{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,22]],"date-time":"2026-10-22T14:45:56Z","timestamp":1792680356445,"version":"4.5.0"},"reference-count":75,"publisher":"Springer Science and Business Media LLC","issue":"5","license":[{"start":{"date-parts":[[2026,10,11]],"date-time":"2026-10-11T00:00:00Z","timestamp":1791676800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"},{"start":{"date-parts":[[2026,10,11]],"date-time":"2026-10-11T00:00:00Z","timestamp":1791676800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"}],"funder":[{"name":"T\u00dcB\u0130TAK-KBAG","award":["124Z673"],"award-info":[{"award-number":["124Z673"]}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Planta"],"published-print":{"date-parts":[[2026,11]]},"DOI":"10.1007\/s00425-026-05197-3","type":"journal-article","created":{"date-parts":[[2026,10,11]],"date-time":"2026-10-11T00:05:18Z","timestamp":1791677118000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Plastome architecture and maternal relationships of cultivated almond (Prunus dulcis) and its wild relatives"],"prefix":"10.1007","volume":"264","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-2425-8244","authenticated-orcid":false,"given":"Yasin","family":"Kaya","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1113-3074","authenticated-orcid":false,"given":"Z\u00fcbeyde U\u011furlu","family":"Ayd\u0131n","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6695-6177","authenticated-orcid":false,"given":"Ali A.","family":"D\u00f6nmez","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2026,10,11]]},"reference":[{"key":"5197_CR1","doi-asserted-by":"publisher","first-page":"57","DOI":"10.1007\/s10341-025-01750-8","volume":"68","author":"N Alhas-Ero\u011flu","year":"2026","unstructured":"Alhas-Ero\u011flu N (2026) Evaluation of international almond trade: how competitive is T\u00fcrkiye in global almond markets? Appl Fruit Sci 68:57. https:\/\/doi.org\/10.1007\/s10341-025-01750-8","journal-title":"Appl Fruit Sci"},{"key":"5197_CR2","doi-asserted-by":"publisher","first-page":"455","DOI":"10.1111\/tpj.14538","volume":"101","author":"T Alioto","year":"2020","unstructured":"Alioto T, Alexiou KG, Bardil A, Barteri F, Castanera R, Cruz F, Dhingra A, Duval H, Fern\u00e1ndez i Mart\u00ed \u00c1, Frias L, Gal\u00e1n B (2020) Transposons played a major role in the diversification between the closely related almond and peach genomes: results from the almond genome sequence. Plant J 101:455\u2013472. https:\/\/doi.org\/10.1111\/tpj.14538","journal-title":"Plant J"},{"key":"5197_CR3","doi-asserted-by":"publisher","first-page":"42","DOI":"10.1186\/s43141-020-00057-3","volume":"18","author":"MH Amar","year":"2020","unstructured":"Amar MH (2020) ycf1-ndhF genes, the most promising plastid genomic barcode, sheds light on phylogeny at low taxonomic levels in Prunus persica. J Genet Eng Biotechnol 18:42. https:\/\/doi.org\/10.1186\/s43141-020-00057-3","journal-title":"J Genet Eng Biotechnol"},{"key":"5197_CR4","doi-asserted-by":"publisher","first-page":"885","DOI":"10.1139\/cjps-2019-0129","volume":"99","author":"MH Amar","year":"2019","unstructured":"Amar MH, Magdy M, Wang L, Zhou H, Zheng B, Jiang X, Atta AH, Han Y (2019) Peach chloroplast genome variation architecture and phylogenomic signatures of cpDNA introgression in Prunus. Can J Plant Sci 99:885\u2013896. https:\/\/doi.org\/10.1139\/cjps-2019-0129","journal-title":"Can J Plant Sci"},{"key":"5197_CR5","doi-asserted-by":"publisher","first-page":"3030","DOI":"10.1093\/bioinformatics\/bty220","volume":"34","author":"A Amiryousefi","year":"2018","unstructured":"Amiryousefi A, Hyv\u00f6nen J, Poczai P (2018) IRscope: an online program to visualize the junction sites of chloroplast genomes. Bioinformatics 34:3030\u20133031. https:\/\/doi.org\/10.1093\/bioinformatics\/bty220","journal-title":"Bioinformatics"},{"key":"5197_CR6","unstructured":"Andrews S (2010) FastQC: a quality control tool for high throughput sequence data. Babraham Bioinformatics. http:\/\/www.bioinformatics.babraham.ac.uk\/projects\/fastqc\/. Accessed 