Vege and Mar: Two Novel hAT MITE Families from Drosophila willistoni
Department of Ecology and Evolutionary Biology, The University of Arizona, Tucson, Arizona|, http://www.100md.com
Abstract|, http://www.100md.com
Two novel families of miniature inverted repeat transposable elements (MITEs), Vege and Mar, are described from Drosophila willistoni. Based on their structures, both element families are hypothesized to belong to the hAT superfamily of transposable elements. Both elements have perfect, inverted terminal repeats and 8-bp target site duplications and were found to have inserted within fixed copies of nonautonomous P elements. Vege is present in all studied D. willistoni populations and appears to have a relatively low copy number. Mar was identified in only a single D. willistoni population, and its copy number is presently unknown. Although MITEs occupy relatively large proportions of the genomes of a broad range of organisms, this may be their first unambiguous identification in any species of the genus Drosophila.|, http://www.100md.com
Key Words: Drosophila willistoni • transposons • MITEs • hAT elements
Introduction6j[[*s, 百拇医药
Although a large array of transposable elements (TEs) have been described from Drosophila genomes, miniature inverted repeat transposable elements (MITEs) are rare or absent in most species of this genus that have been examined, including Drosophila melanogaster. In contrast, MITEs make up large proportions of many other host genomes and are present across a broad taxonomic range of organisms.6j[[*s, 百拇医药
MITEs were first discovered about 10 years ago in maize and have subsequently been identified in many animals and plants, including Homo sapiens, Caenorhabditis elegans, fish and Xenopus species, Arabidopsis thaliana, and a variety of other plants . Within Diptera, MITEs appear to be abundant in the mosquito species Anopheles gambiae, Aedes aegypti, and Culex pipiens. Ten MITE families have been reported to date in Anopheles gambiae ;) and one family reported in Anopheles stephensi . Twelve families have been described in Aedes aegypti and three families described in Culex pipiens .
MITEs are very short nonautonomous elements that are often present in high copy number (>1,000) per family per genome. These elements can occupy significant portions of their host genomes, and can insert close to structural genes, potentially influencing gene action. MITEs have terminal inverted repeats (TIRs) or subterminal inverted repeats (IRs) and are typically smaller than 1,000 bp. They have no coding potential, are AT-rich, and may have a stable secondary structure.'y.#*, http://www.100md.com
Different families of MITEs have common structural features but little if any sequence similarity. Until recently, it was not obvious to which class of transposons (I or II) they should be assigned nor how they attained such high copy numbers. It is now apparent that MITEs are nonautonomous DNA (class II) elements that originated from a subset of autonomous DNA transposons . MITEs are distinct from internally deleted class II elements in that they have no internal homology to their derivative transposons. Instead, they seem to have a propensity for including nonhomologous sequences in their internal regions. Investigations within plants and other organisms have demonstrated that MITEs are active and may be transposed by their parent DNA transposons . MITEs derived from the same superfamily of class II elements are generally similar in size.
In the first systematic attempt at classification , MITEs have been grouped into superfamilies based on their association with superfamilies of transposases. Possible superfamilies of transposase (and MITEs) include Tc1/mariner, PIF/Harbinger, piggyBac/TTAA, and hAT./a6x[rx, 百拇医药
The hAT superfamily of autonomous transposons is so named because members all share homology and transposition characteristics with hobo from Drosophila, Ac from Maize, and Tam3 from the snapdragon . They are class II DNA transposable elements, which transpose with a cut and paste mechanism, and are found in a wide variety of eukaryotic taxa, with many described from plants, nematodes, and fungi. They typically have short TIRs and duplicate 8 bp of host target site DNA (TSD) upon transposition./a6x[rx, 百拇医药
Within insects, a number of hAT superfamily members have been identified. Members of this superfamily include Homer, and the nonautonomous element HLE, from the tephritid fly Batrocera tryoni , Hermes from the housefly Musca domestica , Hermit from the blowfly Lucilia cuprina , and the ancestral element hopper from the tephritid Batrocera dorsalis . Partial hAT-like sequences have also been derived from the Australian bushfly Musca vetustissima ) and the Lepidopterans Heliothis virescens and Helicoverpa zea ).
