Under the rug: Abandoning persistent misconceptions that obfuscate organelle evolution
The advent and advance of next generation sequencing over the past two decades made it possible to accumulate large quantities of sequence reads that could be used to assemble complete or nearly complete organelle genomes (plastome or mitogenome). The result has been an explosive increase in the ava...
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| Published in | Molecular phylogenetics and evolution Vol. 151; p. 106903 |
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| Main Authors | , , , |
| Format | Journal Article |
| Language | English |
| Published |
United States
Elsevier Inc
01.10.2020
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| Subjects | |
| Online Access | Get full text |
| ISSN | 1055-7903 1095-9513 1095-9513 |
| DOI | 10.1016/j.ympev.2020.106903 |
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| Abstract | The advent and advance of next generation sequencing over the past two decades made it possible to accumulate large quantities of sequence reads that could be used to assemble complete or nearly complete organelle genomes (plastome or mitogenome). The result has been an explosive increase in the availability of organelle genome sequences with over 4000 different species of green plants currently available on GenBank. During the same time period, plant molecular biologists greatly enhanced the understanding of the structure, repair, replication, recombination, transcription and translation, and inheritance of organelle DNA. Unfortunately many plant evolutionary biologists are unaware of or have overlooked this knowledge, resulting in misrepresentation of several phenomena that are critical for phylogenetic and evolutionary studies using organelle genomes. We believe that confronting these misconceptions about organelle genome organization, composition, and inheritance will improve our understanding of the evolutionary processes that underly organelle evolution. Here we discuss four misconceptions that can limit evolutionary biology studies and lead to inaccurate phylogenies and incorrect structure of the organellar DNA used to infer organelle evolution. |
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| AbstractList | The advent and advance of next generation sequencing over the past two decades made it possible to accumulate large quantities of sequence reads that could be used to assemble complete or nearly complete organelle genomes (plastome or mitogenome). The result has been an explosive increase in the availability of organelle genome sequences with over 4000 different species of green plants currently available on GenBank. During the same time period, plant molecular biologists greatly enhanced the understanding of the structure, repair, replication, recombination, transcription and translation, and inheritance of organelle DNA. Unfortunately many plant evolutionary biologists are unaware of or have overlooked this knowledge, resulting in misrepresentation of several phenomena that are critical for phylogenetic and evolutionary studies using organelle genomes. We believe that confronting these misconceptions about organelle genome organization, composition, and inheritance will improve our understanding of the evolutionary processes that underly organelle evolution. Here we discuss four misconceptions that can limit evolutionary biology studies and lead to inaccurate phylogenies and incorrect structure of the organellar DNA used to infer organelle evolution. The advent and advance of next generation sequencing over the past two decades made it possible to accumulate large quantities of sequence reads that could be used to assemble complete or nearly complete organelle genomes (plastome or mitogenome). The result has been an explosive increase in the availability of organelle genome sequences with over 4000 different species of green plants currently available on GenBank. During the same time period, plant molecular biologists greatly enhanced the understanding of the structure, repair, replication, recombination, transcription and translation, and inheritance of organelle DNA. Unfortunately many plant evolutionary biologists are unaware of or have overlooked this knowledge, resulting in misrepresentation of several phenomena that are critical for phylogenetic and evolutionary studies using organelle genomes. We believe that confronting these misconceptions about organelle genome organization, composition, and inheritance will improve our understanding of the evolutionary processes that underly organelle evolution. Here we discuss four misconceptions that can limit evolutionary biology studies and lead to inaccurate phylogenies and incorrect structure of the organellar DNA used to infer organelle evolution.The advent and advance of next generation sequencing over the past two decades made it possible to accumulate large quantities of sequence reads that