TY - JOUR AU - Tonti-Filippini, J. AU - Nevill, P. G. AU - Dixon, K. AU - Small, I. PY - 2017 DA - 2017// TI - What can we do with 1000 plastid genomes? JO - Plant J VL - 90 UR - https://doi.org/10.1111/tpj.13491 DO - 10.1111/tpj.13491 ID - Tonti-Filippini2017 ER - TY - JOUR AU - Knoop, V. PY - 2004 DA - 2004// TI - The mitochondrial DNA of land plants: peculiarities in phylogenetic perspective JO - Curr Genet VL - 46 UR - https://doi.org/10.1007/s00294-004-0522-8 DO - 10.1007/s00294-004-0522-8 ID - Knoop2004 ER - TY - JOUR AU - Chaw, S. M. AU - Shih, A. C. AU - Wang, D. AU - Wu, Y. W. AU - Liu, S. M. AU - Chou, T. Y. PY - 2008 DA - 2008// TI - The mitochondrial genome of the gymnosperm Cycas taitungensis contains a novel family of short interspersed elements, Bpu sequences, and abundant RNA editing sites JO - Mol Biol Evol VL - 25 UR - https://doi.org/10.1093/molbev/msn009 DO - 10.1093/molbev/msn009 ID - Chaw2008 ER - TY - JOUR AU - Guo, W. AU - Grewe, F. AU - Fan, W. AU - Young, G. J. AU - Knoop, V. AU - Palmer, J. D. AU - Mower, J. P. PY - 2016 DA - 2016// TI - Ginkgo and Welwitschia mitogenomes reveal extreme contrasts in gymnosperm mitochondrial evolution JO - Mol Biol Evol VL - 33 UR - https://doi.org/10.1093/molbev/msw024 DO - 10.1093/molbev/msw024 ID - Guo2016 ER - TY - JOUR AU - Sullivan, A. l. e. x. i. s. R. AU - Eldfjell, Y. r. i. n. AU - Schiffthaler, B. a. s. t. i. a. n. AU - Delhomme, N. i. c. o. l. a. s. AU - Asp, T. o. r. b. e. n. AU - Hebelstrup, K. i. m. H. AU - Keech, O. l. i. v. i. e. r. AU - Öberg, L. i. s. a. AU - Møller, I. a. n. M. a. x. AU - Arvestad, L. a. r. s. AU - Street, N. a. t. h. a. n. i. e. l. R. AU - Wang, X. i. a. o. -. R. u. PY - 2019 DA - 2019// TI - The Mitogenome of Norway Spruce and a Reappraisal of Mitochondrial Recombination in Plants JO - Genome Biology and Evolution VL - 12 UR - https://doi.org/10.1093/gbe/evz263 DO - 10.1093/gbe/evz263 ID - Sullivan2019 ER - TY - STD TI - Jackman SD, Coombe L, Warren RL, Kirk H, Trinh E, McLeod T, Pleasance S, Pandoh P, Zhao Y, Coope RJ, et al. Largest complete mitochondrial genome of a gymnosperm, Sitka Spruce (Picea sitchensis), indicates complex physical structure. bioRxiv. 2019;601104. ID - ref6 ER - TY - JOUR AU - Nystedt, B. AU - Street, N. R. AU - Wetterbom, A. AU - Zuccolo, A. AU - Lin, Y. C. AU - Scofield, D. G. AU - Vezzi, F. AU - Delhomme, N. AU - Giacomello, S. AU - Alexeyenko, A. PY - 2013 DA - 2013// TI - The Norway spruce genome sequence and conifer genome evolution JO - Nature. VL - 497 UR - https://doi.org/10.1038/nature12211 DO - 10.1038/nature12211 ID - Nystedt2013 ER - TY - JOUR AU - Ran, J. -. H. AU - Shen, T. -. T. AU - Wang, M. -. M. AU - Wang, X. -. Q. PY - 2018 DA - 2018// TI - Phylogenomics resolves the deep phylogeny of seed plants and indicates partial convergent or homoplastic evolution between Gnetales and angiosperms JO - Proc R Soc B VL - 285 UR - https://doi.org/10.1098/rspb.2018.1012 DO - 10.1098/rspb.2018.1012 ID - Ran2018 ER - TY - JOUR AU - Wang, X. -. Q. AU - Ran, J. -. H. PY - 2014 DA - 2014// TI - Evolution and biogeography of gymnosperms JO - Mol Phylogenet Evol VL - 75 UR - https://doi.org/10.1016/j.ympev.2014.02.005 DO - 10.1016/j.ympev.2014.02.005 ID - Wang2014 ER - TY - JOUR AU - Bowe, L. M. AU - Coat, G. AU - dePamphilis, C. W. PY - 2000 DA - 2000// TI - Phylogeny of seed plants based on all three genomic compartments: Extant gymnosperms are monophyletic and Gnetales' closest relatives are conifers JO - Proc Natl Acad Sci USA VL - 97 UR - https://doi.org/10.1073/pnas.97.8.4092 DO - 10.1073/pnas.97.8.4092 ID - Bowe2000 ER - TY - JOUR AU - Lu, Y. AU - Ran, J. -. H. AU - Guo, D. -. M. AU - Yang, Z. -. Y. AU - Wang, X. -. Q. PY - 2014 DA - 2014// TI - Phylogeny and divergence times of gymnosperms inferred from single-copy nuclear genes JO - PLoS One VL - 9 UR - https://doi.org/10.1371/journal.pone.0107679 DO - 10.1371/journal.pone.0107679 ID - Lu2014 ER - TY - BOOK AU - Farjón, A. PY - 2001 DA - 2001// TI - World checklist and bibliography of conifers PB - Royal Bot. Gard CY - Kew, England ID - Farjón2001 ER - TY - JOUR AU - Li, J. -. Y. AU - Wen, Y. -. D. AU - Jiang, C. -. Y. AU - Li, F. AU - Gao, C. -. C. PY - 2000 DA - 2000// TI - A simple and rapid method for isolating mitochondrial plasmid DNA from plant JO - Acta Sci Nat Univ Nankai VL - 33 ID - Li2000 ER - TY - JOUR AU - Khanam, S. M. AU - Naydenov, N. G. AU - Kadowaki, K. I. AU - Nakamura, C. PY - 2007 DA - 2007// TI - Mitochondrial biogenesis as revealed by mitochondrial transcript profiles during germination and early seedling growth in wheat JO - Genes Genet Syst VL - 82 UR - https://doi.org/10.1266/ggs.82.409 DO - 10.1266/ggs.82.409 ID - Khanam2007 ER - TY - JOUR AU - Bolger, A. M. AU - Lohse, M. AU - Usadel, B. PY - 2014 DA - 2014// TI - Trimmomatic: a flexible trimmer for Illumina sequence data JO - Bioinformatics. VL - 30 UR - https://doi.org/10.1093/bioinformatics/btu170 DO - 10.1093/bioinformatics/btu170 ID - Bolger2014 ER - TY - JOUR AU - Zhao, N. AU - Wang, Y. AU - Hua, J. PY - 2018 DA - 2018// TI - The roles of mitochondrion in intergenomic gene transfer in plants: a source and a pool JO - Int J Mol Sci VL - 19 UR - https://doi.org/10.3390/ijms19020547 DO - 10.3390/ijms19020547 ID - Zhao2018 ER - TY - CHAP AU - Knoop, V. o. l. k. e. r. PY - 2012 DA - 2012// TI - Seed Plant Mitochondrial Genomes: Complexity Evolving BT - Advances in Photosynthesis and Respiration PB - Springer Netherlands CY - Dordrecht ID - Knoop2012 ER - TY - JOUR AU - Park, S. AU - Grewe, F. AU - Zhu, A. AU - Ruhlman, T. A. AU - Sabir, J. AU - Mower, J. P. AU - Jansen, R. K. PY - 2015 DA - 2015// TI - Dynamic evolution of Geranium mitochondrial genomes through multiple horizontal and intracellular gene transfers JO - New Phytol VL - 208 UR - https://doi.org/10.1111/nph.13467 DO - 10.1111/nph.13467 ID - Park2015 ER - TY - JOUR AU - Sanchez-Puerta, M. V. AU - Garcia, L. E. AU - Wohlfeiler, J. AU - Ceriotti, L. F. PY - 2017 DA - 2017// TI - Unparalleled replacement of native mitochondrial genes by foreign homologs in a holoparasitic plant JO - New Phytol VL - 214 UR - https://doi.org/10.1111/nph.14361 DO - 10.1111/nph.14361 ID - Sanchez-Puerta2017 ER - TY - JOUR AU - Cheng, N. AU - Lo, Y. S. AU - Ansari, M. I. AU - Ho, K. C. AU - Jeng, S. T. AU - Lin, N. S. AU - Dai, H. PY - 2017 DA - 2017// TI - Correlation between mtDNA complexity and mtDNA replication mode in developing cotyledon mitochondria during mung bean seed germination JO - New Phytol VL - 213 UR - https://doi.org/10.1111/nph.14158 DO - 10.1111/nph.14158 ID - Cheng2017 ER - TY - JOUR AU - Wu, Z. AU - Cuthbert, J. M. AU - Taylor, D. R. AU - Sloan, D. B. PY - 2015 DA - 2015// TI - The massive mitochondrial genome of the angiosperm Silene noctiflora is evolving by gain or loss of entire chromosomes JO - Proc Natl Acad Sci U S A VL - 112 UR - https://doi.org/10.1073/pnas.1421397112 DO - 10.1073/pnas.1421397112 ID - Wu2015 ER - TY - JOUR AU - Gui, S. AU - Wu, Z. AU - Zhang, H. AU - Zheng, Y. AU - Zhu, Z. AU - Liang, D. AU - Ding, Y. PY - 2016 DA - 2016// TI - The mitochondrial genome map of Nelumbo nucifera reveals ancient evolutionary features JO - Sci Rep VL - 6 UR - https://doi.org/10.1038/srep30158 DO - 10.1038/srep30158 ID - Gui2016 ER - TY - JOUR AU - Ye, N. AU - Wang, X. AU - Li, J. AU - Bi, C. AU - Xu, Y. AU - Wu, D. AU - Ye, Q. PY - 2017 DA - 2017// TI - Assembly and comparative analysis of complete mitochondrial genome sequence of an economic plant Salix suchowensis JO - PeerJ. VL - 5 UR - https://doi.org/10.7717/peerj.3148 DO - 10.7717/peerj.3148 ID - Ye2017 ER - TY - JOUR AU - Bankevich, A. AU - Nurk, S. AU - Antipov, D. AU - Gurevich, A. A. AU - Dvorkin, M. AU - Kulikov, A. S. AU - Lesin, V. M. AU - Nikolenko, S. I. AU - Pham, S. AU - Prjibelski, A. D. PY - 2012 DA - 2012// TI - SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing JO - J Comput Biol VL - 19 UR - https://doi.org/10.1089/cmb.2012.0021 DO - 10.1089/cmb.2012.0021 ID - Bankevich2012 ER - TY - JOUR AU - Lang, B. F. AU - Laforest, M. J. AU - Burger, G. PY - 2007 DA - 2007// TI - Mitochondrial introns: a critical view JO - Trends Genet VL - 23 UR - https://doi.org/10.1016/j.tig.2007.01.006 DO - 10.1016/j.tig.2007.01.006 ID - Lang2007 ER - TY - JOUR AU - Sandoval, P. AU - Leon, G. AU - Gomez, I. AU - Carmona, R. AU - Figueroa, P. AU - Holuigue, L. AU - Araya, A. AU - Jordana, X. PY - 2004 DA - 2004// TI - Transfer of RPS14 and RPL5 from the mitochondrion to the nucleus in grasses JO - Gene. VL - 324 UR - https://doi.org/10.1016/j.gene.2003.09.027 DO - 10.1016/j.gene.2003.09.027 ID - Sandoval2004 ER - TY - JOUR AU - Kurihara-Yonemoto, S. AU - Kubo, T. PY - 2010 DA - 2010// TI - Increased accumulation of intron-containing transcripts in rice mitochondria caused by low temperature: is cold-sensitive RNA editing implicated? JO - Curr Genet VL - 56 UR - https://doi.org/10.1007/s00294-010-0320-4 DO - 10.1007/s00294-010-0320-4 ID - Kurihara-Yonemoto2010 ER - TY - JOUR AU - Camacho, C. AU - Coulouris, G. AU - Avagyan, V. AU - Ma, N. AU - Papadopoulos, J. AU - Bealer, K. AU - Madden, T. L. PY - 2009 DA - 2009// TI - BLAST+: architecture and applications JO - BMC Bioinformatics VL - 10 UR - https://doi.org/10.1186/1471-2105-10-421 DO - 10.1186/1471-2105-10-421 ID - Camacho2009 ER - TY - JOUR AU - Chaisson, M. J. AU - Tesler, G. PY - 2012 DA - 2012// TI - Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory JO - BMC Bioinformatics. VL - 13 UR - https://doi.org/10.1186/1471-2105-13-238 DO - 10.1186/1471-2105-13-238 ID - Chaisson2012 ER - TY - JOUR AU - Koren, S. AU - Walenz, B. P. AU - Berlin, K. AU - Miller, J. R. AU - Bergman, N. H. AU - Phillippy, A. M. PY - 2017 DA - 2017// TI - Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation JO - Genome Res VL - 27 UR - https://doi.org/10.1101/gr.215087.116 DO - 10.1101/gr.215087.116 ID - Koren2017 ER - TY - JOUR AU - Walker, B. J. AU - Abeel, T. AU - Shea, T. AU - Priest, M. AU - Abouelliel, A. AU - Sakthikumar, S. AU - Cuomo, C. A. AU - Zeng, Q. AU - Wortman, J. AU - Young, S. K. PY - 2014 DA - 2014// TI - Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement JO - PLoS One VL - 9 UR - https://doi.org/10.1371/journal.pone.0112963 DO - 10.1371/journal.pone.0112963 ID - Walker2014 ER - TY - JOUR AU - Langmead, B. AU - Salzberg, S. L. PY - 2012 DA - 2012// TI - Fast gapped-read alignment with bowtie 2 JO - Nat Methods VL - 9 UR - https://doi.org/10.1038/nmeth.1923 DO - 10.1038/nmeth.1923 ID - Langmead2012 ER - TY - JOUR AU - Kurtz, S. AU - Phillippy, A. AU - Delcher, A. L. AU - Smoot, M. AU - Shumway, M. AU - Antonescu, C. AU - Salzberg, S. L. PY - 2004 DA - 2004// TI - Versatile and open software for comparing large genomes JO - Genome Biol VL - 5 UR - https://doi.org/10.1186/gb-2004-5-2-r12 DO - 10.1186/gb-2004-5-2-r12 ID - Kurtz2004 ER - TY - JOUR AU - Nakamura, T. AU - Yamada, K. D. AU - Tomii, K. AU - Katoh, K. PY - 2018 DA - 2018// TI - Parallelization of MAFFT for large-scale multiple sequence alignments JO - Bioinformatics. VL - 34 UR - https://doi.org/10.1093/bioinformatics/bty121 DO - 10.1093/bioinformatics/bty121 ID - Nakamura2018 ER - TY - JOUR AU - Lowe, T. M. AU - Chan, P. P. PY - 2016 DA - 2016// TI - tRNAscan-SE on-line: integrating search and context for analysis of transfer RNA genes JO - Nucleic Acids Res VL - 44 UR - https://doi.org/10.1093/nar/gkw413 DO - 10.1093/nar/gkw413 ID - Lowe2016 ER - TY - JOUR AU - Conesa, A. AU - Gotz, S. AU - Garcia-Gomez, J. M. AU - Terol, J. AU - Talon, M. AU - Robles, M. PY - 2005 DA - 2005// TI - Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research JO - Bioinformatics. VL - 21 UR - https://doi.org/10.1093/bioinformatics/bti610 DO - 10.1093/bioinformatics/bti610 ID - Conesa2005 ER - TY - JOUR AU - Lohse, M. AU - Drechsel, O. AU - Kahlau, S. AU - Bock, R. PY - 2013 DA - 2013// TI - OrganellarGenomeDRAW--a suite of tools for generating physical maps of plastid and mitochondrial genomes and visualizing expression data sets JO - Nucleic Acids Res VL - 41 UR - https://doi.org/10.1093/nar/gkt289 DO - 10.1093/nar/gkt289 ID - Lohse2013 ER - TY - JOUR AU - Wang, Z. AU - Lian, J. AU - Li, Q. AU - Zhang, P. AU - Zhou, Y. AU - Zhan, X. AU - Zhang, G. PY - 2016 DA - 2016// TI - RES-scanner: a software package for genome-wide identification of RNA-editing sites JO - GigaScience. VL - 5 UR - https://doi.org/10.1186/s13742-016-0143-4 DO - 10.1186/s13742-016-0143-4 ID - Wang2016 ER - TY - JOUR AU - Mower, J. P. PY - 2009 DA - 2009// TI - The PREP suite: predictive RNA editors for plant mitochondrial genes, chloroplast genes and user-defined alignments JO - Nucleic Acids Res VL - 37 UR - https://doi.org/10.1093/nar/gkp337 DO - 10.1093/nar/gkp337 ID - Mower2009 ER - TY - JOUR AU - Wysoker, A. AU - Fennell, T. AU - Ruan, J. AU - Homer, N. AU - Marth, G. AU - Abecasis, G. AU - Durbin, R. J. B. PY - 2009 DA - 2009// TI - The sequence alignment/map (SAM) format and SAMtools JO - Bioinformatics. VL - 25 UR - https://doi.org/10.1093/bioinformatics/btp352 DO - 10.1093/bioinformatics/btp352 ID - Wysoker2009 ER - TY - JOUR AU - Ran, J. -. H. AU - Gao, H. AU - Wang, X. -. Q. PY - 2010 DA - 2010// TI - Fast evolution of the retroprocessed mitochondrial rps3 gene in conifer II and further evidence for the phylogeny of gymnosperms JO - Mol Phylogenet Evol VL - 54 UR - https://doi.org/10.1016/j.ympev.2009.09.011 DO - 10.1016/j.ympev.2009.09.011 ID - Ran2010 ER - TY - JOUR AU - Benson, G. PY - 1999 DA - 1999// TI - Tandem repeats finder: a program to analyze DNA sequences JO - Nucl Acids Res. VL - 27 UR - https://doi.org/10.1093/nar/27.2.573 DO - 10.1093/nar/27.2.573 ID - Benson1999 ER - TY - JOUR AU - Krzywinski, M. AU - Schein, J. AU - Birol, I. AU - Connors, J. AU - Gascoyne, R. AU - Horsman, D. AU - Jones, S. J. AU - Marra, M. A. PY - 2009 DA - 2009// TI - Circos: an information aesthetic for comparative genomics JO - Genome Res VL - 19 UR - https://doi.org/10.1101/gr.092759.109 DO - 10.1101/gr.092759.109 ID - Krzywinski2009 ER - TY - JOUR AU - Kubo, N. AU - Arimura, S. PY - 2010 DA - 2010// TI - Discovery of the rpl10 gene in diverse plant mitochondrial genomes and its probable replacement by the nuclear gene for chloroplast RPL10 in two lineages of angiosperms JO - DNA Res VL - 17 UR - https://doi.org/10.1093/dnares/dsp024 DO - 10.1093/dnares/dsp024 ID - Kubo2010 ER - TY - JOUR AU - Lenz, H. AU - Hein, A. AU - Knoop, V. PY - 2018 DA - 2018// TI - Plant organelle RNA editing and its specificity factors: enhancements of analyses and new database features in PREPACT 3.0 JO - BMC Bioinformatics VL - 19 UR - https://doi.org/10.1186/s12859-018-2244-9 DO - 10.1186/s12859-018-2244-9 ID - Lenz2018 ER - TY - JOUR AU - Richardson, A. O. AU - Rice, D. W. AU - Young, G. J. AU - Alverson, A. J. AU - Palmer, J. D. PY - 2013 DA - 2013// TI - The "fossilized" mitochondrial genome of Liriodendron tulipifera: ancestral gene content and order, ancestral editing sites, and extraordinarily low mutation rate JO - BMC Biol VL - 11 UR - https://doi.org/10.1186/1741-7007-11-29 DO - 10.1186/1741-7007-11-29 ID - Richardson2013 ER - TY - JOUR AU - Adams, K. L. AU - Qiu, Y. L. AU - Stoutemyer, M. AU - Palmer, J. D. PY - 2002 DA - 2002// TI - Punctuated evolution of mitochondrial gene content: high and variable rates of mitochondrial gene loss and transfer to the nucleus during angiosperm evolution JO - Proc Natl Acad Sci U S A VL - 99 UR - https://doi.org/10.1073/pnas.042694899 DO - 10.1073/pnas.042694899 ID - Adams2002 ER - TY - JOUR AU - Adams, K. L. AU - Palmer, J. D. PY - 2003 DA - 2003// TI - Evolution of mitochondrial gene content: gene loss and transfer to the nucleus JO - Mol Phylogenet Evol VL - 29 UR - https://doi.org/10.1016/S1055-7903(03)00194-5 DO - 10.1016/S1055-7903(03)00194-5 ID - Adams2003 ER - TY - JOUR AU - Bonen, L. AU - Calixte, S. PY - 2006 DA - 2006// TI - Comparative analysis of bacterial-origin genes for plant mitochondrial ribosomal proteins JO - Mol Biol Evol VL - 23 UR - https://doi.org/10.1093/molbev/msj080 DO - 10.1093/molbev/msj080 ID - Bonen2006 ER - TY - JOUR AU - Wu, Z. AU - Sloan, D. B. AU - Brown, C. W. AU - Rosenblueth, M. AU - Palmer, J. D. AU - Ong, H. C. PY - 2017 DA - 2017// TI - Mitochondrial retroprocessing promoted functional transfers of rpl5 to the nucleus in grasses JO - Mol Biol Evol VL - 34 UR - https://doi.org/10.1093/molbev/msx170 DO - 10.1093/molbev/msx170 ID - Wu2017 ER - TY - JOUR AU - Sloan, D. B. AU - Warren, J. M. AU - Williams, A. M. AU - Wu, Z. AU - Abdel-Ghany, S. E. AU - Chicco, A. J. AU - Havird, J. C. PY - 2018 DA - 2018// TI - Cytonuclear integration and co-evolution JO - Nat Rev Genet VL - 19 UR - https://doi.org/10.1038/s41576-018-0035-9 DO - 10.1038/s41576-018-0035-9 ID - Sloan2018 ER - TY - JOUR AU - Bergthorsson, U. AU - Adams, K. L. AU - Thomason, B. AU - Palmer, J. D. PY - 2003 DA - 2003// TI - Widespread horizontal transfer of mitochondrial genes in flowering plants JO - Nature. VL - 424 UR - https://doi.org/10.1038/nature01743 DO - 10.1038/nature01743 ID - Bergthorsson2003 ER - TY - JOUR AU - Guo, W. AU - Zhu, A. AU - Fan, W. AU - Mower, J. P. PY - 2017 DA - 2017// TI - Complete mitochondrial genomes from the ferns Ophioglossum californicum and Psilotum nudum are highly repetitive with the largest organellar introns JO - New Phytol VL - 213 UR - https://doi.org/10.1111/nph.14135 DO - 10.1111/nph.14135 ID - Guo2017 ER - TY - JOUR AU - Petersen, G. AU - Cuenca, A. AU - Zervas, A. AU - Ross, G. T. AU - Graham, S. W. AU - Barrett, C. F. AU - Davis, J. I. AU - Seberg, O. PY - 2017 DA - 2017// TI - Mitochondrial genome evolution in Alismatales: size reduction and extensive loss of ribosomal protein genes JO - PLoS One VL - 12 UR - https://doi.org/10.1371/journal.pone.0177606 DO - 10.1371/journal.pone.0177606 ID - Petersen2017 ER - TY - JOUR AU - Rice, D. W. AU - Alverson, A. J. AU - Richardson, A. O. AU - Young, G. J. AU - Sanchez-Puerta, M. V. AU - Munzinger, J. AU - Barry, K. AU - Boore, J. L. AU - Zhang, Y. AU - dePamphilis, C. W. PY - 2013 DA - 2013// TI - Horizontal transfer of entire genomes via mitochondrial fusion in the angiosperm Amborella JO - Science. VL - 342 UR - https://doi.org/10.1126/science.1246275 DO - 10.1126/science.1246275 ID - Rice2013 ER - TY - JOUR AU - Jackman, S. D. AU - Warren, R. L. AU - Gibb, E. A. AU - Vandervalk, B. P. AU - Mohamadi, H. AU - Chu, J. AU - Raymond, A. AU - Pleasance, S. AU - Coope, R. AU - Wildung, M. R. PY - 2015 DA - 2015// TI - Organellar genomes of white spruce (Picea glauca): assembly and annotation JO - Genome Biol Evol. VL - 8 UR - https://doi.org/10.1093/gbe/evv244 DO - 10.1093/gbe/evv244 ID - Jackman2015 ER - TY - JOUR AU - Liu, S. L. AU - Zhuang, Y. AU - Zhang, P. AU - Adams, K. L. PY - 2009 DA - 2009// TI - Comparative analysis of structural diversity and sequence evolution in plant mitochondrial genes transferred to the nucleus JO - Mol Biol Evol VL - 26 UR - https://doi.org/10.1093/molbev/msp011 DO - 10.1093/molbev/msp011 ID - Liu2009 ER - TY - JOUR AU - Kubo, T. AU - Nishizawa, S. AU - Sugawara, A. AU - Itchoda, N. AU - Estiati, A. AU - Mikami, T. PY - 2000 DA - 2000// TI - The complete nucleotide sequence of the mitochondrial genome of sugar beet (Beta vulgaris L.) reveals a novel gene for tRNACys(GCA) JO - Nucl Acids Res. VL - 28 UR - https://doi.org/10.1093/nar/28.13.2571 DO - 10.1093/nar/28.13.2571 ID - Kubo2000 ER - TY - JOUR AU - Sugiyama, Y. AU - Watase, Y. AU - Nagase, M. AU - Makita, N. AU - Yagura, S. AU - Hirai, A. AU - Sugiura, M. PY - 2005 DA - 2005// TI - The complete nucleotide sequence and multipartite organization of the tobacco