BACKGROUND
genomes are highly dynamic.
comparative genome analysis has revealed extensive differences, including inversions, transpositions, reciprocal translocations and duplications, among genomes of different species, as well as among genomes of different strains within the same species.
in particular, duplications had been observed and studied long before any genome sequencing projects were initiated.
for example, the bar "gene" duplication in the fruit fly drosophila melanogaster, which was found to be important in determining eye size, was identified cytologically in the 1920s  <cit> .
now, with the availability of genome sequences of many species, a large number of studies have been carried out to detect in silico and in a genome-wide manner the presence of such duplications  <cit> .
duplications can be classified into three types based on their scales: whole genome duplications, segmental duplications, and single gene duplications.
in 1970s, susumu ohno proposed that gene duplication is the driving force for the generation of new genes and novel biochemical processes  <cit> .
caenorhabditis elegans is a widely used model organism for its small size, short life cycle, well-defined development, ease of manipulation, as well as a compact genome.
in c. elegans, gene duplications have been found to be responsible for the formation of many gene families, including chemosensory gene families  <cit> , transcription factors  <cit> , abc transporters  <cit> , and gene families important in host-pathogen interactions  <cit> .
in contrast to the extensive analyses of individual gene duplications in c. elegans, large scale segmental duplications have received little attention, although they are known to exist  <cit> .
in this project, we have carried out a genome-wide analysis of segmental duplications in c. elegans using a new program called orthocluster  <cit> , and we have experimentally assessed the polymorphism of the largest pair of duplicons in different wild-type  strains of c. elegans as well as the wild isolate–hawaiian strain .
given that we ran orthocluster at the gene level, in which each chromosome is represented as a set of genes with their corresponding order and strandedness, the term "segmental duplication" is used here to describe any group of one or more genes that are found duplicated in the genome.
RESULTS
identification of genome-wide segmental duplications
we applied orthocluster to identify genome-wide segmental duplications in c. elegans.
orthocluster can identify "perfect segmental duplications"–duplications containing no mismatches, "imperfect segmental duplications"–duplications containing a certain level of mismatches , as well as synteny blocks among multiple genomes  <cit> .
in this report, we call each duplicated segment of genes a duplicon  <cit> .
perfect segmental duplications
we identified  <dig>  perfect segmental duplications, which generate  <dig>  duplicons .
note that the number of duplicons is not exactly twice the number of segmental duplications because the same regions can be duplicated more than once.
the majority of the segmental duplications  are intrachromosomal and can be further categorized as tandem  when the corresponding duplicons are found adjacently, or as dispersed  when at least one gene is separating them.
sizes of the identified duplicons vary dramatically, ranging from one to  <dig> genes , or from  <dig> bp to  <dig> kb in size .
the majority of these duplicons contain single genes , while a few contain more than ten genes, consistent with previous observations  <cit>  .
the duplicons are not evenly distributed in different chromosomes, with chromosome v having significantly more duplications than other chromosomes .
the largest pair of duplicons is located on the left arm of chromosome v, and each duplicon contains  <dig> genes with a genomic span of  <dig> kb.
although the presence of this large segmental duplication has been reported in previous studies  <cit> , detailed analysis has not been pursued.
imperfect segmental duplications
search for imperfect segmental duplications revealed larger duplicons, suggesting that some smaller neighboring perfect duplicons can merge to form larger imperfect ones.
as a result, the number of duplicons identified decreased from  <dig>   to  <dig> , generated by  <dig>  imperfect segmental duplications .
molecular comparison of the two largest duplicons
to further characterize the largest segmental duplication, we compared the two duplicons generated by the largest segmental duplication at the base pair level.
first, we observed that the two duplicons are found in tandem on chromosome v between  <dig>  kb and  <dig>  kb in the canonical c. elegans genome sequence that is hosted at wormbase http://www.wormbase.org <cit> .
each duplicon contains  <dig> putative protein-coding genes, most of which are putative chemosensory genes based on wormbase  curation.
additionally, we found identical copies of mariner-like transposable element cemar <dig>  <cit>  flanking the duplicons .
multiple sequence alignment of the dna sequences of these transposons indicated that they are nearly identical .
