Characterization of single nucleotide polymorphisms in chloroplast genomes of Musaceae Juss.
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Abstract
Musaceae Juss., also called the bananas and plantains family contains essential food crops with critical economic value and nutritional and medicinal properties. In this study, complete chloroplast genomes of 55 species of Musaceae, including all three genera of Musa, Musella, and Ensete, were used to characterize single nucleotide polymorphisms. Also, nucleotide diversity among surveyed species was observed. The results showed regions of high genetic variability in the chloroplast genome and genes carrying multiple single-nucleotide polymorphisms specific for species and genera, such as ycf1, ycf2, ndhF, matK, accD, infA, and petL. A biased nucleotide conversion toward G, C, and T suggests a trend in the evolution of the Musaceae chloroplast genomes. Phylogenetic analysis revealed a close relationship between Ensete and Musella genera and confirmed the existence of two clades in the genus Musa. This study summarizes nucleotide diversity, focusing on single-nucleotide polymorphisms, which are helpful for further studies on population genetics and developing molecular markers in Musaceae.
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References
Ahmad, F., Martawi, N. M., Poerba, Y. S., De Jong, H., Schouten, H., & Kema, G. H. J.. (2020). Genetic mapping of Fusarium wilt resistance in a wild banana Musa acuminata ssp. malaccensis accession. Theoretical and Applied Genetics, 133(12), 3409–3418. https://doi.org/10.1007/s00122-020-03677-y
Amorim, E. P., dos Santos-Serejo, J. A., Amorim, V. B. O., Ferreira, C. F., & Silva, S. O. (2011, October). Banana breeding at Embrapa cassava and fruits. In VII International Symposium on Banana: ISHS-ProMusa Symposium on Bananas and Plantains: Towards Sustainable Global Production 986 (pp. 171-176).
Arbeithuber, B., Betancourt, A. J., Ebner, T., & Tiemann-Boege, I. (2015). Crossovers are associated with mutation and biased gene conversion at recombination hotspots. Proceedings of the National Academy of Sciences of the United States of America, 112(7), 2109–2114. https://doi.org/10.1073/pnas.1416622112
Birdsell, J. A. (2002). Integrating Genomics, Bioinformatics, and Classical Genetics to Study the Effects of Recombination on Genome Evolution. Molecular Biology and Evolution, 19(7), 1181–1197. https://doi.org/10.1093/oxfordjournals.molbev.a004176
Brooks, S., Gelman, A., Jones, G., & Meng, X. L. (Eds.). (2011). Handbook of Markov chain monte Carlo. CRC press.
Christelová, P., Valárik, M., Hřibová, E., De Langhe, E., & Doležel, J.. (2011). A multi gene sequence-based phylogeny of the Musaceae (banana) family. BMC Evolutionary Biology, 11(1), 103. https://doi.org/10.1186/1471-2148-11-103
D’Hont, A., Denoeud, F., Aury, J.-M., Baurens, F.-C., Carreel, F., Garsmeur, O., Noel, B., Bocs, S., Droc, G., Rouard, M., Da Silva, C., Jabbari, K., Cardi, C., Poulain, J., Souquet, M., Labadie, K., Jourda, C., Lengellé, J., Rodier-Goud, M., … Wincker, P.. (2012). The banana (Musa acuminata) genome and the evolution of monocotyledonous plants. Nature, 488(7410), 213–217. https://doi.org/10.1038/nature11241
Darling, A. E., Mau, B., & Perna, N. T.. (2010). progressiveMauve: Multiple Genome Alignment with Gene Gain, Loss and Rearrangement. PLOS ONE, 5(6), e11147. https://doi.org/10.1371/journal.pone.0011147
Darriba, D., Taboada, G. L., Doallo, R., & Posada, D.. (2012). jModelTest 2: more models, new heuristics and parallel computing. Nature Methods, 9(8), 772–772. https://doi.org/10.1038/nmeth.2109
Dobrogojski, J., Adamiec, M., & Luciński, R.. (2020). The chloroplast genome: a review. Acta Physiologiae Plantarum, 42(6). https://doi.org/10.1007/s11738-020-03089-x
