Biomics

The first review of plant pan-plastomes has been prepared. While complete chloroplast genomes have already been sequenced for several thousand species, there are currently only about three dozens of presented pan-plastomes. There are publications though, in which the term "pan-plastome" was not used, but in fact the pan-approach was applied to the sequenced multiple chloroplast genomes. The importance of the use of pan-plastomes for phylogenetic studies is noted, since in this case intraspecific differences are taken into account. The need for the compilation and use of consensus plastomes or con-plastomes, which contain only the most frequently occurring major mutations compared to the reference chloroplast genome, is emphasized, as this can lead to a more accurate inference of evolutionary events. Some attention is paid to the terminology used, including historical aspects. A point of view is expressed that more attention should be paid to the sequencing and compilation of plant pan-plastomes.

plastome, pan-plastome, chloroplast genome, chloroplast pangenome, sequencing, higher plants, phylogeny

1. Barchi L, Rabanus-Wallace MT, Prohens J et al. Improved genome assembly and pan-genome provide key insights into eggplant domestication and breeding. Plant J. 2021. V.107(2). P.579-596. doi: 10.1111/tpj.15313
2. Chen N, Sha LN, Wang YL et al. Variation in Plastome Sizes Accompanied by Evolutionary History in Monogenomic Triticeae (Poaceae: Triticeae). Front Plant Sci. 2021. V.12. 741063. doi: 10.3389/fpls.2021.741063
3. Chen Q, Chen L, Teixeira da Silva JA, Yu X. The plastome reveals new insights into the evolutionary and domestication history of peonies in East Asia. BMC Plant Biol. 2023. V.23(1). 243. doi: 10.1186/s12870-023-04246-3
4. Chiba Y. Cytochemical studies on chloroplasts. I. Cytologic demonstration of nucleic acids in chloroplasts. Cytologia. 1951. V.16. P.259-264.
5. Chiba Y, Sugahara K. The nucleic acid content of chloroplasts isolated from spinach and tobacco leaves. Arch Biochem Biophys. 1957. V.71(2). P.367-376. doi: 10.1016/0003-9861(57)90047-4
6. Cho W, Jung JK, Kang MY et al. High-throughput SNP markers for authentication of Korean wheat cultivars based on seven complete plastomes and the nuclear genome. Food Sci Biotechnol. 2022. V.31(4). P.423-431. doi: 10.1007/s10068-022-01043-w
7. Ding Y, Fang Y, Guo L et al. Phylogenic study of Lemnoideae (duckweeds) through complete chloroplast genomes for eight accessions. 2017. V.5. e4186. doi: 10.7717/peerj.4186
8. Go S, Koo H, Jung M et al. Pan-chloroplast genomes for accession-specific marker development in Hibiscus syriacus. Sci Data. 2024. V.11(1). 246. doi: 10.1038/s41597-024-03077-7
9. Goryunova S., Sivolapova A., Polivanova O. et al. Comparative Study of Plastomes in Solanum tuberosum with Different Cytoplasm Types. Plants. 2023. V.12. 3995. doi: 10.3390/plants12233995
10. Goulding SE, Wolfe KH, Olmstead RG, Morden CW. Ebb and flow of the chloroplast inverted repeat. Gen. Genet. 1996. V.252. P.195–206. doi: 10.1007/BF02173220
11. He W, Chen C, Xiang K et al. The History and Diversity of Rice Domestication as Resolved From 1464 Complete Plastid Genomes. Front Plant Sci. 2021. V.12. P.781-793. doi: 10.3389/fpls.2021.781793