could be used to assemble complete or nearly complete organelle genomes (plastome or mitogenome). The result has been an explosive increase in the availability of organelle genome sequences with over 4000 different species of green plants currently available on GenBank. During the same time period, plant molecular biologists greatly enhanced the understanding of the structure, repair, replication, recombination, transcription and translation, and inheritance of organelle DNA. Unfortunately many plant evolutionary biologists are unaware of or have overlooked this knowledge, resulting in misrepresentation of several phenomena that are critical for phylogenetic and evolutionary studies using organelle genomes. We believe that confronting these misconceptions about organelle genome organization, composition, and inheritance will improve our understanding of the evolutionary processes that underly organelle evolution. Here we discuss four misconceptions that can limit evolutionary biology studies and lead to inaccurate phylogenies and incorrect structure of the organellar DNA used to infer organelle evolution. |
| ArticleNumber | 106903 |
| Author | Ruhlman, Tracey A. Jansen, Robert K. Gonçalves, Deise J.P. Mandel, Jennifer R. |
| Author_xml | – sequence: 1 givenname: Deise J.P. surname: Gonçalves fullname: Gonçalves, Deise J.P. email: deisejpg@umich.edu organization: Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA – sequence: 2 givenname: Robert K. surname: Jansen fullname: Jansen, Robert K. organization: Department of Integrative Biology, The University of Texas at Austin, Austin, TX 78713, USA – sequence: 3 givenname: Tracey A. surname: Ruhlman fullname: Ruhlman, Tracey A. organization: Department of Integrative Biology, The University of Texas at Austin, Austin, TX 78713, USA – sequence: 4 givenname: Jennifer R. surname: Mandel fullname: Mandel, Jennifer R. organization: Department of Biological Sciences, Center for Biodiversity Research, University of Memphis, Memphis, TN 38152, USA |
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| Cites_doi | 10.1073/pnas.92.25.11331 10.1105/tpc.160771 10.1007/s11103-011-9762-4 10.1002/ajb2.1048 10.1111/j.1365-313X.2012.05057.x 10.1002/humu.22767 10.1146/annurev.genet.35.102401.090231 10.1534/g3.119.401023 10.1105/tpc.15.00879 10.1139/gen-2015-0090 10.1016/bs.abr.2017.11.017 10.1093/gbe/evz076 10.1038/301092a0 10.1111/nph.12395 10.1007/BF00425847 10.2307/3870324 10.1111/j.1365-294X.2010.04984.x 10.1111/nph.12431 10.1038/hdy.1994.19 10.1007/s00606-019-01610-5 10.1073/pnas.76.1.41 10.1371/journal.pgen.1008373 10.7717/peerj.7747 10.3389/fpls.2015.00883 10.1016/j.jmb.2003.11.020 10.1007/s10265-009-0306-9 10.1002/j.1537-2197.1988.tb11219.x 10.1016/j.ympev.2019.05.030 10.1093/pcp/pcm170 10.1007/s00299-016-1949-3 10.2307/2419070 10.1038/s41559-017-0126 10.1093/sysbio/syaa013 10.1093/jhered/91.6.435 10.1093/sysbio/syx050 10.1093/pcp/pcg121 10.1093/molbev/msi191 10.1002/j.1537-2197.1996.tb12718.x 10.1111/j.1469-8137.2010.03195.x 10.1534/genetics.118.300711 10.1007/s00294-006-0082-1 10.1111/syen.12431 10.1111/j.1365-313X.2007.03278.x 10.1016/j.bbamcr.2013.03.010 10.1038/256708a0 10.1007/BF00336777 10.1111/jse.12579 10.1016/j.ympev.2019.05.022 10.1600/0363644042451008 10.1146/annurev-arplant-043015-112232 10.1093/bioinformatics/btz300 10.1007/s10577-013-9349-9 |
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| Keywords | Patterns of inheritance Mitochondria Plastome phylogenies Single locus Heteroplasmy Chloroplast |
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| References | Wolfe, Randle (b0285) 2004; 29 Kozik, Rowan, Lavelle, Berke, Schranz, Michelmore, Christensen (b0135) 2019; 15 Christensen (b0050) 2018 Phan, Pham, Melton, Ramsey, Daigle, Mandel (b0200) 2019; 35 Bendich (b0020) 1993; 24 Thode, Lohmann, Sanmartín (b0255) 2020 Bendich (b0015) 2004; 16 Hagemann (b0100) 2000; 91 Oldenburg, Bendich (b0180) 2015; 6 Greiner, Rauwolf, Meurer, Herrmann (b0075) 2011; 20 Kim, Kim, Cameron (b0110) 2020 Massouh, Schubert, Yaneva-Roder, Ulbricht-Jones, Zupok, Johnson, Wright, Pellizzer, Sobanski, Bock, Greiner (b0160) 2016; 28 Sloan (b0245) 2013; 200 Oldenburg, Bendich (b0185) 2004; 335 Sato, Sato (b0230) 2013; 1833 Reboud, Zeyl (b0210) 1994; 72 Wicke, Schneeweiss, DePamphilis, Müller, Quandt (b0275) 2011; 76 Vellarikkal, Dhiman, Joshi, Hasija, Sivasubbu, Scaria (b0265) 2015; 36 Walker, Walker-Hale, Vargas, Larson, Stull (b0270) 2019; 7 Birky (b0030) 1995; 92 Sparks, Dale (b0250) 1980; 180 Hagemann (b0105) 2004 Oldenburg, Bendich (b0190) 1996; 8 Breton, Stewart (b0040) 2015; 58 Thyssen, Svab, Maliga (b0260) 2012; 72 Roy, Schreiber (b0225) 2014; 25 Bendich (b0010) 2013; 21 Kmiec, Woloszynska, Janska (b0120) 2006; 50 Wu, Waneka, Sloan (b0290) 2020; 10 Gruenstaeudl (b0080) 2019; 305 Shen, Hittinger, Rokas (b0235) 2017; 1 Maréchal, Brisson (b0155) 2010; 186 Choi, Jansen, Ruhlman (b0045) 2019; 11 Gonçalves, Shimizu, Ortiz, Simpson, Jansen (b0070) 2019; 138 