in contrast, the regions upstream of the beginning of the first cemar <dig> and downstream of the third cemar <dig>  show no significant similarity.
next, we compared dna sequences of the two duplicons, and found that they have  <dig> % sequence identity, with only six small differences .
considering the large size of these duplicons , such high level of similarity is rather surprising.
the biggest difference is a  <dig> bp deletion found in the upstream duplicon .
other differences are limited to one to three nucleotides, and notably, all differences are located in either intergenic regions or within introns of current gene models .
given that these two duplicons are virtually identical, we expect all  <dig> gene models contained in each of these duplicons to be identical.
to our surprise, based on the current wormbase  annotation, only  <dig> of the  <dig> pairs are identical  , suggesting that many of these gene models are defective, and thus need to be improved.
we have thus attempted to improve these gene models using existing est sequence data and their similarity to known paralogous genes that are curated by wormbase curators .
all updated gene models have been submitted to wormbase .
each gene pair is shown in order of appearance from 5' to 3'.
the "method of repair" column suggests a way to fix those gene models that have different peptide sequence, given the lack of supporting information for better improvement.
longest: suggests taking the longest peptide sequence as the correct model.
evidence: suggests considering as correct the member of the pair that has been reported as "person evidence" in wormbase.
genewise: suggest a paralog gene that can be used to predict a gene structure in the region within each member of the pair.
each gene is characterized in terms of est data support as ns  if no intron is supported, ps  if at least one intron is not supported, and fs  if all introns are supported by est data.
*: see text.
experimental characterization of the largest duplicons in c. elegans
the high level of similarity between these two largest duplicons in the c. elegans genome prompted us to hypothesize that they were generated very recently and thus not all wild-type  strains carry them.
to test this hypothesis, we genotyped  <dig> of the n <dig> strains, received from the researchers in the c. elegans community, for the presence of these duplicons.
for each strain, we examined  the presence of the junction between the two largest duplicons  and  the presence of the  <dig> bp unique sequence .
results showed that the  <dig> samples processed can be divided into two groups: a group of  <dig> samples that don't carry the largest duplicon pair , and a group of  <dig> samples that carry the largest duplicon pair .
in addition, this tandem duplication was not found in the c. elegans cb <dig> strain, an isolate from a hawaiian island.
thus, we conclude from these results that the n <dig> worms, which all originated from a common ancestor first established in sydney brenner's lab in 1960s  <cit> , had become polymorphic in this genomic region in laboratory.
this conclusion is further supported by two interesting patterns that emerged from our genotyping assays.
first,  <dig> of the  <dig> cgc  strains  don't have the largest duplicons.
this includes the strain from donald riddle, who originally set up the cgc.
the only one "cgc n <dig> strain"  that carries the largest duplicons is thus likely not a real cgc but was in fact obtained from an alternative source.
second, all  <dig> strains that were obtained from robert horvitz's lab and from the labs that obtained their n <dig> strain directly or indirectly from the horvitz lab  contain the largest duplicons.
we have also tested the existence of the junction in the cosmid f56a <dig>  which was created and used in the c. elegans genome sequencing project  <cit> .
pcr results clearly showed the presence of the duplication junction in the cosmid f56a <dig> , suggesting that this pair of duplicons also exist in the c. elegans strain used for the c. elegans genome sequencing project.
together, these observations support our hypothesis that this large tandem duplication arose as a result of a recent event, after the n <dig> strain was established as a laboratory strain in the early 1970s.
tandem segmental duplications and transposons
the presence of nearly identical cemar <dig> transposons flanking the largest duplicons suggests a possible role of these transposons in the duplication event .
the fact that these duplicons are found in tandem and in a head-to-tail orientation, together with the close to 100% transposon dna identity suggests that this segmental duplication occurred by an unequal crossing over event facilitated by the presence of the cemar <dig> transposons.
the expected outcome of an unequal recombination event is two types of chromosomes: one with the duplicated region and one with a deletion of the same region.
unlike duplication, deletion of  <dig> genes could lead to a reduced evolutionary fitness and loss of the strain.
in order to examine whether this mechanism accounts for other observed tandem duplications, we selected all duplications in the c. elegans genome that are larger than  <dig>  bp that show more than 90% identity at the dna level and examined their correlation to the distribution of transposable elements.
