Molecular identification and genetic diversity analysis of Ocimum basilicum L. using chloroplast matK sequences and Genome-wide SNP markers

Articles in Press

Document Type : Research Paper

Authors

College of Science, Mustansiriyah University, Baghdad, Iraq.

10.22103/jab.2026.27125.1888

Abstract

Objective
The economically significant aromatic crop sweet basil (Ocimum basilicum L.) needs thorough genetic analysis for breeding optimization and germplasm conservation. To clarify genetic diversity and population organization in farmed basil, we combined genome-wide SNP markers with chloroplast DNA barcoding (matK).
Materials and methods
A total of thirty different cultivated O. basilicum accessions were analyzed (10 accessions from three distinct geographic locations) in Baghdad, Iraq. The matK gene from each accession was amplified and sequenced using the Sanger sequencing. Genomic SNPs were generated using the genotyping-by-sequencing (GBS) method. After passing a quality control assessment, 6234 of the SNPs were considered valid high-quality SNPs. Genetic diversity, population structure, and differentiation were analyzed using haplotype analysis, STRUCTURE analysis, principal coordinates analysis (PCA), and statistical evaluation methods, including analysis of molecular variance (AMOVA) and Fst pairwise statistics.
Results
MatK sequencing revealed moderate genetic diversity among eight haplotypes was observed (Hd = 0.685 ± 0.045), whereas an excess of heterozygotes was identified in the SNP analysis (Ho = 0.092 ± 0.038; He = 0.251 ± 0.072; Fis = 0.634 ± 0.089; P < 0.001). Bayesian clustering suggests three genetically distinct populations (K = 3), while AMOVA results indicate 24.3% of the overall genetic variation is attributed to the population (Φst = 0.243, P < 0.001). Collectively, SNP markers exhibit relatively greater resolution than matK and demonstrate a moderate degree of correlation with matK-based genetic relationships (Mantel r = 0.523, P = 0.002).
Conclusions
Independent conservation is required for three genetically distinct populations with limited gene flow. The pronounced heterozygote deficit suggests that crosses between genetically distinct populations may enhance heterosis in breeding programs. Our results provide new biological insights into the genetic architecture of cultivated basil. These insights include the presence of three well-defined genetic clusters, a strong but structured lack of heterozygosity, and partial concordance between the chloroplast and nuclear genomes. These findings could improve our understanding of gene flow, domestication effects, and population differentiation in O. basilicum. Furthermore, they could provide a genomic framework for future breeding and conservation strategies.

Keywords

Abdelaziz, S. A., Khaled, K. A. M., Younis, R. A. A., Al-Kordy, M. A., El-Domyati, F. M., & Moghazee, M. M. (2024). Comparison of four DNA barcoding loci to distinguish between some Apiaceae family species. Beni-Suef University Journal of Basic and Applied Sciences, 13, Article 12. https://doi.org/10.1186/s43088-023-00457-7

Amirteymoori, E., Khezri, A., Dayani, O., Mohammadabadi, M., Khorasani, S., Mousaie, A., & Kazemi-Bonchenari, M. (2021). Effects of linseed processing method (ground versus extruded) and dietary crude protein content on performance, digestibility, ruminal fermentation pattern, and rumen protozoa population in growing lambs. Italian Journal of Animal Science, 20(1), 1506–1517. https://doi.org/10.1080/1828051X.2021.1984324

Arabpour, Z., Mohammadabadi, M., & Khezri, A. (2021). The expression pattern of p32 gene in femur, humeral muscle, back muscle and back fat tissues of Kermani lambs. Agricultural Biotechnology Journal, 13(4), 183–200. https://doi.org/10.22103/jab.2022.18782.1371

Avetisyan, A., Markosian, A., Petrosyan, M., Sahakyan, N., Babayan, A., Aloyan, S., & Trchounian, A. (2017). Chemical composition and some biological activities of the essential oils from basil (Ocimum) different cultivars. BMC Complementary and Alternative Medicine, 17(1), Article 60. https://doi.org/10.1186/s12906-017-1587-5

