Transposable elements: Instability of genes and genomes

Yurchenko, N. N.; Kovalenko, L. V.; Захаров, И. К.

doi:10.1134/s2079059711060141

Cited by 18 publications

(10 citation statements)

References 62 publications

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“…Second, it has been suggested that mobilisation of transposable elements may be a possible cause of the accelerated decline in viability due to insertional mutations, rather than synergistic epistasis, in Mukai´s (1969) mutation-accumulation experiment (Keightley 1996). Inbreeding is one of the several factors known to produce genomic instability (Yurchenko et al 2011; García Guerreiro 2012), so it is possible that an increased mobilisation of transposable elements occurs also in highly inbred lines, mimicking the nonlinear decline in fitness observed. Finally, inbreeding has been shown to produce substantial changes in gene expression (Kristensen et al 2005; Ayroles et al 2009; Paige 2010; García et al 2012), which could modulate the rate of inbreeding depression.…”

Section: Discussionmentioning

confidence: 99%

Accelerated inbreeding depression suggests synergistic epistasis for deleterious mutations in Drosophila melanogaster

et al. 2019

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Epistasis may have important consequences for a number of issues in quantitative genetics and evolutionary biology. In particular, synergistic epistasis for deleterious alleles is relevant to the mutation load paradox and the evolution of sex and recombination. Some studies have shown evidence of synergistic epistasis for spontaneous or induced deleterious mutations appearing in mutation-accumulation experiments. However, many newly arising mutations may not actually be segregating in natural populations because of the erasing action of natural selection. A demonstration of synergistic epistasis for naturally segregating alleles can be achieved by means of inbreeding depression studies, as deleterious recessive allelic effects are exposed in inbred lines. Nevertheless, evidence of epistasis from these studies is scarce and controversial. In this paper, we report the results of two independent inbreeding experiments carried out with two different populations of Drosophila melanogaster. The results show a consistent accelerated inbreeding depression for fitness, suggesting synergistic epistasis among deleterious alleles. We also performed computer simulations assuming different possible models of epistasis and mutational parameters for fitness, finding some of them to be compatible with the results observed. Our results suggest that synergistic epistasis for deleterious mutations not only occurs among newly arisen spontaneous or induced mutations, but also among segregating alleles in natural populations.

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Section: Discussionmentioning

confidence: 99%

Accelerated inbreeding depression suggests synergistic epistasis for deleterious mutations in Drosophila melanogaster

et al. 2019

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“…PCC 8005 also overexpressed a large set of genes involved in the restriction modification mechanism, phage-immunity, and MGEs, possibly indicating radiation-induced genetic rearrangements. MGEs have been shown to be important components of genomic rearrangements (Yurchenko et al 2011).…”

Section: Discussionmentioning

confidence: 99%

Molecular investigation of the radiation resistance of edible cyanobacterium Arthrospira sp. PCC 8005

et al. 2015

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The aim of this work was to characterize in detail the response of Arthrospira to ionizing radiation, to better understand its radiation resistance capacity. Live cells of Arthrospira sp. PCC 8005 were irradiated with 60Co gamma rays. This study is the first, showing that Arthrospira is highly tolerant to gamma rays, and can survive at least 6400 Gy (dose rate of 527 Gy h−1), which identified Arthrospira sp. PCC 8005 as a radiation resistant bacterium. Biochemical, including proteomic and transcriptomic, analysis after irradiation with 3200 or 5000 Gy showed a decline in photosystem II quantum yield, reduced carbon fixation, and reduced pigment, lipid, and secondary metabolite synthesis. Transcription of photo-sensing and signaling pathways, and thiol-based antioxidant systems was induced. Transcriptomics did show significant activation of ssDNA repair systems and mobile genetic elements (MGEs) at the RNA level. Surprisingly, the cells did not induce the classical antioxidant or DNA repair systems, such superoxide dismutase (SOD) enzyme and the RecA protein. Arthrospira cells lack the catalase gene and the LexA repressor. Irradiated Arthrospira cells did induce strongly a group of conserved proteins, of which the function in radiation resistance remains to be elucidated, but which are a promising novel routes to be explored. This study revealed the radiation resistance of Arthrospira, and the molecular systems involved, paving the way for its further and better exploitation.

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“…Although mutations may be harmful, and could lead to different diseases and even death of the individuals, they are the basis of biological evolution for the species. Thus, mutations generate diversity that may provide adaptive advantages to the changing environments, being further selected as a result of the natural selection [15] . The role of TEs in evolution was proposed by Barbara McClintock in the 1980s, since then progress had been made to understand the significance of TEs in genome evolution through the comprehensive study of the structure and function of TEs in different organisms [16] .…”

Section: Introductionmentioning

confidence: 99%

Scanning of Transposable Elements and Analyzing Expression of Transposase Genes of Sweet Potato [Ipomoea batatas]

Ling

Xiang

et al. 2014

PLoS ONE

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BackgroundTransposable elements (TEs) are the most abundant genomic components in eukaryotes and affect the genome by their replications and movements to generate genetic plasticity. Sweet potato performs asexual reproduction generally and the TEs may be an important genetic factor for genome reorganization. Complete identification of TEs is essential for the study of genome evolution. However, the TEs of sweet potato are still poorly understood because of its complex hexaploid genome and difficulty in genome sequencing. The recent availability of the sweet potato transcriptome databases provides an opportunity for discovering and characterizing the expressed TEs.Methodology/Principal FindingsWe first established the integrated-transcriptome database by de novo assembling four published sweet potato transcriptome databases from three cultivars in China. Using sequence-similarity search and analysis, a total of 1,405 TEs including 883 retrotransposons and 522 DNA transposons were predicted and categorized. Depending on mapping sets of RNA-Seq raw short reads to the predicted TEs, we compared the quantities, classifications and expression activities of TEs inter- and intra-cultivars. Moreover, the differential expressions of TEs in seven tissues of Xushu 18 cultivar were analyzed by using Illumina digital gene expression (DGE) tag profiling. It was found that 417 TEs were expressed in one or more tissues and 107 in all seven tissues. Furthermore, the copy number of 11 transposase genes was determined to be 1–3 copies in the genome of sweet potato by Real-time PCR-based absolute quantification.Conclusions/SignificanceOur result provides a new method for TE searching on species with transcriptome sequences while lacking genome information. The searching, identification and expression analysis of TEs will provide useful TE information in sweet potato, which are valuable for the further studies of TE-mediated gene mutation and optimization in asexual reproduction. It contributes to elucidating the roles of TEs in genome evolution.

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Transposable elements: Instability of genes and genomes

Cited by 18 publications

References 62 publications

Accelerated inbreeding depression suggests synergistic epistasis for deleterious mutations in Drosophila melanogaster

Accelerated inbreeding depression suggests synergistic epistasis for deleterious mutations in Drosophila melanogaster

Molecular investigation of the radiation resistance of edible cyanobacterium Arthrospira sp. PCC 8005

Scanning of Transposable Elements and Analyzing Expression of Transposase Genes of Sweet Potato [Ipomoea batatas]

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