Topic
Nuclear DNA
About: Nuclear DNA is a research topic. Over the lifetime, 3933 publications have been published within this topic receiving 185830 citations.
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TL;DR: Based on a large data set of nuclear and plastid DNA sequences, a reconstructed robust phylogeny of Populus using parsimony, maximum likelihood and Bayesian inference methods, showing better resolution at both inter- and intra-sectional level than previous studies.
Abstract: Populus (Salicaceae) is one of the most economically and ecologically important genera of forest trees. The complex reticulate evolution and lack of highly variable orthologous single-copy DNA markers have posed difficulties in resolving the phylogeny of this genus. Based on a large data set of nuclear and plastid DNA sequences, we reconstructed robust phylogeny of Populus using parsimony, maximum likelihood and Bayesian inference methods. The resulting phylogenetic trees showed better resolution at both inter- and intra-sectional level than previous studies. The results revealed that (1) the plastid-based phylogenetic tree resulted in two main clades, suggesting an early divergence of the maternal progenitors of Populus; (2) three advanced sections (Populus, Aigeiros and Tacamahaca) are of hybrid origin; (3) species of the section Tacamahaca could be divided into two major groups based on plastid and nuclear DNA data, suggesting a polyphyletic nature of the section; and (4) many species proved to be of hybrid origin based on the incongruence between plastid and nuclear DNA trees. Reticulate evolution may have played a significant role in the evolution history of Populus by facilitating rapid adaptive radiations into different environments.
72 citations
TL;DR: It is concluded that the palindromic repeats in V. carteri represent a single class of selfish DNA and speculate that the derivation of this element involved the lateral gene transfer of an organelle intron that first appeared in the mitochondrial genome, spreading to the ptDNA through mitochondrion-to-plastid DNA migrations, and eventually arrived in the nucDNA through organelle- to-nucleus DNA transfer events.
Abstract: Background
The magnitude of noncoding DNA in organelle genomes can vary significantly; it is argued that much of this variation is attributable to the dissemination of selfish DNA. The results of a previous study indicate that the mitochondrial DNA (mtDNA) of the green alga Volvox carteri abounds with palindromic repeats, which appear to be selfish elements. We became interested in the evolution and distribution of these repeats when, during a cursory exploration of the V. carteri nuclear DNA (nucDNA) and plastid DNA (ptDNA) sequences, we found palindromic repeats with similar structural features to those of the mtDNA. Upon this discovery, we decided to investigate the diversity and evolutionary implications of these palindromic elements by sequencing and characterizing large portions of mtDNA and ptDNA and then comparing these data to the V. carteri draft nuclear genome sequence.
72 citations
TL;DR: The leading theories explaining the phenomenon of aging are closely related, i.e., aging is due to a decreasing capacity of nDNA repair, which leads to unrepaired nDNA damage, or to an accumulation of mitochondria with damaged mtDNA, which leading to a deficit of cellular energy production.
Abstract: It is generally accepted that mitochondria are able to proliferate evenin postmitotic cells due to their natural turnover and also to satisfyincreased cell energy requirements. However, no detailed studies areavailable, particularly with respect to specific cell types. Since [ 3 H]-thymidine is incorporated not only into nuclear (n) DNA but also intothe DNA of cytoplasmic mitochondria, an autoradiographic approachwas developed at the light microscopy level in order to study basicquestions of mitochondrial (mt) proliferation in organs of rodents insitu via the cytoplasmic incorporation of [ 3 H]-thymidine injected intothe animals 1 h before sacrifice. Experiments carried out on mice afterX-irradiation showed that cytoplasmic labeling was not due to aprocess such as unscheduled nuclear DNA synthesis (nUDS). Further-more, half-lives of mitochondria between 8-23 days were deducedspecifically in relation to cell types. The phase of mtDNA synthesiswas about 75 min. Finally, mt proliferation was measured in brain cellsof mice as a function of age. While all neurons showed a decreasingextent of mtDNA synthesis during old age, nUDS decreased only indistinct cell types of the cortex and hippocampus. We conclude thatthe leading theories explaining the phenomenon of aging are closelyrelated, i.e., aging is due to a decreasing capacity of nDNA repair,which leads to unrepaired nDNA damage, or to an accumulation ofmitochondria with damaged mtDNA, which leads to a deficit ofcellular energy production.
72 citations
TL;DR: The increase or decrease in the copy number of several repetitive sequences examined here may indicate the existence of a directed change in genome size in rice.
Abstract: This paper describes a fluorescence in situ hybridization (FISH) analysis of three different repetitive sequence families, which were mapped to mitotic metaphase chromosomes and extended DNA fibers (EDFs) of the two subspecies of rice (OrYza sativa), indica and japonica (2n = 2x = 24). The repeat families studied were (1) the tandem repeat sequence A (TrsA), a functionally non-significant repeat; (2) the [TTTA-GGG]n telomere sequence, a non-transcribed, tandemly repeated but functionally significant repeat; and (3) the 5S ribosomal RNA (5S rDNA). FISH of the TrsA repeat to metaphase chromosomes of indica and japonica cultivars revealed clear signals at the distal ends of twelve and four chromosomes, respectively. As shown in a previous report, the 17S ribosomal RNA genes (17S rDNA) are located at the nucleolus organizers (NORs) on chromosomes 9 and 10 of the indica cultivar. However, the japonica rice lacked the rDNA signals on chromosome 10. The size of the 5S rDNA repeat block, which was mapped on the chromosome 11 of both cultivars, was 1.22 times larger in the indica than in the japonica genome. The telomeric repeat arrays at the distal ends of all chromosome arms were on average three times longer in the indica genome than in the japonica genome. Flow cytometric measurements revealed that the nuclear DNA content of indica rice is 9.7% higher than that of japonica rice. Our data suggest that different repetitive sequence families contribute significantly to the variation in genome size between indica and japonica rice, though to different extents. The increase or decrease in the copy number of several repetitive sequences examined here may indicate the existence of a directed change in genome size in rice. Possible reasons for this phenomenon of concurrent evolution of various repeat families are discussed.
72 citations
TL;DR: The results indicate that the contribution of mitochondria to the endogenously generated background levels of oxidative damage in the nuclear DNA is negligible.
72 citations