Jansen RK. Plastid genomes of seed plants: advances in photosynthesis and respiration 35. In: Genomics of chloroplasts and mitochondria; 2012.
Google Scholar
Palmer JD. Chloroplast DNA exists in two orientations. Nature. 1983;301(5895):92–3. https://doi.org/10.1038/301092a0.
Article
CAS
Google Scholar
Bock R. Structure, function, and inheritance of plastid genomes. In: Bock R, editor. Book: Structure, function, and inheritance of plastid genomes. ln: Edited by. Berlin, Heidelberg: Springer Berlin Heidelberg; 2007. p. 29–63. https://doi.org/10.1007/4735_2007_0223.
Shinozaki K, Ohme M, Tanaka M, Wakasugi T, Hayashida N, Matsubayashi T, et al. The complete nucleotide-sequence of the tobacco chloroplast genome - its gene organization and expression. EMBO J. 1986;5(9):2043–9. https://doi.org/10.1002/j.1460-2075.1986.tb04464.x.
Article
CAS
PubMed
PubMed Central
Google Scholar
Chumley TW, Palmer JD, Mower JP, Fourcade HM, Calie PJ, Boore JL, et al. The complete chloroplast genome sequence of Pelargonium x hortorum: organization and evolution of the largest and most highly rearranged chloroplast genome of land plants. Mol Biol Evol. 2006;23(11):2175–90. https://doi.org/10.1093/molbev/msl089.
Article
CAS
PubMed
Google Scholar
Wicke S, Schneeweiss GM, de Pamphilis CW, Muller KF, Quandt D. The evolution of the plastid chromosome in land plants: gene content, gene order, gene function. Plant Mol Biol. 2011;76(3–5):273–97. https://doi.org/10.1007/s11103-011-9762-4.
Article
CAS
PubMed
PubMed Central
Google Scholar
Weng ML, Blazier JC, Govindu M, Jansen RK. Reconstruction of the ancestral plastid genome in Geraniaceae reveals a correlation between genome rearrangements, repeats, and nucleotide substitution rates. Mol Biol Evol. 2014;31(3):645–59. https://doi.org/10.1093/molbev/mst257.
Article
CAS
PubMed
Google Scholar
Blazier JC, Jansen RK, Mower JP, Govindu M, Zhang J, Weng ML, et al. Variable presence of the inverted repeat and plastome stability in Erodium. Ann Bot-London. 2016;117(7):1209–20. https://doi.org/10.1093/aob/mcw065.
Article
CAS
Google Scholar
Ruhlman TA, Zhang J, Blazier JC, Sabir JSM, Jansen RK. Recombination-dependent replication and gene conversion homogenize repeat sequences and diversify plastid genome structure. Am J Bot. 2017;104(4):559–72. https://doi.org/10.3732/ajb.1600453.
Article
CAS
PubMed
Google Scholar
Sanderson MJ, Copetti D, Burquez A, Bustamante E, Charboneau JLM, Eguiarte LE, et al. Exceptional reduction of the plastid genome of saguaro cactus (Carnegiea gigantea): loss of the ndh gene suite and inverted repeat. Am J Bot. 2015;102(7):1115–27. https://doi.org/10.3732/ajb.1500184.
Article
CAS
PubMed
Google Scholar
Choi IS, Jansen R, Ruhlman T. Lost and found: return of the inverted repeat in the legume clade defined by its absence. Genome Biol Evol. 2019;11(4):1321–33. https://doi.org/10.1093/gbe/evz076.
Article
CAS
PubMed
PubMed Central
Google Scholar
Jin DM, Wicke S, Gan L, Yang JB, Jin JJ, Yi TS. The loss of the inverted repeat in the putranjivoid clade of Malpighiales. Front Plant Sci. 2020;11. https://doi.org/10.3389/fpls.2020.00942.
Palmer JD, Thompson WF. Chloroplast DNA rearrangements are more frequent when a large inverted repeat sequence is lost. Cell. 1982;29(2):537–50. https://doi.org/10.1016/0092-8674(82)90170-2.
Article
CAS
PubMed
Google Scholar
Guisinger MM, Kuehl JV, Boore JL, Jansen RK. Extreme reconfiguration of plastid genomes in the angiosperm family geraniaceae: rearrangements, repeats, and codon usage. Mol Biol Evol. 2011;28(1):583–600. https://doi.org/10.1093/molbev/msq229.