Within the genus Drosophila, the hobo element is the only hAT element thus far identified. performed a Southern hybridization screen of hobo elements from 134 taxa within the genus Drosophila and found hobo elements restricted to the melanogaster and montium subgroups of the melanogaster species group. Only D. melanogaster and its sibling species, D. simulans and D. mauritiana, contained potentially complete hobo elements. This observation provides additional evidence for a recent origin of hobo within the melanogaster species group, perhaps by horizontal transfer, akin to the recent acquisition of P elements by D. melanogaster. This scenario is also supported by the presence of both H (hobo+) and E (hobo-) strains in D. melanogaster and D. simulans (. Furthermore, the hob element appears to have transferred horizontally within the species group . Using squash and dot blotting, , detected hobo signal from isolated lines of D. willistoni. Although our repeated attempts to isolate hobo from this species have been unsuccessful (unpublished data), recent studies in another laboratory suggest the presence of multiple copies of this TE family (V. Valente, V. Valiati, and C. C. Klein, personal communication). Evidence that hobo-like sequences are an ancient component of Drosophila genomes is provided by the presence of divergent hobo-homologous sequences in the genomes of D. melanogaster E strains and of coding genes with hobo homology in the D. melanogaster genome.
Within plants, and indeed within many other organisms, class II TEs are seldom complete, the vast majority being internally deleted forms created by imprecise transposition . These still have the ability to transpose, as long as an alternative source of transposase, provided by autonomous elements in trans, is available. Many of these, such as naturally deleted forms of hobo and the P element (O'Hare and Rubin 1983), do not qualify as MITEs, because they do possess internal homology to their derivative transposons.$1, 百拇医药
We describe here two new MITE families, Vege and Mar, from Drosophila willistoni, that are associated with the hAT super family of TEs. These may be the first true MITEs identified from Drosophila.$1, 百拇医药
Materials and Methods$1, 百拇医药
PCR and Sequence Analysis$1, 百拇医药
Vege and Mar sequences were discovered incidentally during routine PCR screening for P element deletion derivatives. Briefly, genomic DNA was extracted from 30 adult flies using standard protocols . P elements were amplified from genomic DNA using Taq DNA polymerase (Invitrogen) under standard conditions with the MIR primer (5' CATAAGGTGGTCCCGTCG) homologous to nucleotides 14 to 31 and 2877 to 2894 of the P element TIR . MIR is specific to M-type and canonical P elements. After size fractionation on agarose gels, bands smaller than the full-sized potentially autonomous canonical P element (2907 bp) were gel extracted (Gibco-BRL concert band purification kit) and directly ligated into pCRtopo2.1 using the TopoTA cloning kit (Invitrogen). Potential positives were color selected and PCR amplified from colonies directly using M13 F/R vector primers. Sequences were generated from positive PCR products on an ABI 3100 at the GATC core facility (ARL, University of Arizona). During alignments of all P element deletion derivatives, it was noted that some clones contained regions that were not homologous to P elements in either the forward or reverse orientation. Subsequent GenBank searches using BLAST tools revealed that these sequences had little homology to any banked sequences.