Bolger, A. M., Lohse, M., & Usadel, B. (2014). Trimmomatic: A flexible trimmer for Illumina sequence data. Bioinformatics, 30(15), 2114–2120. https://doi.org/10.1093/bioinformatics/btu170

Carović-Stanko, K., Liber, Z., Besendorfer, V., Javornik, B., Bohanec, B., Kolak, I., & Satovic, Z. (2010). Genetic relations among basil taxa (Ocimum L.) based on molecular markers, nuclear DNA content, and chromosome number. Plant Systematics and Evolution, 285, 13–22. https://doi.org/10.1007/s00606-009-0251-z

CBOL Plant Working Group. (2009). A DNA barcode for land plants. Proceedings of the National Academy of Sciences of the United States of America, 106(31), 12794–12797. https://doi.org/10.1073/pnas.0905845106

Danecek, P., Auton, A., Abecasis, G., Albers, C. A., Banks, E., DePristo, M. A., Handsaker, R. E., Lunter, G., Marth, G. T., Sherry, S. T., McVean, G., Durbin, R., & 1000 Genomes Project Analysis Group. (2011). The variant call format and VCFtools. Bioinformatics, 27(15), 2156–2158. https://doi.org/10.1093/bioinformatics/btr330

Dray, S., & Dufour, A. (2007). The ade4 package: Implementing the duality diagram for ecologists. Journal of Statistical Software, 22(4), 1–20. https://doi.org/10.18637/jss.v022.i04

Du, C., Xiong, T., Dong, Y., Gao, H., Zhang, Y., & Yue, J. (2025). Complete chloroplast genome structural and phylogenetic analysis of Physostegia virginiana (L.) Benth. 1930 (Lamiaceae). Mitochondrial DNA Part B: Resources, 10(8), 736–741. https://doi.org/10.1080/23802359.2025.2528568

Earl, D. A., & vonHoldt, B. M. (2012). STRUCTURE HARVESTER: A website and program for visualizing STRUCTURE output and implementing the Evanno method. Conservation Genetics Resources, 4, 359–361. https://doi.org/10.1007/s12686-011-9548-7

Evanno, G., Regnaut, S., & Goudet, J. (2005). Detecting the number of clusters of individuals using the software STRUCTURE: A simulation study. Molecular Ecology, 14(8), 2611–2620. https://doi.org/10.1111/j.1365-294X.2005.02553.x

Excoffier, L., & Lischer, H. E. L. (2010). Arlequin suite ver 3.5: A new series of programs to perform population genetics analyses under Linux and Windows. Molecular Ecology Resources, 10(3), 564–567. https://doi.org/10.1111/j.1755-0998.2010.02847.x

Farahvashi, M., Mohammadabadi, M., Askari-Hesni, M., Ghanatsaman, Z. A., & Nanaee, H. A. (2026). Population structure of hawksbill turtles (Eretmochelys imbricata) nesting along the Persian Gulf coastline revealed by inter-simple sequence repeat (ISSR) markers. Scientific Reports, 16(1), Article 4753. https://doi.org/10.1038/s41598-025-34749-y

Govindaraj, M., Vetriventhan, M., & Srinivasan, M. (2015). Importance of genetic diversity assessment in crop plants and its recent advances: An overview of its analytical perspectives. Genetics Research International, 2015, Article 431487. https://doi.org/10.1155/2015/431487

Hedrick, P. W. (2005). A standardized genetic differentiation measure. Evolution, 59(8), 1633–1638.

