Cotton Genomics and Genetics 2024, Vol.15, No.2, 112-126 http://cropscipublisher.com/index.php/cgg 124 expression in polyploid species, which is essential for understanding how different gene isoforms contribute to phenotypic diversity. The integration of NGS with other technologies, such as BioNano optical mapping and high-throughput chromosome conformation capture, has further enhanced the resolution and accuracy of genomic studies in cotton. These combined approaches allow for the identification of structural variations and chromosomal rearrangements that may play critical roles in the evolution and domestication of cotton species. Moreover, the application of NGS in metagenomic studies has the potential to explore the cotton microbiome, which could lead to the discovery of beneficial microbial interactions that enhance cotton growth and resilience. Next-generation sequencing technologies have indeed been a game changer in cotton genomics. The rapid advancements in sequencing methods and the development of new technologies have opened up new avenues for research and practical applications in cotton breeding and genetics. The ability to generate high-quality genomic data at a lower cost and in a shorter time frame has democratized access to genomic information, allowing more researchers to contribute to the field. As NGS technologies continue to evolve, it is expected that they will become even more integral to cotton genomics research. Future developments may include further improvements in sequencing accuracy, read length, and data analysis tools, which will enhance our ability to study complex genomes and their regulatory mechanisms. Ultimately, the continued integration of NGS into cotton genomics will drive innovations in cotton breeding, leading to the development of new varieties that meet the demands of a growing global population and changing environmental conditions. By leveraging the power of next-generation sequencing, researchers and breeders can work together to ensure the sustainability and productivity of cotton, securing its place as a vital crop for the future. Acknowledgments The authors extend sincere thanks to two anonymous peer reviewers for their invaluable feedback on the manuscript, whose evaluations and suggestions have greatly contributed to the improvement of the manuscript. Conflict of Interest Disclosure The authors affirm that this research was conducted without any commercial or financial relationships that could be construed as a potential conflict of interest. References Ang M.Y., Low T.Y., Lee P.Y., Nazarie W.F.W.M., Guryev V., and Jamal R., 2019, Proteogenomics: from next-generation sequencing (NGS) and mass spectrometry-based proteomics to precision medicine, Clinica Chimica Acta, 498: 38-46. https://doi.org/10.1016/j.cca.2019.08.010 Athanasopoulou K., Boti M.A., Adamopoulos P.G., Skourou P.C., and Scorilas A., 2021, Third-generation sequencing: the spearhead towards the radical transformation of modern genomics, Life, 12(1): 30. https://doi.org/10.3390/life12010030 Bansal G., Narta K., and Teltumbade M.R., 2018, Next-Generation sequencing: technology, advancements, and applications, Bioinformatics: Sequences, Structures, Phylogeny, 2018: 15-46. https://doi.org/10.1007/978-981-13-1562-6_2 Baptista R.P., Reis-Cunha J.L., DeBarry J.D., Chiari E., Kissinger J.C., Bartholomeu D.C., and Macedo A.M., 2018, Assembly of highly repetitive genomes using short reads: the genome of discrete typing unit III Trypanosoma cruzi strain 231, Microbial Genomics, 4(4): e000156. https://doi.org/10.1099/mgen.0.000156 Begum S., and Banerjee R., 2021, Next generation sequencing data analysis and its applications in agriculture, Bhartiya Krishi Anusandhan Patrika, 36(1): 25-28. https://doi.org/10.18805/BKAP265 Chen T., 2019, Simple and scalable genome analysis with transposase enzyme linked long-read sequencing (TELL-Seq): from haplotype phasing to de novo assembly in a tube, Journal of Biomolecular Techniques: JBT, 30(Suppl): S37. Church A.J., 2020, Next-Generation sequencing, Genomic Medicine: A Practical Guide, 2020: 25-40. https://doi.org/10.1007/978-3-030-22922-1_2
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