[1] Gott JM, Emeson RB. 2000. Functions and mechanisms of RNA editing. Annual Review of Genetics 34:499−531 doi: 10.1146/annurev.genet.34.1.499
[2] Willbanks A, Wood S, Cheng JX. 2021. RNA epigenetics: fine-tuning chromatin plasticity and transcriptional regulation, and the implications in human diseases. Genes 12:627 doi: 10.3390/genes12050627
[3] Jobson RW, Qiu YL. 2008. Did RNA editing in plant organellar genomes originate under natural selection or through genetic drift? Biology Direct 3:43 doi: 10.1186/1745-6150-3-43
[4] Giege P, Brennicke A. 1999. RNA editing in Arabidopsis mitochondria effects 441 C to U changes in ORFs. Proceedings of the National Academy of Sciences of the United States of America 96:15324−29 doi: 10.1073/pnas.96.26.15324
[5] Grewe F, Herres S, Viehöver P, Polsakiewicz M, Weisshaar B, et al. 2011. A unique transcriptome: 1782 positions of RNA editing alter 1406 codon identities in mitochondrial mRNAs of the lycophyte Isoetes engelmannii. Nucleic Acids Research 7:2890−902 doi: 10.1093/nar/gkq1227
[6] Yura K, Go M. 2008. Correlation between amino acid residues converted by RNA editing and functional residues in protein three-dimensional structures in plant organelles. BMC Plant Biology 8:79 doi: 10.1186/1471-2229-8-79
[7] Yura K, Sulaiman S, Hatta Y, Shionyu M, Go M. 2009. RESOPS: a database for analyzing the correspondence of rna editing sites to protein three-dimensional structures. Plant and Cell Physiology 50:1865−73 doi: 10.1093/pcp/pcp132
[8] Schallenberg-Rudinger M, Kindgren P, Zehrmann A, Small I, Knoop V. 2013. A DYW-protein knockout in Physcomitrella affects two closely spaced mitochondrial editing sites and causes a severe developmental phenotype. The Plant Journal 76:420−32 doi: 10.1111/tpj.12304
[9] Meng Y, Chen D, Jin Y, Mao C, Wu P et al. 2010. RNA editing of nuclear transcripts in Arabidopsis thaliana. BMC Genomics 11:S12 doi: 10.1186/1471-2164-11-S4-S12
[10] Daras G, Rigas S, Alatzas A, Samiotaki M, Chatzopoulos D, et al. 2019. LEFKOTHEA regulates nuclear and chloroplast mRNA splicing in plants. Developmental Cell 50:767−79.e7 doi: 10.1016/j.devcel.2019.07.024
[11] McFadden GI. 1999. Endosymbiosis and evolution of the plant cell. Current Opinion in Plant Biology 2:513−19 doi: 10.1016/S1369-5266(99)00025-4
[12] Martin W, Stoebe B, Goremykin V, Hansmann S, Hasegawa M, et al. 1998. Gene transfer to the nucleus and the evolution of chloroplasts. Nature 393:162−65 doi: 10.1038/30234
[13] Primavesi LF, Wu H, Mudd EA, Day A, Jones HD. 2017. Visualisation of plastid degradation in sperm cells of wheat pollen. Protoplasma 254:229−37 doi: 10.1007/s00709-015-0935-x
[14] Qulsum U, Azad MTA, Tsukahara T. 2019. Analysis of tissue-specific RNA editing events of genes involved in RNA editing in Arabidopsis thaliana. Journal of Plant Biology 62:351−58 doi: 10.1007/s12374-018-0452-5
[15] Zhang Y, Giese J, Kerbler SM, Siemiatkowska B, Perez de Souza L, et al. 2021. Two mitochondrial phosphatases, PP2c63 and Sal2, are required for posttranslational regulation of the TCA cycle in Arabidopsis. Molecular Plant 14:1104−18 doi: 10.1016/j.molp.2021.03.023
[16] Takenaka M, Zehrmann A, Verbitskiy D, Kugelmann M, Härtel B, et al. 2012. Multiple organellar RNA editing factor (MORF) family proteins are required for RNA editing in mitochondria and plastids of plants. Proceedings of the National Academy of Sciences of the United States of America 109:5104−9 doi: 10.1073/pnas.1202452109
[17] Ramaswami G, Zhang R, Piskol R, Keegan LP, Deng P, et al. 2013. Identifying RNA editing sites using RNA sequencing data alone. Nature Methods 10:128−32 doi: 10.1038/nmeth.2330
[18] Dharshini SAP, Taguchi YH, Gromiha MM. 2020. Identifying suitable tools for variant detection and differential gene expression using RNA-seq data. Genomics 112:2166−72 doi: 10.1016/j.ygeno.2019.12.011
[19] Zhu Y, Luo H, Zhang X, Song J, Sun C, et al. 2014. Abundant and selective RNA-editing events in the medicinal mushroom Ganoderma lucidum. Genetics 196:1047−57 doi: 10.1534/genetics.114.161414