Jakobsson, M., & Rosenberg, N. A. (2007). CLUMPP: A cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure. Bioinformatics, 23(14), 1801–1806. https://doi.org/10.1093/bioinformatics/btm233

Jannink, J. L., Lorenz, A. J., & Iwata, H. (2010). Genomic selection in plant breeding: From theory to practice. Briefings in Functional Genomics, 9(2), 166–177. https://doi.org/10.1093/bfgp/elq001

Kassem, M. A. (2025). Comparative analysis of chloroplast genomes across 20 plant species reveals evolutionary patterns in gene content, codon usage, and genome structure. International Journal of Plant Biology, 16(3), Article 105. https://doi.org/10.3390/ijpb16030105

Kirankumar, S. I., Balaji, R., Tanuja, & Parani, M. (2023). The complete chloroplast genome of Ocimum basilicum L. var. basilicum (Lamiaceae) and its phylogenetic analysis. Mitochondrial DNA Part B: Resources, 8(11), 1169–1173. https://doi.org/10.1080/23802359.2023.2275835

Kolde, R. (2019). pheatmap: Pretty heatmaps (Version 1.0.12) [R package]. https://CRAN.R-project.org/package=pheatmap

Kumar, A., Rodrigues, V., Saxena, A., Mishra, P., Shukla, A. K., Shasany, A. K., Nazar, N., Sgamma, T., Slater, A., & Sundaresan, V. (2025). Evaluation of the plastid and nuclear DNA barcodes in genus Ocimum towards quality assurance in herbal industry. Industrial Crops and Products, 224, Article 120399. https://doi.org/10.1016/j.indcrop.2024.120399

Kumar, S., Stecher, G., Li, M., Knyaz, C., & Tamura, K. (2018). MEGA X: Molecular Evolutionary Genetics Analysis across computing platforms. Molecular Biology and Evolution, 35(6), 1547–1549. https://doi.org/10.1093/molbev/msy096

Letsiou, S., Madesis, P., Vasdekis, E., Montemurro, C., Grigoriou, M. E., Skavdis, G., Moussis, V., Koutelidakis, A. E., & Tzakos, A. G. (2024). DNA barcoding as a plant identification method. Applied Sciences, 14(4), Article 1415. https://doi.org/10.3390/app14041415

Li, H. (2013). Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM (arXiv:1303.3997). https://doi.org/10.48550/arXiv.1303.3997

McKenna, A., Hanna, M., Banks, E., Sivachenko, A., Cibulskis, K., Kernytsky, A., Garimella, K., Altshuler, D., Gabriel, S., Daly, M., & DePristo, M. A. (2010). The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data. Genome Research, 20(9), 1297–1303. https://doi.org/10.1101/gr.107524.110

Palumbo, F., Qi, P., Pinto, V. B., Devos, K. M., & Barcaccia, G. (2019). Construction of the first SNP-based linkage map using genotyping-by-sequencing and mapping of the male-sterility gene in leaf chicory. Frontiers in Plant Science, 10, Article 276. https://doi.org/10.3389/fpls.2019.00276

Patel, H. K., Fougat, R. S., Kumar, S., Mistry, J. G., & Kumar, M. (2015). Detection of genetic variation in Ocimum species using RAPD and ISSR markers. 3 Biotech, 5(5), 697–707. https://doi.org/10.1007/s13205-014-0269-y

Peakall, R., & Smouse, P. E. (2006). GENALEX 6: Genetic analysis in Excel. Population genetic software for teaching and research. Molecular Ecology Notes, 6(1), 288–295. https://doi.org/10.1111/j.1471-8286.2005.01155.x

Peterson, B. K., Weber, J. N., Kay, E. H., Fisher, H. S., & Hoekstra, H. E. (2012). Double digest RADseq: An inexpensive method for de novo SNP discovery and genotyping in model and non-model species. PLOS ONE, 7(5), Article e37135. https://doi.org/10.1371/journal.pone.0037135

Pritchard, J. K., Stephens, M., & Donnelly, P. (2000). Inference of population structure using multilocus genotype data. Genetics, 155(2), 945–959. https://doi.org/10.1093/genetics/155.2.945

R Core Team. (2014). R: A language and environment for statistical computing. MSOR Connections, 1.