20 June 2026"},{"key":"5197_CR7","doi-asserted-by":"publisher","first-page":"2583","DOI":"10.1093\/bioinformatics\/btx198","volume":"33","author":"S Beier","year":"2017","unstructured":"Beier S, Thiel T, M\u00fcnch T, Scholz U, Mascher M (2017) MISA-web: a web server for microsatellite prediction. Bioinformatics 33:2583\u20132585. https:\/\/doi.org\/10.1093\/bioinformatics\/btx198","journal-title":"Bioinformatics"},{"key":"5197_CR8","doi-asserted-by":"publisher","first-page":"573","DOI":"10.1093\/nar\/27.2.573","volume":"27","author":"G Benson","year":"1999","unstructured":"Benson G (1999) Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res 27:573\u2013580. https:\/\/doi.org\/10.1093\/nar\/27.2.573","journal-title":"Nucleic Acids Res"},{"key":"5197_CR9","doi-asserted-by":"publisher","first-page":"2114","DOI":"10.1093\/bioinformatics\/btu170","volume":"30","author":"AM Bolger","year":"2014","unstructured":"Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30:2114\u20132120. https:\/\/doi.org\/10.1093\/bioinformatics\/btu170","journal-title":"Bioinformatics"},{"key":"5197_CR10","doi-asserted-by":"publisher","DOI":"10.3389\/fpls.2021.779970","volume":"12","author":"H Brukental","year":"2021","unstructured":"Brukental H, Doron-Faigenboim A, Bar-Ya\u2019akov I, Harel-Beja R, Attia Z, Azoulay-Shemer T, Holland D (2021) Revealing the genetic components responsible for the unique photosynthetic stem capability of the wild almond Prunus arabica (Olivier) Meikle. Front Plant Sci 12:779970. https:\/\/doi.org\/10.3389\/fpls.2021.779970","journal-title":"Front Plant Sci"},{"key":"5197_CR11","doi-asserted-by":"publisher","DOI":"10.1007\/s11295-024-01668-4","volume":"20","author":"H Brukental","year":"2024","unstructured":"Brukental H, Doron-Faigenboim A, Bar-Ya\u2019akov I, Harel-Beja R, Trainin T, Hatib K, Holland D (2024) Exploring the wild almond, Prunus arabica (Olivier), as a genetic source for almond breeding. Tree Genet Genomes 20:37. https:\/\/doi.org\/10.1007\/s11295-024-01668-4","journal-title":"Tree Genet Genomes"},{"key":"5197_CR12","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-10-421","volume":"10","author":"C Camacho","year":"2009","unstructured":"Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, Madden TL (2009) BLAST+: architecture and applications. BMC Bioinform 10:421. https:\/\/doi.org\/10.1186\/1471-2105-10-421","journal-title":"BMC Bioinform"},{"key":"5197_CR13","doi-asserted-by":"publisher","first-page":"12794","DOI":"10.1073\/pnas.0905845106","volume":"106","author":"CBOL Plant Working Group","year":"2009","unstructured":"CBOL Plant Working Group (2009) A DNA barcode for land plants. Proc Natl Acad Sci U S A 106:12794\u201312797. https:\/\/doi.org\/10.1073\/pnas.0905845106","journal-title":"Proc Natl Acad Sci U S A"},{"key":"5197_CR14","doi-asserted-by":"publisher","first-page":"i884","DOI":"10.1093\/bioinformatics\/bty560","volume":"34","author":"S Chen","year":"2018","unstructured":"Chen S, Zhou Y, Chen Y, Gu J (2018) Fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics 34:i884\u2013i890. https:\/\/doi.org\/10.1093\/bioinformatics\/bty560","journal-title":"Bioinformatics"},{"key":"5197_CR15","doi-asserted-by":"publisher","DOI":"10.1016\/j.dib.2024.110077","volume":"53","author":"Y Chen","year":"2024","unstructured":"Chen Y, Bao W, Ao D, Bai Y, Huang H, Yang R, Wuyun TN (2024) Chloroplast genome data of five Amygdalus species: clarifying genome structure and phylogenetic relationships. Data Brief 53:110077. https:\/\/doi.org\/10.1016\/j.dib.2024.110077","journal-title":"Data Brief"},{"key":"5197_CR16","doi-asserted-by":"publisher","first-page":"34","DOI":"10.1016\/j.ympev.2014.02.024","volume":"76","author":"S-W Chin","year":"2014","unstructured":"Chin S-W, Shaw J, Haberle R, Wen J, Potter D (2014) Diversification of almonds, peaches, plums and cherries \u2013 molecular systematics and biogeographic history of Prunus (Rosaceae). Mol Phylogenet Evol 76:34\u201348. https:\/\/doi.org\/10.1016\/j.ympev.2014.02.024","journal-title":"Mol Phylogenet