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Journals / Bartın Üniversitesi Uluslararası Fen Bilimleri Dergisi / 2026 / Cilt: 9 Sayı: 1

CHLOROPLAST GENOME SEQUENCING IN BRASSICACEAE AND ITS PHYLOGENETIC APPLICATIONS: A COMPREHENSIVE REVIEW

BRASSICACEAE'DE KLOROPLAST GENOM DİZİLEMESİ VE FİLOGENETİK UYGULAMALARI: KAPSAMLI BİR İNCELEME

Shaima Mahfood Ebrahim Abdulrahman(BARTIN ÜNİVERSİTESİ)
Mehmet Cengiz Karaismailoglu(BARTIN ÜNİVERSİTESİ)
Pages
107–130
Publication Date
2026-07-31
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AI Summary & Key Takeaways

AI Insight
⚡ TL;DR(Too Long; Didn't Read)

Finally, potential future developments were discussed, highlighting the necessity of multi-genome integration, the application of pan-plastome methodologies, and the expanding possibilities of chloroplast synthetic biology and genome editing to improve agriculture.

📌 3 Key Takeaways

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Objective & Hypothesis:The Brassicaceae family is important both scientifically and economically; however, its complex evolutionary history, characterized by rapid diversification, whole-genome duplications, and significant reticular evolution, makes its classification challenging.
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Key Findings & Data:Phylogenetically relevant structural changes, including temporal shifts in the boundaries of inverted repeats (IRs), lineage-specific gene losses (e.g., rps16), and the loss of ndh genes in response to local adaptive pressures, are investigated in this study.
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Conclusion & Impact:Finally, potential future developments were discussed, highlighting the necessity of multi-genome integration, the application of pan-plastome methodologies, and the expanding possibilities of chloroplast synthetic biology and genome editing to improve agriculture.
🔬Design:Review & Systematic Survey
📍Scope:Comprehensive Sample
⚙️Variables:Brassicaceae · kloroplast genomu · plastomik

Abstract

The Brassicaceae family is important both scientifically and economically; however, its complex evolutionary history, characterized by rapid diversification, whole-genome duplications, and significant reticular evolution, makes its classification challenging. The advent of high-throughput next-generation sequencing technology has facilitated the shift from single-locus phylogenomics to whole-plastome phylogenomics, improving our understanding of the family's deep evolutionary relationships. This comprehensive review reinforces our understanding of Brassicaceae chloroplast genomes, highlighting the highly consistent gene content, distinctive base composition patterns, and highly conserved quadruple structure. Phylogenetically relevant structural changes, including temporal shifts in the boundaries of inverted repeats (IRs), lineage-specific gene losses (e.g., rps16), and the loss of ndh genes in response to local adaptive pressures, are investigated in this study. Furthermore, the effectiveness of plastid phylogenics in clarifying taxonomically complex clades was evaluated, while directly addressing common problems such as cytonuclear incompatibility, chloroplast capture, and soft polytomies at key backbone nodes. The article examined newly developed methodologies, including genome scanning, advanced assembly tools such as GetOrganelle, and multispecies merger phylogenetic reconstruction. Finally, potential future developments were discussed, highlighting the necessity of multi-genome integration, the application of pan-plastome methodologies, and the expanding possibilities of chloroplast synthetic biology and genome editing to improve agriculture.

Özet

Brassicaceae familyası hem bilimsel hem de ekonomik açıdan önemlidir; ancak hızlı çeşitlenmeler, tüm genom duplikasyonları ve önemli ağsı evrimle karakterize edilen karmaşık evrimsel tarihi, sınıflandırmasını zorlaştırmaktadır. Yüksek verimli yeni nesil dizileme teknolojisinin ortaya çıkışı, tek lokuslu filogenomikten tüm plastom filogenomikine geçişi kolaylaştırarak, familyanın derin evrimsel ilişkilerine dair anlayışımızı geliştirmiştir. Bu kapsamlı inceleme, Brassicaceae kloroplast genomlarına dair anlayışımızı pekiştirmektedir. Gen içeriklerinin son derece tutarlılığına, ayırt edici baz bileşim kalıplarına ve oldukça korunmuş dörtlü yapısına vurgu yapmaktadır. Ters tekrarların (IR'ler) sınırlarında zamansal değişiklikler, soy hattına özgü gen kayıpları (örneğin rps16) ve yerel adaptif baskılara yanıt olarak ndh genlerinin kaybı da dahil olmak üzere, filogenetikle ilgili yapısal değişiklikler bu çalışmada incelenmiştir. Ayrıca, sitonükleer uyumsuzluk, kloroplast yakalama ve önemli omurga düğümlerindeki yumuşak politomiler gibi yaygın sorunları doğrudan ele alırken, taksonomik olarak karmaşık kladların açıklığa kavuşturulmasında plastid filogenomiğinin etkinliği değerlendirilmiştir. Makale, genom taraması, GetOrganelle gibi gelişmiş montaj araçları ve çok türlü birleşme filogenetik rekonstrüksiyonu da dahil olmak üzere yeni geliştirilen metodolojileri incelemiştir. Son olarak, çoklu genom entegrasyonunun gerekliliğini, pan-plastom metodolojilerinin uygulanmasını ve tarımı geliştirmek için kloroplast sentetik biyolojisi ve genom düzenlemesinin genişleyen olanaklarını vurgulayarak potansiyel gelecekteki gelişmeler tartışılmıştır.

