Variation of the genome size estimate with environmental conditions in Drosophila melanogaster

Nardon, C.; Weiss, Michèle; Vieira, Cristina; Biémont, Christian

doi:10.1002/cyto.a.10061

Cited by 18 publications

(29 citation statements)

References 39 publications

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“…In D. melanogaster, non site-specific non-LTR retrotransposons are usually either recently transposed euchromatic elements dispersed on all chromosome arms, or defective elements accumulated in pericentromeric heterochromatin (Dimitri and Junakovic, 1999). Molecular cytology helps in understanding the distribution and localization of mobile elements even at the population level, by providing a tool for investigating genome size variations along with factors like the geographical or environmental conditions (see, for instance, Nardon et al, 2003). However, the distribution of repeated elements has been relatively poorly documented in fish genomes, and earlier studies have mainly focused on otherwise uncharacterized satellite sequences (for a review, see Phillips, 2001).…”

Section: Discussionmentioning

confidence: 99%

Diversity and clustered distribution of retrotransposable elements in the compact genome of the pufferfish Tetraodon nigroviridis

Fischer

Bouneau²,

Coutanceau³

et al. 2005

Cytogenet Genome Res

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We report the characterization and chromosomal distribution of retroelements in the compact genome of the pufferfish Tetraodon nigroviridis. We have reconstructed partial/complete retroelement sequences, established their phylogenetic relationship to other known eukaryotic retrotransposons, and performed double-color FISH analyses to gain new insights into their patterns of chromosomal distribution. We could identify 43 different reverse transcriptase retrotransposons belonging to the three major known subclasses (14 non-LTR retrotransposons from seven clades, 25 LTR retrotransposons representing the five major known groups, and four Penelope-like elements), and well as two SINEs (non-autonomous retroelements). Such a diversity of retrotransposable elements, which seems to be relatively common in fish but not in mammals, is astonishing in such a compact genome. The total number of retroelements was approximately 3000, roughly representing only 2.6% of the genome of T. nigroviridis. This is much less than in other vertebrate genomes, reflecting the compact nature of the genome of this pufferfish. Major differences in copy number were observed between different clades, indicating differential success in invading and persisting in the genome. Some retroelements displayed evidence of recent activity. Finally, FISH analysis showed that retrotransposable elements preferentially accumulate in specific heterochromatic regions of the genome of T. nigroviridis, revealing a degree of genomic compartmentalization not observed in the human genome.

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Section: Discussionmentioning

confidence: 99%

Diversity and clustered distribution of retrotransposable elements in the compact genome of the pufferfish Tetraodon nigroviridis

Fischer

Bouneau²,

Coutanceau³

et al. 2005

Cytogenet Genome Res

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“…Significant variation in genome size was observed in D. melanogaster when the insects were reared at various temperatures and humidities (Nardon et al 2003). Also, the age of the insects and the temperature of the nuclei solution prior to flow cytometry resulted in a variable genome size in Drosophila (Nardon et al 2003). Older insects had a smaller genome size, whereas a low humidity during insect rearing increased the genome size significantly.…”

Section: Genome Sizementioning

confidence: 93%

“…Apparently, the genome sizes of Trichogramma species are quite different. However, part of these differences can be attributed to variation in the environmental conditions during the experiments (Nardon et al 2003). Significant variation in genome size was observed in D. melanogaster when the insects were reared at various temperatures and humidities (Nardon et al 2003).…”

Section: Genome Sizementioning

confidence: 98%

“…However, part of these differences can be attributed to variation in the environmental conditions during the experiments (Nardon et al 2003). Significant variation in genome size was observed in D. melanogaster when the insects were reared at various temperatures and humidities (Nardon et al 2003). Also, the age of the insects and the temperature of the nuclei solution prior to flow cytometry resulted in a variable genome size in Drosophila (Nardon et al 2003).…”