12. Ishizuka W. Tabata A. Ono K. et al. Draft chloroplast genome of Larix gmelinii var. japonica: insight into intraspecific divergence. Journal of Forest Research. 2017. V.22(6). P.393-398. doi: 10.1080/13416979.2017.1386019
13. Jagendorf A.T., Wildman S.G. The Proteins of Green Leaves. VI. Centrifugal Fractionation of Tobacco Leaf Homogenates and Some Properties of Isolated Chloroplasts. Plant Physiology. V.29(3). P.270–279. doi: 10.1104/pp.29.3.270
14. Jia M, Wang J, Cao D et al. The pan-plastome of Hemerocallis citrina reveals new insights into the genetic diversity and cultivation history of an economically important food plant. BMC Plant Biol. 2024. V.24(1). 44. doi: 10.1186/s12870-023-04668-z
15. Jiang K, Wang ZW, Huang WC, Hu YH. Characterization of two complete chloroplast genomes of Lindera megaphylla (Lauraceae). Mitochondrial DNA B Resour. 2019. V.4(2). P.2851-2852. doi: 10.1080/23802359.2019.1660275
16. Kan J, Nie L, Mi Z et al. Insights into Aquilaria phylogenetics through comparative plastomic resources. For Res (Fayettev). V.4. e030. doi: 10.48130/forres-0024-0028
17. Kan J, Nie L, Wang M et al. The Mendelian pea pan-plastome: insights into genomic structure, evolutionary history, and genetic diversity of an essential food crop. Genomics Communications. 2024. V.1. e004 doi: 10.48130/gcomm-0024-0004
18. Kersten B, Faivre Rampant P et al. Genome Sequences of Populus tremula Chloroplast and Mitochondrion: Implications for Holistic Poplar Breeding. PLoS One. V.11(1). e0147209. doi: 10.1371/journal.pone.0147209
19. Khan A.W., Garg V., Roorkiwal M., et al. Super-Pangenome by Integrating the Wild Side of a Species for Accelerated Crop Improvement. Trends Plant Sci. 2020. V.25(2). P.148-158. doi: 10.1016/j.tplants.2019.10.012
20. Kim K, Lee SC, Lee J et al. Comprehensive Survey of Genetic Diversity in Chloroplast Genomes and 45S nrDNAs within Panax ginseng PLoS One. 2015. V.10(6). e0117159. doi: 10.1371/journal.pone.0117159
21. Krüger M, Abeyawardana OAJ, Juříček M et al. Variation in plastid genomes in the gynodioecious species Silene vulgaris. BMC Plant Biol. 2019. V.19(1). 568. doi: 10.1186/s12870-019-2193-0
22. Kuluev A.R., Matniyazov R.T., Kuluev B.R., Chemeris A.V. Aegilops aucheri — almost forgotten as a separate species — may also be regarded as rather close to a probable ancient donor of subgenome G for polyploid wheats of the timopheevii-zhukovskyi lineage. Biomics. 2024. V.16(4). P.359-368. doi: 10.31301/2221-6197.bmcs.2024-25
23. Kuluev AR, Matniyazov RT, Kuluev BR et al. Complete chloroplast genomes of five Aegilops aucheri accessions having different geographical origins. Mitochondrial DNA A DNA Mapp Seq Anal. 2025. V.35(3-4). P.119-125. doi: 10.1080/24701394.2025.2476401
24. Kuluev B.R., Chemeris D.A., Gerashchenkov G.A. et al. Pangenomics of plants. Biomics. 2025. 17(1). P.42-64. DOI: 10.31301/2221-6197.bmcs.2025-4
25. Lee SR, Oh A, Son DC. Characterization, comparison, and phylogenetic analyses of chloroplast genomes of Euphorbia Sci Rep. 2024. V.14(1). 15352. doi: 10.1038/s41598-024-66102-0
26. Li DM, Pan YG, Liu HL et al. Thirteen complete chloroplast genomes of the Costaceae family: insights into genome structure, selective pressure and phylogenetic relationships. BMC Genomics. 2024. V.25(1). 68. doi: 10.1186/s12864-024-09996-4