Southern Hybridizationstus, 百拇医药
Two micrograms of pooled genomic DNA from approximately 30 flies was digested to completion using PvuII (Gibco-BRL) a null cutter within the two sequenced MITEs. Restricted DNA was elecrophoresed and transferred to nylon membrane (Amersham) using a modified capillary transfer protocol . Radioactive probes were generated from a PCR-derived template amplified from the reference sequences using Radprime DNA labeling (Gibco-BRL). Membranes were hybridized overnight before being washed at high stringency (final wash 65°C, 0.1XSSC, 20 min). Membranes were exposed to Xomat-AR film (Kodak), and scored manually.tus, 百拇医药
Results and Discussiontus, 百拇医药
The initial Vege sequence was found inserted between nu 62 and 63 of a P element (GenBank accession number .1). Sequence analysis demonstrates that this MITE duplicates 8 bp of host DNA (canonical P nu 55 to 62) as a TSD and has 12 bp of perfect TIRs. The complete copy isolated has 33% GC with a size of 884 bp. The sequence has been deposited in GenBank under accession number . TBLASTn searches indicates that Vege has no coding capacity, and BLASTx searches found no significant homology between Vege and GenBank sequences. The orientation of the MITE is ascribed by placing the newly duplicated 8-bp target site at the 3'-end of the element (as assigned by comparing this locus with an orthologous locus lacking the insert). The copy of Vege at this locus is fixed across all populations of D. willistoni sampled (A. J. Holyoake, J. K. Hall, and M. G. Kidwell, unpublished data). Interestingly, this locus is polymorphic for an additional insertion of a mini-me TE at nucleotide position 58 of Vege. By using both inverse PCR and Southern blotting analysis, it was demonstrated that Vege is present in six to seven copies in the D. willistoni haploid genome. Additionally, Vege hybridization patterns are found in D. nebulosa and D. tropicalis, sister species to D. willistoni, but not in D. melanogaster. Internal PCR of the Vege element indicated that it is extremely heterogeneous both in size and sequence, suggesting that these copy numbers may be gross underestimates.
Mar is similar to Vege in that it has 8-bp TSDs and 11-bp perfect TIRs. Mar has 38% GC over 610 bp. The Mar sequence is deposited in GenBank under accession number . Mar is also inserted within a nonautonomous P element and has been detected in a single population of D. willistoni. The Mar insertion is between nu 58 and 59 of the canonical P element, with the TSD of nu 50 to 58. Interestingly, the Mar insertion included a loss of 7 bp of P element sequence immediately adjacent to the 3' insertion site (but after the TSD). TBLASTn and BLASTx analysis indicate that like Vege, Mar has neither coding capacity nor significant sequence homology to known published sequences.h, 百拇医药
We hypothesize that both Vege and Mar are MITE members of the hAT superfamily of TEs. Although autonomous dipteran hAT members (and the nonautonomous HLE element) have different length TIRs and sequence-specific TSDs, there are distinct areas of homology between them ( and ). These homologous nucleotides frequently extend to other, more diverged, members of the hAT superfamily from vertebrates and plants .
fig.ommittedo, 百拇医药
Table 1 TIR Sequences of MITEs Derived from hAT Superfamily TEs and the P Element.o, 百拇医药
fig.ommittedo, 百拇医药
Table 2 TSDs of Dipteran hAT Superfamily Transposons and Derived MITEs in Comparison with That of the P Element.o, 百拇医药
MITE sequences that have been previously linked to the hAT superfamily of TEs have been linked on the basis of a combination of the TIR and TSD similarities. hAT-like MITEs have previously been found in the rice and Arabidopsis genomes , Anopheles gambiae Xenopus , and humans . Each of these (with the exception of Vision) share 8-bp TSDs and have TIRs sharing the consensus sequence specific to hAT elements . Other Dipteran MITEs such as TA-IV-Ag from Anopheles gambiae share similarities with hAT MITE TIRs, but they have a dinucleotide (TA) TSD placing them as pogo-like MITEs in the Tc1/Mariner superfamily .o, 百拇医药
The apparent rarity of Drosophila MITEs may well be related to the relative paucity of class II transposon sources. In contrast to some other taxa, relatively few class II TEs are present within the genus Drosophila . In the euchromatic portion of the D. melanogaster genome that has been sequenced, only 10 out of 54 families are identified as class II transposons . Those present in chromosomes 2R, X, and 4 are limited to 1360, BariI, Foldback, HB1, hobo, hopper, pogo and the S element . A shortage of transposase sources may have limited the formation and expansion of MITE-like elements within this and related species.