altogether  <dig> pairs of tandem duplicons , including the largest tandem duplicons described above, were examined and only five were found to be associated with neighboring transposons, suggesting that transposable elements may play a role in the formation of some, but not all, tandem segmental duplications.
this association is not significantly different from random .
in addition, for all cases associated with transposons, except the largest duplicons, transposons are found in the neighborhood of one duplicon but not perfectly flanked by transposons at edges.
alternatively, it is possible that most of the transposable elements have moved away from the tandem duplication regions after the duplication event.
interestingly, among all tandem duplications , larger duplicon pairs  tend to be arranged in a head-to-tail orientation , while smaller ones are arranged in a tail-to-tail  orientation .
large tandem duplication polymorphism creates a new gene
a detailed examination of the junction between the two largest duplicons revealed that there is a gene  flanking this junction that resides on both duplicons .
this gene contains a glutathione s-transferase n-terminal domain and the gene model is fully supported by est data.
this est data was generated by yuji kohara  <cit> , who generated the est library using a c. elegans strain that contains the largest segmental duplication, based on our genotyping result.
exons in f56a <dig>  derived from exons in f15e <dig>   and y45g12c.
<dig> .
thus, this large segmental duplication leads to the creation of a novel c. elegans gene through an exon shuffling mechanism  <cit> .
the function of this putative new gene is being examined.
discussion and
CONCLUSIONS
in this project we applied orthocluster  <cit> , our newly developed method for a gene-oriented detection and analysis of segmental duplications within the c. elegans genome.
the versatility of this program allowed us to identify both perfect and imperfect segmental duplications, as well as to conclude that most of the identified duplicons are intrachromosomal and relatively small , consistent with previous observations  <cit> .
the largest pair of duplicons that we identified is localized in tandem on chromosome v and contains  <dig> genes.
our detailed analysis revealed that these duplicons are nearly identical, suggesting a very recent duplication event.
this hypothesis is further supported by the following observations.
first, these two duplicons are flanked by nearly identical cemar <dig> transposons , which may have caused a recent unequal crossing over event.
previous studies in c. elegans have shown that transposable elements can cause tandem duplications  <cit> .
a recent study revealed that the cemar <dig> transposons may be active in the c. elegans genome  <cit> , which suggests that this segmental duplication was preceded by a transposition event of the cemar <dig> element.
second, this large segmental duplication is strain-specific.
among  <dig> n <dig> strains genotyped, only  <dig> have the duplication.
since all of these  <dig> n <dig> strains were originated from a common ancestor strain, the large tandem segmental duplication might have occurred once after the establishment of n <dig> as a laboratory c. elegans wild-type strain in 1960s  <cit> .
this ancestor strain was originally obtained from mushroom compost near bristol, england, and was given to sydney brenner by ellsworth dougherty in the spring of  <dig>  <cit> .
from the bristol strain, sydney brenner isolated a hermaphrodite and its progeny was used for establishing a line of hermaphrodites and a line of males.
these were the founder stocks of the n <dig> strains  <cit> .
most likely, after the large segmental duplication was established, it was then propagated to other labs in the c. elegans community.
this idea is consistent with the emerging patterns of the genotyping results–many duplication-carrying strains were obtained from labs that are related.
similarly, the strains that do not carry this large tandem duplication were obtained directly or indirectly from cgc.
additionally, the largest duplicon pair does not exist in the wild c. elegans isolate, the hawaiian strain.
the expression and function of these  <dig> pairs of genes is largely unknown.
since many of these genes  are putative chemosensory genes, chemotaxis experiments  <cit>  can be used to evaluated the impact of this duplication.
the six differences could lie in regulatory elements and thus impact gene expression.
an unexpected result is that a new gene was created through exon shuffling as a byproduct of this large segmental duplication .
the presence of this gene might be beneficial for the organism and thus helped to maintain these duplicons.
the function of this new gene and its potential role in stabilizing the segmental duplication will be examined and reported separately.
an unsettled puzzle is the  <dig> bp unique sequence, which is found only in the downstream largest duplicon in the current c. elegans genome release .