Ramsey, Mandel (b0205) 2019; 2 Doyle (b0060) 1992; 17 Kirk, Tilney-Bassett (b0115) 1978 Kolodner, Tewari (b0125) 1975; 256 Shrestha, Weng, Theriot, Gilbert, Ruhlman, Krosnick, Jansen (b0240) 2019; 138 Palmer (b0195) 1983; 301 Kolodner, Tewari (b0130) 1979; 76 Ruhlman, Jansen (b0215) 2018 Zampini, Truche, Lepage, Tremblay-Belzile, Brisson (b0295) 2017 Leebens-Mack, Raubeson, Cui, Kuehl, Fourcade, Chumley, Boore, Jansen, DePamphilis (b0145) 2005; 22 Gitzendanner, Soltis, Wong, Ruhfel, Soltis (b0065) 2018; 105 Zhang, Liu, Sodmergen (b0300) 2003; 44 Gualberto, Newton (b0085) 2017; 68 Bohra, Jha, Adhimoolam, Bisht, Singh (b0035) 2016; 35 Kuroiwa (b0140) 2010; 123 Corriveau, Coleman (b0055) 1988; 75 Léveillé-Bourret, Starr, Ford, Lemmon, Lemmon (b0150) 2017; 67 Zhang, Wang, Jin, Stull, Bruneau, Cardoso, Queiroz, Moore, Zhang, Chen, Wang, Li, Yi (b0220) 2020; 69 Birky (b0025) 2001; 35 Azhagiri, Maliga (b0005) 2007; 52 Wilton, Zaidi, Makova, Nielsen (b0280) 2018; 20 McCauley (b0170) 2013; 200 Matsushima, Hu, Toyoda, Sodmergen, Sakamoto (b0165) 2008; 49 Mogensen (b0175) 1996; 83 Kmiec (10.1016/j.ympev.2020.106903_b0120) 2006; 50 Kolodner (10.1016/j.ympev.2020.106903_b0130) 1979; 76 Bendich (10.1016/j.ympev.2020.106903_b0010) 2013; 21 Greiner (10.1016/j.ympev.2020.106903_b0075) 2011; 20 Leebens-Mack (10.1016/j.ympev.2020.106903_b0145) 2005; 22 Shen (10.1016/j.ympev.2020.106903_b0235) 2017; 1 Azhagiri (10.1016/j.ympev.2020.106903_b0005) 2007; 52 Corriveau (10.1016/j.ympev.2020.106903_b0055) 1988; 75 Shrestha (10.1016/j.ympev.2020.106903_b0240) 2019; 138 Birky (10.1016/j.ympev.2020.106903_b0030) 1995; 92 Massouh (10.1016/j.ympev.2020.106903_b0160) 2016; 28 Oldenburg (10.1016/j.ympev.2020.106903_b0180) 2015; 6 Kozik (10.1016/j.ympev.2020.106903_b0135) 2019; 15 Thode (10.1016/j.ympev.2020.106903_b0255) 2020 Vellarikkal (10.1016/j.ympev.2020.106903_b0265) 2015; 36 Roy (10.1016/j.ympev.2020.106903_b0225) 2014; 25 Wolfe (10.1016/j.ympev.2020.106903_b0285) 2004; 29 Palmer (10.1016/j.ympev.2020.106903_b0195) 1983; 301 Birky (10.1016/j.ympev.2020.106903_b0025) 2001; 35 Doyle (10.1016/j.ympev.2020.106903_b0060) 1992; 17 Matsushima (10.1016/j.ympev.2020.106903_b0165) 2008; 49 Gitzendanner (10.1016/j.ympev.2020.106903_b0065) 2018; 105 Oldenburg (10.1016/j.ympev.2020.106903_b0185) 2004; 335 Hagemann (10.1016/j.ympev.2020.106903_b0105) 2004 Sloan (10.1016/j.ympev.2020.106903_b0245) 2013; 200 Ruhlman (10.1016/j.ympev.2020.106903_b0215) 2018 Zhang (10.1016/j.ympev.2020.106903_b0220) 2020; 69 Thyssen (10.1016/j.ympev.2020.106903_b0260) 2012; 72 Reboud (10.1016/j.ympev.2020.106903_b0210) 1994; 72 Zampini (10.1016/j.ympev.2020.106903_b0295) 2017 Léveillé-Bourret (10.1016/j.ympev.2020.106903_b0150) 2017; 67 Mogensen (10.1016/j.ympev.2020.106903_b0175) 1996; 83 Wicke (10.1016/j.ympev.2020.106903_b0275) 2011; 76 Kuroiwa (10.1016/j.ympev.2020.106903_b0140) 2010; 123 Ramsey (10.1016/j.ympev.2020.106903_b0205) 2019; 2 Maréchal (10.1016/j.ympev.2020.106903_b0155) 2010; 186 Breton (10.1016/j.ympev.2020.106903_b0040) 2015; 58 Gruenstaeudl (10.1016/j.ympev.2020.106903_b0080) 2019; 305 Bendich (10.1016/j.ympev.2020.106903_b0015) 2004; 16 Hagemann (10.1016/j.ympev.2020.106903_b0100) 2000; 91 Sato (10.1016/j.ympev.2020.106903_b0230) 2013; 1833 Kolodner (10.1016/j.ympev.2020.106903_b0125) 1975; 256 Wu (10.1016/j.ympev.2020.106903_b0290) 2020; 10 Zhang (10.1016/j.ympev.2020.106903_b0300) 2003; 44 Sparks (10.1016/j.ympev.2020.106903_b0250) 1980; 180 Phan (10.1016/j.ympev.2020.106903_b0200) 2019; 35 Oldenburg (10.1016/j.ympev.2020.106903_b0190) 1996; 8 Bohra (10.1016/j.ympev.2020.106903_b0035) 2016; 35 Kirk (10.1016/j.ympev.2020.106903_b0115) 1978 Gonçalves (10.1016/j.ympev.2020.106903_b0070) 2019; 138 Kim (10.1016/j.ympev.2020.106903_b0110) 2020 Choi (10.1016/j.ympev.2020.106903_b0045) 2019; 11 Gualberto (10.1016/j.ympev.2020.106903_b0085) 2017; 68 McCauley (10.1016/j.ympev.2020.106903_b0170) 2013; 200 Wilton (10.1016/j.ympev.2020.106903_b0280) 2018; 20 Bendich (10.1016/j.ympev.2020.106903_b0020) 1993; 24 Christensen (10.1016/j.ympev.2020.106903_b0050) 2018 Walker (10.1016/j.ympev.2020.106903_b0270) 2019; 7 |
| References_xml | – start-page: 2 year: 2004 end-page: 31 ident: b0105 article-title: The sexual inheritance of plant organelles publication-title: Molecular Biology and Biotechnology of Plant Organelles: Chloroplasts and Mitochondria – volume: 35 start-page: 4411 year: 2019 end-page: 4412 ident: b0200 article-title: icHET: Interactive visualization of cytoplasmic heteroplasmy publication-title: Bioinformatics – volume: 1833 start-page: 1979 year: 2013 end-page: 1984 ident: b0230 article-title: Maternal inheritance of mitochondrial DNA by diverse mechanisms to eliminate paternal mitochondrial DNA publication-title: Biochim. Biophys. Acta – volume: 49 start-page: 81 year: 2008 end-page: 91 ident: b0165 article-title: The model plant publication-title: Plant Cell Physiol. – start-page: 119 year: 2017 end-page: 163 ident: b0295 article-title: Plastid genome stability and repair publication-title: Somatic Genome Variation in Animals, Plants, and Microorganisms – volume: 6 start-page: 883 year: 2015 ident: b0180 article-title: DNA maintenance in plastids and mitochondria of plants publication-title: Front. Plant Sci. – volume: 20 start-page: 671 year: 2011 end-page: 691 ident: b0075 article-title: The role of plastids in plant speciation publication-title: Mol. Ecol. – volume: 22 start-page: 1948 year: 2005 end-page: 1963 ident: b0145 article-title: Identifying the basal angiosperm node in chloroplast genome phylogenies: sampling one’s way out of the Felsenstein zone publication-title: Mol. Biol. Evol. – volume: 50 start-page: 149 year: 2006 end-page: 159 ident: b0120 article-title: Heteroplasmy as a common state of mitochondrial genetic information in plants and animals publication-title: Curr. Genet. – volume: 335 start-page: 953 year: 2004 end-page: 970 ident: b0185 article-title: Most chloroplast DNA of maize seedlings in linear molecules with defined ends and branched forms publication-title: J. Mol. Biol. – volume: 186 start-page: 299 year: 2010 end-page: 317 ident: b0155 article-title: Recombination and the maintenance of plant organelle genome stability publication-title: New Phytol. – volume: 105 start-page: 291 year: 2018 end-page: 301 ident: b0065 article-title: Plastid phylogenomic analysis of green plants: a billion years of evolutionary history publication-title: Am. J. Bot. – volume: 20 start-page: 1261 year: 2018 end-page: 1274 ident: b0280 article-title: A population phylogenetic view of mitochondrial heteroplasmy publication-title: Genetics – volume: 28 start-page: 911 year: 2016 end-page: 929 ident: b0160 article-title: Spontaneous chloroplast mutants mostly occur by replication slippage and show a biased pattern in the plastome of publication-title: Plant Cell – volume: 72 start-page: 84 year: 2012 end-page: 88 ident: b0260 article-title: Exceptional inheritance of plastids via pollen in publication-title: Plant J. – volume: 92 start-page: 11331 year: 1995 end-page: 11338 ident: b0030 article-title: Uniparental inheritance of mitochondrial and chloroplast genes: mechanisms and evolution publication-title: Proc. Natl. Acad. Sci. USA – volume: 11 start-page: 1321 year: 2019 end-page: 1333 ident: b0045 article-title: Lost and found: Return of the inverted repeat in the legume clade defined by its absence publication-title: Genome Biol. Evol. – volume: 138 start-page: 219 year: 2019 end-page: 232 ident: b0070 article-title: Incongruence between species tree and gene trees and phylogenetic signal variation in plastid genes publication-title: Mol. Phylogenet. Evol. – volume: 17 start-page: 144 year: 1992 end-page: 163 ident: b0060 article-title: Gene trees and species trees: molecular systematics as one-character taxonomy publication-title: Syst. Bot. – volume: 10 start-page: 1077 year: 2020 end-page: 1086 ident: b0290 article-title: The tempo and mode of angiosperm mitochondrial genome divergence inferred from intraspecific variation in publication-title: G3-Genes Genom. Genet. – year: 2020 ident: b0255 article-title: Evaluating character partitioning and molecular models in plastid phylogenomics at low taxonomic levels: A case study using publication-title: J. Syst. Evol. – volume: 67 start-page: 94 year: 2017 end-page: 112 ident: b0150 article-title: Resolving rapid radiations within angiosperm families using anchored phylogenomics publication-title: Syst. Biol. – volume: 44 start-page: 941 year: 2003 end-page: 951 ident: b0300 article-title: Examination of the cytoplasmic DNA in male reproductive cells to determine the potential for cytoplasmic inheritance in 295 angiosperm species publication-title: Plant Cell Physiol. – volume: 69 start-page: 613 year: 2020 end-page: 622 ident: b0220 article-title: Exploration of plastid phylogenomic conflict yields new insights into the deep relationships of Leguminosae publication-title: Syst. Biol. – volume: 25 start-page: S13 year: 2014 end-page: S14 ident: b0225 article-title: Detecting and quantifying low level gene variants in Sanger sequencing traces using the ab1 peak reporter tool publication-title: J. Biomol. Tech. – volume: 58 start-page: 423 year: 2015 end-page: 431 ident: b0040 article-title: Atypical mitochondrial inheritance patterns in eukaryotes publication-title: Genome – volume: 72 start-page: 132 year: 1994 end-page: 140 ident: b0210 article-title: Organelle inheritance in plants publication-title: Heredity – volume: 35 start-page: 125 year: 2001 end-page: 148 ident: b0025 article-title: The inheritance of genes in mitochondria and chloroplasts: laws, mechanisms, and models publication-title: Annu. Rev. Genet. – volume: 68 start-page: 225 year: 2017 end-page: 252 ident: b0085 article-title: Plant mitochondrial genomes: dynamics and mechanisms of mutation publication-title: Annu. Rev. Plant Biol. – volume: 138 start-page: 53 year: 2019 end-page: 64 ident: b0240 