Evol"},{"key":"5197_CR17","doi-asserted-by":"publisher","first-page":"80","DOI":"10.4161\/fly.19695","volume":"6","author":"P Cingolani","year":"2012","unstructured":"Cingolani P, Platts A, Wang LL, Coon M, Nguyen T, Wang L, Land SJ, Lu X, Ruden DM (2012) A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff. Fly 6:80\u201392. https:\/\/doi.org\/10.4161\/fly.19695","journal-title":"Fly"},{"key":"5197_CR18","doi-asserted-by":"publisher","first-page":"1443","DOI":"10.1002\/j.1537-2197.1988.tb11219.x","volume":"75","author":"JL Corriveau","year":"1988","unstructured":"Corriveau JL, Coleman AW (1988) Rapid screening method to detect potential biparental inheritance of plastid DNA and results for over 200 angiosperm species. Am J Bot 75:1443\u20131458. https:\/\/doi.org\/10.1002\/j.1537-2197.1988.tb11219.x","journal-title":"Am J Bot"},{"key":"5197_CR19","doi-asserted-by":"publisher","DOI":"10.1093\/g3journal\/jkac065","volume":"12","author":"KM D\u2019Amico-Willman","year":"2022","unstructured":"D\u2019Amico-Willman KM, Ouma WZ, Meulia T, Sideli GM, Gradziel TM, Fresnedo-Ram\u00edrez J (2022) Whole-genome sequence and methylome profiling of the almond [Prunus dulcis (Mill.) D.A. Webb] cultivar \u201cNonpareil.\u201d G3 (Bethesda) 12:jkac065. https:\/\/doi.org\/10.1093\/g3journal\/jkac065","journal-title":"G3 (Bethesda)"},{"key":"5197_CR20","doi-asserted-by":"publisher","first-page":"134","DOI":"10.1186\/s13059-016-1004-2","volume":"17","author":"H Daniell","year":"2016","unstructured":"Daniell H, Lin C-S, Yu M, Chang W-J (2016) Chloroplast genomes: diversity, evolution, and applications in genetic engineering. Genome Biol 17:134. https:\/\/doi.org\/10.1186\/s13059-016-1004-2","journal-title":"Genome Biol"},{"key":"5197_CR21","doi-asserted-by":"publisher","first-page":"1092","DOI":"10.1111\/mec.12129","volume":"22","author":"M Delplancke","year":"2013","unstructured":"Delplancke M, Alvarez N, Benoit L, Esp\u00edndola A, Joly HI, Neuenschwander S, Arrigo N (2013) Evolutionary history of almond tree domestication in the Mediterranean basin. Mol Ecol 22:1092\u20131104. https:\/\/doi.org\/10.1111\/mec.12129","journal-title":"Mol Ecol"},{"key":"5197_CR22","doi-asserted-by":"publisher","DOI":"10.1038\/srep08348","volume":"5","author":"W Dong","year":"2015","unstructured":"Dong W, Xu C, Li C, Sun J, Zuo Y, Shi S, Cheng T, Guo J, Zhou S (2015) Ycf1, the most promising plastid DNA barcode of land plants. Sci Rep 5:8348. https:\/\/doi.org\/10.1038\/srep08348","journal-title":"Sci Rep"},{"key":"5197_CR23","unstructured":"D\u00f6nmez AA, \u00d6zmen \u0130 (2001) Numerical taxonomic study on the Pruneae (Rosaceae) tribe in Turkey. In: Proceedings of the 2nd Balkan Botanical Congress, vol 1. \u0130stanbul, pp 179\u2013188"},{"key":"5197_CR24","doi-asserted-by":"publisher","first-page":"49","DOI":"10.1007\/978-94-011-5274-7_10","volume-title":"Progress in botanical research: proceedings of the 1st Balkan Botanical Congress","author":"AA D\u00f6nmez","year":"1998","unstructured":"D\u00f6nmez AA, Y\u0131ld\u0131r\u0131ml\u0131 \u015e (1998) Intraspecific variation of Amygdalus orientalis Miller (Rosaceae). In: Tsekos I, Moustakas M (eds) Progress in botanical research: proceedings of the 1st Balkan Botanical Congress. Kluwer Academic Publishers, Dordrecht, pp 49\u201352"},{"key":"5197_CR25","doi-asserted-by":"publisher","DOI":"10.1186\/s12864-021-07968-6","volume":"22","author":"Z Du","year":"2021","unstructured":"Du Z, Lu K, Zhang K, He Y, Wang H, Chai G, Shi J, Duan Y (2021) The chloroplast genome of Amygdalus L. (Rosaceae) reveals the phylogenetic relationship and divergence time. BMC Genomics 22:645. https:\/\/doi.org\/10.1186\/s12864-021-07968-6","journal-title":"BMC Genomics"},{"key":"5197_CR26","unstructured":"FAO (2023) FAOSTAT: crops and livestock products. Food and Agriculture Organization of the United Nations, Rome. https:\/\/www.fao.org\/faostat\/en\/#data\/QCL. Accessed 20 June 2026"},{"key":"5197_CR27","doi-asserted-by":"publisher","first-page":"665","DOI":"10.1007\/s00294-015-0495-9","volume":"61","author":"B