27. Li J, Pan D, Wang J, Zeng X, Guo S. Pan-Chloroplast Genomes Reveal the Accession-Specific Marker for Gastrodia elata glauca. Int J Mol Sci. 2024. V.25(21). 11603. doi: 10.3390/ijms252111603
28. Li YL, Nie LY, Deng SW et al. Characterization of Firmiana danxiaensis plastomes and comparative analysis of Firmiana: insight into its phylogeny and evolution. BMC Genomics. 2024a. V.25(1). 203. doi: 10.1186/s12864-024-10046-2
29. Lilly JW, Havey MJ, Jackson SA, Jiang J. Cytogenomic analyses reveal the structural plasticity of the chloroplast genome in higher plants. Plant Cell. V.13. P.245–254. doi: 10.1105/tpc.13.2.245
30. Liu H, Hou Z, Xu L et al. Comparative analysis of organellar genomes between diploid and tetraploid Chrysanthemum indicum with its relatives. Front Plant Sci. 2023. V.14. 1228551. doi: 10.3389/fpls.2023.1228551
31. Liu H, Zhao W, Hua W, Liu J. A large-scale population based organelle pan-genomes construction and phylogeny analysis reveal the genetic diversity and the evolutionary origins of chloroplast and mitochondrion in Brassica napus BMC Genomics. 2022. V.23(1). 339. doi: 10.1186/s12864-022-08573-x
32. López MG, Fass M, Rivas JG et al. Plastome genomics in South American maize landraces: chloroplast lineages parallel the geographical structuring of nuclear gene pools. Ann Bot. 2021. V.128(1). P.115-125. doi: 10.1093/aob/mcab038
33. Lu RS, Hu K, Zhang FJ et al. Pan-Plastome of Greater Yam (Dioscorea alata) in China: Intraspecific Genetic Variation, Comparative Genomics, and Phylogenetic Analyses. Int J Mol Sci. 2023. V.24(4). 3341. doi: 10.3390/ijms24043341
34. Magdy M, Ou L, Yu H et al. Pan-plastome approach empowers the assessment of genetic variation in cultivated Capsicum Hortic Res. 2019. V.6. 108. doi: 10.1038/s41438-019-0191-x
35. Mavrodiev EV, Madorsky A. On Pattern-Cladistic Analyses Based on Complete Plastid Genome Sequences. Acta Biotheor. 2023. V.71(4). 22. doi: 10.1007/s10441-023-09475-5
36. Meng J, Wang Y, Song H, Dong W, Dong N. Insights into Phylogeny, Taxonomy, Origins and Evolution of Crataegus and Mespilus, Based on Comparative Chloroplast Genome Analysis. Genes (Basel). 2025 Feb 7;16(2):204. doi: 10.3390/genes16020204
37. Michaelis P. Cytoplasmic inheritance in epilobium and its theoretical significance. Adv Genet. 1954. V.6. P.287-401. doi: 10.1016/S0065-2660(08)60132-7
38. Nah G, Im JH, Kim JW et al. The complete chloroplast genomes of three Korean Echinochloa crus-galli Mitochondrial DNA A DNA Mapp Seq Anal. 2016. V.27(6). P.4357-4358. doi: 10.3109/19401736.2015.1089499
39. Nie L, Liu F, Wang M et al. Plastome data provides new insights into population differentiation and evolution of Ginkgo in the Sichuan Basin of China. BMC Plant Biol. 2025. V.25(1). 48. doi: 10.1186/s12870-024-05977-7
40. Ogihara Y., Isono K., Kojima T. et al. Chinese Spring wheat (Triticum aestivum) chloroplast genome: complete sequence and contig clones. Plant Mol. Bol. Rep. 2000. V.18. P.243-253. doi: 10.1007/BF02823995
41. Ogihara Y, Isono K, Kojima T et al. Structural features of a wheat plastome as revealed by complete sequencing of chloroplast DNA. Mol Genet Genomics. 2002. V.266(5). P.740-746. doi: 10.1007/s00438-001-0606-9
42. Ohyama K, Fukuzawa H, Kohchi T et al. Chloroplast gene organization deduced from complete sequence of liverwort Marchantia polymorpha chloroplast DNA. 1986. V.322. P. 572–574. doi: 10.1038/322572a0.