Article
CAS
PubMed
Google Scholar
Hirao T, Watanabe A, Kurita M, Kondo T, Takata K. Complete nucleotide sequence of the Cryptomeria japonicia D. Don. chloroplast genome and comparative chloroplast genomics: diversified genomic structure of coniferous species. BMC Plant Biol. 2008;8:70. https://doi.org/10.1186/1471-2229-8-70.
Lee HL, Jansen RK, Chumley TW, Kim KJ. Gene relocations within chloroplast genomes of Jasminum and Menodora (Oleaceae) are due to multiple, overlapping inversions. Mol Biol Evol. 2007;24(5):1161–80. https://doi.org/10.1093/molbev/msm036.
Article
CAS
PubMed
Google Scholar
Zhu AD, Guo WH, Gupta S, Fan WS, Mower JP. Evolutionary dynamics of the plastid inverted repeat: the effects of expansion, contraction, and loss on substitution rates. New Phytol. 2016;209(4):1747–56. https://doi.org/10.1111/nph.13743.
Article
CAS
PubMed
Google Scholar
Wolfe KH, Li WH, Sharp PM. Rates of nucleotide substitution vary greatly among plant mitochondrial, chloroplast, and nuclear Dnas. P Natl Acad Sci USA. 1987;84(24):9054–8. https://doi.org/10.1073/pnas.84.24.9054.
Article
CAS
Google Scholar
Perry AS, Wolfe KH. Nucleotide substitution rates in legume chloroplast DNA depend on the presence of the inverted repeat. J Mol Evol. 2002;55(5):501–8. https://doi.org/10.1007/s00239-002-2333-y.
Article
CAS
PubMed
Google Scholar
Magee AM, Aspinall S, Rice DW, Cusack BP, Semon M, Perry AS, et al. Localized hypermutation and associated gene losses in legume chloroplast genomes. Genome Res. 2010;20(12):1700–10. https://doi.org/10.1101/gr.111955.110.
Article
CAS
PubMed
PubMed Central
Google Scholar
Mower JP, Touzet P, Gummow JS, Delph LF, Palmer JD. Extensive variation in synonymous substitution rates in mitochondrial genes of seed plants. BMC Evol Biol. 2007;7(1). https://doi.org/10.1186/1471-2148-7-135.
Cai ZQ, Guisinger M, Kim HG, Ruck E, Blazier JC, McMurtry V, et al. Extensive reorganization of the plastid genome of Trifolium subterraneum (Fabaceae) is associated with numerous repeated sequences and novel DNA insertions. J Mol Evol. 2008;67(6):696–704. https://doi.org/10.1007/s00239-008-9180-7.
Article
CAS
PubMed
Google Scholar
Sabir J, Schwarz E, Ellison N, Zhang J, Baeshen NA, Mutwakil M, et al. Evolutionary and biotechnology implications of plastid genome variation in the inverted-repeat-lacking clade of legumes. Plant Biotechnol J. 2014;12(6):743–54. https://doi.org/10.1111/pbi.12179.
Article
CAS
PubMed
Google Scholar
Dugas DV, Hernandez D, Koenen EJM, Schwarz E, Straub S, Hughes CE, et al. Mimosoid legume plastome evolution: IR expansion, tandem repeat expansions, and accelerated rate of evolution in clpP. Sci Rep-Uk. 2015;5(1). https://doi.org/10.1038/srep16958.
Shrestha B, Gilbert LE, Ruhlman TA, Jansen RK. Rampant nuclear transfer and substitutions of plastid genes in Passiflora. Genome Biol Evol. 2020;12(8):1313–29. https://doi.org/10.1093/gbe/evaa123.
Article
CAS
PubMed
PubMed Central
Google Scholar
Cauz-Santos LA, da Costa ZP, Callot C, Cauet S, Zucchi MI, Berges H, et al. A repertory of rearrangements and the loss of an inverted repeat region in Passiflora chloroplast genomes. Genome Biol Evol. 2020;12(10):1841–57. https://doi.org/10.1093/gbe/evaa155.
Article
CAS
PubMed
PubMed Central
Google Scholar
Shrestha B, Weng ML, Theriot EC, Gilbert LE, Ruhman TA, Krosnick SE, et al. Highly accelerated rates of genomic rearrangements and nucleotide substitutions in plastid genomes of Passiflora subgenus Decaloba. Mol Phylogenet Evol. 2019;138:53–64. https://doi.org/10.1016/j.ympev.2019.05.030.