George","year":"2015","unstructured":"George B, Bhatt BS, Awasthi M, George B, Singh AK (2015) Comparative analysis of microsatellites in chloroplast genomes of lower and higher plants. Curr Genet 61:665\u2013677. https:\/\/doi.org\/10.1007\/s00294-015-0495-9","journal-title":"Curr Genet"},{"key":"5197_CR28","doi-asserted-by":"publisher","first-page":"W59","DOI":"10.1093\/nar\/gkz238","volume":"47","author":"S Greiner","year":"2019","unstructured":"Greiner S, Lehwark P, Bock R (2019) OrganellarGenomeDRAW (OGDRAW) version 1.3.1: expanded toolkit for the graphical visualization of organellar genomes. Nucleic Acids Res 47:W59\u2013W64. https:\/\/doi.org\/10.1093\/nar\/gkz238","journal-title":"Nucleic Acids Res"},{"key":"5197_CR29","doi-asserted-by":"publisher","first-page":"518","DOI":"10.1093\/molbev\/msx281","volume":"35","author":"DT Hoang","year":"2018","unstructured":"Hoang DT, Chernomor O, von Haeseler A, Minh BQ, Vinh LS (2018) UFBoot2: improving the ultrafast bootstrap approximation. Mol Biol Evol 35:518\u2013522. https:\/\/doi.org\/10.1093\/molbev\/msx281","journal-title":"Mol Biol Evol"},{"key":"5197_CR30","doi-asserted-by":"publisher","DOI":"10.1016\/j.ympev.2021.107118","volume":"160","author":"RGJ Hodel","year":"2021","unstructured":"Hodel RGJ, Zimmer E, Wen J (2021) A phylogenomic approach resolves the backbone of Prunus (Rosaceae) and identifies signals of hybridization and allopolyploidy. Mol Phylogenet Evol 160:107118. https:\/\/doi.org\/10.1016\/j.ympev.2021.107118","journal-title":"Mol Phylogenet Evol"},{"key":"5197_CR31","doi-asserted-by":"publisher","DOI":"10.1016\/j.gene.2021.145751","volume":"793","author":"X Huang","year":"2021","unstructured":"Huang X, Tan W, Li F, Liao R, Guo Z, Shi T, Gao Z (2021) The chloroplast genome of Prunus zhengheensis: genome comparative and phylogenetic relationships analysis. Gene 793:145751. https:\/\/doi.org\/10.1016\/j.gene.2021.145751","journal-title":"Gene"},{"key":"5197_CR32","doi-asserted-by":"publisher","DOI":"10.1002\/imo2.25","volume":"1","author":"L Huang","year":"2024","unstructured":"Huang L, Yu H, Wang Z, Xu W (2024) CPStools: a package for analyzing chloroplast genome sequences. iMetaOmics 1:e25. https:\/\/doi.org\/10.1002\/imo2.25","journal-title":"iMetaOmics"},{"key":"5197_CR33","doi-asserted-by":"publisher","DOI":"10.3390\/genes10010023","volume":"10","author":"J-H Jeon","year":"2019","unstructured":"Jeon J-H, Kim S-C (2019) Comparative analysis of the complete chloroplast genome sequences of three closely related East-Asian wild roses (Rosa sect. Synstylae; Rosaceae). Genes 10:23. https:\/\/doi.org\/10.3390\/genes10010023","journal-title":"Genes"},{"key":"5197_CR34","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-020-02154-5","volume":"21","author":"J-J Jin","year":"2020","unstructured":"Jin J-J, Yu W-B, Yang J-B, Song Y, dePamphilis CW, Yi T-S, Li D-Z (2020) GetOrganelle: a fast and versatile toolkit for accurate de novo assembly of organelle genomes. Genome Biol 21:241. https:\/\/doi.org\/10.1186\/s13059-020-02154-5","journal-title":"Genome Biol"},{"key":"5197_CR35","doi-asserted-by":"publisher","first-page":"587","DOI":"10.1038\/nmeth.4285","volume":"14","author":"S Kalyaanamoorthy","year":"2017","unstructured":"Kalyaanamoorthy S, Minh BQ, Wong TKF, von Haeseler A, Jermiin LS (2017) ModelFinder: fast model selection for accurate phylogenetic estimates. Nat Methods 14:587\u2013589. https:\/\/doi.org\/10.1038\/nmeth.4285","journal-title":"Nat Methods"},{"key":"5197_CR36","doi-asserted-by":"publisher","first-page":"772","DOI":"10.1093\/molbev\/mst010","volume":"30","author":"K Katoh","year":"2013","unstructured":"Katoh K, Standley DM (2013) MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol 30:772\u2013780. https:\/\/doi.org\/10.1093\/molbev\/mst010","journal-title":"Mol Biol Evol"},{"key":"5197_CR37","doi-asserted-by":"publisher","first-page":"41","DOI":"10.1080\/10408398.2011.646363","volume":"55","author":"S Kaur","year":"2015","unstructured":"Kaur S, Panesar PS, Bera MB, Kaur V (2015) Simple sequence repeat markers in genetic