mitochondrial genome: comparative analysis of mitochondrial genomes in higher plants JO - Mol Gen Genomics VL - 272 UR - https://doi.org/10.1007/s00438-004-1075-8 DO - 10.1007/s00438-004-1075-8 ID - Sugiyama2005 ER - TY - CHAP AU - Mower, J. P. AU - Sloan, D. B. AU - Alverson, A. J. ED - Wendel, J. H. PY - 2012 DA - 2012// TI - Plant mitochondrial genome diversity: the genomics revolution BT - Plant Genome Diversity Volume 1: plant genomes, their residents, and their evolutionary dynamics. vol. 1 PB - Springer CY - New York UR - https://doi.org/10.1007/978-3-7091-1130-7_9 DO - 10.1007/978-3-7091-1130-7_9 ID - Mower2012 ER - TY - JOUR AU - Gugerli, F. AU - Sperisen, C. AU - Buchler, U. AU - Brunner, I. AU - Brodbeck, S. AU - Palmer, J. D. AU - Qiu, Y. L. PY - 2001 DA - 2001// TI - The evolutionary split of Pinaceae from other conifers: evidence from an intron loss and a multigene phylogeny JO - Mol Phylogenet Evol VL - 21 UR - https://doi.org/10.1006/mpev.2001.1004 DO - 10.1006/mpev.2001.1004 ID - Gugerli2001 ER - TY - JOUR AU - Bonen, L. PY - 2008 DA - 2008// TI - Cis- and trans-splicing of group II introns in plant mitochondria JO - Mitochondrion. VL - 8 UR - https://doi.org/10.1016/j.mito.2007.09.005 DO - 10.1016/j.mito.2007.09.005 ID - Bonen2008 ER - TY - JOUR AU - Slipiko, M. AU - Myszczynski, K. AU - Buczkowska-Chmielewska, K. AU - Baczkiewicz, A. AU - Szczecinska, M. AU - Sawicki, J. PY - 2017 DA - 2017// TI - Comparative analysis of four Calypogeia species revealed unexpected change in evolutionarily-stable Liverwort mitogenomes JO - Genes (Basel) VL - 8 UR - https://doi.org/10.3390/genes8120395 DO - 10.3390/genes8120395 ID - Slipiko2017 ER - TY - JOUR AU - Hepburn, N. J. AU - Schmidt, D. W. AU - Mower, J. P. PY - 2012 DA - 2012// TI - Loss of two introns from the Magnolia tripetala mitochondrial cox2 gene implicates horizontal gene transfer and gene conversion as a novel mechanism of intron loss JO - Mol Biol Evol VL - 29 UR - https://doi.org/10.1093/molbev/mss130 DO - 10.1093/molbev/mss130 ID - Hepburn2012 ER - TY - JOUR AU - Cuenca, A. AU - Ross, T. G. AU - Graham, S. W. AU - Barrett, C. F. AU - Davis, J. I. AU - Seberg, O. AU - Petersen, G. PY - 2016 DA - 2016// TI - Localized retroprocessing as a model of intron loss in the plant mitochondrial genome JO - Genome Biol Evol. VL - 8 UR - https://doi.org/10.1093/gbe/evw148 DO - 10.1093/gbe/evw148 ID - Cuenca2016 ER - TY - JOUR AU - Mourier, T. AU - Jeffares, D. C. PY - 2003 DA - 2003// TI - Eukaryotic intron loss JO - Science. VL - 300 UR - https://doi.org/10.1126/science.1080559 DO - 10.1126/science.1080559 ID - Mourier2003 ER - TY - JOUR AU - Cohen, N. E. AU - Shen, R. AU - Carmel, L. PY - 2012 DA - 2012// TI - The role of reverse transcriptase in intron gain and loss mechanisms JO - Mol Biol Evol VL - 29 UR - https://doi.org/10.1093/molbev/msr192 DO - 10.1093/molbev/msr192 ID - Cohen2012 ER - TY - JOUR AU - Derr, L. K. AU - Strathern, J. N. PY - 1993 DA - 1993// TI - A role for reverse transcripts in gene conversion JO - Nature. VL - 361 UR - https://doi.org/10.1038/361170a0 DO - 10.1038/361170a0 ID - Derr1993 ER - TY - JOUR AU - Grewe, F. AU - Herres, S. AU - Viehover, P. AU - Polsakiewicz, M. AU - Weisshaar, B. AU - Knoop, V. PY - 2011 DA - 2011// TI - A unique transcriptome: 1782 positions of RNA editing alter 1406 codon identities in mitochondrial mRNAs of the lycophyte Isoetes engelmannii JO - Nucl Acids Res VL - 39 UR - https://doi.org/10.1093/nar/gkq1227 DO - 10.1093/nar/gkq1227 ID - Grewe2011 ER - TY - JOUR AU - Nielsen, C. B. AU - Friedman, B. AU - Birren, B. AU - Burge, C. B. AU - Galagan, J. E. PY - 2004 DA - 2004// TI - Patterns of intron gain and loss in fungi JO - PLoS Biol VL - 2 UR - https://doi.org/10.1371/journal.pbio.0020422 DO - 10.1371/journal.pbio.0020422 ID - Nielsen2004 ER - TY - JOUR AU - Zumkeller, S. M. AU - Knoop, V. AU - Knie, N. PY - 2016 DA - 2016// TI - Convergent evolution of