[20] Kim H, Jeong E, Lee SW, Han K. 2003. Computational analysis of hydrogen bonds in protein-RNA complexes for interaction patterns. FEBS Letters 552:231−9 doi: 10.1016/S0014-5793(03)00930-X
[21] Chen Y, Kortemme T, Robertson T, Baker D, Varani G. 2004. A new hydrogen-bonding potential for the design of protein-RNA interactions predicts specific contacts and discriminates decoys. Nucleic Acids Research 32:5147−62 doi: 10.1093/nar/gkh785
[22] Lane N, Martin W. 2010. The energetics of genome complexity. Nature 467:929−34 doi: 10.1038/nature09486
[23] Härtel B, Zehrmann A, Verbitskiy D, Takenaka M. 2013. The longest mitochondrial RNA editing PPR protein MEF12 in Arabidopsis thaliana requires the full-length E domain. RNA Biology 10:1543−8 doi: 10.4161/rna.25484
[24] Matsushita K, Takeuchi O, Standley DM, Kumagai Y, Kawagoe T, et al. 2009. Zc3h12a is an RNase essential for controlling immune responses by regulating mRNA decay. Nature 458:1185−90 doi: 10.1038/nature07924
[25] Zhou W, Karcher D, Bock R. 2014. Identification of enzymes for adenosine-to-inosine editing and discovery of cytidine-to-uridine editing in nucleus-encoded transfer RNAs of Arabidopsis. Plant Physiology 166:1985−97 doi: 10.1104/pp.114.250498
[26] Li Y, Göhl M, Ke K, Vanderwal CD, Spitale RC. 2019. Identification of adenosine-to-inosine RNA editing with acrylonitrile reagents. Organic Letters 21:19 doi: 10.1021/acs.orglett.9b02929
[27] Chateigner-Boutin AL, Small I. 2007. A rapid high-throughput method for the detection and quantification of RNA editing based on high-resolution melting of amplicons. Nucleic Acids Research 35:e114 doi: 10.1093/nar/gkm640
[28] Moro B, Rojas A, Palatnik JF. 2019. Detection of MicroRNA Processing Intermediates Through RNA Ligation Approaches. In Plant MicroRNAs, eds. de Folter S. 1932:XII, 363. New York: Humana Press. pp. 261−83 https://doi.org/10.1007/978-1-4939-9042-9_20
[29] Ramaswami G, Lin W, Piskol R, Tan MH, Davis C, et al. 2012. Accurate identification of human Alu and non-Alu RNA editing sites. Nature methods 9:579−81 doi: 10.1038/nmeth.1982
[30] Le HS, Schulz MH, McCauley BM, Hinman VF, Bar-Joseph Z. 2013. Probabilistic error correction for RNA sequencing. Nucleic Acids Research 10:e109 doi: 10.1093/nar/gkt215
[31] Li H, Homer N. 2010. A survey of sequence alignment algorithms for next-generation sequencing. Briefings in Bioinformatics 11:473−83 doi: 10.1093/bib/bbq015
[32] Tuskan GA, Difazio S, Jansson S, Bohlmann J, Grigoriev I, et al. 2006. The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). Science 313:1596−604 doi: 10.1126/science.1128691
[33] Benjamini Y, Hochberg Y. 1995. Controlling the false discovery rate - a practical and powerful approach to multiple testing. Journal of the Royal Statistical Society: Series B (Methodological) 57:289−300 doi: 10.1111/j.2517-6161.1995.tb02031.x
[34] Cavalier-Smith T. 2004. Only six kingdoms of life. Proceedings of the Royal Society of London Series B: Biological Sciences 271:1251−62 doi: 10.1098/rspb.2004.2705
[35] Jenkins BH, Maguire F, Leonard G, Eaton JD, West S, et al. 2021. Emergent RNA-RNA interactions can promote stability in a facultative phototrophic endosymbiosis. Proceedings of the National Academy of Sciences of the United States of America 118:e2108874118 doi: 10.1073/pnas.2108874118
[36] Martin W, Rujan T, Richly E, Hansen A, Cornelsen S, et al. 2002. Evolutionary analysis of Arabidopsis, cyanobacterial, and chloroplast genomes reveals plastid phylogeny and thousands of cyanobacterial genes in the nucleus. Proceedings of the National Academy of Sciences of the United States of America 99:12246−51 doi: 10.1073/pnas.182432999
[37] Richardson E, Dorrell RG, Howe CJ. 2014. Genome-wide transcript profiling reveals the coevolution of plastid gene sequences and transcript processing pathways in the fucoxanthin dinoflagellate Karlodinium veneficum. Molecular Biology and Evolution 9:2376−86 doi: 10.1093/molbev/msu189