divergence and marker-assisted selection of rice cultivars: a review. Crit Rev Food Sci Nutr 55:41\u201349. https:\/\/doi.org\/10.1080\/10408398.2011.646363","journal-title":"Crit Rev Food Sci Nutr"},{"key":"5197_CR38","doi-asserted-by":"publisher","DOI":"10.1186\/s12864-024-11044-0","volume":"25","author":"S Khojand","year":"2024","unstructured":"Khojand S, Zeinalabedini M, Azizinezhad R, Imani A, Ghaffari MR (2024) Genomic exploration of Iranian almond (Prunus dulcis) germplasm: decoding diversity, population structure, and linkage disequilibrium through genotyping-by-sequencing analysis. BMC Genomics 25:1101. https:\/\/doi.org\/10.1186\/s12864-024-11044-0","journal-title":"BMC Genomics"},{"key":"5197_CR39","unstructured":"Kolde R (2019) pheatmap: pretty heatmaps. R package version 1.0.12. https:\/\/CRAN.R-project.org\/package=pheatmap"},{"key":"5197_CR40","doi-asserted-by":"publisher","first-page":"8369","DOI":"10.1073\/pnas.0503123102","volume":"102","author":"WJ Kress","year":"2005","unstructured":"Kress WJ, Wurdack KJ, Zimmer EA, Weigt LA, Janzen DH (2005) Use of DNA barcodes to identify flowering plants. Proc Natl Acad Sci U S A 102:8369\u20138374. https:\/\/doi.org\/10.1073\/pnas.0503123102","journal-title":"Proc Natl Acad Sci U S A"},{"key":"5197_CR41","doi-asserted-by":"publisher","first-page":"143","DOI":"10.1023\/A:1008690409554","volume":"46","author":"G Ladizinsky","year":"1999","unstructured":"Ladizinsky G (1999) On the origin of almond. Genet Resour Crop Evol 46:143\u2013147. https:\/\/doi.org\/10.1023\/A:1008690409554","journal-title":"Genet Resour Crop Evol"},{"key":"5197_CR42","doi-asserted-by":"publisher","first-page":"2669","DOI":"10.1093\/molbev\/msm193","volume":"24","author":"T Lepage","year":"2007","unstructured":"Lepage T, Bryant D, Philippe H, Lartillot N (2007) A general comparison of relaxed molecular clock models. Mol Biol Evol 24:2669\u20132680. https:\/\/doi.org\/10.1093\/molbev\/msm193","journal-title":"Mol Biol Evol"},{"key":"5197_CR43","doi-asserted-by":"publisher","first-page":"3094","DOI":"10.1093\/bioinformatics\/bty191","volume":"34","author":"H Li","year":"2018","unstructured":"Li H (2018) Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics 34:3094\u20133100. https:\/\/doi.org\/10.1093\/bioinformatics\/bty191","journal-title":"Bioinformatics"},{"key":"5197_CR44","doi-asserted-by":"publisher","first-page":"157","DOI":"10.1111\/brv.12104","volume":"90","author":"X Li","year":"2014","unstructured":"Li X, Yang Y, Henry RJ, Rossetto M, Wang Y, Chen S (2014) Plant DNA barcoding: from gene to genome. Biol Rev 90:157\u2013166. https:\/\/doi.org\/10.1111\/brv.12104","journal-title":"Biol Rev"},{"key":"5197_CR45","unstructured":"Li H (2013) Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv:1303.3997"},{"key":"5197_CR46","doi-asserted-by":"publisher","first-page":"1530","DOI":"10.1093\/molbev\/msaa015","volume":"37","author":"BQ Minh","year":"2020","unstructured":"Minh BQ, Schmidt HA, Chernomor O, Schrempf D, Woodhams MD, von Haeseler A, Lanfear R (2020) IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era. Mol Biol Evol 37:1530\u20131534. https:\/\/doi.org\/10.1093\/molbev\/msaa015","journal-title":"Mol Biol Evol"},{"key":"5197_CR47","doi-asserted-by":"publisher","first-page":"4623","DOI":"10.1073\/pnas.0907801107","volume":"107","author":"MJ Moore","year":"2010","unstructured":"Moore MJ, Soltis PS, Bell CD, Burleigh JG, Soltis DE (2010) Phylogenetic analysis of 83 plastid genes further resolves the early diversification of eudicots. Proc Natl Acad Sci USA 107:4623\u20134628. https:\/\/doi.org\/10.1073\/pnas.0907801107","journal-title":"Proc Natl Acad Sci USA"},{"key":"5197_CR48","doi-asserted-by":"publisher","first-page":"92","DOI":"10.1038\/301092a0","volume":"301","author":"JD Palmer","year":"1983","unstructured":"Palmer JD (1983) Chloroplast DNA exists in two orientations. Nature 301:92\u201393. https:\/\/doi.org\/10.1038\/301092a0","journal-title":"Nature"},{"key":"5197_CR49","doi-asserted-by":"publisher","DOI":"10.3390\/ijms20235940","volume":"20","author":"X