fern-specific mitochondrial group II intron atp1i361g2 and its ancient source paralogue rps3i249g2 and independent losses of intron and RNA editing among Pteridaceae JO - Genome Biol Evol VL - 8 UR - https://doi.org/10.1093/gbe/evw173 DO - 10.1093/gbe/evw173 ID - Zumkeller2016 ER - TY - JOUR AU - Edera, A. A. AU - Gandini, C. L. AU - Sanchez-Puerta, M. V. PY - 2018 DA - 2018// TI - Towards a comprehensive picture of C-to-U RNA editing sites in angiosperm mitochondria JO - Plant Mol Biol VL - 97 UR - https://doi.org/10.1007/s11103-018-0734-9 DO - 10.1007/s11103-018-0734-9 ID - Edera2018 ER - TY - JOUR AU - Bakker, F. T. AU - Breman, F. AU - Merckx, V. PY - 2006 DA - 2006// TI - DNA sequence evolution in fast evolving mitochondrial DNA nad1 exons in Geraniaceae and Plantaginaceae JO - Taxon. VL - 55 UR - https://doi.org/10.2307/25065683 DO - 10.2307/25065683 ID - Bakker2006 ER - TY - JOUR AU - Howad, W. AU - Kempken, F. PY - 1997 DA - 1997// TI - Cell type-specific loss of atp6 RNA editing in cytoplasmic male sterile Sorghum bicolor JO - Proc Natl Acad Sci U S A VL - 94 UR - https://doi.org/10.1073/pnas.94.20.11090 DO - 10.1073/pnas.94.20.11090 ID - Howad1997 ER - TY - JOUR AU - Hu, J. AU - Yi, R. AU - Zhang, H. AU - Ding, Y. PY - 2013 DA - 2013// TI - Nucleo-cytoplasmic interactions affect RNA editing of cox2, atp6 and atp9 in alloplasmic male-sterile rice (Oryza sativa L.) lines JO - Mitochondrion VL - 13 UR - https://doi.org/10.1016/j.mito.2013.01.011 DO - 10.1016/j.mito.2013.01.011 ID - Hu2013 ER - TY - JOUR AU - Takenaka, M. AU - Zehrmann, A. AU - Verbitskiy, D. AU - Härtel, B. AU - Brennicke, A. PY - 2013 DA - 2013// TI - RNA editing in plants and its evolution JO - Annu Rev Genet VL - 47 UR - https://doi.org/10.1146/annurev-genet-111212-133519 DO - 10.1146/annurev-genet-111212-133519 ID - Takenaka2013 ER - TY - JOUR AU - Zabaleta, E. AU - Mouras, A. AU - Hernould, M. AU - Suharsono AU - Araya, A. PY - 1996 DA - 1996// TI - Transgenic male-sterile plant induced by an unedited atp9 gene is restored to fertility by inhibiting its expression with antisense RNA JO - Proc Natl Acad Sci USA VL - 93 UR - https://doi.org/10.1073/pnas.93.20.11259 DO - 10.1073/pnas.93.20.11259 ID - Zabaleta1996 ER - TY - JOUR AU - Tang, W. AU - Luo, C. PY - 2018 DA - 2018// TI - Molecular and functional diversity of RNA editing in plant mitochondria JO - Mol Biotechnol VL - 60 UR - https://doi.org/10.1007/s12033-018-0126-z DO - 10.1007/s12033-018-0126-z ID - Tang2018 ER - TY - JOUR AU - Regina, T. M. AU - Quagliariello, C. PY - 2010 DA - 2010// TI - Lineage-specific group II intron gains and losses of the mitochondrial rps3 gene in gymnosperms JO - Plant Physiol Biochem VL - 48 UR - https://doi.org/10.1016/j.plaphy.2010.05.003 DO - 10.1016/j.plaphy.2010.05.003 ID - Regina2010 ER - TY - JOUR AU - Salmans, M. L. AU - Chaw, S. M. AU - Lin, C. P. AU - Shih, A. C. AU - Wu, Y. W. AU - Mulligan, R. M. PY - 2010 DA - 2010// TI - Editing site analysis in a gymnosperm mitochondrial genome reveals similarities with angiosperm mitochondrial genomes JO - Curr Genet VL - 56 UR - https://doi.org/10.1007/s00294-010-0312-4 DO - 10.1007/s00294-010-0312-4 ID - Salmans2010 ER - TY - JOUR AU - Fan, W. AU - Guo, W. AU - Funk, L. AU - Mower, J. P. AU - Zhu, A. PY - 2019 DA - 2019// TI - Complete loss of RNA editing from the plastid genome and most highly expressed mitochondrial genes of Welwitschia mirabilis JO - Sci China Life Sci VL - 62 UR - https://doi.org/10.1007/s11427-018-9450-1 DO - 10.1007/s11427-018-9450-1 ID - Fan2019 ER - TY - JOUR AU - Dong, S. AU - Zhao, C. AU - Zhang, S. AU - Wu, H. AU - Mu, W. AU - Wei, T. AU - Li, N. AU - Wan, T. AU - Liu, H. AU - Cui, J. PY - 2019 DA - 2019// TI - The amount of RNA editing sites in liverwort organellar genes is correlated with GC content and nuclear PPR protein diversity JO - Genome Biol Evol. VL - 11 UR - https://doi.org/10.1093/gbe/evz232 DO - 10.1093/gbe/evz232 