csrn1-like elements showed a topology similar to that of the pol tree, while the phylogenetic relationships especially among the anopheles elements with different expression strategies could be resolved more evidently with the rapidly evolving gag sequences. the tree proposed that anopheles elements with the separated orfs have evolved from an ancient form with two overlapped orfs. genomic distribution and mobile potential of pwrn1 the copy number of pwrn was estimated over per haploid paragonimus genome via dot blotting. a southern blot analysis showed that these pwrn copies are interspersed throughout the genome, rather than being tandemly arrayed or being clustered at limited loci. however, the blotting could not distinguish the distribution patterns of pwrn between diploid and triploid genomes, mainly due to the high copy number and resulting smeared hybridization signals. for a more detailed comparison of pwrn1-occupied loci, irap analyses were conducted with the individual genomic dnas and pwrn ltr-specific primers. numerous bands were amplified from genomic loci intervened between two copies of pwrn the patterns were found to be homogeneous among the triploid individuals and almost all of the triploid markers were detected in at least one of the diploid genomes, especially with the korean origin. conversely, polymorphic markers were substantially observed among the diploid genomes at intra- and interpopulation levels. analyses of more parasite individuals showed similar results. given the fact that the sporadic replication of an active retrotransposon introduces intergenomic polymorphism, this observation may reflect a differentially preserved mobile potential of pwrn depending on the karyotype of its host genome; the element has maintained the ability to produce progeny copies in diploids, whereas it has ceased to retrointegrate into new genomic loci in the triploid populations. in accordance with this suggestion, mrna transcripts of the element were detected in a diploid population, but not in a triploid one. the intra-genomic expansion of retrotransposons initiates by transcribing their mrnas using host rna polymerase. by adapting to this unique replication mode, host defense mechanisms have diversely evolved by focusing on the protection of transcription and/or destruction of mrna transcripts, including chromatin modification and rna interference. therefore, pwrn was likely to be suppressed at the initial transcription stage in the triploid population, although no relevant mechanism could be addressed in this study. discussion since the first detection of ltr retrotransposons with an unusual capsid protein in a trematode and insect species, a series of similar elements have been isolated from genomes of the other trematodes and insects. they share unique properties such as pbs for t-rnatrp, bp of tsd and tight amino acid conservation in the encoded proteins. the most conspicuous feature, nevertheless, can be found in the amino acid sequences of gag proteins. in general, the first orf contained in various retrotransposons diverge rapidly so that they display low levels of sequence identity to one another, except for the active cys-his motif. however, the proteins of csrn1-like elements have been known to conserve a novel sequence motif of cx2hx9cx3c, instead of the conventional cchc motif. these facts have suggested that members of this clade are originated from an intermediate form of reverse-transcribing elements, which have emerged in the common ancestor of the monophylyl ecdysozoan and lophotrochozoan animals. retrotransposons characterized from the lung fluke and mosquito possessed all of these features and thus, further supported the notion that these elements are selectively expanded in the lower animal taxa. the gag protein of retrotransposons functions as a nucleocapsid protein during the assembly of virus-like particle, which is thought to be an important intermediate in retrotransposition. the origin and functional relevance of gag found in the csrn1-like elements could not be properly addressed, because neither cellular nor the other retrotransposon-related protein was detected during homolog searches based on the blast algorithm and hidden markov models. considering the well-conserved, α-helix-rich secondary structure and the active replication of these elements including csrn, the proteins seem to have nucleic acid-binding capacity to form vlps. malik and eickbush have proposed the chimeric origin of ltr retrotransposons and retroviruses, between a preexisting element and non-ltr element/host gene. this may reflect the genetic flexibility endogenous in the mobile elements to generate novel functional/structural variants. a gag gene equipped in the preexisting element is likely to have been substituted by a presently unidentified host gene with the unusual motif during the evolutionary start point of csrn1-like elements. different expression strategies were observed among the csrn1-like elements. a single primary transcript is responsible for the production of multiple retrotransposon proteins, which are essential for the autonomous replication of the corresponding element, and is subjected to ribosomal frameshifting to maintain a proper ratio between the gag and pol proteins. genetic events including insertion/deletion of single nucleotide around the frameshifting region are occasionally attributable to the generation of retrotransposons with a single fused orf. the gag and pol proteins are produced by proteolytic cleavage of a single translation product in the cases of single-orf variants. the variant form will replace the previous one in the host genome, via the highly efficient vlp formation. the structural variation was not detected with the multiple pwrn copies retrieved by pcr. the ancient copies with two overlapped orfs might have decayed in the paragonimus genome, mainly due to the low propagation rate. otherwise, diagnostic base substitutions in priming regions of the variant copies might lead to a failure in the amplification of the corresponding dna segments. retrotransposons generally show very low retrotransposition and excision rates, and their expansion is largely restricted to germ cells and/or an early developmental stage. these elements, however, become unstable under specific circumstances and can rapidly expand in the host genomes by increasing their replication frequency. the mobile potential of pwrn seemed to be differentially preserved among p. westermani populations; the element maintained its activity in diploids, while a majority of the activity had been suppressed in triploid individuals. in association with the origin of the triploid worms, an allopolyploidic hybridization occurred in ancestral diploids at the intra- or interspecies level has been suggested as a relevant genomic event. irap markers shared in the diploid and triploid worms are likely to represent genomic loci flanked by pwrn copies in the putative ancestral diploids, and may provide further genomic evidence supporting the