Topic
Genome
About: Genome is a research topic. Over the lifetime, 74231 publications have been published within this topic receiving 3819713 citations.
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TL;DR: The changes in DNA sequence that have taken place during the evolution of eukaryotic genomes cannot be accounted for simply by base substitutions; some more complex mutations must have take place as well.
755 citations
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TL;DR: The process of gene loss from chloroplast genomes across the inferred tree is mapped and it is found that independent parallel gene losses in multiple lineages outnumber phylogenetically unique losses by more than 4:1.
Abstract: Photosynthetic eukaryotes, particularly unicellular forms, possess a fossil record that is either wrought with gaps or difficult to interpret, or both. Attempts to reconstruct their evolution have focused on plastid phylogeny, but were limited by the amount and type of phylogenetic information contained within single genes. Among the 210 different protein-coding genes contained in the completely sequenced chloroplast genomes from a glaucocystophyte, a rhodophyte, a diatom, a euglenophyte and five land plants, we have now identified the set of 45 common to each and to a cyanobacterial outgroup genome. Phylogenetic inference with an alignment of 11,039 amino-acid positions per genome indicates that this information is sufficient--but just rarely so--to identify the rooted nine-taxon topology. We mapped the process of gene loss from chloroplast genomes across the inferred tree and found that, surprisingly, independent parallel gene losses in multiple lineages outnumber phylogenetically unique losses by more that 4:1. We identified homologues of 44 different plastid-encoded proteins as functional nuclear genes of chloroplast origin, providing evidence for endosymbiotic gene transfer to the nucleus in plants.
754 citations
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United States Department of Energy1, J. Craig Venter Institute2, Heidelberg University3, University of California, Berkeley4, University of California, Irvine5, Technische Universität München6, National Institutes of Health7, Pomona College8, Salk Institute for Biological Studies9, University of Kiel10, National Institute of Genetics11, University of Vienna12, University of Kansas13, University of Innsbruck14, Dartmouth College15, North Carolina State University16, Ludwig Maximilian University of Munich17
TL;DR: Comparisons of the Hydra genome to the genomes of other animals shed light on the evolution of epithelia, contractile tissues, developmentally regulated transcription factors, the Spemann–Mangold organizer, pluripotency genes and the neuromuscular junction.
Abstract: The freshwater cnidarian Hydra was first described in 17021 and has been the object of study for 300 years. Experimental studies of Hydra between 1736 and 1744 culminated in the discovery of asexual reproduction of an animal by budding, the first description of regeneration in an animal, and successful transplantation of tissue between animals2. Today, Hydra is an important model for studies of axial patterning3, stem cell biology4 and regeneration5. Here we report the genome of Hydra magnipapillata and compare it to the genomes of the anthozoan Nematostella vectensis6 and other animals. The Hydra genome has been shaped by bursts of transposable element expansion, horizontal gene transfer, trans-splicing, and simplification of gene structure and gene content that parallel simplification of the Hydra life cycle. We also report the sequence of the genome of a novel bacterium stably associated with H. magnipapillata. Comparisons of the Hydra genome to the genomes of other animals shed light on the evolution of epithelia, contractile tissues, developmentally regulated transcription factors, the Spemann–Mangold organizer, pluripotency genes and the neuromuscular junction.
754 citations
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TL;DR: The process by which novel structure and function could have arisen during evolution are considered speculatively in terms of the authors' gene regulation theory.
Abstract: Recent experimental information on DNA sequence repetition is reviewed, and the significance of both repetitive and non-repetitive sequence considered. Included are a summary of data on the distribution of genome sizes in animals, new experiments on interspecific DNA homology, the distribution of sequence frequencies, and the interspersion of repetitive sequences within the genome. Aspects of the process of evolution are considered at the level of change in the DNA. the process by which novel structure and function could have arisen during evolution are considered speculatively in terms of the authors' gene regulation theory (Britten and Davidson, 1969).
753 citations
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TL;DR: A greater complexity of the human genome in the form of variation of longer and more complex repetitive DNA that can now be largely resolved with the application of this longer-read sequencing technology is suggested.
Abstract: The human genome is arguably the most complete mammalian reference assembly, yet more than 160 euchromatic gaps remain and aspects of its structural variation remain poorly understood ten years after its completion. To identify missing sequence and genetic variation, here we sequence and analyse a haploid human genome (CHM1) using single-molecule, real-time DNA sequencing. We close or extend 55% of the remaining interstitial gaps in the human GRCh37 reference genome--78% of which carried long runs of degenerate short tandem repeats, often several kilobases in length, embedded within (G+C)-rich genomic regions. We resolve the complete sequence of 26,079 euchromatic structural variants at the base-pair level, including inversions, complex insertions and long tracts of tandem repeats. Most have not been previously reported, with the greatest increases in sensitivity occurring for events less than 5 kilobases in size. Compared to the human reference, we find a significant insertional bias (3:1) in regions corresponding to complex insertions and long short tandem repeats. Our results suggest a greater complexity of the human genome in the form of variation of longer and more complex repetitive DNA that can now be largely resolved with the application of this longer-read sequencing technology.
753 citations