Tree Genetics and Molecular Breeding 2024, Vol.14, No.3, 106-118 http://genbreedpublisher.com/index.php/tgmb 107 This study provides a comprehensive overview of the current state of tree genomic research, highlighting key achievements and identifying ongoing challenges. By synthesizing findings from recent studies, this study maps the full genome of trees and decode their functions from leaves to roots. This includes exploring the genetic basis of traits related to growth, adaptation, and resistance, as well as understanding the ecological and evolutionary implications of these traits. Ultimately, this study seeks to inform future research directions and applications in tree breeding, conservation, and ecosystem management, contributing to the sustainable management of forest resources in a changing world. 2 Technological Advances in Tree Genome Sequencing 2.1 Evolution of sequencing technologies: from sanger to next-generation sequencing The journey of sequencing technologies began with the advent of Sanger sequencing in the 1970s, which revolutionized the field by allowing the complete sequencing of genomes for the first time. Sanger sequencing, also known as the chain termination method, dominated the field for over three decades due to its accuracy and reliability (Dijk et al., 2018; Sharma et al., 2018). However, the need for higher throughput and cost-effective solutions led to the development of next-generation sequencing (NGS) technologies. NGS technologies, often referred to as the second-generation sequencing, brought about a paradigm shift by enabling massively parallel sequencing of millions of DNA fragments simultaneously. This leap significantly reduced the cost and time required for sequencing, making it accessible for large-scale genomic studies (Bansal et al., 2018; Levy and Boone, 2018). Key NGS platforms include Illumina's sequencing by synthesis and Ion Torrent's semiconductor sequencing, both of which are characterized by short-read lengths but high accuracy (Kumar et al., 2019; Hu et al., 2021). The limitations of short-read sequencing, such as difficulties in resolving repetitive regions and large genomic rearrangements, paved the way for third-generation sequencing technologies. These long-read sequencing methods, exemplified by Pacific Biosciences and Oxford Nanopore technologies, offer much longer read lengths, which are crucial for accurate genome assembly and detecting complex structural variations (Dijk et al., 2018; Hu et al., 2021). Despite initial concerns about accuracy, recent advancements have significantly improved the precision of long-read sequencing (Hu et al., 2021). 2.2 Impact of high-throughput sequencing on tree genomic studies The introduction of high-throughput sequencing has had a profound impact on tree genomic studies. NGS technologies have enabled comprehensive genomic analyses of various tree species, facilitating the discovery of genetic variations, gene functions, and evolutionary relationships (Bansal et al., 2018; Satam et al., 2024). The ability to sequence entire genomes rapidly and cost-effectively has accelerated research in areas such as tree breeding, conservation genetics, and understanding tree responses to environmental changes (Sharma et al., 2018). High-throughput sequencing has also enhanced transcriptomic studies, allowing researchers to investigate gene expression patterns and regulatory mechanisms in trees. This has provided insights into complex traits such as growth, disease resistance, and adaptation to abiotic stresses (Satam et al., 2024). Moreover, the application of NGS in metagenomics has expanded our understanding of tree-microbe interactions, which are critical for tree health and productivity (Sharma et al., 2018). The integration of high-throughput sequencing data with advanced bioinformatics tools has further amplified the impact of these technologies. Sophisticated algorithms and computational pipelines have been developed to handle the vast amounts of data generated, enabling accurate assembly, annotation, and analysis of tree genomes (Bansal et al., 2018; Satam et al., 2024). 2.3 Future prospects: emerging technologies and their potential The future of tree genome sequencing looks promising with the continuous evolution of sequencing technologies. Emerging methodologies, such as single-molecule sequencing and nanopore-based approaches, are expected to overcome current limitations and provide even greater accuracy and efficiency (Anderson, 2018; Kumar et al.,
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