Drenth, A., & Kema, G. (2021). The Vulnerability of Bananas to Globally Emerging Disease Threats. Phytopathology, 111(12), 2146–2161. https://doi.org/10.1094/PHYTO-07-20-0311-RVW
Droc, G., Lariviere, D., Guignon, V., Yahiaoui, N., This, D., Garsmeur, O., Dereeper, A., Hamelin, C., Argout, X., Dufayard, J.-F., Lengelle, J., Baurens, F.-C., Cenci, A., Pitollat, B., D'Hont, A., Ruiz, M., Rouard, M., Bocs, S (2013). The Banana Genome Hub Database. DOI: http://10.1093/database/bat035
Duan, H., Guo, J., Xuan, L., Wang, Z., Li, M., Yin, Y., & Yang, Y.. (2020). Comparative chloroplast genomics of the genus Taxodium. BMC Genomics, 21(1). https://doi.org/10.1186/s12864-020-6532-1
Edgar, R. C.. (2004). MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research, 32(5), 1792–1797. https://doi.org/10.1093/nar/gkh340
Food and Agriculture Organization of the United Nations (FAO) (n.d.). FAOSTAT (2021). Statistics | Food and Agriculture Organization of the United Nations. https://www.fao.org/faostat/en/#home
Food and Agriculture Organization of the United Nations (FAO) (n.d.). FAOSTAT (2022). Statistics | Food and Agriculture Organization of the United Nations. https://www.fao.org/faostat/en/#home
Fu, N., Ji, M., Rouard, M., Yan, H.-F., & Ge, X.-J.. (2022). Comparative plastome analysis of Musaceae and new insights into phylogenetic relationships. BMC Genomics, 23(1). https://doi.org/10.1186/s12864-022-08454-3
Geneious Prime 2022.2. (2022, June 14). Geneious | Bioinformatics Software for Sequence Data Analysis. https://www.geneious.com/
Guindon, S., & Gascuel, O. (2003). A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Systematic Biology, 52(5), 696–704. https://doi.org/10.1080/10635150390235520
Guo, Y., Yang, J., Li, H., & Zhao, H. (2021). Chloroplast Genomes of Two Species of Cypripedium: Expanded Genome Size and Proliferation of AT-Biased Repeat Sequences. Frontiers in Plant Science, 12. https://doi.org/10.3389/fpls.2021.609729
Häkkinen, M. (2013). Reappraisal of sectional taxonomy in Musa (Musaceae). Taxon, 62(4), 809–813. https://doi.org/10.12705/624.3
Heslop-Harrison, J. S., & Schwarzacher, T. (2007). Review: Domestication, Genomics and the Future for Banana. Annals of Botany, 100(5), 1073-1084. https://doi.org/10.1093/aob/mcm191
Ibarra-Laclette, E., Albert, V. A., Herrera-Estrella, A., & Herrera-Estrella, L.. (2011). Is GC bias in the nuclear genome of the carnivorous plant Utricularia driven by ROS-based mutation and biased gene conversion?. Plant Signaling & Behavior, 6(11), 1631–1634. https://doi.org/10.4161/psb.6.11.17657
Igwe, D. O., Ihearahu, O. C., Osano, A. A., Acquaah, G., & Ude, G. N.. (2021). Genetic Diversity and Population Assessment of Musa L. (Musaceae) Employing CDDP Markers. Plant Molecular Biology Reporter, 39(4), 801–820. https://doi.org/10.1007/s11105-021-01290-x
International Tropical Fruits Network. (2016, March 16). Banana - Nutritional Value. Retrieved March 21, 2023, from https://www.itfnet.org/v1/2016/03/banana-nutritional-value/
Jones, D. R. (2007, September). Disease and pest constraints to banana production. In III International Symposium on Banana: ISHS-ProMusa Symposium on Recent Advances in Banana Crop Protection for Sustainable 828 (pp. 21-36).
Kostka, D., Hubisz, M. J., Siepel, A., & Pollard, K. S. (2012). The Role of GC-Biased Gene Conversion in Shaping the Fastest Evolving Regions of the Human Genome. Molecular Biology and Evolution, 29(3), 1047–1057. https://doi.org/10.1093/molbev/msr279
Kumar, K. P. S., Bhowmik, D., Duraivel, S., & Umadevi, M. (2012). Traditional and Medicinal Uses of Banana. Journal of Pharmacognosy and Phytochemistry, 1(3).