Rochette, N. C., Rivera-Colón, A. G., & Catchen, J. M. (2019). Stacks 2: Analytical methods for paired-end sequencing improve RADseq-based population genomics. Molecular Ecology, 28(21), 4737–4754. https://doi.org/10.1111/mec.15253

Rosenberg, N. A. (2004). DISTRUCT: A program for the graphical display of population structure. Molecular Ecology Notes, 4(1), 137–138. https://doi.org/10.1046/j.1471-8286.2003.00566.x

Rozas, J., Ferrer-Mata, A., Sánchez-DelBarrio, J. C., Guirao-Rico, S., Librado, P., Ramos-Onsins, S. E., & Sánchez-Gracia, A. (2017). DnaSP 6: DNA sequence polymorphism analysis of large data sets. Molecular Biology and Evolution, 34(12), 3299–3302. https://doi.org/10.1093/molbev/msx248

Schnable, P. S., & Springer, N. M. (2013). Progress toward understanding heterosis in crop plants. Annual Review of Plant Biology, 64, 71–88. https://doi.org/10.1146/annurev-arplant-042110-103827

Shah, P., Jain, N., Gawande, N., Sharma, T., Devanathan, K., Sankaranarayanan, S., & Balaji, R. (2026). Advancing plant DNA barcoding: Integrating chloroplast genome sequencing, cryptic diversity discovery and machine learning. Molecular Biology Reports, 53(1), Article 550. https://doi.org/10.1007/s11033-026-11736-8

Sloan, D. B., Warren, J. M., Williams, A. M., Wu, Z., Abdel-Ghany, S. E., Chicco, A. J., & Havird, J. C. (2018). Cytonuclear integration and co-evolution. Nature Reviews Genetics, 19(10), 635–648. https://doi.org/10.1038/s41576-018-0035-9

Varshney, R. K., Graner, A., & Sorrells, M. E. (2005). Genomics-assisted breeding for crop improvement. Trends in Plant Science, 10(12), 621–630. https://doi.org/10.1016/j.tplants.2005.10.004

Waits, L. P., Luikart, G., & Taberlet, P. (2001). Estimating the probability of identity among genotypes in natural populations: Cautions and guidelines. Molecular Ecology, 10(1), 249–256. https://doi.org/10.1046/j.1365-294x.2001.01185.x

Wickham, H. (2016). Data analysis. In ggplot2: Elegant graphics for data analysis (pp. 189–201). Springer. https://doi.org/10.1007/978-3-319-24277-4

Woolliams, J. A., Berg, P., Dagnachew, B. S., & Meuwissen, T. H. (2015). Genetic contributions and their optimization. Journal of Animal Breeding and Genetics, 132(2), 89–99. https://doi.org/10.1111/jbg.12148

Zhakipbekov, K., Turgumbayeva, A., Akhelova, S., Bekmuratova, K., Blinova, O., Utegenova, G., Shertaeva, K., Sadykov, N., Tastambek, K., Saginbazarova, A., Urazgaliyev, K., Tulegenova, G., Zhalimova, Z., & Karasova, Z. (2024). Antimicrobial and other pharmacological properties of Ocimum basilicum, Lamiaceae. Molecules, 29(2), Article 388. https://doi.org/10.3390/molecules29020388

References

Abdelaziz, S. A., Khaled, K. A. M., Younis, R. A. A., Al-Kordy, M. A., El-Domyati, F. M., & Moghazee, M. M. (2024). Comparison of four DNA barcoding loci to distinguish between some Apiaceae family species. Beni-Suef University Journal of Basic and Applied Sciences, 13, Article 12. https://doi.org/10.1186/s43088-023-00457-7

Amirteymoori, E., Khezri, A., Dayani, O., Mohammadabadi, M., Khorasani, S., Mousaie, A., & Kazemi-Bonchenari, M. (2021). Effects of linseed processing method (ground versus extruded) and dietary crude protein content on performance, digestibility, ruminal fermentation pattern, and rumen protozoa population in growing lambs. Italian Journal of Animal Science, 20(1), 1506–1517. https://doi.org/10.1080/1828051X.2021.1984324

