- Open Access
Identification, characterization and comparative genomics of chimpanzee endogenous retroviruses
© Polavarapu et al.; BioMed Central Ltd. 2006
- Received: 29 March 2006
- Accepted: 25 May 2006
- Published: 28 June 2006
Retrotransposons, the most abundant and widespread class of eukaryotic transposable elements, are believed to play a significant role in mutation and disease and to have contributed significantly to the evolution of genome structure and function. The recent sequencing of the chimpanzee genome is providing an unprecedented opportunity to study the functional significance of these elements in two closely related primate species and to better evaluate their role in primate evolution.
We report here that the chimpanzee genome contains at least 42 separate families of endogenous retroviruses, nine of which were not previously identified. All but two (CERV 1/PTERV1 and CERV 2) of the 42 families of chimpanzee endogenous retroviruses were found to have orthologs in humans. Molecular analysis (PCR and Southern hybridization) of CERV 2 elements demonstrates that this family is present in chimpanzee, bonobo, gorilla and old-world monkeys but absent in human, orangutan and new-world monkeys. A survey of endogenous retroviral positional variation between chimpanzees and humans determined that approximately 7% of all chimpanzee-human INDEL variation is associated with endogenous retroviral sequences.
Nine families of chimpanzee endogenous retroviruses have been transpositionally active since chimpanzees and humans diverged from a common ancestor. Seven of these transpositionally active families have orthologs in humans, one of which has also been transpositionally active in humans since the human-chimpanzee divergence about six million years ago. Comparative analyses of orthologous regions of the human and chimpanzee genomes have revealed that a significant portion of INDEL variation between chimpanzees and humans is attributable to endogenous retroviruses and may be of evolutionary significance.
- Long Terminal Repeat
- Additional Data File
- Long Terminal Repeat Retrotransposon
- Chimpanzee Genome
- Reverse Transcriptase Sequence
Retrotransposons are the most abundant and widespread class of eukaryotic transposable elements. For example, >30% of the mouse genome , >50% of the maize genome  and >60% of the human genome  are composed of retrotransposon sequences. This group of transposable elements is made up of short interspersed nuclear elements (SINEs), long interspersed nuclear elements (LINEs) and long terminal repeat (LTR) retrotransposons/endogenous retroviruses, all of which replicate via reverse transcription of an RNA intermediate . The biological significance of retrotransposons ranges from their contribution to mutation (for example, ) and disease (for example, [6, 7]) to their role in gene and genome evolution (for example, [8–10]).
The recent sequencing of the chimpanzee genome has provided an unprecedented opportunity to not only compare the full complement of retrotransposons in two closely related primate species but to gain insight into the role these elements may have played in human evolution. We have combined the use of an LTR retrotransposon search algorithm, LTR_STRUC , with a systematic series of iterative TBLASTN searches to identify the endogenous retroviruses present in the Ensembl chimpanzee database . Since LTR_STRUC searches for LTR retrotransposons/endogenous retroviruses based on structure rather than homology, elements are often identified that go undetected in traditional BLAST searches (for example, ).
LTR_STRUC is designed specifically to find full-length LTR retrotransposons/endogenous retroviruses, that is, ones having two LTRs and a pair of target site duplications (TSDs) . Thus, we complemented our search by using reverse transcriptase (RT) sequences from LTR_STRUC-identified elements as query sequences in an iterative series of TBLASTN searches. This allowed us to identify structurally aberrant elements not directly detected by LTR_STRUC. Finally, a series TBLASTN searches were carried out using, as query sequences, previously reported human RT sequences for which orthologues were not identified by our previous two searches.
The chimpanzee genome contains at least 42 families of endogenous retroviruses
Using the procedure described above, we identified a total of 425 full-length chimpanzee endogenous retroviruses. This is certainly an underestimate of the number of endogenous retroviruses in the chimpanzee genome because we consciously excluded any sequences that could not be unambiguously identified as an endogenous retrovirus. The majority of these endogenous retroviruses (395/425 or 93%) were identified directly by LTR_STRUC or by homology to LTR_STRUC-identified elements.
Previously characterized RT sequences from a variety of species used for comparison in phylogenies
Name of retrovirus
Rabbit endogenous retrovirus
Golden hamster intracisternal A-particle H18
Simian SRV-1 type D retrovirus
Mouse mammary tumor virus
Rous sarcoma virus
Human foamy virus
Feline foamy virus
Human immunodeficiency virus 1
Bovine leukemia virus
Baboon endogenous virus
Feline leukemia virus
Moloney murine leukemia virus
Porcine endogenous retrovirus
Mus dunni endogenous virus
Gibbon ape leukemia virus
Koala type C endogenous virus
Representative sequences from each family of chimpanzee endogenous retroviruses
Family name: chimp family (orthologous human family)
Location on chromosome (chromosome no: position)
5' and 3' LTR % identity
Length of 5'/3' LTRs (bp)
Target site repeats
Element length (bp)
CERV 3 (HERVS71)
CERV 4 (HERV3)
CERV 5 (HERV15)
CERV 6 (HERV 1*)
CERV 7 (Harlequin)
CERV 8 (HERVE)
CERV 9 (HERV 2*)
CERV 10 (HERVH48)
CERV 11 (HERV-H)
CERV 12 (HERVFH19)
CERV 13 (PRIMA4)
CERV 14 (HERV 5*)
CERV 15 (HERV-P)
CERV 16 (HERV-17)
CERV 17 (HERV30)
CERV 18 (HERV 9)
Arg, Lys, Pro
CERV 19 (PABL_B)
CERV 20 (HERVP71A)
CERV 21 (HERV 4*)
CERV 22 (HERV 6*)
CERV 23 (HERV 7*)
CERV 24 (HERV 10*)
CERV 25 (HERV 11*)
CERV 26 (HERV 12*)
CERV 27 (HERVI)
CERV 28 (HERVIP10F)
CERV 29 (HERVG25)
CERV 30 (HERVK10)
CERV 31 (HERVK14)
CERV 32 (HERVK14C)
CERV 33 (HERVK(C4))
CERV 34 (HERVK9)
CERV 35 (HERVK13)
CERV 36 (HERVK11D)
CERV 37 (HERVK11)
CERV 38 (HERVK3)
CERV 39 (HERVK22)
CERV 40 (HERV S)
CERV 41 (HERV16)
CERV 42 (HERVL)
Consistent with the consensus nomenclature used for human endogenous retroviruses (HERV) , we here refer to the chimpanzee endogenous retroviral families by the acronym CERV (for chimp endogenous retrovirus). Distinct families are indicated by number (for example, CERV 1 to CERV 42). In the single instance where the CERV acronym refers to a previously named element/family, we include the pre-existing nomenclature as well (CERV 1/PTERV1). In those cases where a CERV family has an orthologue in humans, the name of the orthologous HERV family is given in parentheses (for example, CERV 3(HERVS71)).