list Dm-mPogo and SGM-IS as the only known Drosophila MITEs. Dm-mPogo, with dinucleotide (TA) TSDs and perfect 21 bp (or imperfect 25 bp) long TIRs are essentially identical over their length to the sequence of the autonomous pogo element and may actually be considered severely truncated non autonomous versions of these elements . Likewise, SGM-IS sequences have recently been identified as members of the mini-me element family, common among species of the genus Drosophila . Mini-me TEs have one terminal and one subterminal repeat, have no TSDs, and may have hairpin formation at the 5' terminus when single stranded. These and other factors lead the authors to conclude that these elements may be a new group of non-LTR retroposon . It may be, therefore, that there are no previously described true MITEs in the genus Drosophila.:8], 百拇医药
Within the willistoni species group of Sophophora, no hAT TE members are known, although recent studies have indicated the presence of hobo-related elements in this group (V. Valente, V. Valiate, and C. C. Klein personal communication). The presence of hAT-related MITEs and the polytypic insertion pattern of the Mar element suggest that D. willistoni does have hAT elements and that they may have provided a transposase source for the movement of hAT-related MITEs in recent times. Given that hAT elements have been shown to cross-mobilize other hAT sequences in vivo it is plausible that any hAT element present in this species could mobilize Vege and Mar.
Presently, it is not possible to say if Vege and Mar are closely related to any one of the sequenced hAT elements from other species. Vege and the Anopheles gambiae MITE Pegasus share 100% similarity over their overlapping TIRs, However, Pegasus TSDs don't conform well to the Dipteran consensus .+kp, 百拇医药
To conclude, we have described here what may be the first true MITEs from a Drosophila genome. We hypothesize, based on TIR and TSD similarities, that both Vege and Mar belong to a hAT superfamily of MITEs found across a broad taxonomic range of organisms. Although the current absence of hAT autonomous TEs within the willistoni species group of Drosophila is not consistent with this finding, we predict that hAT elements will eventually be found in these species.+kp, 百拇医药
Acknowledgements+kp, 百拇医药
We thank Cédric Feschotte for comments and insights into the identity of these sequences. We are grateful to Vera Valente, Victor Valiate, Chirlei C. Klein, and Zhijian Tu for access to unpublished results. This work was supported by National Science Foundation Grant DEB-9815754 awarded to M.G.K.
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Accepted for publication September 13, 2002.(Andrew J. Holyoake and Margaret G. Kidwell)
Abstract|, http://www.100md.com
Two novel families of miniature inverted repeat transposable elements (MITEs), Vege and Mar, are described from Drosophila willistoni. Based on their structures, both element families are hypothesized to belong to the hAT superfamily of transposable elements. Both elements have perfect, inverted terminal repeats and 8-bp target site duplications and were found to have inserted within fixed copies of nonautonomous P elements. Vege is present in all studied D. willistoni populations and appears to have a relatively low copy number. Mar was identified in only a single D. willistoni population, and its copy number is presently unknown. Although MITEs occupy relatively large proportions of the genomes of a broad range of organisms, this may be their first unambiguous identification in any species of the genus Drosophila.|, http://www.100md.com
Key Words: Drosophila willistoni • transposons • MITEs • hAT elements
Introduction6j[[*s, 百拇医药
Although a large array of transposable elements (TEs) have been described from Drosophila genomes, miniature inverted repeat transposable elements (MITEs) are rare or absent in most species of this genus that have been examined, including Drosophila melanogaster. In contrast, MITEs make up large proportions of many other host genomes and are present across a broad taxonomic range of organisms.6j[[*s, 百拇医药
MITEs were first discovered about 10 years ago in maize and have subsequently been identified in many animals and plants, including Homo sapiens, Caenorhabditis elegans, fish and Xenopus species, Arabidopsis thaliana, and a variety of other plants . Within Diptera, MITEs appear to be abundant in the mosquito species Anopheles gambiae, Aedes aegypti, and Culex pipiens. Ten MITE families have been reported to date in Anopheles gambiae ;) and one family reported in Anopheles stephensi . Twelve families have been described in Aedes aegypti and three families described in Culex pipiens .