Article
CAS
PubMed
Google Scholar
Rabah SO, Shrestha B, Hajrah NH, Sabir MJ, Alharby HF, Sabir MJ, et al. Passiflora plastome sequencing reveals widespread genomic rearrangements. J Syst Evol. 2019;57(1):1–14. https://doi.org/10.1111/jse.12425.
Article
Google Scholar
Goulding SE, Olmstead RG, Morden CW, Wolfe KH. Ebb and flow of the chloroplast inverted repeat. Mol Gen Genet. 1996;252(1–2):195–206. https://doi.org/10.1007/BF02173220.
Article
CAS
PubMed
Google Scholar
Day A, Madesis P. DNA replication, recombination, and repair in plastids. In: Bock R, editor. Book: DNA replication, recombination, and repair in plastids. ln: Edited by. Berlin, Heidelberg: Springer Berlin Heidelberg; 2007. p. 65–119. https://doi.org/10.1007/4735_2007_0231.
Choi IS, Jansen R, Ruhlman T. Caught in the act: variation in plastid genome inverted repeat expansion within and between populations of Medicago minima. Ecol Evol. 2020;10(21):12129–37. https://doi.org/10.1002/ece3.6839.
Article
PubMed
PubMed Central
Google Scholar
Jansen RK, Wojciechowski MF, Sanniyasi E, Lee SB, Daniell H. Complete plastid genome sequence of the chickpea (Cicer arietinum) and the phylogenetic distribution of rps12 and clpP intron losses among legumes (Leguminosae). Mol Phylogenet Evol. 2008;48(3):1204–17. https://doi.org/10.1016/j.ympev.2008.06.013.
Article
CAS
PubMed
PubMed Central
Google Scholar
Gurdon C, Maliga P. Two distinct plastid genome configurations and unprecedented intraspecies length variation in the accD coding region in Medicago truncatula. DNA Res. 2014;21(4):417–27. https://doi.org/10.1093/dnares/dsu007.
Article
CAS
PubMed
PubMed Central
Google Scholar
Palmer JD, Osorio B, Aldrich J, Thompson WF. Chloroplast DNA evolution among legumes: loss of a large inverted repeat occurred prior to other sequence rearrangements. Curr Genet. 1987;11(4):275–86. https://doi.org/10.1007/BF00355401.
Article
CAS
Google Scholar
Wojciechowski MF, Lavin M, Sanderson MJ. A phylogeny of legumes (Leguminosae) based on analyses of the plastid matK gene resolves many well-supported subclades within the family. Am J Bot. 2004;91(11):1846–62. https://doi.org/10.3732/ajb.91.11.1846.
Article
CAS
PubMed
Google Scholar
Wu CS, Wang YN, Hsu CY, Lin CP, Chaw SM. 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. 2011;3:1284–95. https://doi.org/10.1093/gbe/evr095.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ruhlman TA, Jansen RK. The plastid genomes of flowering plants. Methods Mol Biol. 2014;1132:3–38. https://doi.org/10.1007/978-1-62703-995-6_1.
Article
CAS
PubMed
Google Scholar
Schwarz EN, Ruhlman TA, Weng ML, Khiyami MA, Sabir JSM, Hajarah NH, et al. Plastome-wide nucleotide substitution rates reveal accelerated rates in Papilionoideae and correlations with genome features across legume subfamilies. J Mol Evol. 2017;84(4):187–203. https://doi.org/10.1007/s00239-017-9792-x.
Article
CAS
PubMed
Google Scholar
Moghaddam M, Kazempour-Osaloo S. Extensive survey of the ycf4 plastid gene throughout the IRLC legumes: Robust evidence of its locus and lineage specific accelerated rate of evolution, pseudogenization and gene loss in the tribe Fabeae. Plos One. 2020;15(3):e0229846. https://doi.org/10.1371/journal.pone.0229846.
Kode V, Mudd EA, Iamtham S, Day A. The tobacco plastid accD gene is essential and is required for leaf development. Plant J. 2005;44(2):237–44. https://doi.org/10.1111/j.1365-313X.2005.02533.x.
Article
CAS
PubMed
Google Scholar
Peltier JB, Ripoll DR, Friso G, Rudella A, Cai Y, Ytterberg J, et al. Clp protease complexes from photosynthetic and non-photosynthetic plastids and mitochondria of plants, their predicted three-dimensional structures, and functional implications. J Biol Chem. 2004;279(6):4768–81. https://doi.org/10.1074/jbc.M309212200.
