Abramson, J., Adler J., Dunger J., et al., 2024. Accurate structure prediction of biomolecular interactions with AlphaFold 3. Nature. 630(8016), 493-500. Ayabe, H., Toyoda, A., Iwamoto, A., et al., 2023. Mitochondrial gene defects in Arabidopsis can broadly affect mitochondrial gene expression through copy number. Plant Physiology. 191, 2256-2275. Ayala-Garcia, V.M., Baruch-Torres, N., Garcia-Medel, P.L., et al., 2018. Plant organellar DNA polymerases paralogs exhibit dissimilar nucleotide incorporation fidelity. FEBS J. 285, 4005-4018. Baruch-Torres, N., Brieba, L.G., 2017. Plant organellar DNA polymerases are replicative and translesion DNA synthesis polymerases. Nucleic Acids Res. 45, 10751-10763. Bi, G.Q., Zhao, S.J., Yao, J.W., et al., 2024. Near telomere-to-telomere genome of the model plant Physcomitrium patens. Nat Plants. 10, 327-343. Brieba, L.G., 2019. Structure-function analysis reveals the singularity of plant mitochondrial DNA replication components: A Mosaic and Redundant System. Plants (Basel). 8, 533. Chen, C.J., Wu, Y., Li, J.W., et al., 2023. TBtools-II: A "one for all, all for one" bioinformatics platform for biological big-data mining. Mol Plant. 16, 1733-1742. Chen, T.T., Chen, X., Zhang, S.S., et al., 2021. The genome sequence archive Family: toward explosive data growth and diverse data types. Genomics Proteomics & Bioinformatics. 19, 578-583. Chevigny, N., Schatz-Daas, D., Lotfi, F. et al., 2020. DNA Repair and the Stability of the Plant Mitochondrial Genome. Int J Mol Sci. 21, 328. Cupp, J.D., Nielsen, B.L., 2013. Arabidopsis thaliana organellar DNA polymerase IB mutants exhibit reduced mtDNA levels with a decrease in mitochondrial area density. Physiol Plant. 149, 91-103. Cupp, J.D., Nielsen, B.L., 2014. Minireview: DNA replication in plant mitochondria. Mitochondrion. 19, 231-237. Czernecki, D., Nourisson, A., Legrand, P., et al., 2023. Reclassification of family A DNA polymerases reveals novel functional subfamilies and distinctive structural features. Nucleic Acids Res. 51, 4488-4507. Danecek, P., McCarthy, S.A., 2017. BCFtools/csq: haplotype-aware variant consequences. Bioinformatics. 33, 2037-2039. Edmondson, A.C., Song, D., Alvarez, L.A., et al., 2005. Characterization of a mitochondrially targeted single-stranded DNA-binding protein in Arabidopsis thaliana. Mol Genet Genomics. 273, 115-122. Fuchs, P., Rugen, N., Carrie, C., et al., 2020. Single organelle function and organization as estimated from Arabidopsis mitochondrial proteomics. Plant J. 101, 420-441. Garcia-Medel, P.L., Baruch-Torres, N., Peralta-Castro, A., 2019. Plant organellar DNA polymerases repair double-stranded breaks by microhomology-mediated end-joining. Nucleic Acids Res. 47, 3028-3044. Gualberto, J.M., Newton, K.J., 2017. Plant mitochondrial genomes: dynamics and mechanisms of mutation. Annu Rev Plant Biol. 68, 225-252. Hernandez, A.J., Richardson, C.C., 2019. Gp2.5, the multifunctional bacteriophage T7 single-stranded DNA binding protein. Seminars in Cell & Developmental Biology. 86, 92-101. Hou, X.R., Wang, D.P., Cheng, Z.K., et al., 2022. A near-complete assembly of an Arabidopsis thaliana genome. Mol Plant. 15, 1247-1250. Jain, C., Rhie, A., Zhang, H.W., Chu,C., et al., 2020. Weighted minimizer sampling improves long read mapping. Bioinformatics. 36, i111-i118. Klodova, B., Potesil, D., Steinbachova, L., et al., 2023. Regulatory dynamics of gene expression in the developing male gametophyte of Arabidopsis. Plant Reprod. 36, 213-241. Lang, D., Ullrich, K.K., Murat, F., et al., 2018. The Physcomitrella patens chromosome-scale assembly reveals moss genome structure and evolution. Plant J. 93, 515-533. Li, D.Q., Wu, X.B., Wang, H.F., et al., 2021. Defective mitochondrial function by mutation in THICK ALEURONE 1 encoding a mitochondrion-targeted single-stranded DNA-binding protein leads to increased aleurone cell layers and improved nutrition in rice. Mol Plant. 