Pang","year":"2019","unstructured":"Pang X, Liu H, Wu S, Yuan Y, Li H, Dong J, Liu Z, An C, Su Z, Li B (2019) Species identification of oaks (Quercus L., Fagaceae) from gene to genome. Int J Mol Sci 20:5940. https:\/\/doi.org\/10.3390\/ijms20235940","journal-title":"Int J Mol Sci"},{"key":"5197_CR50","doi-asserted-by":"publisher","first-page":"419","DOI":"10.1093\/bioinformatics\/btp696","volume":"26","author":"E Paradis","year":"2010","unstructured":"Paradis E (2010) Pegas: an R package for population genetics with an integrated\u2013modular approach. Bioinformatics 26:419\u2013420. https:\/\/doi.org\/10.1093\/bioinformatics\/btp696","journal-title":"Bioinformatics"},{"key":"5197_CR51","doi-asserted-by":"publisher","first-page":"436","DOI":"10.1016\/j.ympev.2013.02.008","volume":"67","author":"E Paradis","year":"2013","unstructured":"Paradis E (2013) Molecular dating of phylogenies by likelihood methods: a comparison of models and a new information criterion. Mol Phylogenet Evol 67:436\u2013444. https:\/\/doi.org\/10.1016\/j.ympev.2013.02.008","journal-title":"Mol Phylogenet Evol"},{"key":"5197_CR52","doi-asserted-by":"publisher","first-page":"526","DOI":"10.1093\/bioinformatics\/bty633","volume":"35","author":"E Paradis","year":"2019","unstructured":"Paradis E, Schliep K (2019) Ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R. Bioinformatics 35:526\u2013528. https:\/\/doi.org\/10.1093\/bioinformatics\/bty633","journal-title":"Bioinformatics"},{"key":"5197_CR53","doi-asserted-by":"publisher","DOI":"10.1186\/1741-7007-7-84","volume":"7","author":"M Parks","year":"2009","unstructured":"Parks M, Cronn R, Liston A (2009) Increasing phylogenetic resolution at low taxonomic levels using massively parallel sequencing of chloroplast genomes. BMC Biol 7:84. https:\/\/doi.org\/10.1186\/1741-7007-7-84","journal-title":"BMC Biol"},{"key":"5197_CR54","doi-asserted-by":"publisher","first-page":"539","DOI":"10.1007\/s11033-021-06749-4","volume":"49","author":"ST Parvathy","year":"2022","unstructured":"Parvathy ST, Udayasuriyan V, Bhadana V (2022) Codon usage bias. Mol Biol Rep 49:539\u2013565. https:\/\/doi.org\/10.1007\/s11033-021-06749-4","journal-title":"Mol Biol Rep"},{"key":"5197_CR55","doi-asserted-by":"publisher","first-page":"142","DOI":"10.1016\/S0169-5347(00)02097-8","volume":"16","author":"J Provan","year":"2001","unstructured":"Provan J, Powell W, Hollingsworth PM (2001) Chloroplast microsatellites: new tools for studies in plant ecology and evolution. Trends Ecol Evol 16:142\u2013147. https:\/\/doi.org\/10.1016\/S0169-5347(00)02097-8","journal-title":"Trends Ecol Evol"},{"key":"5197_CR56","unstructured":"R Core Team (2023) R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna. https:\/\/www.R-project.org\/"},{"key":"5197_CR57","doi-asserted-by":"publisher","first-page":"1543","DOI":"10.3390\/molecules20011543","volume":"20","author":"S Raveendar","year":"2015","unstructured":"Raveendar S, Lee G-A, Jeon Y-A, Lee Y-J, Lee J-R, Cho G-T, Cho J-H, Park J-H, Ma K-H, Chung J-W (2015) Cross-amplification of Vicia sativa subsp. sativa microsatellites across 22 other Vicia species. Molecules 20:1543\u20131550. https:\/\/doi.org\/10.3390\/molecules20011543","journal-title":"Molecules"},{"key":"5197_CR58","doi-asserted-by":"publisher","first-page":"217","DOI":"10.1111\/j.2041-210X.2011.00169.x","volume":"3","author":"LJ Revell","year":"2012","unstructured":"Revell LJ (2012) Phytools: an R package for phylogenetic comparative biology (and other things). Methods Ecol Evol 3:217\u2013223. https:\/\/doi.org\/10.1111\/j.2041-210X.2011.00169.x","journal-title":"Methods Ecol Evol"},{"key":"5197_CR59","doi-asserted-by":"publisher","first-page":"539","DOI":"10.1093\/sysbio\/sys029","volume":"61","author":"F Ronquist","year":"2012","unstructured":"Ronquist F, Teslenko M, van der Mark P, Ayres DL, Darling A, H\u00f6hna S, Larget B, Liu L, Suchard MA, Huelsenbeck JP (2012) MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Syst Biol 61:539\u2013542. https:\/\/doi.org\/10.1093\/sysbio\/sys029","journal-title":"Syst