43. Palmer J.D., Jansen R.K., Michaels H.J. et al. Chloroplast DNA variation and plant phylogeny. Annals of the Missouri Botanical Garden. 1988. V.75. P.1180–1206. doi: 10.2307/2399279
44. Pfanzelt S, Albach DC, von Hagen KB. Extremely low levels of chloroplast genome sequence variability in Astelia pumila (Asteliaceae, Asparagales). PeerJ. 2019. V.7. e6244. doi: 10.7717/peerj.6244
45. Qu XJ, Zou D, Zhang RY et al. Progress, challenge and prospect of plant plastome annotation. Front Plant Sci. 2023. V.14. 1166140. doi: 10.3389/fpls.2023.1166140
46. Renner O. Die pflanzlichen plastiden als selbstandige elemente der genetischen konstitution. math.-phys. Klasse Sachs. Akad. Wiss. Leipzig. 1934. V.86. P. 241–266.
47. Ruhlman TA, Jansen RK. Plastid Genomes of Flowering Plants: Essential Principles. In Chloroplast Biotechnology; Humana: New York, NY, USA, 2021. P. 3–47. doi: 10.1007/978-94-007-2920-9_5
48. Sabir J.S., Arasappan D., Bahieldin A. et al. Whole mitochondrial and plastid genome SNP analysis of nine date palm cultivars reveals plastid heteroplasmy and close phylogenetic relationships among cultivars. PLoS One. 2014. V. 9(4). e94158. doi: 10.1371/journal.pone.0094158
49. Sancho R, Cantalapiedra CP, López-Alvarez D et al. Comparative plastome genomics and phylogenomics of Brachypodium: flowering time signatures, introgression and recombination in recently diverged ecotypes. New Phytol. 2018. V.218(4). P.1631-1644. doi: 10.1111/nph.14926
50. Scarampi A, Lawrence JM, Bombelli P et al. Polyploid cyanobacterial genomes provide a reservoir of mutations, allowing rapid evolution of herbicide resistance. Current Biology. 2025. V.35(7). P.1549-1561. doi: 10.1016/j.cub.2025.02.044
51. Scheunert A, Dorfner M, Lingl T, Oberprieler C. Can we use it? On the utility of de novo and reference-based assembly of Nanopore data for plant plastome sequencing. PLoS One. 2020. V.15(3). e0226234. doi: 10.1371/journal.pone.0226234
52. Shinozaki K, Ohme M, Tanaka M et al. The complete nucleotide sequence of the tobacco chloroplast genome: its gene organization and expression. EMBO J. V.5(9). P.2043-2049. doi: 10.1002/j.1460-2075.1986.tb04464.x
53. Sielemann K, Pucker B, Schmidt N et al. Complete pan-plastome sequences enable high resolution phylogenetic classification of sugar beet and closely related crop wild relatives. BMC Genomics. 2022. V.23(1). 113. doi: 10.1186/s12864-022-08336-8
54. Song BN, Liu CK, Deng JJ et al. Genome skimming provides evidence to accept two new genera (Apiaceae) separated from the Peucedanuml. Front Plant Sci. 2025. V.15. 1518418. doi: 10.3389/fpls.2024.1518418
55. Song Y, Li C, Liu L et al. The population genomic analyses of chloroplast genomes shed new insights on the complicated ploidy and evolutionary history in Fragaria. Front Plant Sci. 2023. V.13. 1065218. doi: 10.3389/fpls.2022.1065218
56. Starkenburg SR, Kwon KJ, Jha RK et al. A pangenomic analysis of the Nannochloropsis organellar genomes reveals novel genetic variations in key metabolic genes. BMC Genomics. 2014. V.15. 212. doi: 10.1186/1471-2164-15-212