Arabpour, Z., Mohammadabadi, M., & Khezri, A. (2021). The expression pattern of p32 gene in femur, humeral muscle, back muscle and back fat tissues of Kermani lambs. Agricultural Biotechnology Journal, 13(4), 183–200. https://doi.org/10.22103/jab.2022.18782.1371

Avetisyan, A., Markosian, A., Petrosyan, M., Sahakyan, N., Babayan, A., Aloyan, S., & Trchounian, A. (2017). Chemical composition and some biological activities of the essential oils from basil (Ocimum) different cultivars. BMC Complementary and Alternative Medicine, 17(1), Article 60. https://doi.org/10.1186/s12906-017-1587-5

Bolger, A. M., Lohse, M., & Usadel, B. (2014). Trimmomatic: A flexible trimmer for Illumina sequence data. Bioinformatics, 30(15), 2114–2120. https://doi.org/10.1093/bioinformatics/btu170

Carović-Stanko, K., Liber, Z., Besendorfer, V., Javornik, B., Bohanec, B., Kolak, I., & Satovic, Z. (2010). Genetic relations among basil taxa (Ocimum L.) based on molecular markers, nuclear DNA content, and chromosome number. Plant Systematics and Evolution, 285, 13–22. https://doi.org/10.1007/s00606-009-0251-z

CBOL Plant Working Group. (2009). A DNA barcode for land plants. Proceedings of the National Academy of Sciences of the United States of America, 106(31), 12794–12797. https://doi.org/10.1073/pnas.0905845106

Danecek, P., Auton, A., Abecasis, G., Albers, C. A., Banks, E., DePristo, M. A., Handsaker, R. E., Lunter, G., Marth, G. T., Sherry, S. T., McVean, G., Durbin, R., & 1000 Genomes Project Analysis Group. (2011). The variant call format and VCFtools. Bioinformatics, 27(15), 2156–2158. https://doi.org/10.1093/bioinformatics/btr330

Dray, S., & Dufour, A. (2007). The ade4 package: Implementing the duality diagram for ecologists. Journal of Statistical Software, 22(4), 1–20. https://doi.org/10.18637/jss.v022.i04

Du, C., Xiong, T., Dong, Y., Gao, H., Zhang, Y., & Yue, J. (2025). Complete chloroplast genome structural and phylogenetic analysis of Physostegia virginiana (L.) Benth. 1930 (Lamiaceae). Mitochondrial DNA Part B: Resources, 10(8), 736–741. https://doi.org/10.1080/23802359.2025.2528568

Earl, D. A., & vonHoldt, B. M. (2012). STRUCTURE HARVESTER: A website and program for visualizing STRUCTURE output and implementing the Evanno method. Conservation Genetics Resources, 4, 359–361. https://doi.org/10.1007/s12686-011-9548-7

Evanno, G., Regnaut, S., & Goudet, J. (2005). Detecting the number of clusters of individuals using the software STRUCTURE: A simulation study. Molecular Ecology, 14(8), 2611–2620. https://doi.org/10.1111/j.1365-294X.2005.02553.x

Excoffier, L., & Lischer, H. E. L. (2010). Arlequin suite ver 3.5: A new series of programs to perform population genetics analyses under Linux and Windows. Molecular Ecology Resources, 10(3), 564–567. https://doi.org/10.1111/j.1755-0998.2010.02847.x

Farahvashi, M., Mohammadabadi, M., Askari-Hesni, M., Ghanatsaman, Z. A., & Nanaee, H. A. (2026). Population structure of hawksbill turtles (Eretmochelys imbricata) nesting along the Persian Gulf coastline revealed by inter-simple sequence repeat (ISSR) markers. Scientific Reports, 16(1), Article 4753. https://doi.org/10.1038/s41598-025-34749-y

Govindaraj, M., Vetriventhan, M., & Srinivasan, M. (2015). Importance of genetic diversity assessment in crop plants and its recent advances: An overview of its analytical perspectives. Genetics Research International, 2015, Article 431487. https://doi.org/10.1155/2015/431487

Hedrick, P. W. (2005). A standardized genetic differentiation measure. Evolution, 59(8), 1633–1638.