Leister, D. (2003). Chloroplast research in the genomic age. Trends in Genetics, 19(1), 47-56. https://doi.org/10.1016/S0168-9525(02)00003-3
Lesecque, Y., Mouchiroud, D., & Duret, L. (2013). GC-Biased Gene Conversion in Yeast Is Specifically Associated with Crossovers: Molecular Mechanisms and Evolutionary Significance. Molecular Biology and Evolution, 30(6), 1409–1419. https://doi.org/10.1093/molbev/mst056
Liu, H., Huang, J., Sun, X., Li, J., Hu, Y., Yu, L., Liti, G., Tian, D., Hurst, L. D., & Yang, S. (2018). Tetrad analysis in plants and fungi finds large differences in gene conversion rates but no GC bias. Nature Ecology and Evolution, 2(1), 164–173. https://doi.org/10.1038/s41559-017-0372-7
Liu, Z., Kress, W. J., & Li, Z. (2010). Phylogenetic Analyses of the Banana Family (Musaceae) Based on Nuclear Ribosomal (ITS) and Chloroplast (trnL-F) Evidence. Taxon, 59(1), 20-28. https://doi.org/10.2307/27757047
Mmeka, E. C., Adesoye, A. I., Vroh, B. I., & Ubaoji, K. I. (2013). Single nucleotide polymorphism (SNP) markers discovery within Musa spp (plantain landraces, AAB genome) for use in beta carotene (Provitamin A) trait mapping. American Journal of Biology and Life Sciences, 1(1), 11-19.
Marais, G. A. B. (2003). Biased gene conversion: implications for genome and sex evolution. Trends in Genetics, 19(6), 330–338. https://doi.org/10.1016/s0168-9525(03)00116-1
Marin, D. H., Romero, R. A., Guzman, M., & Sutton, T. B. (2003). Black Sigatoka: an increasing threat to banana cultivation. Plant disease, 87(3), 208-222.
Martin, G., Baurens, F.-C., Cardi, C., Aury, J.-M., & D’Hont, A.. (2013). The Complete Chloroplast Genome of Banana (Musa acuminata, Zingiberales): Insight into Plastid Monocotyledon Evolution. PLOS ONE, 8(6), e67350. https://doi.org/10.1371/journal.pone.0067350
Moghaddam, M., Ohta, A., Shimizu, M., Terauchi, R., & Kazempour-Osaloo, S.. (2022). The complete chloroplast genome of Onobrychis gaubae (Fabaceae-Papilionoideae): comparative analysis with related IR-lacking clade species. BMC Plant Biology, 22(1). https://doi.org/10.1186/s12870-022-03465-4
Mugal, C. F., Weber, C. C., & Ellegren, H. (2015). GC-biased gene conversion links the recombination landscape and demography to genomic base composition. BioEssays, 37(12), 1317–1326. https://doi.org/10.1002/bies.201500058
Muyle, A., & Marais, G. (2016). Mating Systems in Plants, Genome Evolution and. Encyclopedia of Evolutionary Biology, 480-492. https://doi.org/10.1016/B978-0-12-800049-6.00320-6
Ohyama, K. (1996). Chloroplast and Mitochondrial Genomes from a Liverwort, Marchantia polymorpha—Gene Organization and Molecular Evolution—. Bioscience, Biotechnology, and Biochemistry, 60(1), 16–24. https://doi.org/10.1271/bbb.60.16
Ohyama, K., Fukuzawa, H., Kohchi, T., Shirai, H., Sano, T., Sano, S., Umesono, K., Shiki, Y., Takeuchi, M., Chang, Z., Aota, S., Inokuchi, H., & Ozeki, H. (1986). Chloroplast gene organization deduced from complete sequence of liverwort Marchantia polymorpha chloroplast DNA. Nature, 322(6079), 572–574. https://doi.org/10.1038/322572a0
Palmer, J. D., Jansen, R. K., Michaels, H. J., Chase, M. W., & Manhart, J. R. (1988). Chloroplast DNA Variation and Plant Phylogeny. Annals of the Missouri Botanical Garden, 75(4), 1180-1206. https://doi.org/10.2307/2399279
Perrier, X., Langhe, E. D., Donohue, M., Lentfer, C., Vrydaghs, L., Bakry, F., Carreel, F., Hippolyte, I., Horry, P., Jenny, C., Lebot, V., Risterucci, M., Tomekpe, K., Doutrelepont, H., Ball, T., Manwaring, J., & Denham, T. (2011). Multidisciplinary perspectives on banana (Musa spp.) domestication. Proceedings of the National Academy of Sciences of the United States of America, 108(28), 11311-11318. https://doi.org/10.1073/pnas.1102001108
Pessia, E., Popa, A., Mousset, S., Rezvoy, C., Duret, L., & Marais, G. a. B. (2012). Evidence for Widespread GC-biased Gene Conversion in Eukaryotes. Genome Biology and Evolution, 4(7), 675–682. https://doi.org/10.1093/gbe/evs052
Probojati, R. T., Listyorini, D., Sulisetijono, S., & Wahyudi, D. (2021). Phylogeny and estimated genetic divergence times of banana cultivars (Musa spp.) from Java Island by maturase K (matK) genes. Bulletin of the National Research Centre, 45(1), 1-13. https://doi.org/10.1186/s42269-021-00492-3
Rambaut, A., & Drummond, A. J. (2012). FigTree version 1.4. 0.