MITEs are very short nonautonomous elements that are often present in high copy number (>1,000) per family per genome. These elements can occupy significant portions of their host genomes, and can insert close to structural genes, potentially influencing gene action. MITEs have terminal inverted repeats (TIRs) or subterminal inverted repeats (IRs) and are typically smaller than 1,000 bp. They have no coding potential, are AT-rich, and may have a stable secondary structure.'y.#*, http://www.100md.com
Different families of MITEs have common structural features but little if any sequence similarity. Until recently, it was not obvious to which class of transposons (I or II) they should be assigned nor how they attained such high copy numbers. It is now apparent that MITEs are nonautonomous DNA (class II) elements that originated from a subset of autonomous DNA transposons . MITEs are distinct from internally deleted class II elements in that they have no internal homology to their derivative transposons. Instead, they seem to have a propensity for including nonhomologous sequences in their internal regions. Investigations within plants and other organisms have demonstrated that MITEs are active and may be transposed by their parent DNA transposons . MITEs derived from the same superfamily of class II elements are generally similar in size.
In the first systematic attempt at classification , MITEs have been grouped into superfamilies based on their association with superfamilies of transposases. Possible superfamilies of transposase (and MITEs) include Tc1/mariner, PIF/Harbinger, piggyBac/TTAA, and hAT./a6x[rx, 百拇医药
The hAT superfamily of autonomous transposons is so named because members all share homology and transposition characteristics with hobo from Drosophila, Ac from Maize, and Tam3 from the snapdragon . They are class II DNA transposable elements, which transpose with a cut and paste mechanism, and are found in a wide variety of eukaryotic taxa, with many described from plants, nematodes, and fungi. They typically have short TIRs and duplicate 8 bp of host target site DNA (TSD) upon transposition./a6x[rx, 百拇医药
Within insects, a number of hAT superfamily members have been identified. Members of this superfamily include Homer, and the nonautonomous element HLE, from the tephritid fly Batrocera tryoni , Hermes from the housefly Musca domestica , Hermit from the blowfly Lucilia cuprina , and the ancestral element hopper from the tephritid Batrocera dorsalis . Partial hAT-like sequences have also been derived from the Australian bushfly Musca vetustissima ) and the Lepidopterans Heliothis virescens and Helicoverpa zea ).
Within the genus Drosophila, the hobo element is the only hAT element thus far identified. performed a Southern hybridization screen of hobo elements from 134 taxa within the genus Drosophila and found hobo elements restricted to the melanogaster and montium subgroups of the melanogaster species group. Only D. melanogaster and its sibling species, D. simulans and D. mauritiana, contained potentially complete hobo elements. This observation provides additional evidence for a recent origin of hobo within the melanogaster species group, perhaps by horizontal transfer, akin to the recent acquisition of P elements by D. melanogaster. This scenario is also supported by the presence of both H (hobo+) and E (hobo-) strains in D. melanogaster and D. simulans (. Furthermore, the hob element appears to have transferred horizontally within the species group . Using squash and dot blotting, , detected hobo signal from isolated lines of D. willistoni. Although our repeated attempts to isolate hobo from this species have been unsuccessful (unpublished data), recent studies in another laboratory suggest the presence of multiple copies of this TE family (V. Valente, V. Valiati, and C. C. Klein, personal communication). Evidence that hobo-like sequences are an ancient component of Drosophila genomes is provided by the presence of divergent hobo-homologous sequences in the genomes of D. melanogaster E strains and of coding genes with hobo homology in the D. melanogaster genome.
