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      Plant Organelle Genome Replication

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          Abstract

          Mitochondria and chloroplasts perform essential functions in respiration, ATP production, and photosynthesis, and both organelles contain genomes that encode only some of the proteins that are required for these functions. The proteins and mechanisms for organelle DNA replication are very similar to bacterial or phage systems. The minimal replisome may consist of DNA polymerase, a primase/helicase, and a single-stranded DNA binding protein (SSB), similar to that found in bacteriophage T7. In Arabidopsis, there are two genes for organellar DNA polymerases and multiple potential genes for SSB, but there is only one known primase/helicase protein to date. Genome copy number varies widely between type and age of plant tissues. Replication mechanisms are only poorly understood at present, and may involve multiple processes, including recombination-dependent replication (RDR) in plant mitochondria and perhaps also in chloroplasts. There are still important questions remaining as to how the genomes are maintained in new organelles, and how genome copy number is determined. This review summarizes our current understanding of these processes.

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          Comparative organization of chloroplast genomes.

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            Evolutionary dynamics of the plastid inverted repeat: the effects of expansion, contraction, and loss on substitution rates.

            Rates of nucleotide substitution were previously shown to be several times slower in the plastid inverted repeat (IR) compared with single-copy (SC) regions, suggesting that the IR provides enhanced copy-correction activity. To examine the generality of this synonymous rate dependence on the IR, we compared plastomes from 69 pairs of closely related species representing 52 families of angiosperms, gymnosperms, and ferns. We explored the breadth of IR boundary shifts in land plants and demonstrate that synonymous substitution rates are, on average, 3.7 times slower in IR genes than in SC genes. In addition, genes moved from the SC into the IR exhibit lower synonymous rates consistent with other IR genes, while genes moved from the IR into the SC exhibit higher rates consistent with other SC genes. Surprisingly, however, several plastid genes from Pelargonium, Plantago, and Silene have highly accelerated synonymous rates despite their IR localization. Together, these results provide strong evidence that the duplicative nature of the IR reduces the substitution rate within this region. The anomalously fast-evolving genes in Pelargonium, Plantago, and Silene indicate localized hypermutation, potentially induced by a higher level of error-prone double-strand break repair in these regions, which generates substitutional rate variation.
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              Mitochondrial genomes: anything goes.

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                Author and article information

                Journal
                Plants (Basel)
                Plants (Basel)
                plants
                Plants
                MDPI
                2223-7747
                21 September 2019
                October 2019
                : 8
                : 10
                : 358
                Affiliations
                [1 ]Department of Microbiology & Molecular Biology, Brigham Young University, Provo, UT 84602, USA; stewart.morley@ 123456usda.gov
                [2 ]Agricultural Biotechnology Division, National Institute for Biotechnology & Genetic Engineering, Jhang Road, Faisalabad, Punjab 44000, Pakistan; niazbloch@ 123456yahoo.com
                Author notes
                [* ]Correspondence: brentnielsen@ 123456byu.edu ; Tel.: +1-801-422-1102
                [†]

                Current address: United States Department of Agriculture, 975 Warson Rd, St. Louis, Mo 63132, USA.

                Author information
                https://orcid.org/0000-0002-9391-2089
                https://orcid.org/0000-0001-6300-4816
                Article
                plants-08-00358
                10.3390/plants8100358
                6843274
                31546578
                6a0486c1-93f2-47a3-9517-1d80e754bec5
                © 2019 by the authors.

                Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license ( http://creativecommons.org/licenses/by/4.0/).

                History
                : 13 August 2019
                : 18 September 2019
                Categories
                Review

                dna replication,recombination-dependent replication (rdr),plant mitochondrial dna,chloroplast dna,dna repair

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