Endogenous retroviral families of the chimpanzee genome
LTR retrotransposons and retroviruses are grouped into three major classes . Class I contains elements related to the gammaretroviruses (for example, Moloney murine leukemia virus (MuLV; accession no. AF033811), gibbon ape leukemia virus (GALV; accession no. M26927) and feline leukemia virus (FeLV; accession no. M18247)). Class II elements are related to betaretroviruses (for example, mouse mammary tumor virus (MMTV; accession no. NC_001503), rabbit endogenous retrovirus (RERV; accession no. AF480925)). Class III elements are distantly related to spumaviruses (for example, human foamy virus (HFV; accession no. Y07725), feline foamy virus (FeFV; accession no. AJ223851)). Of the 42 chimpanzee families identified in our study, 29 belong to class I, 10 to class II and 3 to class III (Figure 1).
While there is a precedence for classifying human endogenous retroviruses into families based on their tRNA primer-binding sites (for example, HERV K (lysine tRNA binding site)) , we find that such groupings do not accurately reflect the phylogenetic groupings of CERVs. For example, some members of the CERV 21 family have a proline tRNA binding site whereas other members of this same family utilize threonine tRNA as a primer. Conversely, phylogenetically divergent CERV families may share the same tRNA binding site (for example, members of the CERV 27 (HERV I) and CERV 30 (HERVK10) have lysine tRNA binding sites) (Table 2). Thus, primer binding sites appear to be an evolutionarily labile feature and thus not a reliable indicator of phylogenetic relationships among chimpanzee endogenous retroviruses. A similar conclusion has been drawn for LTR retrotransposons in Caenorhabditis elegans .
Full-length CERVs are typically between 7,000 and 10,000 base-pairs (bp) in length. Consistent with what has been reported for LTR retrotransposons/endogenous retroviruses in other species [17–19], CERV target site duplications (TSDs) range in size from 4 to 6 bp in length. With the exception of a few mutated copies, CERVs have the same canonical dinucleotides terminating the LTRs as have been reported for LTR retrotransposons/endogenous retroviruses in other species (TG/CA) [17–19]. CERV LTRs are typically 400 to 600 bp in length, although some LTRs are variant in size due to INDELs. For example, the LTRs of a member of the CERV 4 (HERV 3) family are 1,591 bp in length due to the insertion of an Alu element at some point in the evolutionary history of this lineage. The following is a more detailed characterization of the three classes of CERVs.
Class I: families 1 to 29
The CERV families 1 through 29 group with the class I retroviruses (Figure 1; Additional data file 2). The average size of full-length class I CERVs is 8,443 bp. These elements range in size from 2,268 to 13,135 bp in length. Much of this variation is due to INDELs associated with non-functional elements. The average size of LTRs associated with full-length class I CERV elements is 544 bp (range 195 to 1,591 bp). Class I CERV elements display considerable variation in their tRNA binding sites, even within families (Table 2). The most frequently used tRNA primer for class I CERV families (28%) is proline tRNA.
Because the LTRs of endogenous retroviruses are synthesized from a single template during reverse transcription, they are identical at the DNA sequence level upon integration . Using the primate pseudogene nucleotide substitution rate of 0.16% divergence per million years [20, 21], the relative integration time or age of CERV elements can be estimated from the level of sequence divergence existing between the element's 5' and 3' LTRs. The Jukes-Cantor model was used to correct for the presence of multiple mutations at the same site, back mutations and convergent substitutions . Although caution must be taken when using LTR divergence to estimate the age of individual elements because of confounding processes such as recombination and conversion, (for example, [23, 24]), the method is able to provide useful age estimates, at least to a first approximation (for example, ). Using this method, we estimate that the age of full-length class I CERV elements ranges from 0.8 to 82.9 million years (MY).
Full length elements representing at least three class I CERV families, CERV 1/PTERV1, CERV 2 and CERV 3 (HERVS71) have been recently transpositionally active as indicated by the presence of an unoccupied pre-integration site at the corresponding locus in humans. Inconsistent with this view is the fact that one of the chimpanzee-specific CERV 3 (HERVS71) insertions located on the Y chromosome displays an atypically high level of LTR-LTR sequence divergence (9%), indicative of it having inserted about 28 million years ago (MYA). However, the clear absence of this insert, both in the sequenced human genome (pre-integration site in tact) and in the genomes of several randomly sampled ethnically and geographically diverse humans (data not shown), indicates that this element most likely inserted after the chimpanzee-human divergence (about 6 MYA) and that the exceptionally high level of LTR-LTR sequence divergence is due to an inter-element recombination or conversion event [23, 24]. All other class I CERV elements are much older and have not been reproductively active since well before chimpanzees and humans diverged from a common ancestor.