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Cite This Article

Abdulrahman, S. M. E., Karaismailoglu, M. C. (2026). CHLOROPLAST GENOME SEQUENCING IN BRASSICACEAE AND ITS PHYLOGENETIC APPLICATIONS: A COMPREHENSIVE REVIEW. Bartın Üniversitesi Uluslararası Fen Bilimleri Dergisi, Cilt: 9 Sayı: 1, 107–130. https://doi.org/10.55930/jonas.1926887

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References (55)

  1. Aguilar, A. G., Arreguin, P., Bejar, I., Castro, A., Chavarria, M. D., Chavez, O., Cruz-Martinez, J., De la Cruz-Ortiz, R. J., Degrandis-Figueroa, P. L., Gonzalez, K., Gutierrez-Vargas, M. E., Hill, M., Hughey, J. R., Jones, C. M., Kennamore, K., Lopez, V., Nelson, M. M., Lopez Magana, I., Magana-Zavala, J., Martinez, B. S., Mendez Gutierrez, V., Mendoza, B., Morales, J. E., Ochoa, S., Perea-Lopez, R., Perez-Rizo, J., Quiroz-Contreras, D., Ramirez, E. C., Ramirez, F., Ramirez, I., Rozin, T., Salazar, M. G., Saldana-Landeros, P., Sosa, J., Vega-Valencia, J., Villanueva, A., Villicana, R., & Zambrano, J. (2026). Complete chloroplast genome of the federally endangered Menzies' wallflower Erysimum menziesii (Brassicaceae, Anthophyta) from California, USA. Microbiology Resource Announcements, 15(3), e01298-25. https://doi.org/10.1128/mra.01298-25
  2. Al-Shehbaz, I. A. (2025). The Brassicaceae then and now: advancements in the past three decades, a review. Ann Bot, mcaf055.
  3. An, H., Qi, X., Gaynor, M. L., Hao, Y., Gebken, S. C., Mabry, M. E. & Pires, J. C. (2019). Transcriptome and organellar sequencing highlights the complex origin and diversification of allotetraploid Brassica napus. Nat Commun, 10, 2878.
  4. Bailey, C. D., Koch, M. A., Mayer, M., Mummenhoff, K., O'Kane, S. L., Warwick, S. I., Windham, M. D. & Al-Shehbaz, I. A. (2006). Toward a global phylogeny of the Brassicaceae. Mol Biol Evol, 23(11), 2142-2160.
  5. Bankevich, A., Nurk, S., Antipov, D., Gurevich, A. A., Dvorkin, M., Kulikov, A. S. & Pevzner, P. A. (2012). SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol, 19(5), 455-477.
  6. Beilstein, M. A., Al-Shehbaz, I. A. & Kellogg, E. A. (2006). Brassicaceae phylogeny and trichome evolution. American Journal of Botany, 93(4), 607-619.
  7. Beilstein, M. A., Al-Shehbaz, I. A., Mathews, S. & Kellogg, E. A. (2008). Brassicaceae phylogeny inferred from phytochrome A and ndhF sequence data: Tribes and trichomes revisited. American Journal of Botany, 95(10), 1307-1327.
  8. Birky, C. W. (2001). The inheritance of genes in mitochondria and chloroplasts: laws, mechanisms, and models. Annu Rev Genet, 35, 125-148.
  9. Brock, J. R., Mandáková, T., McKain, M., Lysak, M. A. & Olsen, K. M. (2022). Chloroplast phylogenomics in Camelina (Brassicaceae) reveals multiple origins of polyploid species and the maternal lineage of C. sativa. Hortic Res, 9, uhab050.
  10. Cauz-Santos, L. A., Da Costa, Z. P., Callot, C., Cauet, S., Zucchi, M. I., Bergès, H. & Vieira, M. L. C. (2025). Plastome structural rearrangements and evolutionary dynamics in plants. New Phytol, 246, 2405-2415.
  11. Couvreur, T. L. P., Franzke, A., Al-Shehbaz, I. A., Bakker, F. T., Koch, M. A. & Mummenhoff, K. (2010). Molecular phylogenetics, temporal diversification, and principles of evolution in the mustard family (Brassicaceae). Mol Biol Evol, 27(1), 55-71.
