[1] Armenise, L., Simeone, M., Piredda, R., et al., 2012. Validation of DNA barcoding as an efficient tool for taxon identification and detection of species diversity in Italian conifers. Eur. J. For. Res. 131, 1337-1353. [2] Bell, D., Lin, Q., Gerelle, W.K., et al., 2020. Organellomic data sets confirm a cryptic consensus on (unrooted) land-plant relationships and provide new insights into bryophyte molecular evolution. Am. J. Bot. 107, 91-115. [3] Bentolila, S., Heller, W.P., Sun, T., et al., 2012. Rip1, a member of an arabidopsis protein family, interacts with the protein rare1 and broadly affects RNA editing. Proc. Natl. Acad. Sci. U.S.A. 109, 8372-8373. [4] Bowe, L.M., dePamphilis, C.W.W., 1996. Effects of RNA editing and gene processing on phylogenetic reconstruction. Mol. Biol. Evol. 13,1159-1166. [5] Burleigh, J.G., Mathews, S., 2004. Phylogenetic signal in nucleotide data from seed plants: implications for resolving the seed plant tree of life. Am. J. Bot. 91, 1599-1613. [6] Cox, C.J., Li, B., Foster, P.G., et al., 2014. Conflicting phylogenies for early land plants are caused by composition biases among synonymous substitutions. Syst. Biol. 63, 272-279. [7] Cuenca, A., Petersen, G., Seberg, O., et al., 2010. Are substitution rates and RNA editing correlated? BMC Evol. Biol. 10, 1-15. [8] Dong, S., Zhao, C., Zhang, S., et al., 2019. The amount of RNA editing sites in liverwort organellar genes is correlated with GC content and nuclear PPR protein diversity. Genome Biol. Evol. 11, 3233-3239. [9] Dong, S.S., Li, H.L., Goffinet, B., et al., 2022. Exploring the impact of RNA editing on mitochondrial phylogenetic analyses in liverworts, an early land plant lineage. J. Systemat. Evol. 60, 16-22. [10] Du, X.Y., Lu, J.M., Li, D.Z., 2020. Extreme plastid RNA editing may confound phylogenetic reconstruction: a case study of Selaginella (lycophytes). Plant Divers. 42, 356-361. [11] Edera, A.A., Gandini, C.L., Sanchez-Puerta, M.V., 2018. Towards a comprehensive picture of C-to-U RNA editing sites in angiosperm mitochondria. Plant Mol. Biol. 97, 215-231. [12] Gitzendanner, M.A., Soltis, P.S., Wong, G.K.S., et al., 2018. Plastid phylogenomic analysis of green plants: a billion years of evolutionary history. Am. J. Bot. 105, 291-301. [13] Gray, M.W., 2012. Evolutionary origin of RNA editing. Biochemistry 51, 5235-5242. [14] Groth-Malonek, M., Pruchner, D., Grewe, F., et al., 2005. Ancestors of trans-splicing mitochondrial introns support serial sister group relationships of hornworts and mosses with vascular plants. Mol. Biol. Evol. 22, 117-125. [15] Guo, W., Grewe, F., Fan, W., et al., 2016. Ginkgo and Welwitschia mitogenomes reveal extreme contrasts in gymnosperm mitochondrial evolution. Mol. Biol. Evol. 33, 1448-1460. [16] Guo, W., Zhu, A., Fan, W., et al., 2017. Complete mitochondrial genomes from the ferns Ophioglossum californicum and Psilotum nudum are highly repetitive with the largest organellar introns. New Phytol. 213, 391-403. [17] Hecht, J., Grewe, F., Knoop, V., 2011. Extreme RNA editing in coding islands and abundant microsatellites in repeat sequences of Selaginella moellendorffii mitochondria: the root of frequent plant mtDNA recombination in early tracheophytes. Genome Biol. Evol. 3, 344-358. [18] Huelsenbeck, J.P., 1995. Performance of phylogenetic methods in simulation. Syst. Biol. 44, 17-48. [19] Ichinose, M., Sugita, M., 2016. RNA editing and its molecular mechanism in plant organelles. Genes 8, 5. [20] Knoop, V., 2011. When you can't trust the DNA: RNA editing changes transcript sequences. Cell. Mol. Life Sci. 68, 567-586. [21] Kuck, P., Longo, G.C., 2014. Fasconcat-g: extensive functions for multiple sequence alignment preparations concerning phylogenetic studies. Front. Zool. 11, 1-8. [22] Lanfear, R., Calcott, B., Ho, S.Y.W., et al., 2012. Partitionfinder: combined selection of partitioning schemes and substitution models for phylogenetic analyses. Mol. Biol. Evol. 29, 1695-1701. [23] Leebens-Mack, J.H., Barker, M.S., Carpenter, E.J., et al., 2019. One thousand plant transcriptomes and the phylogenomics of green plants. Nature 574, 679-685. [24] Liu, Y., Cox, C.J., Wang, W., et al., 2014. Mitochondrial phylogenomics of early land plants: mitigating the effects of saturation, compositional