Class II: families 30 to 39
The CERV families 30 through 39 group with class II retroviruses (Figure 1; Additional data file 3). All Class II CERV families have orthologues in humans. The average size of full-length class II CERVs is 7,670 bp. This class of CERV elements range in size from 2,564 to 12,803 bp in length. As with class I elements, much of the size variation among class II elements is due to INDELs associated with non-functional elements. The average size of LTRs associated with full-length class II CERV elements is 544 bp (range 243 to 1,139 bp). Consistent with the fact that class II CERVs are orthologous to human HERV K elements, all but one family of class II CERV elements have lysine tRNA binding sites. The sole exception, CERV 39 (HERV K22), has a methionine tRNA binding site (Table 2). It has recently been proposed that HERV K22 be renamed HERV M to reflect its distinct primer binding site . Unlike the other class II CERV elements, the CERV 39 (HERV K22) family clusters closely with the betaretrovirus (MMTV, SRV-1) (Figure 1; Additional data file 3).
CERV 36 (HERV K11D) is the second oldest family of class II CERV elements. We estimate that CERV 36 (HERV K11D) elements have not been transpositionally active for about 25 MY. We found that several members of the CERV 36 (HERV K11D) display the same deletion within the gag-pol regions of their genomes, suggesting that this deletion occurred prior to their transposition. Thus, this subfamily of CERV 36 (HERV K11D) elements comprised, at one time, non-autonomous elements and acquired essential replicative functions in trans.
Class III: families 40 to 42
The CERV families 40 (HERV S), 41 (HERV 16) and 42 (HERV L) group with class III retroviruses and are related to spumaviruses  (Figure 1; Additional data file 4). All class III CERV families have orthologues in humans. The average size of full-length class III CERVs is 6,758 bp. This class of CERV elements range in size from 2,980 to 13,271 bp in length. Again, much of this size variation is due to INDELs in this uniformly non-functional class of CERV elements. The average size of LTRs associated with full-length class III CERV elements is 446 bp (range 254 to 831 bp). CERV 40 elements have a serine tRNA binding site while CERV 42 elements have a leucine tRNA binding site (Table 2). Due to sequence ambiguities, we were unable to determine the tRNA binding site for CERV 41 elements (Table 2). Class III CERV elements are the oldest group of endogenous retroviruses in the chimpanzee genome. The estimated age of these elements ranges from 30 to 145 MY.
Two CERV families have no human orthologues
With more than 100 members, CERV 1/PTERV1 is one of the most abundant families of endogenous retroviruses in the chimpanzee genome. CERV 1/PTERV1 elements range in size from 5 to 8.8 kb in length, are bordered by inverted terminal repeats (TG and CA) and are characterized by 4 bp TSDs (Table 2). The LTRs of the CERV 1/PTERV1 family of elements range from 379 to 414 bp in length. CERV 1/PTERV1 elements have a proline tRNA primer binding site (Table 2). LTR sequence identity among CERV 1/PTERV1 elements ranges from 97.1% to 99.7%.
We found that a number of CERV 1/PTERV1 elements with high (>99%) LTR-LTR sequence identity have large (1 to 2 kb) deletions within the RT encoding region of their genomes. It is likely that these are non-autonomous elements that have inserted relatively recently by acquiring RT functions in trans, presumably from autonomous CERV 1/PTERV1 elements. Instances of recently inserted LTR retrotransposons/endogenous retroviruses lacking RT-encoding functions have previously been detected in the genomes of humans  and other species of both plants [18, 33] and animals (for example, ).
This is the second family of chimpanzee endogenous retroviruses with no orthologue in the human genome. We identified ten solo LTRs and eight full-length copies of CERV 2 elements in the chimpanzee genome although, because of incomplete sequencing, we could identify the LTRs for only four of the eight full-length elements. CERV 2 elements are typically larger than CERV 1/PTERV1 elements, ranging in size from 8 to 10 kb in length. CERV 2 elements are bordered by inverted terminal repeats (TG and CA), have 4 bp TSDs (Table 2) and a proline tRNA primer binding site (Table 2). The LTRs of the CERV 2 family of elements range from 486 to 497 bp in length. Based on their LTR sequence identity (98.07% to 99.6%), we estimate that full-length CERV 2 elements were transpositionally active in the chimpanzee genome between 1.3 and 6.0 MYA. Thus, the majority of CERV 2 elements were biologically active after the divergence of chimpanzees and humans from a common ancestor.
Endogenous retroviral positional variation between chimpanzees and humans
Comparative analyses of orthologous regions of the human and chimpanzee genomes has revealed a number of instances where relatively large spans of sequence present in one species are not present in the other [34, 35]. It has been proposed that these gaps or INDELs may be of evolutionary significance (for example, ). To determine the proportion of these gaps (human gaps are sequences present in chimpanzees but absent in humans; chimpanzee gaps are sequences present in humans but absent in chimpanzees) involving endogenous retroviruses, we utilized the human gap and chimpanzee gap datasets available at the UCSC Genome Bioinformatics web site  that were generated by aligning the chimpanzee genome with the human genome build HG16 [37, 38]. These datasets include gaps of sizes ranging from 80 bp to 12.0 kb. Gap sequences from the datasets >5,000 bp (1,330 sequences), the typical length of full-length LTR retrotransposons/retroviruses, were blasted against the NCBI non-redundant protein database  using BlastX . BLAST was used to identify species-specific full-length endogenous retroviral insertions in humans and chimpanzees. A total of 41 chimpanzee gap sequences and 31 human gap sequences were found to have significant similarity (e < 0.01) with retroviral sequences.