Biol"},{"key":"5197_CR60","doi-asserted-by":"publisher","first-page":"3299","DOI":"10.1093\/molbev\/msx248","volume":"34","author":"J Rozas","year":"2017","unstructured":"Rozas J, Ferrer-Mata A, S\u00e1nchez-DelBarrio JC, Guirao-Rico S, Librado P, Ramos-Onsins SE, S\u00e1nchez-Gracia A (2017) DnaSP 6: DNA sequence polymorphism analysis of large data sets. Mol Biol Evol 34:3299\u20133302. https:\/\/doi.org\/10.1093\/molbev\/msx248","journal-title":"Mol Biol Evol"},{"key":"5197_CR61","doi-asserted-by":"publisher","first-page":"W686","DOI":"10.1093\/nar\/gki366","volume":"33","author":"P Schattner","year":"2005","unstructured":"Schattner P, Brooks AN, Lowe TM (2005) The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs. Nucleic Acids Res 33:W686\u2013W689. https:\/\/doi.org\/10.1093\/nar\/gki366","journal-title":"Nucleic Acids Res"},{"key":"5197_CR62","unstructured":"Seemann T (2015) Snippy: fast bacterial variant calling from NGS reads. https:\/\/github.com\/tseemann\/snippy. Accessed 20 June 2026"},{"key":"5197_CR63","doi-asserted-by":"publisher","first-page":"1281","DOI":"10.1093\/nar\/15.3.1281","volume":"15","author":"PM Sharp","year":"1987","unstructured":"Sharp PM, Li W-H (1987) The codon adaptation index: a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Res 15:1281\u20131295. https:\/\/doi.org\/10.1093\/nar\/15.3.1281","journal-title":"Nucleic Acids Res"},{"key":"5197_CR64","doi-asserted-by":"publisher","DOI":"10.1186\/s12870-024-04999-5","volume":"24","author":"L Shen","year":"2024","unstructured":"Shen L, Chen S, Liang M, Qu S, Feng S, Wang D, Wang G (2024) Comparative analysis of codon usage bias in chloroplast genomes of ten medicinal species of Rutaceae. BMC Plant Biol 24:424. https:\/\/doi.org\/10.1186\/s12870-024-04999-5","journal-title":"BMC Plant Biol"},{"key":"5197_CR65","doi-asserted-by":"publisher","DOI":"10.1101\/192112","author":"AM Thomson","year":"2017","unstructured":"Thomson AM, Vargas OM, Dick CW (2017) Comparative analysis of 24 chloroplast genomes yields highly informative genetic markers for the Brazil nut family (Lecythidaceae). bioRxiv. https:\/\/doi.org\/10.1101\/192112","journal-title":"bioRxiv"},{"key":"5197_CR66","doi-asserted-by":"publisher","first-page":"W6","DOI":"10.1093\/nar\/gkx391","volume":"45","author":"M Tillich","year":"2017","unstructured":"Tillich M, Lehwark P, Pellizzer T, Ulbricht-Jones ES, Fischer A, Bock R, Greiner S (2017) GeSeq: versatile and accurate annotation of organelle genomes. Nucleic Acids Res 45:W6\u2013W11. https:\/\/doi.org\/10.1093\/nar\/gkx391","journal-title":"Nucleic Acids Res"},{"key":"5197_CR67","doi-asserted-by":"publisher","first-page":"926","DOI":"10.1080\/11263504.2021.1979678","volume":"156","author":"Z U\u011furlu Ayd\u0131n","year":"2022","unstructured":"U\u011furlu Ayd\u0131n Z, Kaya Y, D\u00f6nmez AA (2022) DNA barcoding evaluation of geophytes: comparative efficiency of three barcode loci for Anemone (Ranunculaceae) and Gladiolus (Iridaceae). Plant Biosyst 156:926\u2013937. https:\/\/doi.org\/10.1080\/11263504.2021.1979678","journal-title":"Plant Biosyst"},{"key":"5197_CR68","doi-asserted-by":"publisher","first-page":"3985","DOI":"10.1534\/g3.116.032672","volume":"6","author":"D Velasco","year":"2016","unstructured":"Velasco D, Hough J, Aradhya M, Ross-Ibarra J (2016) Evolutionary genomics of peach and almond domestication. G3 (Bethesda) 6:3985\u20133993. https:\/\/doi.org\/10.1534\/g3.116.032672","journal-title":"G3 (Bethesda)"},{"key":"5197_CR69","doi-asserted-by":"publisher","first-page":"1751","DOI":"10.3732\/ajb.1500299","volume":"102","author":"JF Walker","year":"2015","unstructured":"Walker JF, Jansen RK, Zanis MJ, Emery NC (2015) Sources of inversion variation in the small single copy (SSC) region of chloroplast genomes. Am J Bot 102:1751\u20131752. https:\/\/doi.org\/10.3732\/ajb.1500299","journal-title":"Am J Bot"},{"key":"5197_CR70","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-020-67264-3","volume":"10","author":"W Wang","year":"2020","unstructured":"Wang W, Yang T, Wang H-L, Li Z-J, Ni J-W, Su S, Xu