14, 1343-1361. Lu, S.N., Wang, J.Y, Chitsaz, F., et al., 2020. CDD/SPARCLE: the conserved domain database in 2020. Nucleic Acids Res. 48, D265-D268. Marchler-Bauer, A., Bryant, S.H., 2004. CD-Search: protein domain annotations on the fly. Nucleic Acids Res. 32, W327-331. Misra, C.S., Sousa, A. G.G., Barros, P.M., et al., 2023. Cell-type-specific alternative splicing in the Arabidopsis germline. Plant Physiol 192, 85-101. Morley, S.A., Ahmad, N., Nielsen, B.L., 2019. Plant organelle genome replication. Plants (Basel). 8, 358. Morley, S.A., Nielsen, B.L., 2016. Chloroplast DNA copy number changes during plant development in organelle DNA polymerase mutants. Front Plant Sci. 7, 57. Morley, S.A., Peralta-Castro, A., Brieba, L.G., et al., 2019. Arabidopsis thaliana organelles mimic the T7 phage DNA replisome with specific interactions between Twinkle protein and DNA polymerases Pol1A and Pol1B. BMC Plant Biol. 19, 241. Qian, J., Li M., Zheng M., et al., 2021. Arabidopsis SSB1, a mitochondrial single-stranded DNA-binding protein, is involved in ABA response and mitochondrial RNA splicing. Plant Cell Physiol. 62, 1321-1334. Qian, J., Zheng, M., Wang, L.G., et al., 2022. Arabidopsis mitochondrial single-stranded DNA-binding proteins SSB1 and SSB2 are essential regulators of mtDNA replication and homologous recombination. J Integr Plant Biol. 64, 1952-1965. Shedge, V., Davila, J., Arrieta-Montiel, M.P., et al., 2010. Extensive rearrangement of the Arabidopsis mitochondrial genome elicits cellular conditions for thermotolerance. Plant Physiol. 152, 1960-1970. Shereda, R.D., Kozlov, A.G., Lohman, T.M., et al., 2008. SSB as an organizer/mobilizer of genome maintenance complexes. Crit Rev Biochem Mol Biol. 43, 289-318. Shinn, M.K., Kozlov, A.G., Nguyen, B., et al., 2019. Are the intrinsically disordered linkers involved in SSB binding to accessory proteins? Nucleic Acids Res. 47, 8581-8594. Sloan, D.B., Alverson, A.J., Chuckalovcak, J.P., et al., 2012. Rapid evolution of enormous, multichromosomal genomes in flowering plant mitochondria with exceptionally high mutation rates. PLoS Biol. 10, e1001241. Wallet, C., Ret, M.L., Bergdoll, M., et al., 2015. The RECG1 DNA translocase is a key factor in recombination surveillance, repair, and segregation of the mitochondrial DNA in Arabidopsis. Plant Cell. 27, 2907-2925. Wang J., Zou Y., Mower J.P., et al., 2024. Rethinking the mutation hypotheses of plant organellar DNA. Genomics Communications. 1, e003. Wolfe, K.H., L, W.H., Sharp, P.M., 1987. Rates of nucleotide substitution vary greatly among plant mitochondrial chloroplast and nuclear DNAs. Proc Natl Acad Sci U S A. 84, 8054-9058. Wu, Z.Q., Waneka, G., Broz, A.K., et al., 2020. MSH1 is required for maintenance of the low mutation rates in plant mitochondrial and plastid genomes. Proc Natl Acad Sci U S A. 117, 16448-16455. Wu, Z.Q., Liao, X.Z., Zhang, X.N., et al., 2020. Genomic architectural variation of plant mitochondria-A review of multichromosomal structuring. Journal of Systematics and Evolution. 60, 160-168. Wynn, E.L., Christensen, A.C. et al., 2019. Repeats of unusual size in plant mitochondrial genomes: identification, incidence and evolution. G3 Genes Genomes Genetics. 9, 549-559. Xue, Y.B., Bao, Y.M., Zhang, Z., et al., 2022. Database resources of the national genomics data center, China national center for bioinformation in 2022. Nucleic Acids Res. 50, D27-D38. Zhang, D., Gao, F.L, Jakovlic, I., 2020. PhyloSuite: An integrated and scalable desktop platform for streamlined molecular sequence data management and evolutionary phylogenetics studies. Mol Ecol Resour. 20, 348-355. Zhang, L.G., Ma, J., Shen, Z.R., et al., 2022. Low copy numbers for mitochondrial DNA moderates the strength of nuclear-cytoplasmic incompatibility in plants. J Integr Plant Biol. 65, 739-754. Zou, Y., Zhu, W.D., Sloan, D.B., et al., 2022. Long-read sequencing characterizes mitochondrial and plastid genome variants in Arabidopsis msh1 mutants. Plant J. 112, 738-755. Zwonitzer, K.D., Tressel, L.G., Wu, Z.Q., et al., 2024. Genome copy number predicts extreme evolutionary rate variation in plant mitochondrial DNA. Proc Natl Acad Sci U S A. 121, e2317240121. |