Cotton Genomics and Genetics 2024, Vol.15, No.2, 112-126 http://cropscipublisher.com/index.php/cgg 123 their ability to resolve repeat sequences and large genomic rearrangements, which are challenging for short-read sequencing methods (Kumar et al., 2019). These advancements hold great potential for improving our understanding of cotton genomics and facilitating more precise genetic modifications. 7.2 Integration with other omics technologies The integration of NGS with other omics technologies, such as transcriptomics, proteomics, metabolomics, and epigenomics, is becoming increasingly important in the field of genomics. This multi-omics approach allows for a comprehensive understanding of the biological processes underlying cotton growth, development, and stress responses (Donlin et al., 2019; Do et al., 2021). For instance, proteogenomics, which combines NGS and mass spectrometry-based proteomics, has been instrumental in identifying novel coding sequences and patient-specific proteoforms in cancer research, and similar approaches can be applied to cotton genomics to identify key regulatory proteins and pathways (Ang et al., 2019). The integration of these diverse datasets can provide a holistic view of the molecular mechanisms in cotton, enabling the development of more resilient and high-yielding varieties. 7.3 Potential for sustainable cotton production The application of NGS technologies in cotton genomics holds significant promise for sustainable cotton production. By enabling the identification of genetic variations and stress-responsive genes, NGS can facilitate the development of cotton varieties that are more resistant to biotic and abiotic stresses (Begum and Banerjee, 2021; Yang et al., 2021). This is particularly important in the context of climate change, where crops are increasingly exposed to extreme weather conditions and new pest pressures. Additionally, the integration of NGS with other omics technologies can help in understanding the complex interactions between genes and environmental factors, leading to the development of cotton varieties that require fewer inputs such as water, fertilizers, and pesticides (Yang et al., 2021). Ultimately, these advancements can contribute to more sustainable and environmentally friendly cotton production practices. The future of cotton genomics is bright, with emerging NGS technologies and the integration of multi-omics approaches paving the way for significant advancements. These innovations hold the potential to enhance our understanding of cotton biology, improve crop resilience, and promote sustainable agricultural practices. 8 Concluding Remarks Next-generation sequencing (NGS) technologies have revolutionized the field of genomics, providing unprecedented insights into the genetic makeup of organisms, including cotton. The evolution from Sanger sequencing to NGS has significantly increased sequencing output while reducing time and cost. Short-read sequencing technologies, such as Illumina and Ion Torrent, have been widely used due to their high accuracy, although they are limited by read length. On the other hand, long-read sequencing technologies, such as Pacific Biosciences and Oxford Nanopore, offer longer read lengths, which are crucial for resolving complex genomic regions, albeit with initially lower accuracy. Recent advancements have improved the accuracy of long-read technologies, making them more viable for comprehensive genomic studies. In cotton genomics, NGS has enabled the characterization of alternative splicing events, which are crucial for understanding gene regulation and diversity in polyploid species like cotton. The development of reference-grade genome assemblies for Gossypium hirsutum and Gossypium barbadense has provided valuable resources for evolutionary and functional genomic studies, as well as for breeding programs aimed at improving fiber quality. Additionally, NGS has facilitated the identification of quantitative trait loci (QTL) associated with desirable traits, further enhancing cotton breeding efforts. The advancements in NGS technologies have profound implications for cotton genomics. The ability to generate high-quality, comprehensive genome assemblies allows for a deeper understanding of the genetic basis of important traits, such as fiber quality and yield. This knowledge can be directly applied to breeding programs, enabling the development of cotton varieties with superior characteristics. Furthermore, the identification of alternative splicing events and their regulatory mechanisms provides insights into the complexity of gene
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