article-title: Highly accelerated rates of genomic rearrangements and nucleotide substitutions in plastid genomes of publication-title: Mol. Phylogenet. Evol. – volume: 256 start-page: 708 year: 1975 end-page: 711 ident: b0125 article-title: Chloroplast DNA from higher plants replicates by both the Cairns and the rolling circle mechanism publication-title: Nature – volume: 76 start-page: 273 year: 2011 end-page: 297 ident: b0275 article-title: The evolution of the plastid chromosome in land plants: gene content, gene order, gene function publication-title: Plant Mol. Biol. – volume: 16 start-page: 1661 year: 2004 end-page: 1666 ident: b0015 article-title: Circular chloroplast chromosome: the grand illusion publication-title: Plant Cell – volume: 200 start-page: 978 year: 2013 end-page: 985 ident: b0245 article-title: One ring to rule them all? Genome sequencing provides new insights into the ‘master circle’ model of plant mitochondrial DNA structure publication-title: New Phytol. – volume: 35 start-page: 967 year: 2016 end-page: 993 ident: b0035 article-title: Cytoplasmic male sterility (CMS) in hybrid breeding in field crops publication-title: Plant Cell Rep. – volume: 15 start-page: e1008373 year: 2019 ident: b0135 article-title: The alternative reality of plant mitochondrial DNA: One ring does not rule them all publication-title: PLoS Genet. – volume: 305 start-page: 827 year: 2019 end-page: 836 ident: b0080 article-title: Why the monophyly of Nymphaeaceae currently remains indeterminate: an assessment based on gene-wise plastid phylogenomics publication-title: Plant. Syst. Evol. – start-page: 223 year: 2018 end-page: 262 ident: b0215 article-title: Chapter Eight – Aberration or analogy? The atypical plastomes of Geraniaceae publication-title: Advances in Botanical Research, Plastid Genome Evolution – year: 1978 ident: b0115 article-title: The Plastids. Their Chemistry, Structure, Growth and Inheritance – volume: 21 start-page: 287 year: 2013 end-page: 296 ident: b0010 article-title: DNA abandonment and the mechanisms of uniparental inheritance of mitochondria and chloroplasts publication-title: Chromosome Res. – volume: 91 start-page: 435 year: 2000 end-page: 440 ident: b0100 article-title: Erwin Baur or Carl Correns: who really created the theory of plastid inheritance? publication-title: J. Hered. – volume: 2 start-page: 1 year: 2019 end-page: 40 ident: b0205 article-title: When one genome is not enough: Organellar heteroplasmy in plants publication-title: Annu. Plant Rev. – volume: 29 start-page: 1011 year: 2004 end-page: 1020 ident: b0285 article-title: Recombination, heteroplasmy, haplotype polymorphism, and paralogy in plastid genes: implications for plant molecular systematics publication-title: Syst. Bot. – volume: 52 start-page: 817 year: 2007 end-page: 823 ident: b0005 article-title: Exceptional paternal inheritance of plastids in publication-title: Plant J. – volume: 200 start-page: 966 year: 2013 end-page: 977 ident: b0170 article-title: Paternal leakage, heteroplasmy, and the evolution of plant mitochondrial genomes publication-title: New Phytol. – volume: 301 start-page: 92 year: 1983 end-page: 93 ident: b0195 article-title: Chloroplast DNA exists in two orientations publication-title: Nature – start-page: 11 year: 2018 end-page: 32 ident: b0050 article-title: Mitochondrial DNA repair and genome evolution publication-title: Annual Plant Reviews Book Series – volume: 24 start-page: 279 year: 1993 end-page: 290 ident: b0020 article-title: Reaching for the ring: the study of mitochondrial genome structure publication-title: Curr. Genet. – volume: 83 start-page: 383 year: 1996 end-page: 404 ident: b0175 article-title: The hows and whys of cytoplasmic inheritance in seed plants publication-title: Am. J. Bot. – volume: 123 start-page: 207 year: 2010 end-page: 230 ident: b0140 article-title: Review of cytological studies on cellular and molecular mechanisms of uniparental (maternal or paternal) inheritance of plastid and mitochondrial genomes induced by active digestion of organelle nuclei (nucleoids) publication-title: J. Plant Res. – volume: 8 start-page: 447 year: 1996 end-page: 461 ident: b0190 article-title: Size and structure of replicating mitochondrial DNA in cultured tobacco cells publication-title: Plant Cell – volume: 76 start-page: 41 year: 1979 end-page: 45 ident: b0130 article-title: Inverted repeats in chloroplast DNA from higher plants publication-title: Proc. Natl. Acad. Sci. USA – volume: 75 start-page: 1443 year: 1988 end-page: 1458 ident: b0055 article-title: Rapid screening method to detect potential biparental inheritance of plastid DNA and results for over 200 angiosperm species publication-title: Am. J. Bot. – volume: 7 start-page: e7747 year: 2019 ident: b0270 article-title: Characterizing gene tree conflict in plastome-inferred phylogenies publication-title: PeerJ – volume: 36 start-page: 419 year: 2015 end-page: 424 ident: b0265 article-title: Mit-o-matic: A