  12. Daniell, H., Lin, C. S., Yu, M. & Chang, W. J. (2016). Chloroplast genomes: diversity, evolution, and applications in genetic engineering. Genome Biol, 17, 134.
  13. Dierckxsens, N., Mardulyn, P. & Smits, G. (2017). NOVOPlasty: de novo assembly of organelle genomes from whole genome data. Nucleic Acids Res, 45(4), e18.
  14. Dominicus, L. J. M. A., Al-Shehbaz, I. A., German, D. A., Mummenhoff, K., Hay, N. M., Lysák, M. A., Koch, M. A., Lens, F. & Hendriks, K. P. (2025). Mitoplastomic discordance in Brassicaceae phylogenomics confirms the complex evolutionary history of the family. Ann Bot, 2019, 1-16.
  15. Edger, P. P., Hall, J. C., Harkess, A., Tang, M., Coombs, J., Mohammadin, S., Schranz, M. E., Xiong, Z., Leebens-Mack, J., Meyers, B. C., Sytsma, K. J., Koch, M. A., Al-Shehbaz, I. A. & Pires, J. C. (2018). Brassicales phylogeny inferred from 72 plastid genes: A reanalysis of the phylogenetic localization of two paleopolyploid events and origin of novel chemical defenses. American Journal of Botany, 105(3), 463-469.
  16. Eshel, G., Duppen, N., Wang, G., Oh, D.-H., Kazachkova, Y., Herzyk, P., Amtmann, A., Gordon, M., Chalifa-Caspi, V., Oscar, M. A., Bar-David, S., Marshall-Colon, A., Dassanayake, M. & Barak, S. (2022). Positive selection and heat-response transcriptomes reveal adaptive features of the Brassicaceae desert model, Anastatica hierochuntica. New Phytol, 236(3), 1006-1026.
  17. Fu, J. & Zhang, J. (2026). Editing and synthetic engineering of chloroplast genomes. Plant Commun, 7(3), 101783.
  18. German, D. A., Hendriks, K. P., Koch, M. A., Lens, F., Lysak, M. A., Bailey, C. D. & Al-Shehbaz, I. A. (2023). An updated classification of the Brassicaceae (Cruciferae). PhytoKeys, 220, 127-144.
  19. Go, S., Koo, H., Jung, M., Hong, S., Yi, G. & Kim, Y. M. (2024). Pan-chloroplast genomes for accession-specific marker development in Hibiscus syriacus. Sci Data, 11, 246.
  20. Guo, X., Liu, J., Hao, G., Zhang, L., Mao, K., Wang, X., Zhang, D., Ma, T., Hu, Q., Al-Shehbaz, I. A. & Koch, M. A. (2017). Plastome phylogeny and early diversification of Brassicaceae. BMC Genomics, 18(1), 1–9.
  21. Guo, X., Mandáková, T., Trachtová, K., Özüdoğru, B., Liu, J. & Lysak, M. A. (2021). Linked by ancestral bonds: multiple whole-genome duplications and reticulate evolution in a Brassicaceae tribe. Mol Biol Evol, 38(5), 1695-1714.
  22. Hendriks, K. P., Kiefer, C., Al-Shehbaz, I. A., Bailey, C. D., Huysduynen, A. H. van, Nikolov, L. A., Nauheimer, L., Zuntini, A. R., German, D. A., Franzke, A., Koch, M. A., Lysak, M. A., Toro-Núñez, Ó., Özüdoğru, B., Invernón, V. R., Walden, N., Maurin, O., Hay, N. M., Shushkov, P. & Lens, F. (2022). Global phylogeny of the Brassicaceae provides important insights into gene discordance. BioRxiv, September, 2022.09.01.506188.
  23. Hendriks, K. P., Kiefer, C., Al-Shehbaz, I. A., Bailey, C. D., Hooft van Huysduynen, A., Nikolov, L. A. & Lens, F. (2023). Global Brassicaceae phylogeny based on filtering of 1,000-gene dataset. Curr Biol, 33(19), 4052-4068.e6. Huang, C. H., Sun, R., Hu, Y., Zeng, L., Zhang, N., Cai, L. & Ma, H. (2016). Resolution of Brassicaceae phylogeny using nuclear genes uncovers nested radiations and supports convergent morphological evolution. Mol Biol Evol, 33(2), 394-412.