in all  <dig> strains that carry the duplication, the  <dig> bp unique sequence is found in both duplicons.
interestingly, the sequence of the strain available at wormbase shows that this  <dig> bp sequence is found only in one of the duplicons–the downstream duplicon.
further examination of the genomic region harboring this putative deletion in the upstream duplicon shows that it is repetitive, containing several copies of a single complex repeat type  .
the difference between these two types of strains  could be explained by strain-specific deletion in the strain used for the c. elegans genome sequencing project.
the possibility that the  <dig> bp sequence is an assembly error has not been ruled out.
recent studies have proven that large genomic differences exist between the laboratory n <dig> c. elegans strain and the hawaiian c. elegans strain, in addition to many snps discovered previously  <cit> .
for example, maydan and colleagues  <cit>  discovered a ~2% gene variation between n <dig> c. elegans strain and the cb <dig> hawaiian c. elegans strain using array comparative genome hybridization  array.
they uncovered significant variations, including deletions and copy-number differences.
more recently, projects using illumina solexa sequencing methods revealed extensive differences  even between different c. elegans laboratory strains  <cit>  at the base-pair resolution.
our study reveals for the first time that different laboratory n <dig> strains can acquire and accumulate large-scale differences.
our discovery stresses the importance of taking into account variations in different laboratory strains when solving inconsistencies in results from different labs.
our results, together with recent results using acgh or solexa sequencing methods, have thus clearly established that different n <dig> strains contain extensive differences in their genomic sequences.
for robust research and for effective communication between different research groups, we recommend that labs should regularly start fresh from frozen c. elegans aliquot and should acquire n <dig> worms directly from cgc instead of from neighboring labs.
more importantly, we recommend that each lab should keep a detailed record of the history of the n <dig> worms used.
furthermore, the n <dig> strain containing this large segmental duplication that is used in over one third of all c. elegans labs, should also be maintained and highlighted in cgc as a reference.
additionally, since the current c. elegans genome  carries the largest duplicons  while the current cgc n <dig> strain does not, the cgc n <dig> strain, which is widely used in c. elegans labs, should be fully sequenced, assembled, analyzed, and compared with the current wormbase genome.

 genomes are highly dynamic. comparative genome analysis has revealed extensive differences, including inversions, transpositions, reciprocal translocations and duplications, among genomes of different species, as well as among genomes of different strains within the same species. in particular, duplications had been observed and studied long before any genome sequencing projects were initiated. for example, the bar "gene" duplication in the fruit fly drosophila melanogaster, which was found to be important in determining eye size, was identified cytologically in the 1920s. now, with the availability of genome sequences of many species, a large number of studies have been carried out to detect in silico and in a genome-wide manner the presence of such duplications. duplications can be classified into three types based on their scales: whole genome duplications, segmental duplications, and single gene duplications. in 1970s, susumu ohno proposed that gene duplication is the driving force for the generation of new genes and novel biochemical processes. caenorhabditis elegans is a widely used model organism for its small size, short life cycle, well-defined development, ease of manipulation, as well as a compact genome. in c. elegans, gene duplications have been found to be responsible for the formation of many gene families, including chemosensory gene families, transcription factors, abc transporters, and gene families important in host-pathogen interactions. in contrast to the extensive analyses of individual gene duplications in c. elegans, large scale segmental duplications have received little attention, although they are known to exist. in this project, we have carried out a genome-wide analysis of segmental duplications in c. elegans using a new program called orthocluster, and we have experimentally assessed the polymorphism of the largest pair of duplicons in different wild-type strains of c. elegans as well as the wild isolate–hawaiian strain. given that we ran orthocluster at the gene level, in which each chromosome is represented as a set of genes with their corresponding order and strandedness, the term "segmental duplication" is used here to describe any group of one or more genes that are found duplicated in the genome.  