comprehensive computational pipeline for clinical evaluation of mitochondrial variations from next-generation sequencing datasets publication-title: Hum. Mutat. – volume: 1 start-page: 1 year: 2017 end-page: 10 ident: b0235 article-title: Contentious relationships in phylogenomic studies can be driven by a handful of genes publication-title: Nat. Ecol. Evol. – volume: 180 start-page: 351 year: 1980 end-page: 355 ident: b0250 article-title: Characterization of 3H-labeled supercoiled mitochondrial DNA from tobacco suspension culture cells publication-title: Mol. Gen. Genet. – year: 2020 ident: b0110 article-title: How well to multispecies coalescent methods perform with mitochondrial genomic data? A case study of butterflies and moths (Insecta: Lepdoptera) publication-title: Entomol. Syst. – volume: 92 start-page: 11331 year: 1995 ident: 10.1016/j.ympev.2020.106903_b0030 article-title: Uniparental inheritance of mitochondrial and chloroplast genes: mechanisms and evolution publication-title: Proc. Natl. Acad. Sci. USA doi: 10.1073/pnas.92.25.11331 – volume: 16 start-page: 1661 year: 2004 ident: 10.1016/j.ympev.2020.106903_b0015 article-title: Circular chloroplast chromosome: the grand illusion publication-title: Plant Cell doi: 10.1105/tpc.160771 – volume: 76 start-page: 273 year: 2011 ident: 10.1016/j.ympev.2020.106903_b0275 article-title: The evolution of the plastid chromosome in land plants: gene content, gene order, gene function publication-title: Plant Mol. Biol. doi: 10.1007/s11103-011-9762-4 – volume: 105 start-page: 291 year: 2018 ident: 10.1016/j.ympev.2020.106903_b0065 article-title: Plastid phylogenomic analysis of green plants: a billion years of evolutionary history publication-title: Am. J. Bot. doi: 10.1002/ajb2.1048 – volume: 72 start-page: 84 year: 2012 ident: 10.1016/j.ympev.2020.106903_b0260 article-title: Exceptional inheritance of plastids via pollen in Nicotiana sylvestris with no detectable paternal mitochondrial DNA in the progeny publication-title: Plant J. doi: 10.1111/j.1365-313X.2012.05057.x – start-page: 2 year: 2004 ident: 10.1016/j.ympev.2020.106903_b0105 article-title: The sexual inheritance of plant organelles – volume: 36 start-page: 419 year: 2015 ident: 10.1016/j.ympev.2020.106903_b0265 article-title: Mit-o-matic: A comprehensive computational pipeline for clinical evaluation of mitochondrial variations from next-generation sequencing datasets publication-title: Hum. Mutat. doi: 10.1002/humu.22767 – volume: 35 start-page: 125 year: 2001 ident: 10.1016/j.ympev.2020.106903_b0025 article-title: The inheritance of genes in mitochondria and chloroplasts: laws, mechanisms, and models publication-title: Annu. Rev. Genet. doi: 10.1146/annurev.genet.35.102401.090231 – volume: 10 start-page: 1077 year: 2020 ident: 10.1016/j.ympev.2020.106903_b0290 article-title: The tempo and mode of angiosperm mitochondrial genome divergence inferred from intraspecific variation in Arabidopsis thaliana publication-title: G3-Genes Genom. Genet. doi: 10.1534/g3.119.401023 – volume: 28 start-page: 911 year: 2016 ident: 10.1016/j.ympev.2020.106903_b0160 article-title: Spontaneous chloroplast mutants mostly occur by replication slippage and show a biased pattern in the plastome of Oenothera publication-title: Plant Cell doi: 10.1105/tpc.15.00879 – volume: 58 start-page: 423 year: 2015 ident: 10.1016/j.ympev.2020.106903_b0040 article-title: Atypical mitochondrial inheritance patterns in eukaryotes publication-title: Genome doi: 10.1139/gen-2015-0090 – start-page: 223 year: 2018 ident: 10.1016/j.ympev.2020.106903_b0215 article-title: Chapter Eight – Aberration or analogy? The atypical plastomes of Geraniaceae doi: 10.1016/bs.abr.2017.11.017 – volume: 11 start-page: 1321 year: 2019 ident: 10.1016/j.ympev.2020.106903_b0045 article-title: Lost and found: Return of the inverted repeat in the legume clade defined by its absence publication-title: Genome Biol. Evol. doi: 10.1093/gbe/evz076 – volume: 301 start-page: 92 year: 1983 ident: 10.1016/j.ympev.2020.106903_b0195 article-title: Chloroplast DNA exists in two orientations publication-title: Nature doi: 10.1038/301092a0 – volume: 200 start-page: 978 year: 2013 ident: 10.1016/j.ympev.2020.106903_b0245 article-title: One ring to rule them all? Genome sequencing provides new insights into the ‘master circle’ model of plant mitochondrial DNA structure publication-title: New Phytol. doi: 10.1111/nph.12395 – volume: 180 start-page: 351 year: 1980 ident: 10.1016/j.ympev.2020.106903_b0250 article-title: Characterization of 3H-labeled supercoiled mitochondrial DNA from tobacco suspension culture cells publication-title: Mol. Gen. Genet. doi: 10.1007/BF00425847 – volume: 8 start-page: 447 year: 1996 ident: 10.1016/j.ympev.2020.106903_b0190 article-title: Size and structure of replicating mitochondrial DNA in cultured tobacco cells publication-title: Plant Cell doi: 10.2307/3870324 – volume: 20 start-page: 671 year: 2011 ident: 10.1016/j.ympev.2020.106903_b0075 