  24. Jin, J. J., Yu, W. Bin, Yang, J. B., Song, Y., Depamphilis, C. W., Yi, T. S. & Li, D. Z. (2020). GetOrganelle: A fast and versatile toolkit for accurate de novo assembly of organelle genomes. Genome Biology, 21(1), 1–31.
  25. Kagale, S., Robinson, S. J., Nixon, J., Xiao, R., Huebert, T., Condie, J. & Parkin, I. A. (2014). Polyploid evolution of the Brassicaceae during the Cenozoic era. Plant Cell, 26(7), 2777-2791.
  26. Karaismailoğlu, M. C., Eldem, V., İnal, B. & Balcı, M. A. (2025). Biosystematics studies of endemic Thlaspi violascens Boiss. and T. densiflorum Boiss. & Kotschy: Highlights on molecular and morphological identification. Flora, 322, 152644.
  27. Karaismailoğlu, M. C., Inal, B. & Erol, O. (2022). A systematic study of the Thlaspi s.l. taxa in sections Nomisma, Thlaspi and Pterotropis from Turkey based on fruit morphological and molecular data. Acta Botanica Croatica, 81(2), 197-205.
  28. Liu, B., Feng, L., Huang, Y., Yang, Y., Li, C., Kang, T., Xing, Y. & Xu, L. (2026). Complete chloroplast genome and phylogenetic analysis of Cardamine leucantha L. 1836 (Brassicaceae). Mitochondrial DNA Part B Resour, 11(1), 19-194.
  29. Liu, J., Zhou, S. Z., Liu, Y. L., Zhao, B. Y., Yu, D., Zhong, M. C. & Li, D. Z. (2024). Genomes of Meniocus linifolius and Tetracme quadricornis reveal the ancestral karyotype and genomic features of core Brassicaceae. Plant Commun, 5, 100878.
  30. Liu, L. M., Du, X. Y., Guo, C. & Li, D. Z. (2020). Resolving robust phylogenetic relationships of core Brassicaceae using genome skimming data. J Syst Evol, 59(3), 442-453.
  31. Liu, T., Hu, Z., Xu, L., Luo, X., Zou, L., Li, S. & An, X. (2025). Complete Chloroplast Genome Sequence Structure and Phylogenetic Analysis of Brassica juncea var. multiceps (Brassicaceae). Agronomy, 15, 2501.
  32. Mabry, M. E., Abrahams, R. S., Al-Shehbaz, I. A., Baker, W. J., Barak, S., Barker, M. S. & Harkess, A. E. (2023). Complementing model species with model clades. Plant Cell, 36(5), 1205-1226.
  33. Magdy, M., Ou, L., Yu, H., Chen, R., Zhou, Y., Hassan, H. & Zou, X. (2019). Pan-plastome approach empowers the assessment of genetic variation in cultivated Capsicum species. Hortic Res, 6, 108.
  34. Mandáková, T., Li, Z., Barker, M. S. & Lysak, M. A. (2017). Diverse genome organization following 13 independent mesopolyploid events in Brassicaceae contrasts with convergent patterns of gene retention. Plant J, 91(1), 3-21.
  35. Mirarab, S., Reaz, R., Bayzid, M. S., Zimmermann, T., Swenson, M. S. & Warnow, T. (2014). ASTRAL: genome-scale coalescent-based species tree estimation. Bioinformatics, 30, i541-i548.
  36. Nguyen, L. T., Schmidt, H. A., von Haeseler, A. & Minh, B. Q. (2015). IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol, 32(1), 268-274.
  37. Nikolov, L. A., Shushkov, P., Nevado, B., Gan, X., Al-Shehbaz, I. A., Filatov, D. & Tsiantis, M. (2019). Resolving the backbone of the Brassicaceae phylogeny for investigating trait diversity. New Phytol, 222(3), 1638-1651.
  38. Raubeson, L. A., Peery, R., Chumley, T. W., Dziubek, C., Fourcade, H. M., Boore, J. L. & Jansen, R. K. (2007). Comparative chloroplast genomics: Analyses including new sequences from the angiosperms Nuphar advena and Ranunculus macranthus. BMC Genomics, 8, 174.
