The<i>hobo</i>-related elements in the<i>melanogaster</i>species group

Ortiz, Mauro de Freitas; Loreto, Élgion Lúcio Silva

doi:10.1017/s0016672308009312

Cited by 18 publications

(6 citation statements)

References 44 publications

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“…We found 28 homozygous euchromatic TE insertions, which are predominantly LTR and defective hobo elements, suggesting a high rate of euchromatic TE insertions (∼0.08 insertion/gen). That we observed a predominance of LTR and hobo elements among the new TE insertions mirrors their recent spread in D. melanogaster populations ( Pascual and Periquet 1991 ; Periquet et al 1994 ; Bowen and McDonald 2001 ; De Freitas Ortiz and Silva Loreto 2008 ). The abundance of defective hobo elements among the new insertions is particularly interesting given that these hobo elements lack the transposase enzyme necessary for mobilization.…”

Section: Discussionsupporting

confidence: 69%

Rapid Low-Cost Assembly of the Drosophila melanogaster Reference Genome Using Low-Coverage, Long-Read Sequencing

Solares

Chakraborty

Miller

et al. 2018

G3 Genes|Genomes|Genetics

103

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Accurate and comprehensive characterization of genetic variation is essential for deciphering the genetic basis of diseases and other phenotypes. A vast amount of genetic variation stems from large-scale sequence changes arising from the duplication, deletion, inversion, and translocation of sequences. In the past 10 years, high-throughput short reads have greatly expanded our ability to assay sequence variation due to single nucleotide polymorphisms. However, a recent de novo assembly of a second Drosophila melanogaster reference genome has revealed that short read genotyping methods miss hundreds of structural variants, including those affecting phenotypes. While genomes assembled using high-coverage long reads can achieve high levels of contiguity and completeness, concerns about cost, errors, and low yield have limited widespread adoption of such sequencing approaches. Here we resequenced the reference strain of D. melanogaster (ISO1) on a single Oxford Nanopore MinION flow cell run for 24 hr. Using only reads longer than 1 kb or with at least 30x coverage, we assembled a highly contiguous de novo genome. The addition of inexpensive paired reads and subsequent scaffolding using an optical map technology achieved an assembly with completeness and contiguity comparable to the D. melanogaster reference assembly. Comparison of our assembly to the reference assembly of ISO1 uncovered a number of structural variants (SVs), including novel LTR transposable element insertions and duplications affecting genes with developmental, behavioral, and metabolic functions. Collectively, these SVs provide a snapshot of the dynamics of genome evolution. Furthermore, our assembly and comparison to the D. melanogaster reference genome demonstrates that high-quality de novo assembly of reference genomes and comprehensive variant discovery using such assemblies are now possible by a single lab for under $1,000 (USD).

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Section: Discussionsupporting

confidence: 69%

Rapid Low-Cost Assembly of the Drosophila melanogaster Reference Genome Using Low-Coverage, Long-Read Sequencing

Solares

Chakraborty

Miller

et al. 2018

G3 Genes|Genomes|Genetics

103

View full text Add to dashboard Cite

show abstract

“…We found 28 homozygous euchromatic TE insertions, which are predominantly LTR and defective hobo elements, suggesting a high rate of euchromatic TE insertions (~0.08 insertion/gen). That we observed a predominance of LTR and hobo elements among the new TE insertions mirrors their recent spread in D. melanogaster populations (Pascual and Periquet 1991;Periquet et al 1994;Bowen and McDonald 2001;De Freitas Ortiz and Silva Loreto 2008). The abundance of defective hobo elements among the new insertions is particularly interesting given that these hobo elements lack the transposase enzyme necessary for mobilization.…”

Section: Discussionsupporting

confidence: 54%

Rapid low-cost assembly of the Drosophila melanogaster reference genome using low-coverage, long-read sequencing