The presence of an endogenous retroviral sequence in chimpanzees that is missing at an orthologous genomic position in humans can be due to a novel insertion in chimpanzees or deletion of the element in humans. Similarly, the presence of an endogenous retroviral sequence in humans that is missing at an orthologous genomic position in chimpanzees can be due to novel insertion in humans or due to deletion of the element in chimpanzees. Because endogenous retroviruses do not precisely excise from insertion sites , it is possible to distinguish between these two possibilities. If a region in humans orthologous to the position of an endogenous retroviral insertion in chimpanzees contains a remnant of endogenous retroviral sequence (for example, fragmented element or solo LTR), we score the gap as a deletion in humans. If the orthologous region contains no remnant of the endogenous retrovirus but the pre-integration genomic sequence can be clearly identified, we score the gap as an insertion in chimpanzees. The same rules apply for the analogous dataset of the endogenous retroviral sequences present in humans but absent in chimpanzees.
Endogenous retrovirus INDEL sequences (>5000 bp) present in chimpanzees but absent in humans
CERV 18 (HERV9)
CERV 32 (HERVK14C)
2 (1 I + 1 D)
CERV 30 (HERVK10)
CERV 42 (HERVL)
CERV 17 (HERV30)
CERV 3 (HERVS71)
CERV 28 (HERVIP10F)
CERV 7 (Harlequin)
CERV 34 (HERVK9)
Endogenous retrovirus INDEL sequences (>5000 bp) present in humans but absent in chimpanzees
9 (8 I +1 D)
CERV 30 (HERVK10)
CERV 11 (HERVH)
CERV 18 (HERV9)
CERV 16 (HERV17)
CERV 34 (HERVK9)
CERV 37 (HERVK11)
CERV 35 (HERVK13)
CERV 3 (HERVS71)
CERV 42 (HERVL)
CERV 7 (Harlequin)
CERV 28 (HERVIP10F)
CERV 19 (PABL_B)
Since solo LTRs and fragmented endogenous retroviral copies are typically ten to a hundred times more abundant than full-length elements in humans [14, 41], we extended our survey to determine the extent to which INDEL variation between humans and chimpanzees is associated with solo LTRs and/or fragmented endogenous retroviral sequences. We again utilized datasets (human gaps and chimp gaps) available at the UCSC Genome Bioinformatics web site . We used 'Repeat Masker' (AF Smit and P Green, unpublished data) to identify all interspersed repeats, that is, all transposable elements present in the datasets, and to subsequently extract endogenous retroviral homologous sequences.
Gap sequences were divided into two types: 'Mosaic type' gap sequences are defined as those composed of more than one category of interspersed repeats (for example, endogenous retrovirus inserted within a LINE element); and 'Single type' gap sequences are defined as those composed of only sequences homologous to endogenous retroviruses. Single type gap sequences were further divided into two categories: category 1 comprises those gap sequences composed entirely of an endogenous retroviral sequence; and category 2 comprises those gap sequences composed of endogenous retrovirus and non-interspersed repeat sequences. The above categorizations are useful in distinguishing gaps due to deletions in one species from the gaps due to insertions in the other species. Instances of mosaic type and single type category 2 gaps are deletions in that species while the gaps that belong to single type category 1 are either deletions in that species or insertions in the other species. Because endogenous retroviruses do not excise precisely  from the insertion sites, these later gaps can be further characterized as the result of insertions or deletions.
Endogenous retrovirus INDELs (80 bp to 12.0 kb) in humans and chimpanzees
Gaps with interspersed repeats
Gaps containing endogenous retrovirus sequences
Category 2 gaps
Category 1 gaps
85 (25 full ln + 60 solo LTRs)
12 (2 full ln + 10 solo LTRs)
CERV 30 (HERVK10)
78 (8 full ln + 70 solo LTRs)
43 (1 full ln + 42 solo LTRs)
CERV 3 (HERVS71)
1 (1 full ln)
CERV 11 (HERVH/LTR7)
CERV 37 (HERVK11/MER11C)
CERV 34 (HERVK9/MER9)
CERV 18 (HERV9)
CERV 35 (HERVK13/LTR13)
A total of 1,608 chimpanzee gap sequences contained endogenous retroviral sequences (758 mosaic type and 850 single type (557 category 1+ 293 category 2). As stated above, 758 mosaic types and 293 single type category 2 are deletions in chimpanzees. Of the 557 that belonged to single type category 1, 79 are new insertions in humans while the remaining 478 are deletions in chimpanzees (Table 5).
Consistent with the copy number of CERV 30 (HERVK10) species-specific full-length insertions (Table 4), the insertions of solo LTRs from this family were higher in humans (78) than in chimpanzees (43) since they diverged from the common ancestor (Table 5). Apart from CERV 30 (HERVK10) insertions in both the genomes, five other endogenous retroviral families continued to be active in chimpanzees, resulting in solo LTR or fragmented insertions while only one new insertion from MER31B occurred in humans since they diverged from the common ancestor (Table 5).
Once considered parasitic sequences of little or no adaptive significance [42, 43], transposable elements are today generally recognized as significant contributors to human regulatory (for example, ) and structural (for example, ) gene evolution. The recent sequencing of the chimpanzee genome is providing a unique opportunity to conduct comparative genomic analyses of primate transposable elements.