identification of genome-wide segmental duplications we applied orthocluster to identify genome-wide segmental duplications in c. elegans. orthocluster can identify "perfect segmental duplications"–duplications containing no mismatches, "imperfect segmental duplications"–duplications containing a certain level of mismatches, as well as synteny blocks among multiple genomes. in this report, we call each duplicated segment of genes a duplicon. perfect segmental duplications we identified perfect segmental duplications, which generate duplicons. note that the number of duplicons is not exactly twice the number of segmental duplications because the same regions can be duplicated more than once. the majority of the segmental duplications are intrachromosomal and can be further categorized as tandem when the corresponding duplicons are found adjacently, or as dispersed when at least one gene is separating them. sizes of the identified duplicons vary dramatically, ranging from one to genes, or from bp to kb in size. the majority of these duplicons contain single genes, while a few contain more than ten genes, consistent with previous observations. the duplicons are not evenly distributed in different chromosomes, with chromosome v having significantly more duplications than other chromosomes. the largest pair of duplicons is located on the left arm of chromosome v, and each duplicon contains genes with a genomic span of kb. although the presence of this large segmental duplication has been reported in previous studies, detailed analysis has not been pursued. imperfect segmental duplications search for imperfect segmental duplications revealed larger duplicons, suggesting that some smaller neighboring perfect duplicons can merge to form larger imperfect ones. as a result, the number of duplicons identified decreased from to, generated by imperfect segmental duplications. molecular comparison of the two largest duplicons to further characterize the largest segmental duplication, we compared the two duplicons generated by the largest segmental duplication at the base pair level. first, we observed that the two duplicons are found in tandem on chromosome v between kb and kb in the canonical c. elegans genome sequence that is hosted at wormbase http://www.wormbase.org. each duplicon contains putative protein-coding genes, most of which are putative chemosensory genes based on wormbase curation. additionally, we found identical copies of mariner-like transposable element cemar flanking the duplicons. multiple sequence alignment of the dna sequences of these transposons indicated that they are nearly identical. in contrast, the regions upstream of the beginning of the first cemar and downstream of the third cemar show no significant similarity. next, we compared dna sequences of the two duplicons, and found that they have % sequence identity, with only six small differences. considering the large size of these duplicons, such high level of similarity is rather surprising. the biggest difference is a bp deletion found in the upstream duplicon. other differences are limited to one to three nucleotides, and notably, all differences are located in either intergenic regions or within introns of current gene models. given that these two duplicons are virtually identical, we expect all gene models contained in each of these duplicons to be identical. to our surprise, based on the current wormbase annotation, only of the pairs are identical, suggesting that many of these gene models are defective, and thus need to be improved. we have thus attempted to improve these gene models using existing est sequence data and their similarity to known paralogous genes that are curated by wormbase curators. all updated gene models have been submitted to wormbase. each gene pair is shown in order of appearance from 5' to 3'. the "method of repair" column suggests a way to fix those gene models that have different peptide sequence, given the lack of supporting information for better improvement. longest: suggests taking the longest peptide sequence as the correct model. evidence: suggests considering as correct the member of the pair that has been reported as "person evidence" in wormbase. genewise: suggest a paralog gene that can be used to predict a gene structure in the region within each member of the pair. each gene is characterized in terms of est data support as ns if no intron is supported, ps if at least one intron is not supported, and fs if all introns are supported by est data. *: see text. experimental characterization of the largest duplicons in c. elegans the high level of similarity between these two largest duplicons in the c. elegans genome prompted us to hypothesize that they were generated very recently and thus not all wild-type strains carry them. to test this hypothesis, we genotyped of the n strains, received from the researchers in the c. elegans community, for the presence of these duplicons. for each strain, we examined the presence of the junction between the two largest duplicons and the presence of the bp unique sequence. results showed that the samples processed can be divided into two groups: a group of samples that don't carry the largest duplicon pair, and a group of samples that carry the largest duplicon pair. in addition, this tandem duplication was not found in the c. elegans cb strain, an isolate from a hawaiian island. thus, we conclude from these results that the n worms, which all originated from a common ancestor first established in sydney brenner's lab in 1960s, had become polymorphic in this genomic region in laboratory. this conclusion is further supported by two interesting patterns that emerged from our genotyping assays. first, of the cgc strains don't have the largest duplicons. this includes the strain from donald riddle, who originally set up the cgc. the only one "cgc n strain" that carries the largest duplicons is thus likely not a real cgc but was in fact obtained from an alternative source. second, all strains that were obtained from robert horvitz's lab and from the labs that obtained their n strain directly