Solares

Chakraborty

Miller

et al. 2018

Preprint

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Accurate and comprehensive characterization of genetic variation is essential for deciphering the genetic basis of diseases and other phenotypes. A vast amount of genetic variation stems from large-scale sequence changes arising from the duplication, deletion, inversion, and translocation of sequences. In the past 10 years, highthroughput short reads have greatly expanded our ability to assay sequence variation due to single nucleotide polymorphisms. However, a recent de novo assembly of a second Drosophila melanogaster reference genome has revealed that short read genotyping methods miss hundreds of structural variants, including those affecting phenotypes. While genomes assembled using high-coverage long reads can achieve high levels of contiguity and completeness, concerns about cost, errors, and low yield have limited widespread adoption of such sequencing approaches. Here we resequenced the reference strain of D. melanogaster (ISO1) on a single Oxford Nanopore MinION flow cell run for 24 hours. Using only reads longer than 1 kb or with at least 30x coverage, we assembled a highly contiguous de novo genome. The addition of inexpensive paired reads and subsequent scaffolding using an optical map technology achieved an assembly with completeness and contiguity comparable to the D. melanogaster reference assembly. Comparison of our assembly to the reference assembly of ISO1 uncovered a number of structural variants (SVs), including novel LTR transposable element insertions and duplications affecting genes with developmental, behavioral, and metabolic functions. Collectively, these SVs provide a snapshot of the dynamics of genome evolution. Furthermore, our assembly and comparison to the D.melanogaster reference genome demonstrates that high-quality de novo assembly of reference genomes and comprehensive variant discovery using such assemblies are now possible by a single lab for under $1,000 (USD).

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“…In Drosophila, few MITEs have been characterized to date, and the copy number has not exceeded 100 [40–42]. Furthermore, few mariner MITEs have been described, the most notable case being the MiHsmar1 family in humans [43].…”

Section: Discussionmentioning

confidence: 99%

“…The de novo formation hypothesis (that similar solo-TIR-like sequences close to each other may generate these short non-autonomous TEs) has not found empirical support to date. The alternative hypothesis assumes an internal deletion of the autonomous element, with degeneration or substitution of internal sequence [40, 47]. Amplification could result from the recognition of TIRs by the transposase of active copies from the same lineage or from distantly related lineages [48].…”

Section: Discussionmentioning

confidence: 99%

Genomic landscape and evolutionary dynamics of mariner transposable elements within the Drosophila genus

et al. 2014

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BackgroundThe mariner family of transposable elements is one of the most widespread in the Metazoa. It is subdivided into several subfamilies that do not mirror the phylogeny of these species, suggesting an ancient diversification. Previous hybridization and PCR studies allowed a partial survey of mariner diversity in the Metazoa. In this work, we used a comparative genomics approach to access the genus-wide diversity and evolution of mariner transposable elements in twenty Drosophila sequenced genomes.ResultsWe identified 36 different mariner lineages belonging to six distinct subfamilies, including a subfamily not described previously. Wide variation in lineage abundance and copy number were observed among species and among mariner lineages, suggesting continuous turn-over. Most mariner lineages are inactive and contain a high proportion of damaged copies. We showed that, in addition to substitutions that rapidly inactivate copies, internal deletion is a major mechanism contributing to element decay and the generation of non-autonomous sublineages. Hence, 23% of copies correspond to several Miniature Inverted-repeat Transposable Elements (MITE) sublineages, the first ever described in Drosophila for mariner. In the most successful MITEs, internal deletion is often associated with internal rearrangement, which sheds light on the process of MITE origin. The estimation of the transposition rates over time revealed that all lineages followed a similar progression consisting of a rapid amplification burst followed by a rapid decrease in transposition. We detected some instances of multiple or ongoing transposition bursts. Different amplification times were observed for mariner lineages shared by different species, a finding best explained by either horizontal transmission or a reactivation process. Different lineages within one species have also amplified at different times, corresponding to successive invasions. Finally, we detected a preference for insertion into short TA-rich regions, which appears to be specific to some subfamilies.ConclusionsThis analysis is the first comprehensive survey of this family of transposable elements at a genus scale. It provides precise measures of the different evolutionary processes that were hypothesized previously for this family based on PCR data analysis. mariner lineages were observed at almost all “life cycle” stages: recent amplification, subsequent decay and potential (re)-invasion or invasion of genomes.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-727) contains supplementary material, which is available to authorized users.

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Thehobo-related elements in themelanogasterspecies group

Cited by 18 publications

References 44 publications

Rapid Low-Cost Assembly of the Drosophila melanogaster Reference Genome Using Low-Coverage, Long-Read Sequencing

Rapid Low-Cost Assembly of the Drosophila melanogaster Reference Genome Using Low-Coverage, Long-Read Sequencing

Rapid low-cost assembly of the Drosophila melanogaster reference genome using low-coverage, long-read sequencing

Genomic landscape and evolutionary dynamics of mariner transposable elements within the Drosophila genus

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