article-title: The role of plastids in plant speciation publication-title: Mol. Ecol. doi: 10.1111/j.1365-294X.2010.04984.x – volume: 200 start-page: 966 year: 2013 ident: 10.1016/j.ympev.2020.106903_b0170 article-title: Paternal leakage, heteroplasmy, and the evolution of plant mitochondrial genomes publication-title: New Phytol. doi: 10.1111/nph.12431 – volume: 72 start-page: 132 year: 1994 ident: 10.1016/j.ympev.2020.106903_b0210 article-title: Organelle inheritance in plants publication-title: Heredity doi: 10.1038/hdy.1994.19 – volume: 305 start-page: 827 year: 2019 ident: 10.1016/j.ympev.2020.106903_b0080 article-title: Why the monophyly of Nymphaeaceae currently remains indeterminate: an assessment based on gene-wise plastid phylogenomics publication-title: Plant. Syst. Evol. doi: 10.1007/s00606-019-01610-5 – volume: 76 start-page: 41 year: 1979 ident: 10.1016/j.ympev.2020.106903_b0130 article-title: Inverted repeats in chloroplast DNA from higher plants publication-title: Proc. Natl. Acad. Sci. USA doi: 10.1073/pnas.76.1.41 – volume: 15 start-page: e1008373 year: 2019 ident: 10.1016/j.ympev.2020.106903_b0135 article-title: The alternative reality of plant mitochondrial DNA: One ring does not rule them all publication-title: PLoS Genet. doi: 10.1371/journal.pgen.1008373 – volume: 7 start-page: e7747 year: 2019 ident: 10.1016/j.ympev.2020.106903_b0270 article-title: Characterizing gene tree conflict in plastome-inferred phylogenies publication-title: PeerJ doi: 10.7717/peerj.7747 – volume: 6 start-page: 883 year: 2015 ident: 10.1016/j.ympev.2020.106903_b0180 article-title: DNA maintenance in plastids and mitochondria of plants publication-title: Front. Plant Sci. doi: 10.3389/fpls.2015.00883 – volume: 25 start-page: S13 year: 2014 ident: 10.1016/j.ympev.2020.106903_b0225 article-title: Detecting and quantifying low level gene variants in Sanger sequencing traces using the ab1 peak reporter tool publication-title: J. Biomol. Tech. – volume: 335 start-page: 953 year: 2004 ident: 10.1016/j.ympev.2020.106903_b0185 article-title: Most chloroplast DNA of maize seedlings in linear molecules with defined ends and branched forms publication-title: J. Mol. Biol. doi: 10.1016/j.jmb.2003.11.020 – volume: 123 start-page: 207 year: 2010 ident: 10.1016/j.ympev.2020.106903_b0140 article-title: Review of cytological studies on cellular and molecular mechanisms of uniparental (maternal or paternal) inheritance of plastid and mitochondrial genomes induced by active digestion of organelle nuclei (nucleoids) publication-title: J. Plant Res. doi: 10.1007/s10265-009-0306-9 – volume: 75 start-page: 1443 year: 1988 ident: 10.1016/j.ympev.2020.106903_b0055 article-title: Rapid screening method to detect potential biparental inheritance of plastid DNA and results for over 200 angiosperm species publication-title: Am. J. Bot. doi: 10.1002/j.1537-2197.1988.tb11219.x – volume: 138 start-page: 53 year: 2019 ident: 10.1016/j.ympev.2020.106903_b0240 article-title: Highly accelerated rates of genomic rearrangements and nucleotide substitutions in plastid genomes of Passiflora subgenus Decaloba publication-title: Mol. Phylogenet. Evol. doi: 10.1016/j.ympev.2019.05.030 – volume: 49 start-page: 81 year: 2008 ident: 10.1016/j.ympev.2020.106903_b0165 article-title: The model plant Medicago truncatula exhibits biparental plastid inheritance publication-title: Plant Cell Physiol. doi: 10.1093/pcp/pcm170 – volume: 2 start-page: 1 year: 2019 ident: 10.1016/j.ympev.2020.106903_b0205 article-title: When one genome is not enough: Organellar heteroplasmy in plants publication-title: Annu. Plant Rev. – volume: 35 start-page: 967 year: 2016 ident: 10.1016/j.ympev.2020.106903_b0035 article-title: Cytoplasmic male sterility (CMS) in hybrid breeding in field crops publication-title: Plant Cell Rep. doi: 10.1007/s00299-016-1949-3 – year: 1978 ident: 10.1016/j.ympev.2020.106903_b0115 – volume: 17 start-page: 144 year: 1992 ident: 10.1016/j.ympev.2020.106903_b0060 article-title: Gene trees and species trees: molecular systematics as one-character taxonomy publication-title: Syst. Bot. doi: 10.2307/2419070 – volume: 1 start-page: 1 year: 2017 ident: 10.1016/j.ympev.2020.106903_b0235 article-title: Contentious relationships in phylogenomic studies can be driven by a handful of genes publication-title: Nat. Ecol. Evol. doi: 10.1038/s41559-017-0126 – start-page: 119 year: 2017 ident: 10.1016/j.ympev.2020.106903_b0295 article-title: Plastid genome stability and repair – volume: 69 start-page: 613 year: 2020 ident: 10.1016/j.ympev.2020.106903_b0220 article-title: Exploration of plastid phylogenomic conflict yields new insights into the deep relationships of Leguminosae publication-title: Syst. Biol. doi: 10.1093/sysbio/syaa013 – volume: 91 start-page: 435 year: 2000 ident: 10.1016/j.ympev.2020.106903_b0100 article-title: Erwin Baur or Carl Correns: who really created the theory of plastid inheritance? publication-title: J. Hered. doi: 10.1093/jhered/91.6.435 – volume: 67 start-page: 94 year: 2017 ident: 10.1016/j.ympev.2020.106903_b0150 article-title: Resolving rapid radiations within angiosperm families using anchored phylogenomics publication-title: Syst. Biol. doi: 10.1093/sysbio/syx050 – volume: 44 start-page: 941 year: 2003 ident: 10.1016/j.ympev.2020.106903_b0300 article-title: Examination of the cytoplasmic DNA in male reproductive cells to determine the potential for cytoplasmic inheritance in 295 angiosperm species publication-title: Plant Cell Physiol. doi: 10.1093/pcp/pcg121 – volume: 22 start-page: 1948 year: 2005 ident: 10.1016/j.ympev.2020.106903_b0145 article-title: Identifying the basal angiosperm node in chloroplast genome phylogenies: sampling one’s way out of the Felsenstein zone publication-title: Mol. Biol. Evol. doi: 10.1093/molbev/msi191 – volume: 83 start-page: 383 year: 1996 ident: 10.1016/j.ympev.2020.106903_b0175 article-title: The hows and whys of cytoplasmic inheritance in seed plants publication-title: Am. J. Bot. doi: 10.1002/j.1537-2197.1996.tb12718.x – start-page: 11 year: 2018 ident: 10.1016/j.ympev.2020.106903_b0050 article-title: Mitochondrial DNA repair and genome evolution – volume: 186 start-page: 299 year: 2010 ident: 10.1016/j.ympev.2020.106903_b0155 article-title: Recombination and the maintenance of plant organelle genome stability publication-title: New Phytol. doi: 10.1111/j.1469-8137.2010.03195.x – volume: 20 start-page: 1261 year: 2018 ident: 10.1016/j.ympev.2020.106903_b0280 article-title: A population phylogenetic view of mitochondrial heteroplasmy publication-title: Genetics doi: 10.1534/genetics.118.300711 – volume: 50 start-page: 149 year: 2006 ident: 10.1016/j.ympev.2020.106903_b0120 article-title: Heteroplasmy as a common state of mitochondrial genetic information in plants and animals publication-title: Curr. Genet. doi: 10.1007/s00294-006-0082-1 – year: 2020 ident: 10.1016/j.ympev.2020.106903_b0110 article-title: How well to multispecies coalescent methods perform with mitochondrial genomic data? A case study of butterflies and moths (Insecta: Lepdoptera) publication-title: Entomol. Syst. doi: 10.1111/syen.12431 – volume: 52 start-page: 817 year: 2007 ident: 10.1016/j.ympev.2020.106903_b0005 article-title: Exceptional paternal inheritance of plastids in Arabidopsis suggests that low-frequency leakage of plastids via pollen may be universal in plants publication-title: Plant J. doi: 10.1111/j.1365-313X.2007.03278.x – volume: 1833 start-page: 1979 year: 2013 ident: 10.1016/j.ympev.2020.106903_b0230 article-title: Maternal inheritance of mitochondrial DNA by diverse mechanisms to eliminate paternal mitochondrial DNA publication-title: Biochim. Biophys. Acta doi: 10.1016/j.bbamcr.2013.03.010 – volume: 256 start-page: 708 year: 1975 ident: 10.1016/j.ympev.2020.106903_b0125 article-title: Chloroplast DNA from higher plants replicates by both the Cairns and the rolling circle mechanism publication-title: Nature doi: 10.1038/256708a0 – volume: 24 start-page: 279 year: 1993 ident: 10.1016/j.ympev.2020.106903_b0020 article-title: Reaching for the ring: the study of mitochondrial genome structure publication-title: Curr. Genet. doi: 10.1007/BF00336777 – year: 2020 ident: 10.1016/j.ympev.2020.106903_b0255 article-title: Evaluating character partitioning and molecular models in plastid phylogenomics at low taxonomic levels: A case study using Amphilophium (Bignonieae, Bignoniaceae) publication-title: J. Syst. Evol. doi: 10.1111/jse.12579 – volume: 138 start-page: 219 year: 2019 ident: 10.1016/j.ympev.2020.106903_b0070 article-title: Incongruence between species tree and gene trees and phylogenetic signal variation in plastid genes publication-title: Mol. Phylogenet. Evol. doi: 10.1016/j.ympev.2019.05.022 – volume: 29 start-page: 1011 year: 2004 ident: 10.1016/j.ympev.2020.106903_b0285 article-title: Recombination, heteroplasmy, haplotype polymorphism, and paralogy in plastid genes: implications for plant molecular systematics publication-title: Syst. Bot. doi: 10.1600/0363644042451008 – volume: 68 start-page: 225 year: 2017 ident: 10.1016/j.ympev.2020.106903_b0085 article-title: Plant mitochondrial genomes: dynamics and mechanisms of mutation publication-title: Annu. Rev. Plant Biol. doi: 10.1146/annurev-arplant-043015-112232 – volume: 35 start-page: 4411 year: 2019 ident: 10.1016/j.ympev.2020.106903_b0200 article-title: icHET: Interactive visualization of cytoplasmic heteroplasmy publication-title: Bioinformatics doi: 10.1093/bioinformatics/btz300 – volume: 21 start-page: 287 year: 2013 ident: 10.1016/j.ympev.2020.106903_b0010 article-title: DNA abandonment and the mechanisms of uniparental inheritance of mitochondria and chloroplasts publication-title: Chromosome Res. doi: 10.1007/s10577-013-9349-9 |
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| Title | Under the rug: Abandoning persistent misconceptions that obfuscate organelle evolution |
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