or indirectly from the horvitz lab contain the largest duplicons. we have also tested the existence of the junction in the cosmid f56a which was created and used in the c. elegans genome sequencing project. pcr results clearly showed the presence of the duplication junction in the cosmid f56a, suggesting that this pair of duplicons also exist in the c. elegans strain used for the c. elegans genome sequencing project. together, these observations support our hypothesis that this large tandem duplication arose as a result of a recent event, after the n strain was established as a laboratory strain in the early 1970s. tandem segmental duplications and transposons the presence of nearly identical cemar transposons flanking the largest duplicons suggests a possible role of these transposons in the duplication event. the fact that these duplicons are found in tandem and in a head-to-tail orientation, together with the close to 100% transposon dna identity suggests that this segmental duplication occurred by an unequal crossing over event facilitated by the presence of the cemar transposons. the expected outcome of an unequal recombination event is two types of chromosomes: one with the duplicated region and one with a deletion of the same region. unlike duplication, deletion of genes could lead to a reduced evolutionary fitness and loss of the strain. in order to examine whether this mechanism accounts for other observed tandem duplications, we selected all duplications in the c. elegans genome that are larger than bp that show more than 90% identity at the dna level and examined their correlation to the distribution of transposable elements. altogether pairs of tandem duplicons, including the largest tandem duplicons described above, were examined and only five were found to be associated with neighboring transposons, suggesting that transposable elements may play a role in the formation of some, but not all, tandem segmental duplications. this association is not significantly different from random. in addition, for all cases associated with transposons, except the largest duplicons, transposons are found in the neighborhood of one duplicon but not perfectly flanked by transposons at edges. alternatively, it is possible that most of the transposable elements have moved away from the tandem duplication regions after the duplication event. interestingly, among all tandem duplications, larger duplicon pairs tend to be arranged in a head-to-tail orientation, while smaller ones are arranged in a tail-to-tail orientation. large tandem duplication polymorphism creates a new gene a detailed examination of the junction between the two largest duplicons revealed that there is a gene flanking this junction that resides on both duplicons. this gene contains a glutathione s-transferase n-terminal domain and the gene model is fully supported by est data. this est data was generated by yuji kohara, who generated the est library using a c. elegans strain that contains the largest segmental duplication, based on our genotyping result. exons in f56a derived from exons in f15e and y45g12c.. thus, this large segmental duplication leads to the creation of a novel c. elegans gene through an exon shuffling mechanism. the function of this putative new gene is being examined. discussion and  in this project we applied orthocluster, our newly developed method for a gene-oriented detection and analysis of segmental duplications within the c. elegans genome. the versatility of this program allowed us to identify both perfect and imperfect segmental duplications, as well as to conclude that most of the identified duplicons are intrachromosomal and relatively small, consistent with previous observations. the largest pair of duplicons that we identified is localized in tandem on chromosome v and contains genes. our detailed analysis revealed that these duplicons are nearly identical, suggesting a very recent duplication event. this hypothesis is further supported by the following observations. first, these two duplicons are flanked by nearly identical cemar transposons, which may have caused a recent unequal crossing over event. previous studies in c. elegans have shown that transposable elements can cause tandem duplications. a recent study revealed that the cemar transposons may be active in the c. elegans genome, which suggests that this segmental duplication was preceded by a transposition event of the cemar element. second, this large segmental duplication is strain-specific. among n strains genotyped, only have the duplication. since all of these n strains were originated from a common ancestor strain, the large tandem segmental duplication might have occurred once after the establishment of n as a laboratory c. elegans wild-type strain in 1960s. this ancestor strain was originally obtained from mushroom compost near bristol, england, and was given to sydney brenner by ellsworth dougherty in the spring of. from the bristol strain, sydney brenner isolated a hermaphrodite and its progeny was used for establishing a line of hermaphrodites and a line of males. these were the founder stocks of the n strains. most likely, after the large segmental duplication was established, it was then propagated to other labs in the c. elegans community. this idea is consistent with the emerging patterns of the genotyping results–many duplication-carrying strains were obtained from labs that are related. similarly, the strains that do not carry this large tandem duplication were obtained directly or indirectly from cgc. additionally, the