X-Q (2020a) Comparative and phylogenetic analyses of the complete chloroplast genomes of six almond species (Prunus spp. L.). Sci Rep 10:10137. https:\/\/doi.org\/10.1038\/s41598-020-67264-3","journal-title":"Sci Rep"},{"key":"5197_CR71","doi-asserted-by":"publisher","DOI":"10.7717\/peerj.8251","volume":"8","author":"Z-J Wang","year":"2020","unstructured":"Wang Z-J, Xu B-B, Li B, Zhou Q-Q, Wang G-Y, Jiang X-Z, Wang C-C, Xu Z-D (2020b) Comparative analysis of codon usage patterns in chloroplast genomes of six Euphorbiaceae species. PeerJ 8:e8251. https:\/\/doi.org\/10.7717\/peerj.8251","journal-title":"PeerJ"},{"key":"5197_CR72","doi-asserted-by":"publisher","first-page":"273","DOI":"10.1007\/s11103-011-9762-4","volume":"76","author":"S Wicke","year":"2011","unstructured":"Wicke S, Schneeweiss GM, dePamphilis CW, M\u00fcller KF, Quandt D (2011) The evolution of the plastid chromosome in land plants: gene content, gene order, gene function. Plant Mol Biol 76:273\u2013297. https:\/\/doi.org\/10.1007\/s11103-011-9762-4","journal-title":"Plant Mol Biol"},{"key":"5197_CR73","doi-asserted-by":"publisher","DOI":"10.1007\/978-3-319-24277-4","volume-title":"Ggplot2: elegant graphics for data analysis","author":"H Wickham","year":"2016","unstructured":"Wickham H (2016) Ggplot2: elegant graphics for data analysis, 2nd edn. Springer, New York","edition":"2nd edn"},{"key":"5197_CR74","doi-asserted-by":"publisher","DOI":"10.1038\/s41438-019-0171-1","volume":"6","author":"S Xue","year":"2019","unstructured":"Xue S, Shi T, Luo W, Ni X, Iqbal S, Ni Z, Huang X, Yao D, Shen Z, Gao Z (2019) Comparative analysis of the complete chloroplast genome among Prunus mume, P. armeniaca and P. salicina. Hortic Res 6:89. https:\/\/doi.org\/10.1038\/s41438-019-0171-1","journal-title":"Hortic Res"},{"key":"5197_CR75","doi-asserted-by":"publisher","DOI":"10.7717\/peerj.8210","volume":"7","author":"X Zhao","year":"2019","unstructured":"Zhao X, Yan M, Ding Y, Huo Y, Yuan Z (2019) Characterization and comparative analysis of the complete chloroplast genome sequence from Prunus avium \u201cSummit.\u201d PeerJ 7:e8210. https:\/\/doi.org\/10.7717\/peerj.8210","journal-title":"PeerJ"}],"container-title":["Planta"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s00425-026-05197-3.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1007\/s00425-026-05197-3","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s00425-026-05197-3.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,10,22]],"date-time":"2026-10-22T14:32:52Z","timestamp":1792679572000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/article\/10.1007\/s00425-026-05197-3"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,10,11]]},"references-count":75,"journal-issue":{"issue":"5","published-print":{"date-parts":[[2026,11]]}},"alternative-id":["5197"],"URL":"https:\/\/doi.org\/10.1007\/s00425-026-05197-3","relation":{},"ISSN":["0032-0935","1432-2048"],"issn-type":[{"value":"0032-0935","type":"print"},{"value":"1432-2048","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,10,11]]},"assertion":[{"value":"6 August 2026","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"3 October 2026","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"11 October 2026","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"The authors declare that they have no competing financial or non-financial interests, directly or indirectly related to this manuscript.","order":1,"name":"Ethics","label":"Conflict of interest","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"Not applicable. This study did not involve human participants, animals or endangered species; plant material was collected from wild populations in Turkey in accordance with national legislation and institutional guidelines.","order":2,"name":"Ethics","label":"Ethical approval","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"Not applicable.","order":3,"name":"Ethics","label":"Consent to participate and consent for publication","group":{"name":"EthicsHeading","label":"Declarations"}}],"article-number":"164"}}