Within plants, and indeed within many other organisms, class II TEs are seldom complete, the vast majority being internally deleted forms created by imprecise transposition . These still have the ability to transpose, as long as an alternative source of transposase, provided by autonomous elements in trans, is available. Many of these, such as naturally deleted forms of hobo and the P element (O'Hare and Rubin 1983), do not qualify as MITEs, because they do possess internal homology to their derivative transposons.$1, 百拇医药
We describe here two new MITE families, Vege and Mar, from Drosophila willistoni, that are associated with the hAT super family of TEs. These may be the first true MITEs identified from Drosophila.$1, 百拇医药
Materials and Methods$1, 百拇医药
PCR and Sequence Analysis$1, 百拇医药
Vege and Mar sequences were discovered incidentally during routine PCR screening for P element deletion derivatives. Briefly, genomic DNA was extracted from 30 adult flies using standard protocols . P elements were amplified from genomic DNA using Taq DNA polymerase (Invitrogen) under standard conditions with the MIR primer (5' CATAAGGTGGTCCCGTCG) homologous to nucleotides 14 to 31 and 2877 to 2894 of the P element TIR . MIR is specific to M-type and canonical P elements. After size fractionation on agarose gels, bands smaller than the full-sized potentially autonomous canonical P element (2907 bp) were gel extracted (Gibco-BRL concert band purification kit) and directly ligated into pCRtopo2.1 using the TopoTA cloning kit (Invitrogen). Potential positives were color selected and PCR amplified from colonies directly using M13 F/R vector primers. Sequences were generated from positive PCR products on an ABI 3100 at the GATC core facility (ARL, University of Arizona). During alignments of all P element deletion derivatives, it was noted that some clones contained regions that were not homologous to P elements in either the forward or reverse orientation. Subsequent GenBank searches using BLAST tools revealed that these sequences had little homology to any banked sequences.
Southern Hybridizationstus, 百拇医药
Two micrograms of pooled genomic DNA from approximately 30 flies was digested to completion using PvuII (Gibco-BRL) a null cutter within the two sequenced MITEs. Restricted DNA was elecrophoresed and transferred to nylon membrane (Amersham) using a modified capillary transfer protocol . Radioactive probes were generated from a PCR-derived template amplified from the reference sequences using Radprime DNA labeling (Gibco-BRL). Membranes were hybridized overnight before being washed at high stringency (final wash 65°C, 0.1XSSC, 20 min). Membranes were exposed to Xomat-AR film (Kodak), and scored manually.tus, 百拇医药
Results and Discussiontus, 百拇医药
The initial Vege sequence was found inserted between nu 62 and 63 of a P element (GenBank accession number .1). Sequence analysis demonstrates that this MITE duplicates 8 bp of host DNA (canonical P nu 55 to 62) as a TSD and has 12 bp of perfect TIRs. The complete copy isolated has 33% GC with a size of 884 bp. The sequence has been deposited in GenBank under accession number . TBLASTn searches indicates that Vege has no coding capacity, and BLASTx searches found no significant homology between Vege and GenBank sequences. The orientation of the MITE is ascribed by placing the newly duplicated 8-bp target site at the 3'-end of the element (as assigned by comparing this locus with an orthologous locus lacking the insert). The copy of Vege at this locus is fixed across all populations of D. willistoni sampled (A. J. Holyoake, J. K. Hall, and M. G. Kidwell, unpublished data). Interestingly, this locus is polymorphic for an additional insertion of a mini-me TE at nucleotide position 58 of Vege. By using both inverse PCR and Southern blotting analysis, it was demonstrated that Vege is present in six to seven copies in the D. willistoni haploid genome. Additionally, Vege hybridization patterns are found in D. nebulosa and D. tropicalis, sister species to D. willistoni, but not in D. melanogaster. Internal PCR of the Vege element indicated that it is extremely heterogeneous both in size and sequence, suggesting that these copy numbers may be gross underestimates.
Mar is similar to Vege in that it has 8-bp TSDs and 11-bp perfect TIRs. Mar has 38% GC over 610 bp. The Mar sequence is deposited in GenBank under accession number . Mar is also inserted within a nonautonomous P element and has been detected in a single population of D. willistoni. The Mar insertion is between nu 58 and 59 of the canonical P element, with the TSD of nu 50 to 58. Interestingly, the Mar insertion included a loss of 7 bp of P element sequence immediately adjacent to the 3' insertion site (but after the TSD). TBLASTn and BLASTx analysis indicate that like Vege, Mar has neither coding capacity nor significant sequence homology to known published sequences.h, 百拇医药
We hypothesize that both Vege and Mar are MITE members of the hAT superfamily of TEs. Although autonomous dipteran hAT members (and the nonautonomous HLE element) have different length TIRs and sequence-specific TSDs, there are distinct areas of homology between them ( and ). These homologous nucleotides frequently extend to other, more diverged, members of the hAT superfamily from vertebrates and plants .