57. Su Q, Liu L, Zhao M et al. The complete chloroplast genomes of seventeen Aegilops tauschii: genome comparative analysis and phylogenetic inference. PeerJ. 2020. V.8. e8678. doi: 10.7717/peerj.8678
58. Swiatek M, Greiner S, Kemp S et al. PCR analysis of pulsed-field gel electrophoresis-purified plastid DNA, a sensitive tool to judge the hetero-/homoplastomic status of plastid transformants. Curr Genet. 2003. V.43(1). P.45-53. doi: 10.1007/s00294-003-0369-4
59. Szandar K, Jakub S, Paukszto Ł et al. Are the Organellar Genomes Useful for Fine Scale Population Structure Analysis of Endangered Plants?-A Case Study of Pulsatilla patens (L.) Mill. Genes (Basel). V.14(1). 67. doi: 10.3390/genes14010067
60. Tang J, Xia H, Cao M et al. A comparison of rice chloroplast genomes. Plant Physiol. 2004. V.135(1). P.412-420. doi: 10.1104/pp.103.031245
61. Teshome GE, Mekbib Y, Hu G, Li ZZ, Chen J. Comparative analyses of 32 complete plastomes of Tef (Eragrostis tef) accessions from Ethiopia: phylogenetic relationships and mutational hotspots. 2020. V.8. e9314. doi: 10.7717/peerj.9314
62. Tomasello S, Manzo E, Karbstein K. Comparative plastome assembly of the yellow ironweed (Verbesina alternifolia) using Nanopore and Illumina reads. Front Plant Sci. 2024. V.15. 1429494. doi: 10.3389/fpls.2024.1429494
63. Wang J, Kan J, Wang J et al. The pan-plastome of Prunus mume: insights into Prunus diversity, phylogeny, and domestication history. Front Plant Sci. 2024. V.15. 1404071. doi: 10.3389/fpls.2024.1404071
64. Wang J, Kan S, Liao X et al. Plant organellar genomes: much done, much more to do. Trends Plant Sci. 2024a. V.29(7). P.754-769. doi: 10.1016/j.tplants.2023.12.014
65. Wang J, Liao X, Gu C et al. The Asian lotus (Nelumbo nucifera) pan-plastome: diversity and divergence in a living fossil grown for seed, rhizome, and aesthetics. Ornamental Plant Research. 2022. V.2. 2. doi: 10.48130/OPR-2022-0002
66. Wang J, Liao X, Li Y et al. Comparative Plastomes of Curcuma alismatifolia (Zingiberaceae) Reveal Diversified Patterns among 56 Different Cut-Flower Cultivars. Genes (Basel). V.14(9). 1743. doi: 10.3390/genes14091743
67. Wang J, Mu W, Yang T et al. Targeted enrichment of novel chloroplast-based probes reveals a large-scale phylogeny of 412 bamboos. BMC Plant Biol. 2021. V.21(1). 76. doi: 10.1186/s12870-020-02779-5
68. Wang X, Zhang R, Wang D et al. Molecular Structure and Variation Characteristics of the Plastomes from Six Malus baccata (L.) Borkh. Individuals and Comparative Genomic Analysis with Other Malus Biomolecules. 2023a. V.13(6). 962. doi: 10.3390/biom13060962
69. Wettstein Fr. von. Ueber plasmatische Vererbung, sowie Plasma- und Genwirkung. Nachr. Ges. Wise. Goltingen. Jahresber. 1926. P. 250-281.
70. Winkler H. Verbreitung und Ursache der Parthenogenesis im Pflanzen- und Tierreiche. 1920. Jena: Gustav Fischer Verlag. 250 s.