largest duplicon pair does not exist in the wild c. elegans isolate, the hawaiian strain. the expression and function of these pairs of genes is largely unknown. since many of these genes are putative chemosensory genes, chemotaxis experiments can be used to evaluated the impact of this duplication. the six differences could lie in regulatory elements and thus impact gene expression. an unexpected result is that a new gene was created through exon shuffling as a byproduct of this large segmental duplication. the presence of this gene might be beneficial for the organism and thus helped to maintain these duplicons. the function of this new gene and its potential role in stabilizing the segmental duplication will be examined and reported separately. an unsettled puzzle is the bp unique sequence, which is found only in the downstream largest duplicon in the current c. elegans genome release. in all strains that carry the duplication, the bp unique sequence is found in both duplicons. interestingly, the sequence of the strain available at wormbase shows that this bp sequence is found only in one of the duplicons–the downstream duplicon. further examination of the genomic region harboring this putative deletion in the upstream duplicon shows that it is repetitive, containing several copies of a single complex repeat type. the difference between these two types of strains could be explained by strain-specific deletion in the strain used for the c. elegans genome sequencing project. the possibility that the bp sequence is an assembly error has not been ruled out. recent studies have proven that large genomic differences exist between the laboratory n c. elegans strain and the hawaiian c. elegans strain, in addition to many snps discovered previously. for example, maydan and colleagues discovered a ~2% gene variation between n c. elegans strain and the cb hawaiian c. elegans strain using array comparative genome hybridization array. they uncovered significant variations, including deletions and copy-number differences. more recently, projects using illumina solexa sequencing methods revealed extensive differences even between different c. elegans laboratory strains at the base-pair resolution. our study reveals for the first time that different laboratory n strains can acquire and accumulate large-scale differences. our discovery stresses the importance of taking into account variations in different laboratory strains when solving inconsistencies in results from different labs. our results, together with recent results using acgh or solexa sequencing methods, have thus clearly established that different n strains contain extensive differences in their genomic sequences. for robust research and for effective communication between different research groups, we recommend that labs should regularly start fresh from frozen c. elegans aliquot and should acquire n worms directly from cgc instead of from neighboring labs. more importantly, we recommend that each lab should keep a detailed record of the history of the n worms used. furthermore, the n strain containing this large segmental duplication that is used in over one third of all c. elegans labs, should also be maintained and highlighted in cgc as a reference. additionally, since the current c. elegans genome carries the largest duplicons while the current cgc n strain does not, the cgc n strain, which is widely used in c. elegans labs, should be fully sequenced, assembled, analyzed, and compared with the current wormbase genome. 
over the last years since the original publication in the c. elegans genome has been scrutinized and the last gaps were filled in november which present a unique opportunity for examining genome-wide segmental duplications. here, we performed analysis of the c. elegans genome in search for segmental duplications using a new tool–orthocluster–we have recently developed. in fact, only strains carry this large segmental duplication, suggesting a very recent duplication event in the c. elegans genome. the largest pair of duplicons, kb in length located on the left arm of chromosome v, was further characterized. they are nearly identical at the dna level and each duplicon contains putative protein coding genes. genotyping of wild-type strains obtained from different labs in the c. elegans community revealed that not all strains contain this duplication.
 the nematode caenorhabditis elegans was the first multicellular organism to have its genome fully sequenced. over the last years since the original publication in the c. elegans genome has been scrutinized and the last gaps were filled in november which present a unique opportunity for examining genome-wide segmental duplications.  here, we performed analysis of the c. elegans genome in search for segmental duplications using a new tool–orthocluster–we have recently developed. we detected duplicated segments–duplicons–ranging in size from bp to kb. the largest pair of duplicons, kb in length located on the left arm of chromosome v, was further characterized. they are nearly identical at the dna level and each duplicon contains putative protein coding genes. genotyping of wild-type strains obtained from different labs in the c. elegans community revealed that not all strains contain this duplication. in fact, only strains carry this large segmental duplication, suggesting a very recent duplication event in the c. elegans genome.  this report represents the first demonstration that the c. elegans laboratory wild-type n strains has acquired large-scale differences. 