Section: Genome Sizementioning

confidence: 98%

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NOR activity and repeat sequences of the paternal sex ratio chromosome of the parasitoid wasp Trichogramma kaykai

et al. 2005

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Part of the male population of the wasp Trichogramma kaykai carries a B chromosome that manipulates its host sex ratio in favour of males. The only known repeat on this paternal sex ratio (PSR) chromosome is the 45S rDNA, which includes here five different internal transcribed spacer 2 (ITS2) sequences. In this report, we describe that only part of these ITS2 sequences is transcribed. The absence of transcription of some ITS2 sequences might explain the presence of multiple ITS2 sequences on the PSR chromosome since homogenization of rDNA spacers is thought to occur only in transcribed regions. Analysis of the only other known tandem repeat in Trichogramma, the EcoRI repeat, showed that it is absent from the PSR chromosome, and that the T. kaykai EcoRI repeat has 98 and 77% DNA sequence homology with the T. deion and T. brassicae EcoRI repeats, respectively. The size of the PSR chromosome measures 9 Mbp and is equal to 3.9% of the haploid T. kaykai genome. Finally, fluorescent in situ hybridization with a pool of high and moderate repetitive T. kaykai DNA (C0t-50) revealed only a very few major tandem repeats on the Trichogramma genome and only 45S rDNA on the PSR chromosome.

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“…Several recent reviews and commentaries have covered the following areas: the technical limitations of Feulgen cytometry in nuclear DNA amount estimation (Nardon et al, 2003;Greilhuber, 2008), phenotypic impacts of repetitive DNA in flowering plants (Meagher and Vassiliadis, 2005), rapid changes in plant genomes (Henikoff, 2005), the types of somagenetic variations that usually do not change the genome size (Li, 2008) and nuclear gene-induced mitochondrial DNA variation (Abdelnoor et al, 2003;Albert et al, 2003). This review gives emphasis to the variation that affects the nuclear genome size or DNA content.…”

Section: Introductionmentioning

confidence: 99%

Developmental and environmental variation in genomes

2009

Heredity

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The genetic make-up of an organism, established at fertilization, is not conventionally expected to change during development unless mutation occurs. However, there is actually evidence that considerable variation can arise. Some of these changes may occur in response to the environment. This article reviews such variations in genome size or DNA content (excluding ploidy-level changes). The variation can be generated by processes, including high-frequency chromosomal recombination, transposition, cis-element-enhanced gene amplification and repetitivesequence-based changes in nuclear DNA content. Environmentally induced and developmentally regulated genomic variation (ED-genomic variation or ED-genetic variation) can be found in both coding and non-coding sequences, and is often non-Mendelian in its inheritance pattern. Changes can depend on development (for example, propagation method, seed/fruit position on plants, embryo stage, etc.) and occur in response to the environment (for example, light, temperature, herbicide, salinity, fertilizer, land slope direction, pathogen infection, etc.). Some plants have meiotic (or rejuvenation) corrections, which restore their genome sizes to a certain degree. However, Mendelian inheritance and acquired inheritance of the variants occur, and both inheritance types may be different expressions evolved for the same adaptive responses. With this perspective, the terms 'pure-breeding line' or 'stable cultivar' may only be appropriate for a given mode of reproduction or propagation, and for a given environment. ED-genomic variation appears to be an essential component of differentiation, development and adaptation. Consequently, modern molecular biology tools, such as microarray hybridization and new sequencing technology, should be directed towards a more comprehensive evaluation of ED-genomic variation.

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Variation of the genome size estimate with environmental conditions in Drosophila melanogaster

Cited by 18 publications

References 39 publications

Diversity and clustered distribution of retrotransposable elements in the compact genome of the pufferfish <i>Tetraodon nigroviridis</i>

Diversity and clustered distribution of retrotransposable elements in the compact genome of the pufferfish <i>Tetraodon nigroviridis</i>

NOR activity and repeat sequences of the paternal sex ratio chromosome of the parasitoid wasp Trichogramma kaykai

Developmental and environmental variation in genomes

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