Distribution of complete and defective copies of the Tol1 transposable element in natural populations of the medaka fish Oryzias latipes

Koga, Akihiko; Wakamatsu, Yuko; Sakaizumi, Mitsuru; Hamaguchi, Satoshi; Shimada, Atsuko

doi:10.1266/ggs.84.345

Cited by 8 publications

(5 citation statements)

References 37 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Approximately 200 Tol1 copies are present in the diploid medaka fish genome, the majority of which are nonautonomous. Moreover, individual fish that do not contain an autonomous copy can often be found (Koga et al 2009). …”

Section: Transposition Activity Of Tol1mentioning

confidence: 99%

“…For this reason, Tol2 is considered to be a recent invader of the medaka fish genome (Koga et al 2000). In contrast, Tol1 is an ancient resident of the medaka fish genome because the majority of Tol1 copies are defective copies (Koga et al 2009). The present study suggests that even an old transposable element can contribute to the generation of genetic variation when triggered by a transposition burst.…”

Section: Contribution To Genetic Variationmentioning

confidence: 99%

“…Approximately 200 Tol1 copies reside in a diploid medaka fish genome, and their chromosomal locations differ from fish to fish (Koga et al 2009). This fact suggests that Tol1 is also active in the germline of the medaka fish.…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Spontaneous germline excision ofTol1, a DNA-based transposable element naturally occurring in the medaka fish genome

Watanabe¹,

Koga²,

Nakamura³

et al. 2014

Genome

Self Cite

View full text Add to dashboard Cite

DNA-based transposable elements are ubiquitous constituents of eukaryotic genomes. Vertebrates are, however, exceptional in that most of their DNA-based elements appear to be inactivated. The Tol1 element of the medaka fish, Oryzias latipes, is one of the few elements for which copies containing an undamaged gene have been found. Spontaneous transposition of this element in somatic cells has previously been demonstrated, but there is only indirect evidence for its germline transposition. Here, we show direct evidence of spontaneous excision in the germline. Tyrosinase is the key enzyme in melanin biosynthesis. In an albino laboratory strain of medaka fish, which is homozygous for a mutant tyrosinase gene in which a Tol1 copy is inserted, we identified de novo reversion mutations related to melanin pigmentation. The gamete-based reversion rate was as high as 0.4%. The revertant fish carried the tyrosinase gene from which the Tol1 copy had been excised. We previously reported the germline transposition of Tol2, another DNA-based element that is thought to be a recent invader of the medaka fish genome. Tol1 is an ancient resident of the genome. Our results indicate that even an old element can contribute to genetic variation in the host genome as a natural mutator.

show abstract

Section: Transposition Activity Of Tol1mentioning

confidence: 99%

Section: Contribution To Genetic Variationmentioning

confidence: 99%

See 1 more Smart Citation

Spontaneous germline excision ofTol1, a DNA-based transposable element naturally occurring in the medaka fish genome

Watanabe¹,

Koga²,

Nakamura³

et al. 2014

Genome

Self Cite

View full text Add to dashboard Cite

show abstract

“…1). We first conducted surveys using the 12 samples that had been materials for our previous surveys (Koga et al, 2000), and the 32 samples that had been used in another study to examine the distribution of the Tol1 element (Koga et al, 2009). Having found the short version of Tol2 in some samples originating from local populations in northern Japan, we added six samples collected in or around these regions, and eight more samples from locations in areas where the sampling density had previously been relatively low.…”

Section: (Ii) Fish Samplesmentioning

confidence: 99%

Occurrence of a short variant of theTol2transposable element in natural populations of the medaka fish

et al. 2010

Self Cite

View full text Add to dashboard Cite

Tol2 is a member of the hAT (hobo/Activator/Tam3) transposable element family, residing as 10-30 copies per diploid genome in the medaka fish. We previously reported that this element is highly homogeneous in structure at both the restriction map level and the nucleotide sequence level. It was, however, possible that there is variation of such a low frequency as not to have been detected in our previous surveys, in which samples from 12 geographical locations were used. In the present study, we first conducted searches of genome sequence databases of medaka, and found a 119-bp-long internal deletion. We then conducted a survey of samples from 58 locations for this deletion by performing PCR preceded by restriction enzyme digestion to increase the sensitivity to this deletion. We found that copies suffering this deletion have spread, or have been generated by multiple origins, in the northern-to-central part of mainland Japan. Thus, although the high homogeneity in structure is a distinct feature of Tol2, variation does exist at low frequencies in natural populations of medaka. The current status of Tol2 is expected to provide information with which results of future surveys can be compared for clarification of determinants of population dynamics of this DNA-based element.

show abstract

“…Genomic DNA (5 mg for each lane) was digested with the restriction enzymes and hybridized with the probes shown above the panels. Methods were as described in Koga et al (2009). Each hybridization band is expected to represent a restriction fragment consisting of part of Tol2 and its flanking chromosomal region.…”

mentioning

confidence: 99%

Under-representation of repetitive sequences in whole-genome shotgun sequence databases: an illustration using a recently acquired transposable element

Koga

2012

Genome

Self Cite

View full text Add to dashboard Cite

It is widely accepted in a conceptual framework that repetitive sequences, especially those with high sequence homogeneity among copies, tend to be under-represented in whole-genome shotgun sequence databases, because of the difficulty of assembling sequence reads into contigs. Although this is easily inferred, there is no quantitative illustration of this phenomenon. An example using a currently used database is expected to contribute to the intuitive understanding of how serious the under-representation is. The present study provides the first quantitative example (in the case of 16 copies of virtually identical, 4.7-kb sequences in a genome of 7 × 10 (8) bp) by comparing the results of BLAST searches of a sequence database (contig N50; 9.8 kb) with those of Southern blot analysis of genomic DNA. This has revealed that the internal regions of the repetitive sequences are under-represented to a striking extent.

show abstract

Distribution of complete and defective copies of the Tol1 transposable element in natural populations of the medaka fish Oryzias latipes

Cited by 8 publications

References 37 publications

Spontaneous germline excision ofTol1, a DNA-based transposable element naturally occurring in the medaka fish genome

Spontaneous germline excision ofTol1, a DNA-based transposable element naturally occurring in the medaka fish genome

Occurrence of a short variant of theTol2transposable element in natural populations of the medaka fish

Under-representation of repetitive sequences in whole-genome shotgun sequence databases: an illustration using a recently acquired transposable element

Contact Info

Product

Resources

About