Retrotransposons are the most abundant class of transposable elements. For example, retrotransposons comprise at least 60% of the human genome  and results presented here and elsewhere  suggest that the number of endogenous retroviruses in chimpanzees may be higher than in humans. In this paper, we present the results of the first systematic search for endogenous retroviruses in the chimpanzee genome. We have identified 425 full-length endogenous retroviruses in the chimpanzee genome that can be grouped into 42 independent lineages or families (Figure 1). All but two families of chimpanzee endogenous retroviruses were found to have orthologues in humans (Table 2). In contrast, we have found that all known families of human endogenous retroviruses have orthologues in chimpanzees. The two CERV families without orthologues in the human genome display a patchy distribution among primates (Figure 5) and our data suggest that at least some members of both families have been transpositionally active in the chimpanzee lineage after the divergence of chimpanzees and humans from a common ancestor.
We estimate that chimpanzee endogenous retroviruses range in age from about 0.8 to 145 MY. Nine families of chimpanzee endogenous retroviruses have been transpositionally active in chimpanzees while two families of human endogenous retroviruses have been transpositionally active in humans since they diverged from a common ancestor (Table 5). Thus, while some families of endogenous retroviruses have not been transpositionally active within the primate lineage, others have and continued to be active since chimpanzees and humans diverged from a common ancestor.
It has been estimated that 3.5% of the sequence differences between chimpanzees and humans is due to INDELs [34, 35] and that this INDEL variation may be of particular evolutionary significance . We have determined that approximately 7% of all chimpanzee-human INDEL variation is attributable to the presence or absence of endogenous retroviral sequences. The potential biological/evolutionary significance of this variation is currently under investigation.
Emerging evidence indicates that retrotransposons have played a significant role in gene and genome evolution (for example, [8–10]). The identification, characterization and comparative genomics of chimpanzee endogenous retroviruses presented in this report should not only help contribute to our understanding of the functional significance of these elements in chimpanzees but to a better appreciation of the role of endogenous retroviruses in primate evolution.
Initial dataset scanning
The 2.73 GB chimpanzee genomic sequence  obtained from the Ensembl database was scanned for the presence of endogenous retroviruses using a structure based program, LTR_STRUC (LTR retrotransposon structure program) . LTR_STRUC scans the genomic sequence for the presence of similar regions of length typical for LTRs (LTR pairs) and within the expected size of a full-length LTR retrotransposon/endogenous retrovirus. If the putative LTRs are found, the program then searches for additional retrotransposon features, such as primer binding sites (PBSs), poly-purine tracts (PPTs), target site repeats (TSRs), and assigns a reliability score to the hit based on the presence or absence of each of these features. A total of 2,056 hits were reported as the putative endogenous retroviruses in the chimpanzee genomic sequence, of which only 97 encoded RT.
Sequence analysis for identifying the RT coding sequence
The 97 putative elements for which the presence of RT sequence was reported by LTR_STRUC were subjected to sequence analysis to identify the RT coding region. Briefly, sequence analysis involves aligning the amino acid sequence of the three reading frames reported by the search algorithm (the strand encoding RT protein is determined based on the presence of PBSs and PPTs) with previously annotated retroviral proteins using ClustalX  followed by manually checking of the three ORFs for the RT conserved motifs previously described [46, 47]. From this sequence analysis we were able to identify RT conserved motifs for 25 hits.
Identification of additional elements
The 25 RT sequences obtained from sequence analysis were augmented by conducting exhaustive sequence similarity searches using these sequences as queries against the 2.73 GB chimpanzee genomic sequence  using the TBLASTN program [40, 48] to obtain an extensive set of endogenous retroviruses in the sequenced genome. Around 2,000 RT sequences were obtained by automatically parsing the TBLASTN search results for the hits above a threshold of 70% identity and covering a length of one-third of the query sequence using a perl script. After removing duplicates obtained during automatic parsing, we were left with 1,088 RT sequences.
Identification of full length elements
The 1,088 RT sequences identified in the TBLASTN searches were checked for the presence of LTRs on either side of the RT as a criterion for full-length elements. This was done by examining the DNA sequences 7,000 bp on either side of the RT sequence, aligning them against each other using the program BLAST2SEQ and manually checking the hits for the presence of canonical dinucleotides, target site repeats and other LTR characteristic features. LTRs were identified for 395 of the 1,088 elements that had RT sequences. Thirty elements from previously reported human RT sequences for which orthologues were not identified in the above searches were added to our dataset, resulting in a total of 425 elements.
Multiple sequence alignments and phylogenetic analysis
A multiple alignment was constructed from the DNA sequences of the RT region of 425 full-length elements together with representative members from the three classes of vertebrate retroviruses/LTR retrotransposons (Table 1)  using the program ClustalX . We chose to use DNA sequence in making the multiple alignment and building the phylogenetic tree rather than amino acid sequence because of the presence of numerous frame shift mutations and stop codons in the elements. The multiple alignment was manually adjusted in the MEGA alignment browser . A neighbor joining tree was generated from the alignment using MEGA2 with p-distance and pairwise deletions as parameters and bootstrap values were obtained from 1,000 replicates.
Grouping the elements into families
The full-length elements were grouped into families based on the bootstrap values generated in the phylogenetic tree. Phylogenetically well supported clusters with high boot strap values were used to group the elements into families (Figure 1). The most recent element that is still intact is used as the representative element for each family (Table 2).
Identification of the primer binding site
A 100 bp region downstream of the 5' LTR of full-length elements was searched against the chimp tRNA database downloaded from [50, 51] using the program FASTA . The 3' end of tRNA that matched with the reverse complement of the sequence over a stretch of 14 to 22 bp was assigned as a tRNA primer of the element (Table 2).
