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Corresponding author: Hiroshi Hori, Division of Biological Sciences, Graduate School of Science, Nagoya University, Nagoya 464-8602, Japan., hori{at}bio.nagoya-u.ac.jp (E-mail)
Communicating editor: M. J. SIMMONS
| ABSTRACT |
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Tol2 is a transposable element of the terminal-inverted-repeat class, residing in the genome of the medaka fish Oryzias latipes. The genus Oryzias contains more than 10 species for which phylogenetic relationships have previously been estimated. To infer the history of Tol2 in this genus we performed genomic Southern blots and PCR analyses of 10 of the species. It was revealed that Tol2 occurs in 2 of the 10 species (O. curvinotus and O. latipes) and that the length and the restriction map structure of Tol2 are identical in the two cases. Further, sequencing analysis revealed an extremely low level of divergence compared with that in a nuclear gene. These results suggest recent incorporation of Tol2 into one or both of the two species, implying horizontal transfer of Tol2 from one species to the other or into them both from a common source.
TRANSPOSABLE elements are repetitive sequences capable of moving from one chromosomal location to another. Several transposable elements, or transposable element families, are known to be distributed across species, genera, or even higher taxa. When the phylogeny of a transposable element is incongruent with the phylogeny of its host species, horizontal transfer of the element between species is often suggested as the explanation (for reviews, see ![]()
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Well-known examples of horizontal transfer are represented by the P element (![]()
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We here report high nucleotide sequence similarity of a transposable element in two fish species, the most likely explanation for which is horizontal transfer. Tol2 is a terminal-inverted-repeat transposable element residing in the genome of the medaka fish Oryzias latipes (![]()
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| MATERIALS AND METHODS |
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Medaka fish:
This species (O. latipes) inhabits East Asia, including China, Korea, and Japan, and demonstrates geographical variation. According to data on isozyme frequencies, there are four regional populations: [1] Northern Japan, [2] Southern Japan, [3] Eastern Korea, and [4] China and Western Korea (![]()
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Other species:
Nine species of the genus Oryzias were obtained from the World Medaka Aquarium of the Nagoya City Higashiyama Zoological Garden. The nine species, in addition to O. latipes, are listed in Fig 1 with the present consensus on their phylogenetic relationships and their original collection sites. Detailed phylogenetic trees are available in ![]()
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Analysis of genomic DNA:
Southern blotting and subsequent hybridization experiments were performed as described by ![]()
For the 10 species of the genus Oryzias, a 4-µg aliquot of genomic DNA was used for each gel slot. For the species outside the genus, 20 µg was used. The implications of this difference are described in the DISCUSSION.
Hybridization probes:
The Tol2 element was first identified as a DNA fragment inserted into the tyrosinase gene of an albino mutant fish (![]()
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Other molecular techniques:
PCR, cloning, and sequencing were conducted as previously described (![]()
| RESULTS |
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Distribution of Tol2 among species:
Fig 3 illustrates autodiagrams of Southern blots to determine the presence of Tol2 in the 10 species of the genus Oryzias and other species outside the genus. Genomic DNAs were digested with BglII, which has a single cutting site in the Tol2-tyr sequence. In Fig 3A where probe Tyr-Bg (part of the medaka fish tyrosinase gene) was used, one or two hybridization signals were observed for all the fishes of the genus Oryzias, the swordtail fish, and zebrafish. In Fig 3B for which the hybridization conditions were the same as those for Fig 3A and probe L(0)R(4.7) (the entire Tol2 element) was used, strong hybridization signals, consisting of multiple bands, were observed for O. curvinotus and O. latipes. No signals were observed with the other 8 species of the genus Oryzias. For confirmation, an additional four fish samples for each of the 8 Oryzias species were examined by the same method as for Fig 3B and no bands due to Tol2 were observed (data not shown).
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Genomic DNAs from swordtail fish and humans also lacked bands due to the Tol2 element. However, in the lanes for zebrafish and chicken, multiple weak signals were observed.