  39. Ren, T., Xun, L., Jia, Y. & Li, B. (2024). Complete Plastomes of Ten Rorippa Species (Brassicaceae): Comparative Analysis and Phylogenetic Relationships. Agronomy, 14, 913.
  40. Ronquist, F., Teslenko, M., van der Mark, P., Ayres, D. L., Darling, A., Höhna, S. & Huelsenbeck, J. P. (2012). MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Syst Biol, 61, 539-542.
  41. Schulz, O. E. (1936). Cruciferae. In: Engler A, Prantl K, editors. Die natürlichen Pflanzenfamilien. Leipzig: Engelmann.
  42. Stamatakis, A. (2014). RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics, 30(9), 1312-1313.
  43. Tang, S., Liu, J., Zhu, Z., An, X., Dong, J., Luo, X., Chen, C., Liu, T., Zou, L., Li, S. & An, X. (2026). Complete Chloroplast Genome Characteristics and Phylogenetic Analysis of Brassica juncea L. International Journal of Molecular Sciences, 27, 2882. https://doi.org/10.3390/ijms27062882.
  44. Walden, N., German, D. A., Wolf, E. M., Kiefer, M., Rigault, P., Huang, X. C. & Koch, M. A. (2020). Nested whole-genome duplications coincide with diversification and high morphological disparity in Brassicaceae. Nat Commun, 11, 3795.
  45. Wicke, S., Schneeweiss, G. M., dePamphilis, C. W., Müller, K. F. & Quandt, D. (2011). The evolution of the plastid chromosome in land plants: gene content, gene order, gene function. Plant Mol Biol, 76, 273-297.
  46. Wolf, E., Gaquerel, E., Scharmann, M., Yant, L. & Koch, M. A. (2021). Evolutionary footprints of a cold relic in a rapidly warming world. eLife, 10, e71572.
  47. Wolfe, K. H., Li, W. H. & Sharp, P. M. (1987). Rates of nucleotide substitution vary greatly among plant mitochondrial, chloroplast, and nuclear DNAs. Proc Natl Acad Sci, 84(24), 9054-9058.
  48. Xian, W., Bao, Z., Vorbrugg, S., Gautam, A. & Weigel, D. (2025). Organellar genome variation at the population scale. bioRxiv, 2025, 01.
  49. Yang, Q., Bi, H., Yang, W., Li, T., Jiang, J., Zhang, L., Liu, J. & Hu, Q. (2020). The Genome Sequence of Alpine Megacarpaea delavayi Identifies Species-Specific Whole-Genome Duplication. Front. Genet., 11, 1-9.
  50. Zhang, C., Rabiee, M., Sayyari, E. & Mirarab, S. (2018). ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees. BMC Bioinformatics, 19(6), 15-30.
  51. Zhang, Z., Shi, X., Tian, H., Qiu, J., Ma, H. & Tan, D. (2024). Complete Chloroplast Genome of Megacarpaea megalocarpa and Comparative Analysis with Related Species from Brassicaceae. Genes, 15, 886.
  52. Zhang, Z., Tao, M., Shan, X., Pan, Y., Sun, C., Song, L. & Dai, Z. (2022). Characterization of the complete chloroplast genome of Brassica oleracea var. italica and phylogenetic relationships in Brassicaceae. PLoS ONE, 17(2), e0263310.
  53. Zhou, W., Armijos, C. E., Lee, C., Lu, R., Wang, J., Ruhlman, T. A. & Jones, C. D. (2023). Plastid genome assembly using long-read data. Mol Ecol Resour, 23(6), 1442-1457.
  54. Zhu, A., Guo, W., Gupta, S., Fan, W. & Mower, J. P. (2016). Evolutionary dynamics of the plastid inverted repeat: The effects of expansion, contraction, and loss on substitution rates. New Phytol, 209(4), 1747-1756.
  55. Zhu, B., Qian, F., Hou, Y., Yang, W., Cai, M. & Wu, X. (2021). Complete chloroplast genome features and phylogenetic analysis of Eruca sativa (Brassicaceae). PLoS ONE, 16(3), e0248556.