heterogeneity, and codon-usage bias. Syst. Biol. 63, 862-878. [25] Liu, Y., Wang, S., Li, L., et al., 2022. The Cycas genome and the early evolution of seed plants. Native Plants 8, 389-401. [26] Malek, O., Lattig, K., Hiesel, R., et al., 1996. RNA editing in bryophytes and a molecular phylogeny of land plants. EMBO J. 15, 1403-1411. [27] Oldenkott, B., Yamaguchi, K., Tsuji-Tsukinoki, S., et al., 2014. Chloroplast RNA editing going extreme: more than 3400 events of C-to-U editing in the chloroplast transcriptome of the lycophyte Selaginella uncinata. RNA 20, 1499-1506. [28] Owens, J.N., Wilson, V.R., 1999. Cytoplasmic inheritance in Podocarpus totara (podocarpaceae). In IV International Conifer Conference vol 615, 171-172. [29] Petersen, G., Seberg, O., Davis, J.I., et al., 2006. RNA editing and phylogenetic reconstruction in two monocot mitochondrial genes. Taxon 55, 871-886. [30] Picardi, E., Quagliariello, C., 2008. Is plant mitochondrial RNA editing a source of phylogenetic incongruence? An answer from in silico and in vivo data sets. BMC Bioinf. 9, S14. [31] Ran, J.-H., Gao, H., Wang, X.-Q., 2010. Fast evolution of the retroprocessed mitochondrial rps3 gene in Conifer II and further evidence for the phylogeny of gymnosperms. Mol. Phylogenet. Evol. 54, 136-149. [32] Ran, J.H., Shen, T.T., Wang, M.M., et al., 2018. Phylogenomics resolves the deep phylogeny of seed plants and indicates partial convergent or homoplastic evolution between Gnetales and angiosperms. P. Roy. Soc. B-Biol. Sci. 285, 20181012. [33] Regier, J.C., Shultz, J.W., Zwick, A., et al., 2010. Arthropod relationships revealed by phylogenomic analysis of nuclear protein-coding sequences. Nature 463, 1079-1083. [34] Rice, D.W., Alverson, A.J., Richardson, A.O., et al., 2013. Horizontal transfer of entire genomes via mitochondrial fusion in the angiosperm Amborella. Science 342, 1468-1473. [35] Richardson, A.O., Rice, D.W., Young, G.J., et al., 2013. The "fossilized" mitochondrial genome of Liriodendron tulipifera: ancestral gene content and order, ancestral editing sites, and extraordinarily low mutation rate. BMC Biol. 11, 29. [36] Rudinger, M., Polsakiewicz, M., Knoop, V., 2008. Organellar RNA editing and plant-specific extensions of pentatricopeptide repeat proteins in jungermanniid but not in marchantiid liverworts. Mol. Biol. Evol. 25, 1405-1414. [37] Rudinger, M., Volkmar, U., Lenz, H., et al., 2012. Nuclear dyw-type ppr gene families diversify with increasing rna editing frequencies in liverwort and moss mitochondria. J. Mol. Evol. 7, 37-51. [38] Schallenberg-Rudinger, M., Lenz, H., Polsakiewicz, M., et al., 2014. A survey of PPR proteins identifies DYW domains like those of land plant RNA editing factors in diverse eukaryotes. RNA Biol. 10, 1549-1556. [39] Schmidt, H.A., Strimmer, K., Vingron, M., et al., 2002. Tree-puzzle: maximum likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics 18, 502-504. [40] Sloan, D.B., 2017. Nuclear and mitochondrial RNA editing systems have opposite effects on protein diversity. Biol. Lett. 13, 20170314. [41] Smith, D.R., 2009. Unparalleled GC content in the plastid DNA of Selaginella. Plant Mol. Biol. 71, 627. [42] Soltis, D.E., Soltis, P.S., Zanis, M.J., 2002. Phylogeny of seed plants based on evidence from eight genes. Am. J. Bot. 89, 1670-1681. [43] Stamatakis, A., 2014. RaxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 9, 1312-1313. [44] Wang, I.X., So, E., Devlin, J.L., et al., 2013. ADAR regulates RNA editing, transcript stability, and gene expression. Cell Rep. 5, 849-860. [45] Wang, X.Q., Ran, J.H., 2014. Evolution and biogeography of gymnosperms. Mol. Phylogenet. Evol. 75, 24-40. [46] Wu, C.S., Wang, Y.N., Hsu, C.Y., et al., 2011. Loss of different inverted repeat copies from the chloroplast genomes of Pinaceae and cupressophytes and influence of heterotachy on the evaluation of gymnosperm phylogeny. Genome Biol. Evol. 3, 1284-1295. [47] Yang, Y., Ferguson, D.K., Liu, B., et al., 2022. Recent advances on phylogenomics of gymnosperms and a new classification. Plant Divers. 44, 340-350. [48] Zhong, B., Yonezawa, T., Zhong, Y., et al., 2010. The position of Gnetales among seed plants: overcoming pitfalls of chloroplast phylogenomics. Mol. Biol. Evol. 27, 2855-2863. |