proposed mechanism. together with biotic/abiotic stresses such as aridity, polyploidization can boost the mobile potential of various retrotransposons. therefore, it was unexpected to find that pwrn is less active in triploid genomes. host genome surveillance for retrotransposons is likely to be reinforced in association with an increase in genomic dosage. alternatively, pwrn itself would give a feedback effect as a mechanism to compensate for the amplified copy number, following the hybridization process. phylogenetic and comparative analyses with the multiple pwrn copy sequences will be informative to elucidate the evolutionary status/mode of the element among the paragonimus populations with different polyploidy. there have been various reports on the comparison of p. westermani genomes to address the issue regarding the origin of polyploid genomes. molecular data such as the nucleotide sequences of mitochondrial and ribosomal dnas dichotomized the genomes into the northeast and south asian groups, but failed in establishing more detailed relationships among the northeast populations with different polyploidy. the retrointegration of retrotransposons is an irreversible event and the integration site is randomly selected. these characteristics of mobile elements are particularly suitable for the comparative population studies at the intra- and interspecies levels. in this study, we provided molecular evidence demonstrating genomic conservation and/or diversification between korean diploids and triploids by analyzing intergenomic distributions of pwrn. the data suggests that irap and locus-specific typing of active retrotransposons can be an informative genetic marker in exploring the flow of haplotypes among p. westermani populations, and in elucidating the controversial hypotheses on the origin of the triploid populations. in plants, transposable elements are believed to be reactivated very early following polyploid formation and thus contribute to genetic diversity in the polyploidy species. however, understanding on the role of these elements in polyploidy evolution is just beginning to emerge. the polyploid genomes are less common in animals than in plants. our results on the suppressed mobile activity of pwrn in the triploid paragonimus genomes can boost research to examine the evolutionary impacts of retrotransposons in polyploid animal genomes.  with the completion of genome projects from numerous eukaryotic organisms, comprehensive studies on the mobile genetic elements have been conducted with the whole genomic sequences. these studies have broadened our knowledge on the dynamics and impacts of retrotransposons in the host genomes. despite the rapid accumulation of data, however, only limited information is currently available from a few species in the wide phylum platyhelminthes. it is apparent that these invertebrate animal genomes contain diverse retrotransposons and that these elements are actively involved in the remodeling and diversification of their host genomes. our results on the csrn1-like elements of p. westermani and a. gambiae, especially in association with the diversified expression strategies, can make a significant step toward a better understanding of evolutionary episode within the unique csrn clade of ltr retrotransposons, which is specifically expanded in the lower animal taxa. the differentially preserved mobile potential of pwrn and resulting genomic polymorphism in diploid individuals will also be helpful in designing a comparative genomic study with the northeast asian populations of p. westermani. 
the mobile potential of pwrn was likely to be maintained differentially in association with the karyotype of host genomes, as was examined by the presence/absence of intergenomic polymorphism and mrna transcripts. the pwrn1-associated genomic polymorphism, which is substantial in diploids, will also be informative in addressing genomic diversification following inter-/intra-specific hybridization in p. westermani populations. our results on the structural diversity of csrn1-like elements can provide a molecular tool to dissect a more detailed evolutionary episode of ltr retrotransposons. these elements, designated pwrn and agcr- – agcr- conserved unique features including a t-rnatrp primer binding site and the unusual chcc signature of gag proteins. these reverse transcribing elements, which show a complex evolutionary pathway with diverse intermediate forms, have been comprehensively analyzed from a wide range of host genomes, while the information remains limited to only a few species in the phylum platyhelminthes. retrotransposons have been known to involve in the remodeling and evolution of host genome. they evolved heterogeneous expression strategies: a single fused orf, two separate orfs with an identical reading frame and two orfs overlapped by - frameshifting. phylogenetic analyses suggested that the elements with the separate orfs had evolved from an ancestral form with the overlapped orfs. their flanking ltrs displayed >97% nucleotide identities and thus, these elements were likely to have expanded recently in the trematode and insect genomes.
 retrotransposons have been known to involve in the remodeling and evolution of host genome. these reverse transcribing elements, which show a complex evolutionary pathway with diverse intermediate forms, have been comprehensively analyzed from a wide range of host genomes, while the information remains limited to only a few species in the phylum platyhelminthes.  a ltr retrotransposon and its homologs with a strong phylogenetic affinity toward csrn of clonorchis sinensis were isolated from a trematode parasite paragonimus westermani via a degenerate pcr method and from an insect species anopheles gambiae by in silico analysis of the whole mosquito genome, respectively. these elements, designated pwrn and agcr- – agcr- conserved unique features including a t-rnatrp primer binding site and the unusual chcc signature of gag proteins. their flanking ltrs displayed >97% nucleotide identities and thus, these elements were likely to have expanded recently in the trematode and insect genomes. they evolved heterogeneous expression strategies: a single fused orf, two separate orfs with an identical reading frame and two orfs overlapped by - frameshifting. phylogenetic analyses suggested that the elements with the separate orfs had evolved from an ancestral form with the overlapped orfs. the mobile potential of pwrn was likely to be maintained differentially in association with the karyotype of host genomes, as was examined by the presence/absence of intergenomic polymorphism and mrna transcripts.  our results on the structural diversity of csrn1-like elements can provide a molecular tool to dissect a more detailed evolutionary episode of ltr retrotransposons. the pwrn1-associated genomic polymorphism, which is substantial in diploids, will also be informative in addressing genomic diversification following inter-/intra-specific hybridization in p. westermani populations. 