Evolutionary analysis of CERV 1/PTERV1 and CERV 2 LTR sequences
Mulitple alignment was generated from the LTRs for each family using ClustalX . A neighbor joining tree was generated from the alignment using MEGA3  with Jukes-Cantor model  and pairwise deletions as parameters and bootstrap values were obtained from 1,000 replicates. The age of each subfamily was estimated by calculating the average of pairwise distances between all sequences in that subfamily and using the primate pseudogene nucleotide substitution rate of 0.16% divergence per million years [20, 21].
Molecular analysis: PCR and Southern hybridization
Primate DNA samples were purchased form Coriell cell repository (catalog no. PRP00001 and PRP00003) (Coriell institute for medical research, Camden, NJ, USA).
Polymerase chain reaction
Primers were designed in the conserved RT, gag, LTR and env regions of the CERV 2 element using the program PRIMER3 . PCR amplification conditions were as follows: initial denaturation for 4.5 minutes at 94°C, 30 cycles of 30 s denaturation at 94°C, 30 s annealing at 57°C, 40 s elongation at 72°C and a final 1-cycle extension of 7 minutes at 72°C. The PCR products were then visualized on 1% (w/v) agarose gel.
Primate DNA was restriction enzyme digested, transferred to a nylon membrane and hybridized as described previously . Nested PCR amplified products in RT and gag regions of CERV 2 elements were radioactively labeled and used as probes for hybridization. The same amount of DNA was loaded in all the lanes, with DNA samples in the order: human (Homo sapiens), chimpanzee (Pan troglodytes), orangutan (Pongo pygmaeus), crab eating monkey (Macaca fascicularis), rhesus monkey (Macaca mulatto), red-chested mustached tamari (Saguinus labiatus), ring-tailed lemur (Lemur catta), pig tailed monkey (Macaca nemestrina), black headed spider monkey (Ateles geoffroyi), wooly monkey (Lagothrix lagotricha).
The following additional data are available with the online version of this paper. Additional data file 1 contains a description of the nine CERV families for which human orthologues were not identified previously. Additional data file 2 is a RT-based neighbor-joining tree for class I chimpanzee endogenous retroviruses. The distances (corrected 'p' using Jukes-Cantor model) appear next to each of the branches. RT sequences from species other than chimp, listed in Table 1, are included for comparison. The outgroup is class III element HFV (human foamy virus; see Table 1 and Additional data file 4). Additional data file 3 is a RT-based neighbor-joining tree for class II chimpanzee endogenous retroviruses. The distances (corrected 'p' using Jukes-Cantor model) appear next to each of the branches. RT sequences from species other than chimp, listed in Table 1, are included for comparison. The outgroup is class I element from CERV 1/PTERV1 family (see Table 2 and Additional data file 2). Additional data file 4 is a RT-based neighbor-joining tree for class III chimpanzee endogenous retroviruses. The distances (corrected 'p' using Jukes-Cantor model) appear next to each of the branches. RT sequences from species other than chimp, listed in Table 1, are included for comparison. The outgroup is class I element BaEV (baboon endogenous retrovirus; see Table 1 and Additional data file 2). Additional data file 5 is an unrooted neighbour joining phylogenetic tree built from solo LTRs and 5' and 3' LTRs of full-length elements of the CERV1/PTERV1 family. Bootstrap values are shown on the tree. The average pairwise distances (corrected 'p' using Jukes-Cantor model) for each subfamily and the estimated ages are shown. Additional data file 6 is an unrooted neighbour joining phylogenetic tree built from solo LTRs of the CERV 1/PTERV1 family. Bootstrap values are shown in the tree. The average pairwise distances (corrected 'p' using Jukes-Cantor model) for each subfamily and the estimated ages are shown.
We thank Lilya Matyunina for help with Southern hybridization. This research was supported by a grant from the Georgia Institute of Technology Research Foundation.
- Waterston RH, Lindblad-Toh K, Birney E, Rogers J, Abril JF, Agarwal P, Agarwala R, Ainscough R, Alexandersson M, An P, et al: Initial sequencing and comparative analysis of the mouse genome. Nature. 2002, 420: 520-562. 10.1038/nature01262.PubMedView ArticleGoogle Scholar
- SanMiguel P, Tikhonov A, Jin YK, Motchoulskaia N, Zakharov D, Melake-Berhan A, Springer PS, Edwards KJ, Lee M, Avramova Z, et al: Nested retrotransposons in the intergenic regions of the maize genome. Science. 1996, 274: 765-768. 10.1126/science.274.5288.765.PubMedView ArticleGoogle Scholar
- Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, FitzHugh W, et al: Initial sequencing and analysis of the human genome. Nature. 2001, 409: 860-921. 10.1038/35057062.PubMedView ArticleGoogle Scholar