ID - Dong2019 ER - TY - JOUR AU - Skippington, E. AU - Barkman, T. J. AU - Rice, D. W. AU - Palmer, J. D. PY - 2015 DA - 2015// TI - Miniaturized mitogenome of the parasitic plant Viscum scurruloideum is extremely divergent and dynamic and has lost all nad genes JO - Proc Natl Acad Sci U S A VL - 112 UR - https://doi.org/10.1073/pnas.1504491112 DO - 10.1073/pnas.1504491112 ID - Skippington2015 ER - TY - JOUR AU - Sloan, D. B. AU - Alverson, A. J. AU - Chuckalovcak, J. P. AU - Wu, M. AU - McCauley, D. E. AU - Palmer, J. D. AU - Taylor, D. R. PY - 2012 DA - 2012// TI - Rapid evolution of enormous, multichromosomal genomes in flowering plant mitochondria with exceptionally high mutation rates JO - PLoS Biol VL - 10 UR - https://doi.org/10.1371/journal.pbio.1001241 DO - 10.1371/journal.pbio.1001241 ID - Sloan2012 ER - TY - JOUR AU - Kubo, T. AU - Mikami, T. PY - 2007 DA - 2007// TI - Organization and variation of angiosperm mitochondrial genome JO - Physiol Plant VL - 129 UR - https://doi.org/10.1111/j.1399-3054.2006.00768.x DO - 10.1111/j.1399-3054.2006.00768.x ID - Kubo2007 ER - TY - JOUR AU - Goremykin, V. V. AU - Lockhart, P. J. AU - Viola, R. AU - Velasco, R. PY - 2012 DA - 2012// TI - The mitochondrial genome of Malus domestica and the import-driven hypothesis of mitochondrial genome expansion in seed plants JO - Plant J VL - 71 UR - https://doi.org/10.1111/j.1365-313X.2012.05014.x DO - 10.1111/j.1365-313X.2012.05014.x ID - Goremykin2012 ER - TY - JOUR AU - Alverson, A. J. AU - Zhuo, S. AU - Rice, D. W. AU - Sloan, D. B. AU - Palmer, J. D. PY - 2011 DA - 2011// TI - The mitochondrial genome of the legume Vigna radiata and the analysis of recombination across short mitochondrial repeats JO - PLoS One VL - 6 UR - https://doi.org/10.1371/journal.pone.0016404 DO - 10.1371/journal.pone.0016404 ID - Alverson2011 ER - TY - JOUR AU - Alverson, A. J. AU - Wei, X. X. AU - Rice, D. W. AU - Stern, D. B. AU - Barry, K. AU - Palmer, J. D. PY - 2010 DA - 2010// TI - Insights into the evolution of mitochondrial genome size from complete sequences of Citrullus lanatus and Cucurbita pepo (cucurbitaceae) JO - Mol Biol Evol VL - 27 UR - https://doi.org/10.1093/molbev/msq029 DO - 10.1093/molbev/msq029 ID - Alverson2010 ER - TY - JOUR AU - Knoop, V. AU - Unseld, M. AU - Marienfeld, J. AU - Brandt, P. AU - Sünkel, S. AU - Ullrich, H. AU - Brennicke, A. PY - 1996 DA - 1996// TI - copia-, gypsy-and LINE-like retrotransposon fragments in the mitochondrial genome of Arabidopsis thaliana JO - Genetics. VL - 142 ID - Knoop1996 ER - TY - JOUR AU - Yang, J. AU - Liu, G. AU - Zhao, N. AU - Chen, S. AU - Liu, D. AU - Ma, W. AU - Hu, Z. AU - Zhang, M. PY - 2016 DA - 2016// TI - Comparative mitochondrial genome analysis reveals the evolutionary rearrangement mechanism in Brassica JO - Plant Biol (Stuttg) VL - 18 UR - https://doi.org/10.1111/plb.12414 DO - 10.1111/plb.12414 ID - Yang2016 ER - TY - JOUR AU - Lynch, M. AU - Koskella, B. AU - Schaack, S. PY - 2006 DA - 2006// TI - Mutation pressure and the evolution of organelle genomic architecture JO - Science. VL - 311 UR - https://doi.org/10.1126/science.1118884 DO - 10.1126/science.1118884 ID - Lynch2006 ER - TY - JOUR AU - Christensen, A. C. PY - 2013 DA - 2013// TI - Plant mitochondrial genome evolution can be explained by DNA repair mechanisms JO - Genome Biol Evol. VL - 5 UR - https://doi.org/10.1093/gbe/evt069 DO - 10.1093/gbe/evt069 ID - Christensen2013 ER - TY - JOUR AU - Christensen, A. C. PY - 2014 DA - 2014// TI - Genes and junk in plant mitochondria-repair mechanisms and selection JO - Genome Biol Evol. VL - 6 UR - https://doi.org/10.1093/gbe/evu115 DO - 10.1093/gbe/evu115 ID - Christensen2014 ER - TY - JOUR AU - Smith, D. R. PY - 2016 DA - 2016// TI - The mutational hazard hypothesis of organelle genome evolution: 10 years on JO - Mol Ecol VL - 25 UR - https://doi.org/10.1111/mec.13742 DO - 10.1111/mec.13742 ID - Smith2016 ER -