fig.ommittedo, 百拇医药
Table 1 TIR Sequences of MITEs Derived from hAT Superfamily TEs and the P Element.o, 百拇医药
fig.ommittedo, 百拇医药
Table 2 TSDs of Dipteran hAT Superfamily Transposons and Derived MITEs in Comparison with That of the P Element.o, 百拇医药
MITE sequences that have been previously linked to the hAT superfamily of TEs have been linked on the basis of a combination of the TIR and TSD similarities. hAT-like MITEs have previously been found in the rice and Arabidopsis genomes , Anopheles gambiae Xenopus , and humans . Each of these (with the exception of Vision) share 8-bp TSDs and have TIRs sharing the consensus sequence specific to hAT elements . Other Dipteran MITEs such as TA-IV-Ag from Anopheles gambiae share similarities with hAT MITE TIRs, but they have a dinucleotide (TA) TSD placing them as pogo-like MITEs in the Tc1/Mariner superfamily .o, 百拇医药
The apparent rarity of Drosophila MITEs may well be related to the relative paucity of class II transposon sources. In contrast to some other taxa, relatively few class II TEs are present within the genus Drosophila . In the euchromatic portion of the D. melanogaster genome that has been sequenced, only 10 out of 54 families are identified as class II transposons . Those present in chromosomes 2R, X, and 4 are limited to 1360, BariI, Foldback, HB1, hobo, hopper, pogo and the S element . A shortage of transposase sources may have limited the formation and expansion of MITE-like elements within this and related species.
list Dm-mPogo and SGM-IS as the only known Drosophila MITEs. Dm-mPogo, with dinucleotide (TA) TSDs and perfect 21 bp (or imperfect 25 bp) long TIRs are essentially identical over their length to the sequence of the autonomous pogo element and may actually be considered severely truncated non autonomous versions of these elements . Likewise, SGM-IS sequences have recently been identified as members of the mini-me element family, common among species of the genus Drosophila . Mini-me TEs have one terminal and one subterminal repeat, have no TSDs, and may have hairpin formation at the 5' terminus when single stranded. These and other factors lead the authors to conclude that these elements may be a new group of non-LTR retroposon . It may be, therefore, that there are no previously described true MITEs in the genus Drosophila.:8], 百拇医药
Within the willistoni species group of Sophophora, no hAT TE members are known, although recent studies have indicated the presence of hobo-related elements in this group (V. Valente, V. Valiate, and C. C. Klein personal communication). The presence of hAT-related MITEs and the polytypic insertion pattern of the Mar element suggest that D. willistoni does have hAT elements and that they may have provided a transposase source for the movement of hAT-related MITEs in recent times. Given that hAT elements have been shown to cross-mobilize other hAT sequences in vivo it is plausible that any hAT element present in this species could mobilize Vege and Mar.
Presently, it is not possible to say if Vege and Mar are closely related to any one of the sequenced hAT elements from other species. Vege and the Anopheles gambiae MITE Pegasus share 100% similarity over their overlapping TIRs, However, Pegasus TSDs don't conform well to the Dipteran consensus .+kp, 百拇医药
To conclude, we have described here what may be the first true MITEs from a Drosophila genome. We hypothesize, based on TIR and TSD similarities, that both Vege and Mar belong to a hAT superfamily of MITEs found across a broad taxonomic range of organisms. Although the current absence of hAT autonomous TEs within the willistoni species group of Drosophila is not consistent with this finding, we predict that hAT elements will eventually be found in these species.+kp, 百拇医药
Acknowledgements+kp, 百拇医药
We thank Cédric Feschotte for comments and insights into the identity of these sequences. We are grateful to Vera Valente, Victor Valiate, Chirlei C. Klein, and Zhijian Tu for access to unpublished results. This work was supported by National Science Foundation Grant DEB-9815754 awarded to M.G.K.
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Accepted for publication September 13, 2002.(Andrew J. Holyoake and Margaret G. Kidwell)