71. Wu Z, Tembrock LR, Ge S. Are differences in genomic data sets due to true biological variants or errors in genome assembly: an example from two chloroplast genomes. PLoS One. 2015. V.10(2). e0118019. doi: 10.1371/journal.pone.0118019
72. Xia L, Wang H, Zhao X et al. Chloroplast Pan-Genomes and Comparative Transcriptomics Reveal Genetic Variation and Temperature Adaptation in the Cucumber. Int J Mol Sci. V.24(10). 8943. doi: 10.3390/ijms24108943
73. Xiong Y., Xiong Y-L., Jia X-J. et al. Divergence in Elymus sibiricus is related to geography and climate oscillation: A new look from pan-chloroplast genome data. J Syst Evol. V.62(4). P.794-808. DOI: 10.1111/jse.13020
74. Yan X-L., Kan S-L., Wang M-X. et al. Genetic diversity and evolution of the plastome in allotetraploid cotton (Gossypium). J Syst Evol . 2024. V.6. P.1118-1136. doi: 10.1111/jse.13070
75. Yang J, Park CG, Cho MS, Kim SC. Wasabi Gone Wild? Origin and Characterization of the Complete Plastomes of Ulleung Island Wasabi (Eutrema japonicum; Brassicaceae) and Other Cultivars in Korea. Genes (Basel). 2024. V.15(4). 457. doi: 10.3390/genes15040457
76. Yoshida T, Furihata HY, Kawabe A. Patterns of Genomic Integration of Nuclear Chloroplast DNA Fragments in Plant Species. DNA 2014. V.2(21). P.127–140. doi: 10.1093/dnares/dst045
77. Yukawa M, Tsudzuki T, Sugiura M. The chloroplast genome of Nicotiana sylvestris and Nicotiana tomentosiformis: complete sequencing confirms that the Nicotiana sylvestris progenitor is the maternal genome donor of Nicotiana tabacum. Mol Genet Genomics. 2006. V.275(4). P.367-373. doi: 10.1007/s00438-005-0092-6
78. Zhang S, Wang J, He W et al. Variation in mitogenome structural conformation in wild and cultivated lineages of sorghum corresponds with domestication history and plastome evolution. BMC Plant Biol. 2023. V.23(1). 91. doi: 10.1186/s12870-023-04104-2
79. Zhang T, Chen X, Yan W et al. Comparative Analysis of Chloroplast Pan-Genomes and Transcriptomics Reveals Cold Adaptation in Medicago sativa. Int J Mol Sci. 2024. V.25(3). 1776. doi: 10.3390/ijms25031776
80. Zhang T, Li M, Zhu X et al. Comparative Chloroplast Genomes Analysis Provided Adaptive Evolution Insights in Medicago ruthenica. Int J Mol Sci. 2024a. V.25(16). 8689. doi: 10.3390/ijms25168689
81. Zhou J, He W, Wang J et al. The pan-plastome of tartary buckwheat (Fagopyrum tataricum): key insights into genetic diversity and the history of lineage divergence. BMC Plant Biol. 2023. V.23(1). 212. doi: 10.1186/s12870-023-04218-7
82. Zhou J, Zhang S, Wang J et al. Chloroplast genomes in Populus (Salicaceae): comparisons from an intensively sampled genus reveal dynamic patterns of evolution. Sci Rep. 2021. V.11(1). 9471. doi: 10.1038/s41598-021-88160-4
83. Zhou Y, Shang XH, Xiao L et al. Comparative plastomes of Pueraria montana lobata (Leguminosae: Phaseoleae) and closely related taxa: insights into phylogenomic implications and evolutionary divergence. BMC Genomics. 2023a. V.24(1). 299. doi: 10.1186/s12864-023-09356-8
84. Zimmermann HH, Harms L, Epp LS et al. Chloroplast and mitochondrial genetic variation of larches at the Siberian tundra-taiga ecotone revealed by de novo assembly. PLoS One. V.14(7). e0216966. doi: 10.1371/journal.pone.0216966