Article
CAS
PubMed
Google Scholar
Kikuchi S, Bedard J, Hirano M, Hirabayashi Y, Oishi M, Imai M, et al. Uncovering the protein translocon at the chloroplast inner envelope membrane. Science. 2013;339(6119):571–4. https://doi.org/10.1126/science.1229262.
Article
CAS
PubMed
Google Scholar
Sveinsson S, Cronk Q. Evolutionary origin of highly repetitive plastid genomes within the clover genus (Trifolium). BMC Evol Biol. 2014;14(1):228. https://doi.org/10.1186/s12862-014-0228-6.
Article
CAS
PubMed
PubMed Central
Google Scholar
Schwarz EN, Ruhlman TA, Sabir JSM, Hajrah NH, Alharbi NS, Al-Malki AL, et al. Plastid genome sequences of legumes reveal parallel inversions and multiple losses of rps16 in papilionoids. J Syst Evol. 2015;53(5):458–68. https://doi.org/10.1111/jse.12179.
Article
Google Scholar
Gantt JS, Baldauf SL, Calie PJ, Weeden NF, Palmer JD. Transfer of Rpl22 to the nucleus greatly preceded its loss from the chloroplast and involved the gain of an intron. EMBO J. 1991;10(10):3073–8. https://doi.org/10.1002/j.1460-2075.1991.tb07859.x.
Article
CAS
PubMed
PubMed Central
Google Scholar
Millen RS, Olmstead RG, Adams KL, Palmer JD, Lao NT, Heggie L, et al. Many parallel losses of infA from chloroplast DNA during angiosperm evolution with multiple independent transfers to the nucleus. Plant Cell. 2001;13(3):645–58. https://doi.org/10.1105/tpc.13.3.645.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ueda M, Nishikawa T, Fujimoto M, Takanashi H, Arimura S, Tsutsumi N, et al. Substitution of the gene for chloroplast RPS16 was assisted by generation of a dual targeting signal. Mol Biol Evol. 2008;25(8):1566–75. https://doi.org/10.1093/molbev/msn102.
Article
CAS
PubMed
Google Scholar
Sinn BT, Sedmak DD, Kelly LM, Freudenstein JV. Total duplication of the small single copy region in the angiosperm plastome: rearrangement and inverted repeat instability in Asarum. Am J Bot. 2018;105(1):71–84. https://doi.org/10.1002/ajb2.1001.
Article
CAS
PubMed
Google Scholar
Ansell SW, Schneider H, Pedersen N, Grundmann M, Russell SJ, Vogel JC. Recombination diversifies chloroplast trnF pseudogenes in Arabidopsis lyrata. J Evolution Biol. 2007;20(6):2400–11. https://doi.org/10.1111/j.1420-9101.2007.01397.x.
Article
CAS
Google Scholar
Wang RJ, Cheng CL, Chang CC, Wu CL, Su TM, Chaw SM. Dynamics and evolution of the inverted repeat-large single copy junctions in the chloroplast genomes of monocots. BMC Evol Biol. 2008;8(1). https://doi.org/10.1186/1471-2148-8-36.
Ogihara Y, Ohsawa T. Molecular analysis of the complete set of length mutations found in the plastomes of Triticum-Aegilops species. Genome. 2002;45(5):956–62. https://doi.org/10.1139/g02-046.
Article
CAS
PubMed
Google Scholar
Marechal A, Parent JS, Veronneau-Lafortune F, Joyeux A, Lang BF, Brisson N. Whirly proteins maintain plastid genome stability in Arabidopsis. P Natl Acad Sci USA. 2009;106(34):14693–8. https://doi.org/10.1073/pnas.0901710106.
Article
Google Scholar
Kwon T, Huq E, Herrin DL. Microhomology-mediated and nonhomologous repair of a double-strand break in the chloroplast genome of Arabidopsis. P Natl Acad Sci USA. 2010;107(31):13954–9. https://doi.org/10.1073/pnas.1004326107.
Article
Google Scholar
Chen JY, Wu GL, Shrestha N, Wu S, Guo W, Yin M, et al. Phylogeny and species delimitation of Chinese Medicago (Leguminosae) and its relatives based on molecular and morphological evidence. Front Plant Sci. 2021;11. https://doi.org/10.3389/fpls.2020.619799.
Doyle JJ. A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem Bull. 1987;19:11-15.
Andrews S. FastQC: a quality control tool for high throughput sequence data; 2010.
Google Scholar
Dierckxsens N, Mardulyn P, Smits G. NOVOPlasty: de novo assembly of organelle genomes from whole genome data. Nucleic Acids Res. 2017;45(4):e18. https://doi.org/10.1093/nar/gkw955.