- Boeke JD, Stoye JP: Retrotransposons, endogenous retroviruses, and the evolution of retroelements. Retroviruses. Edited by: Coffin JM, Hughes SH, Varmus H. 1997, Plainview, NY: Cold Spring Harbor Laboratory Press, 343-435.Google Scholar
- Green MM: Mobile DNA elements and spontaneous gene mutation. Eukaryotic Transposable Elements as Mutagenic Agents. Edited by: Lambert E, McDonald JF, Weinstein LB. 1988, Cold Spring Harbor, NY: Cold Spring Harbor Laboratory, 41-50.Google Scholar
- Kazazian HH: Mobile elements and disease. Curr Opin Genet Dev. 1998, 8: 343-350. 10.1016/S0959-437X(98)80092-0.PubMedView ArticleGoogle Scholar
- Deininger PL, Batzer MA: Alu repeats and human disease. Mol Genet Metab. 1999, 67: 183-193. 10.1006/mgme.1999.2864.PubMedView ArticleGoogle Scholar
- McDonald JF: Evolution and consequences of transposable elements. Curr Opin Genet Dev. 1993, 3: 855-864. 10.1016/0959-437X(93)90005-A.PubMedView ArticleGoogle Scholar
- Britten RJ: DNA sequence insertion and evolutionary variation in gene regulation. Proc Natl Acad Sci USA. 1996, 93: 9374-9377. 10.1073/pnas.93.18.9374.PubMedPubMed CentralView ArticleGoogle Scholar
- Brosius J: RNAs from all categories generate retrosequences that may be exapted as novel genes or regulatory elements. Gene. 1999, 238: 115-134. 10.1016/S0378-1119(99)00227-9.PubMedView ArticleGoogle Scholar
- McCarthy EM, McDonald JF: LTR_STRUC: a novel search and identification program for LTR retrotransposons. Bioinformatics. 2003, 19: 362-367. 10.1093/bioinformatics/btf878.PubMedView ArticleGoogle Scholar
- Chimpanzee Genome Browser. [http://www.ensembl.org/Pan_troglodytes/]
- Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG: The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 1997, 25: 4876-4882. 10.1093/nar/25.24.4876.PubMedPubMed CentralView ArticleGoogle Scholar
- Polavarapu N, Bowen NJ, McDonald JF: Newly identified families of Human Endogenous Retroviruses (HERVs). J Virol. 2006, 80: 4640-4642. 10.1128/JVI.80.9.4640-4642.2006.PubMedPubMed CentralView ArticleGoogle Scholar
- Smit AF: Interspersed repeats and other mementos of transposable elements in mammalian genomes. Curr Opin Genet Dev. 1999, 9: 657-663. 10.1016/S0959-437X(99)00031-3.PubMedView ArticleGoogle Scholar
- Ganko EW, Fielman KT, McDonald JF: Evolutionary history of Cer elements and their impact on the C. elegans genome. Genome Res. 2001, 11: 2066-2074. 10.1101/gr.196201.PubMedPubMed CentralView ArticleGoogle Scholar
- Bowen NJ, McDonald JF: Genomic analysis of Caenorhabditis elegans reveals ancient families of retroviral-like elements. Genome Res. 1999, 9: 924-935. 10.1101/gr.9.10.924.PubMedView ArticleGoogle Scholar
- McCarthy EM, Liu J, Lizhi G, McDonald JF: Long terminal repeat retrotransposons of Oryza sativa. Genome Biol. 2002, 3: RESEARCH0053-10.1186/gb-2002-3-10-research0053.PubMedPubMed CentralView ArticleGoogle Scholar
- McCarthy EM, McDonald JF: Long terminal repeat retrotransposons of Mus musculus. Genome Biol. 2004, 5: R14-10.1186/gb-2004-5-3-r14.PubMedPubMed CentralView ArticleGoogle Scholar
- Costas J, Naveira H: Evolutionary history of the human endogenous retrovirus family ERV9. Mol Biol Evol. 2000, 17: 320-330.PubMedView ArticleGoogle Scholar
- Kapitonov V, Jurka J: The age of Alu subfamilies. J Mol Evol. 1996, 42: 59-65. 10.1007/BF00163212.PubMedView ArticleGoogle Scholar
- Jukes TH, Cantor CR: Evolution of Protein Molecules. 1969, New York: Academic PressView ArticleGoogle Scholar
- Hughes JF, Coffin JM: Human endogenous retroviral elements as indicators of ectopic recombination events in the primate genome. Genetics. 2005, 171: 1183-1194. 10.1534/genetics.105.043976.PubMedPubMed CentralView ArticleGoogle Scholar
- Johnson WE, Coffin JM: Constructing primate phylogenies from ancient retrovirus sequences. Proc Natl Acad Sci USA. 1999, 96: 10254-10260. 10.1073/pnas.96.18.10254.PubMedPubMed CentralView ArticleGoogle Scholar
- Bowen NJ, McDonald JF: Drosophila euchromatic LTR retrotransposons are much younger than the host species in which they reside. Genome Res. 2001, 11: 1527-1540. 10.1101/gr.164201.PubMedPubMed CentralView ArticleGoogle Scholar
- Lavie L, Medstrand P, Schempp W, Meese E, Mayer J: Human endogenous retrovirus family HERV-K(HML-5): status, evolution, and reconstruction of an ancient betaretrovirus in the human genome. J Virol. 2004, 78: 8788-8798. 10.1128/JVI.78.16.8788-8798.2004.PubMedPubMed CentralView ArticleGoogle Scholar
- Barbulescu M, Turner G, Seaman MI, Deinard AS, Kidd KK, Lenz J: Many human endogenous retrovirus K (HERV-K) proviruses are unique to humans. Curr Biol. 1999, 9: 861-868. 10.1016/S0960-9822(99)80390-X.PubMedView ArticleGoogle Scholar
- Medstrand P, Mager DL: Human-specific integrations of the HERV-K endogenous retrovirus family. J Virol. 1998, 72: 9782-9787.PubMedPubMed CentralGoogle Scholar
- Turner G, Barbulescu M, Su M, Jensen-Seaman MI, Kidd KK, Lenz J: Insertional polymorphisms of full-length endogenous retroviruses in humans. Curr Biol. 2001, 11: 1531-1535. 10.1016/S0960-9822(01)00455-9.PubMedView ArticleGoogle Scholar