Distribution and variation of Tol2 in O. curvinotus and O. latipes:
Fig 4 shows an autodiagram of a Southern blot to determine the presence of Tol2 in an O. curvinotus sample and 12 samples of O. latipes. All 13 samples exhibited multiple bands hybridizing to probe L(0)Pv(0.5). Although this probe contains the left terminal inverted repeat (17 bp), it does not yield a signal for the right terminal inverted repeat (19 bp), as confirmed in a preliminary experiment using a Tol2 clone as the target (data not shown). The numbers of bands observed are shown in Fig 4. In the O. latipes samples, they are distributed in the range between 10 and 25, with an average of 16. This range is not very different from that observed for a single local population (11 to 30, with an average of 19; ![]()
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It has previously been shown, using various parts of Tol2 as probes, that Tol2 copies are highly homogeneous in their restriction map structures in fish samples from a single local population (![]()
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Sequencing analysis of Tol2 copies:
We have previously sequenced five Tol2 copies randomly chosen from genomic libraries of O. latipes and found that they are identical over the entire 4.7-kb element (![]()
Sequencing analysis of the tyrosinase gene region:
The tyrosinase gene is a single-copy gene located on one of the chromosomes (![]()
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Distribution of Tol2 copies in the genome:
O. latipes, O. curvinotus, and O. luzonensis have the same chromosome number, 2n = 48, and their karyotypes are similar to one another (![]()
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) was then crossed to a female of O. luzonensis (G2
), and 10 fish of their progeny (G3-1 to -10), together with the parents, were analyzed in a Southern blot for transmission patterns of Tol2 copies between generations 2 and 3. Fig 9 shows the autodiagram obtained. The male parent (G2
) contains 15 copies, which were transmitted to the progeny without novel insertion events, because new bands were not present in the progeny. The copy numbers in the progeny (G3) were between 5 and 10, with an average of 6.7. The 15 bands carried by the male parent were numbered from the top to the bottom as shown in the photograph. Fisher's exact probability tests were conducted for all possible combinations of 2 bands out of the 15, and a significant association (P < 0.01) was shown only for the combination of bands no. 1 and no. 9. Therefore, the copies represented by these 2 bands appeared to be closely linked to each other on the same chromosome, and the other copies appeared to be transmitted independently of one another. Thus, the Tol2 copies are dispersed in the genome.
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| DISCUSSION |
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Distribution of Tol2:
Tol2 was first found in the medaka fish O. latipes (![]()
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Weak hybridization signals with Tol2 were observed for zebrafish and chicken. We conducted further Southern blot analysis of zebrafish using probes L(0)Pv(0.5), Pv(0.5)Pv(3.1), and Ps(2.4)Ps(4.3) under the same conditions as for Fig 3B. Similar signals were observed for probe Pv(0.5)Pv(3.1) but not for the other two probes (data not shown). It has been reported (![]()
Hybridization signals were not observed for the swordtail fish and human samples. Tol2 thus seems to be absent in these species or else might be too divergent to be detected with Southern blotting. It should be noted that the detectability in the hybridization analysis decreases as the genome size of the target species increases. To overcome this problem, we used 20 µg of genomic DNA for species outside the genus Oryzias, five times as much as for those within the genus (4 µg). The sizes of haploid genomes are 0.680.85 x 109 bp for the medaka fish (![]()
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Phylogeny of fish species:
The relationship among O. latipes, O. curvinotus, and O. luzonensis has been studied from various aspects. ![]()
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Molecular phylogenetic studies including the three species have also been completed. ![]()
Possibility of horizontal transfer:
No deletion copies of Tol2 were detected, while heterogeneity in size due to the presence of internally deleted, smaller copies is common in the hAT family members (![]()
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An alternative explanation of the sequence homogeneity of Tol2 is to postulate a strong selective constraint on the Tol2 sequence. However, this is difficult to reconcile with the fact that Tol2 contains introns with a total length of 1992 bp (![]()
A new transposition event was not observed in the last generation of crosses (Fig 7 and Fig 8). Similarly, Southern blot analysis of an inbred strain did not give evidence for transposition in the last few generations (![]()
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Time and place of horizontal transfer:
One of the possibilities about the time of occurrence of the horizontal transfer is that it took place after the collection of the original samples because the materials used in the present study have been maintained as fish stocks for 310 years. In other words, it might be that there was transfer of Tol2 among the laboratory stocks. This possibility, however, is negligible because the two species have been maintained in different places: O. curvinotus has been in the Nagoya City Zoological Garden and the O. latipes stocks have been in our lab at the University of Tokyo. The two species have not undergone encounter with each other before DNA preparation. Thus, it is more likely that the horizontal transfer occurred in nature.
As to where in nature horizontal transfer occurred, overlapping distribution areas of the two species may be a likely supposition. O. latipes is distributed in a wide range in East Asia, from Japan to China. O. curvinotus inhabits Southern China and Vietnam. It was examined whether the habitats of these two species overlap, with samples collected at various locations in China, but none was observed (![]()
Concerning mechanisms involved in the horizontal transfer and also the direction of the horizontal transfer, our results so far obtained provide no suggestions.
Generality of horizontal transfer:
Horizontal transfer may be considered general at least for mariner/Tc1 family elements because of (1) their presence in diverse organisms (![]()
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| ACKNOWLEDGMENTS |
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We are grateful to H. Hashikawa, M. Sato, and S. Susaki for providing the fish samples. We also thank K. Naruse, T. Iwamatsu, and D. L. Hartl for helpful discussions. This work was partly supported by grant nos. 09680672 and 10216025 to A.K. and nos. 08640786 and 09554053 to H.H. from the Ministry of Education, Science, Sports and Culture of Japan and also by the Takeda Science Foundation to A.K.
Manuscript received October 4, 1999; Accepted for publication January 25, 2000.
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