Jakobsson, M., & Rosenberg, N. A. (2007). CLUMPP: A cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure. Bioinformatics, 23(14), 1801–1806. https://doi.org/10.1093/bioinformatics/btm233

Jannink, J. L., Lorenz, A. J., & Iwata, H. (2010). Genomic selection in plant breeding: From theory to practice. Briefings in Functional Genomics, 9(2), 166–177. https://doi.org/10.1093/bfgp/elq001

Kassem, M. A. (2025). Comparative analysis of chloroplast genomes across 20 plant species reveals evolutionary patterns in gene content, codon usage, and genome structure. International Journal of Plant Biology, 16(3), Article 105. https://doi.org/10.3390/ijpb16030105

Kirankumar, S. I., Balaji, R., Tanuja, & Parani, M. (2023). The complete chloroplast genome of Ocimum basilicum L. var. basilicum (Lamiaceae) and its phylogenetic analysis. Mitochondrial DNA Part B: Resources, 8(11), 1169–1173. https://doi.org/10.1080/23802359.2023.2275835

Kolde, R. (2019). pheatmap: Pretty heatmaps (Version 1.0.12) [R package]. https://CRAN.R-project.org/package=pheatmap

Kumar, A., Rodrigues, V., Saxena, A., Mishra, P., Shukla, A. K., Shasany, A. K., Nazar, N., Sgamma, T., Slater, A., & Sundaresan, V. (2025). Evaluation of the plastid and nuclear DNA barcodes in genus Ocimum towards quality assurance in herbal industry. Industrial Crops and Products, 224, Article 120399. https://doi.org/10.1016/j.indcrop.2024.120399

Kumar, S., Stecher, G., Li, M., Knyaz, C., & Tamura, K. (2018). MEGA X: Molecular Evolutionary Genetics Analysis across computing platforms. Molecular Biology and Evolution, 35(6), 1547–1549. https://doi.org/10.1093/molbev/msy096

Letsiou, S., Madesis, P., Vasdekis, E., Montemurro, C., Grigoriou, M. E., Skavdis, G., Moussis, V., Koutelidakis, A. E., & Tzakos, A. G. (2024). DNA barcoding as a plant identification method. Applied Sciences, 14(4), Article 1415. https://doi.org/10.3390/app14041415

Li, H. (2013). Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM (arXiv:1303.3997). https://doi.org/10.48550/arXiv.1303.3997

McKenna, A., Hanna, M., Banks, E., Sivachenko, A., Cibulskis, K., Kernytsky, A., Garimella, K., Altshuler, D., Gabriel, S., Daly, M., & DePristo, M. A. (2010). The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data. Genome Research, 20(9), 1297–1303. https://doi.org/10.1101/gr.107524.110

Palumbo, F., Qi, P., Pinto, V. B., Devos, K. M., & Barcaccia, G. (2019). Construction of the first SNP-based linkage map using genotyping-by-sequencing and mapping of the male-sterility gene in leaf chicory. Frontiers in Plant Science, 10, Article 276. https://doi.org/10.3389/fpls.2019.00276

Patel, H. K., Fougat, R. S., Kumar, S., Mistry, J. G., & Kumar, M. (2015). Detection of genetic variation in Ocimum species using RAPD and ISSR markers. 3 Biotech, 5(5), 697–707. https://doi.org/10.1007/s13205-014-0269-y

Peakall, R., & Smouse, P. E. (2006). GENALEX 6: Genetic analysis in Excel. Population genetic software for teaching and research. Molecular Ecology Notes, 6(1), 288–295. https://doi.org/10.1111/j.1471-8286.2005.01155.x