Tillich M, Lehwark P, Pellizzer T, Ulbricht-Jones ES, Fischer A, Bock R, et al. GeSeq - versatile and accurate annotation of organelle genomes. Nucleic Acids Res. 2017;45(W1):W6–W11. https://doi.org/10.1093/nar/gkx391.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lowe TM, Chan PP. tRNAscan-SE on-line: integrating search and context for analysis of transfer RNA genes. Nucleic Acids Res. 2016;44(W1):W54–7. https://doi.org/10.1093/nar/gkw413.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kearse M, Moir R, Wilson A, Stones-Havas S, Cheung M, Sturrock S, et al. Geneious basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics. 2012;28(12):1647–9. https://doi.org/10.1093/bioinformatics/bts199.
Article
PubMed
PubMed Central
Google Scholar
Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, et al. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol. 2011;29(7):644–U130. https://doi.org/10.1038/nbt.1883.
Article
CAS
PubMed
PubMed Central
Google Scholar
McGinnis S, Madden TL. BLAST: at the core of a powerful and diverse set of sequence analysis tools. Nucleic Acids Res. 2004;32(Web Server):W20–5. https://doi.org/10.1093/nar/gkh435.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lohse M, Drechsel O, Kahlau S, Bock R. OrganellarGenomeDRAW-a suite of tools for generating physical maps of plastid and mitochondrial genomes and visualizing expression data sets. Nucleic Acids Res. 2013;41(W1):W575–81. https://doi.org/10.1093/nar/gkt289.
Article
PubMed
PubMed Central
Google Scholar
Darling AE, Mau B, Perna NT. progressiveMauve: multiple genome alignment with gene gain, loss and rearrangement. Plos One. 2010;5(6):e11147. https://doi.org/10.1371/journal.pone.0011147.
Benson G. Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res. 1999;27(2):573–80. https://doi.org/10.1093/nar/27.2.573.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kurtz S, Choudhuri JV, Ohlebusch E, Schleiermacher C, Stoye J, Giegerich R. REPuter: the manifold applications of repeat analysis on a genomic scale. Nucleic Acids Res. 2001;29(22):4633–42. https://doi.org/10.1093/nar/29.22.4633.
Article
CAS
PubMed
PubMed Central
Google Scholar
Frazer KA, Pachter L, Poliakov A, Rubin EM, Dubchak I. VISTA: computational tools for comparative genomics. Nucleic Acids Res. 2004;32(Web Server):W273–9. https://doi.org/10.1093/nar/gkh458.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zhang R, Wang YH, Jin JJ, Stull GW, Bruneau A, Cardoso D, et al. Exploration of plastid phylogenomic conflict yields new insights into the deep relationships of Leguminosae. Syst Biol. 2020;69(4):613–22. https://doi.org/10.1093/sysbio/syaa013.
Article
CAS
PubMed
PubMed Central
Google Scholar
Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 2013;30(4):772–80. https://doi.org/10.1093/molbev/mst010.
Article
CAS
PubMed
PubMed Central
Google Scholar
Rozas J, Ferrer-Mata A, Sanchez-DelBarrio JC, Guirao-Rico S, Librado P, Ramos-Onsins SE, et al. DnaSP 6: DNA sequence polymorphism analysis of large data sets. Mol Biol Evol. 2017;34(12):3299–302. https://doi.org/10.1093/molbev/msx248.
Article
CAS
PubMed
Google Scholar
Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, et al. Clustal W and clustal X version 2.0. Bioinformatics. 2007;23(21):2947–8. https://doi.org/10.1093/bioinformatics/btm404.
Article
CAS
PubMed
Google Scholar
Guindon S, Dufayard JF, Hordijk W, Lefort V, Gascuel O. PhyML: fast and accurate phylogeny reconstruction by maximum likelihood. Infect Genet Evol. 2009;9(3):384–5.
Google Scholar
Posada D. jModelTest: phylogenetic model averaging. Mol Biol Evol. 2008;25(7):1253–6. https://doi.org/10.1093/molbev/msn083.
Article
CAS
PubMed
Google Scholar
Yang ZH. PAML 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol. 2007;24(8):1586–91. https://doi.org/10.1093/molbev/msm088.
Article
CAS
PubMed
Google Scholar
Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics. 2014;30(9):1312–3. https://doi.org/10.1093/bioinformatics/btu033.
Article
CAS
PubMed
PubMed Central
Google Scholar