- Yohn CT, Jiang Z, McGrath SD, Hayden KE, Khaitovich P, Johnson ME, Eichler MY, McPherson JD, Zhao S, Paabo S, Eichler EE: Lineage-specific expansions of retroviral insertions within the genomes of African great apes but not humans and orangutans. PLoS Biol. 2005, 3: e110-10.1371/journal.pbio.0030110.PubMedPubMed CentralView ArticleGoogle Scholar
- Belshaw R, Pereira V, Katzourakis A, Talbot G, Paces J, Burt A, Tristem M: Long-term reinfection of the human genome by endogenous retroviruses. Proc Natl Acad Sci USA. 2004, 101: 4894-4899. 10.1073/pnas.0307800101.PubMedPubMed CentralView ArticleGoogle Scholar
- Smit AF: Identification of a new, abundant superfamily of mammalian LTR-transposons. Nucleic Acids Res. 1993, 21: 1863-1872.PubMedPubMed CentralView ArticleGoogle Scholar
- Jiang N, Bao Z, Temnykh S, Cheng Z, Jiang J, Wing RA, McCouch SR, Wessler SR: Dasheng: a recently amplified nonautonomous long terminal repeat element that is a major component of pericentromeric regions in rice. Genetics. 2002, 161: 1293-1305.PubMedPubMed CentralGoogle Scholar
- Mikkelsen T, Hillier LW, Eichler EE, Zody MC, David JB, Yang S, Enard W, Hellmann I, Lindblad-Toh K, Altheide TK, et al: Initial sequence of the chimpanzee genome and comparison with the human genome. Nature. 2005, 437: 69-87. 10.1038/nature04072.View ArticleGoogle Scholar
- Britten RJ: Divergence between samples of chimpanzee and human DNA sequences is 5%, counting indels. Proc Natl Acad Sci USA . 2002, 99: 13633-13635. 10.1073/pnas.172510699.PubMedPubMed CentralView ArticleGoogle Scholar
- UCSC Genome Bioinformatics. [http://genome.ucsc.edu]
- Karolchik D, Baertsch R, Diekhans M, Furey TS, Hinrichs A, Lu YT, Roskin KM, Schwartz M, Sugnet CW, Thomas DJ, et al: The UCSC Genome Browser Database. Nucleic Acids Res. 2003, 31: 51-54. 10.1093/nar/gkg129.PubMedPubMed CentralView ArticleGoogle Scholar
- Karolchik D, Hinrichs AS, Furey TS, Roskin KM, Sugnet CW, Haussler D, Kent WJ: The UCSC Table Browser data retrieval tool. Nucleic Acids Res. 2004, 32 (Database issue): D493-496. 10.1093/nar/gkh103.PubMedPubMed CentralView ArticleGoogle Scholar
- Entrez Protein Database. [http://0-www.ncbi.nlm.nih.gov.brum.beds.ac.uk/entrez/query.fcgi?db=Protein]
- Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ: Basic local alignment search tool. J Mol Biol. 1990, 215: 403-410. 10.1006/jmbi.1990.9999.PubMedView ArticleGoogle Scholar
- Stoye JP: Endogenous retroviruses: still active after all these years?. Curr Biol. 2001, 11: R914-916. 10.1016/S0960-9822(01)00553-X.PubMedView ArticleGoogle Scholar
- Orgel LE, Crick FH: Selfish DNA: the ultimate parasite. Nature. 1980, 284: 604-607. 10.1038/284604a0.PubMedView ArticleGoogle Scholar
- Doolittle WF, Sapienza C: Selfish genes, the phenotype paradigm and genome evolution. Nature. 1980, 284: 601-603. 10.1038/284601a0.PubMedView ArticleGoogle Scholar
- Jordan IK, Rogozin IB, Glazko GV, Koonin EV: Origin of a substantial fraction of human regulatory sequences from transposable elements. Trends Genet. 2003, 19: 68-72. 10.1016/S0168-9525(02)00006-9.PubMedView ArticleGoogle Scholar
- Nekrutenko A, Li WH: Transposable elements are found in a large number of human protein-coding genes. Trends Genet. 2001, 17: 619-621. 10.1016/S0168-9525(01)02445-3.PubMedView ArticleGoogle Scholar
- Xiong Y, Eickbush TH: Origin and evolution of retroelements based upon their reverse transcriptase sequences. EMBO J. 1990, 9: 3353-3362.PubMedPubMed CentralGoogle Scholar
- Xiong Y, Eickbush TH: Similarity of reverse transcriptase-like sequences of viruses, transposable elements, and mitochondrial introns. Mol Biol Evol. 1988, 5: 675-690.PubMedGoogle Scholar
- Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997, 25: 3389-3402. 10.1093/nar/25.17.3389.PubMedPubMed CentralView ArticleGoogle Scholar
- Kumar S, Tamura K, Nei M: MEGA3: Integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief Bioinform. 2004, 5: 150-163. 10.1093/bib/5.2.150.PubMedView ArticleGoogle Scholar
- Lowe TM, Eddy SR: tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 1997, 25: 955-964. 10.1093/nar/25.5.955.PubMedPubMed CentralView ArticleGoogle Scholar
- Chimpanzee tRNA Database. [http://lowelab.ucsc.edu/GtRNAdb/Ptrog/]
- Pearson WR, Lipman DJ: Improved tools for biological sequence comparison. Proc Natl Acad Sci USA. 1988, 85: 2444-2448. 10.1073/pnas.85.8.2444.PubMedPubMed CentralView ArticleGoogle Scholar
- Rozen S, Skaletsky H: Primer3 on the WWW for general users and for biologist programmers. Methods Mol Biol. 2000, 132: 365-386.PubMedGoogle Scholar
- Daly TM, Rafii A, Martin RA, Zehnbauer BA: Novel polymorphism in the FMR1 gene resulting in a "pseudodeletion" of FMR1 in a commonly used fragile X assay. J Mol Diagn. 2000, 2: 128-131.PubMedPubMed CentralView ArticleGoogle Scholar
This article is published under license to BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.