[38] Dorrell RG, Howe CJ. 2012. What makes a chloroplast? Reconstructing the establishment of photosynthetic symbioses Journal of Cell Science 125:1865−75 doi: 10.1242/jcs.102285
[39] Ling Q, Jarvis P. 2013. Dynamic regulation of endosymbiotic organelles by ubiquitination. Trends in Cell Biology 23:399−408 doi: 10.1016/j.tcb.2013.04.008
[40] Den Herder G, Yoshida S, Antolín-Llovera M, Ried MK, Parniske M. 2012. Lotus japonicus E3 ligase SEVEN IN ABSENTIA4 destabilizes the symbiosis receptor-like kinase SYMRK and negatively regulates rhizobial infection. The Plant Cell 24:1691−707 doi: 10.1105/tpc.110.082248
[41] Davy SK, Allemand D, Weis VM. 2012. Cell biology of cnidarian-dinoflagellate symbiosis. Microbiology and Molecular Biology Reviews 76:229−61 doi: 10.1128/MMBR.05014-11
[42] Sergey I, Fedorova Elena E, Erik L, Stephane DM, Andrea G, et al. 2012. Rhizobium-legume symbiosis shares an exocytotic pathway required for arbuscule formation. Proceedings of the National Academy of Sciences of the United States of America 109:8316−21 doi: 10.1073/pnas.1200407109
[43] Sasaki T, Yukawa Y, Miyamoto T, Obokata J, Sugiura M. 2003. Identification of RNA editing sites in chloroplast transcripts from the maternal and paternal progenitors of tobacco (Nicotiana tabacum): comparative analysis shows the involvement of distinct trans-factors for ndhB editing. Molecular Biology and Evolution 7:1028−35 doi: 10.1093/molbev/msg098
[44] Xu G, Zhang J. 2014. Human coding RNA editing is generally nonadaptive. Proceedings of the National Academy of Sciences of the United States of America 111:3769−74 doi: 10.1073/pnas.1321745111
[45] Okuda K, Hammani K, Tanz SK, Peng L, Fukao Y, et al. 2010. The pentatricopeptide repeat protein OTP82 is required for RNA editing of plastid ndhB and ndhG transcripts. The Plant Journal 61:339−49 doi: 10.1111/j.1365-313X.2009.04059.x
[46] Goodstein DM, Shu S, Howson R, Neupane R, Hayes RD, et al. 2012. Phytozome: a comparative platform for green plant genomics. Nucleic Acids Research 40:D1178−D1186 doi: 10.1093/nar/gkr944
[47] Unseld M, Marienfeld JR, Brandt P, Brennicke A. 1997. The mitochondrial genome of Arabidopsis thaliana contains 57 genes in 366, 924 nucleotides. Nature Genetics 15:57−61 doi: 10.1038/ng0197-57
[48] Sato S, Nakamura Y, Kaneko T, Asamizu E, Tabata S. 1999. Complete structure of the chloroplast genome of Arabidopsis thaliana. DNA Research 6:283−90 doi: 10.1093/dnares/6.5.283
[49] Lamesch P, Berardini TZ, Li D, Swarbreck D, Wilks C, et al. 2012. The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools. Nucleic Acids Research 40:D1202−D1210 doi: 10.1093/nar/gkr1090
[50] Langmead B, Salzberg SL. 2012. Fast gapped-read alignment with Bowtie 2. Nature Methods 9:357−59 doi: 10.1038/nmeth.1923
[51] Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, et al. 2009. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25:2078−9 doi: 10.1093/bioinformatics/btp352
[52] Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, et al. 2009. BLAST+: architecture and applications. BMC Bioinformatics 10:421 doi: 10.1186/1471-2105-10-421
[53] Lurin C, Andreés C, Aubourg S, Bellaoui M, Bitton F, et al. 2004. Genome-wide analysis of Arabidopsis pentatricopeptide repeat proteins reveals their essential role in organelle biogenesis. The Plant Cell 16:2089−103 doi: 10.1105/tpc.104.022236
[54] Finn RD, Bateman A, Clements J, Coggill P, Eberhardt RY, et al. 2014. Pfam: the protein families database. Nucleic Acids Research 42:D222−D230 doi: 10.1093/nar/gkt1223
[55] Marchler-Bauer A, Lu SN, Anderson JB, Chitsaz F, Derbyshire MK, et al. 2011. CDD: a Conserved Domain Database for the functional annotation of proteins. Nucleic Acids Research 39:D225−D229 doi: 10.1093/nar/gkq1189
[56] Nie J, Stewart R, Zhang H, Thomson JA, Ruan F, et al. 2011. TF-Cluster: a pipeline for identifying functionally coordinated transcription factors via network decomposition of the shared coexpression connectivity matrix (SCCM). BMC Systems Biology 5:53 doi: 10.1186/1752-0509-5-53