Peterson, B. K., Weber, J. N., Kay, E. H., Fisher, H. S., & Hoekstra, H. E. (2012). Double digest RADseq: An inexpensive method for de novo SNP discovery and genotyping in model and non-model species. PLOS ONE, 7(5), Article e37135. https://doi.org/10.1371/journal.pone.0037135

Pritchard, J. K., Stephens, M., & Donnelly, P. (2000). Inference of population structure using multilocus genotype data. Genetics, 155(2), 945–959. https://doi.org/10.1093/genetics/155.2.945

R Core Team. (2014). R: A language and environment for statistical computing. MSOR Connections, 1.

Rochette, N. C., Rivera-Colón, A. G., & Catchen, J. M. (2019). Stacks 2: Analytical methods for paired-end sequencing improve RADseq-based population genomics. Molecular Ecology, 28(21), 4737–4754. https://doi.org/10.1111/mec.15253

Rosenberg, N. A. (2004). DISTRUCT: A program for the graphical display of population structure. Molecular Ecology Notes, 4(1), 137–138. https://doi.org/10.1046/j.1471-8286.2003.00566.x

Rozas, J., Ferrer-Mata, A., Sánchez-DelBarrio, J. C., Guirao-Rico, S., Librado, P., Ramos-Onsins, S. E., & Sánchez-Gracia, A. (2017). DnaSP 6: DNA sequence polymorphism analysis of large data sets. Molecular Biology and Evolution, 34(12), 3299–3302. https://doi.org/10.1093/molbev/msx248

Schnable, P. S., & Springer, N. M. (2013). Progress toward understanding heterosis in crop plants. Annual Review of Plant Biology, 64, 71–88. https://doi.org/10.1146/annurev-arplant-042110-103827

Shah, P., Jain, N., Gawande, N., Sharma, T., Devanathan, K., Sankaranarayanan, S., & Balaji, R. (2026). Advancing plant DNA barcoding: Integrating chloroplast genome sequencing, cryptic diversity discovery and machine learning. Molecular Biology Reports, 53(1), Article 550. https://doi.org/10.1007/s11033-026-11736-8

Sloan, D. B., Warren, J. M., Williams, A. M., Wu, Z., Abdel-Ghany, S. E., Chicco, A. J., & Havird, J. C. (2018). Cytonuclear integration and co-evolution. Nature Reviews Genetics, 19(10), 635–648. https://doi.org/10.1038/s41576-018-0035-9

Varshney, R. K., Graner, A., & Sorrells, M. E. (2005). Genomics-assisted breeding for crop improvement. Trends in Plant Science, 10(12), 621–630. https://doi.org/10.1016/j.tplants.2005.10.004

Waits, L. P., Luikart, G., & Taberlet, P. (2001). Estimating the probability of identity among genotypes in natural populations: Cautions and guidelines. Molecular Ecology, 10(1), 249–256. https://doi.org/10.1046/j.1365-294x.2001.01185.x

Wickham, H. (2016). Data analysis. In ggplot2: Elegant graphics for data analysis (pp. 189–201). Springer. https://doi.org/10.1007/978-3-319-24277-4

Woolliams, J. A., Berg, P., Dagnachew, B. S., & Meuwissen, T. H. (2015). Genetic contributions and their optimization. Journal of Animal Breeding and Genetics, 132(2), 89–99. https://doi.org/10.1111/jbg.12148

Zhakipbekov, K., Turgumbayeva, A., Akhelova, S., Bekmuratova, K., Blinova, O., Utegenova, G., Shertaeva, K., Sadykov, N., Tastambek, K., Saginbazarova, A., Urazgaliyev, K., Tulegenova, G., Zhalimova, Z., & Karasova, Z. (2024). Antimicrobial and other pharmacological properties of Ocimum basilicum, Lamiaceae. Molecules, 29(2), Article 388. https://doi.org/10.3390/molecules29020388

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