Rijzaani, H., Bayer, P. E., Rouard, M., Doležel, J., Batley, J., & Edwards, D.. (2022). The pangenome of banana highlights differences between genera and genomes. The Plant Genome, 15(1). https://doi.org/10.1002/tpg2.20100
Ronquist, F., Teslenko, M., Ayres, D. L., Darling, A., Höhna, S., Larget, B., Liu, L., Suchard, M. A., & Huelsenbeck, J. P. (2012). MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space. Systematic Biology, 61(3), 539-542. https://doi.org/10.1093/sysbio/sys029
Royal Botanic Gardens Kew (n.d.). Musaceae Juss. Plant of the World Online. https://powo.science.kew.org/taxon/urn:lsid:ipni.org:names:30000849-2
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.
Sardos, J., Breton, C., Perrier, X., Carpentier, S., Paofa, J., Rouard, M., & Roux, N. (2022). Hybridization, missing wild ancestors and the domestication of cultivated diploid bananas. Frontiers in Plant Science, 13. https://doi.org/10.3389/fpls.2022.969220
Sarma, U., Govila, V. K., & Yadav, A. (2019). The traditional and therapeutic use of banana and its plant-based delicacies in ethnic Assamese cuisine and religious rituals from Northeast India. Journal of Ethnic Foods, 7(21). https://doi.org/10.1186/s42779-020-00053-5
Sayers, E. W., Bolton, E. E., Brister, J. R., Canese, K., Chan, J., Comeau, D. C., Connor, R., Funk, K., Kelly, C., Kim, S., Madej, T., Marchler-Bauer, A., Lanczycki, C., Lathrop, S., Lu, Z., Thibaud-Nissen, F., Murphy, T., Phan, L., Skripchenko, Y., Tse, T., … Sherry, S. T. (2022). Database resources of the national center for biotechnology information. Nucleic acids research, 50(D1), D20–D26. https://doi.org/10.1093/nar/gkab1112
Simmonds, N. W., & Shepherd, K. (1955). The taxonomy and origins of the cultivated bananas. Botanical Journal of the Linnean Society, 55(359), 302-312.
Šimoníková, D., Čížková, J., Zoulová, V., Christelová, P., & Hřibová, E.. (2022). Advances in the Molecular Cytogenetics of Bananas, Family Musaceae. Plants, 11(4), 482. https://doi.org/10.3390/plants11040482
Thangavelu, R., Loganathan, M., Arthee, R., Prabakaran, M., & Uma, S. (2020). Fusarium wilt: a threat to banana cultivation and its management. CABI Reviews, (2020), 1-24.
Till, B. J., Jankowicz-Cieslak, J., Sági, L., Huynh, O. A., Utsushi, H., Swennen, R., Terauchi, R., & Mba, C.. (2010). Discovery of nucleotide polymorphisms in the Musa gene pool by Ecotilling. Theoretical and Applied Genetics, 121(7), 1381–1389. https://doi.org/10.1007/s00122-010-1395-5
Zhang, Z., Zhang, D.-S., Zou, L., & Yao, C.-Y.. (2022). Comparison of chloroplast genomes and phylogenomics in the Ficus sarmentosa complex (Moraceae). PLOS ONE, 17(12), e0279849. https://doi.org/10.1371/journal.pone.0