Decoding the Genetic Code: Scientific Exploration of the Telomere-to-telomere (T2T) Genome

With the development of third-generation sequencing technology, genome assembly has entered a new era. The combination of multiple sequencing methods can combine the strengths of each, resulting in higher-quality assembly results. Telomere-to-Telomere (T2T) genome refers to a zero gap genome that is assembled at the T2T level of one or more chromosomes through the combination of multiple sequencing technologies, such as Pacific Biosciences High-Fidelity (PacBio HiFi), Oxford Nanopore Technologies (ONT) Ultra-long, High-throughput Chromosome Conformation Capture (Hi-C), and others. High-quality reference genomes are the basis for genomics research, and the T2T genome has enabled the exploration of unknown areas of the genome, such as telomeres and centromeres, which has provided a more in-depth direction for research. This review provides a comprehensive overview of the T2T genome, reviewing the development of sequencing technologies and then outlining sequencing strategies, assembly methods, quality assessment processes, and analysis software for the T2T genome with practical examples. Representative T2T genomic species of plants, animals, and microorganisms (e.g., human, Arabidopsis, brewer's yeast, and so on) are presented separately. A summary of the potential and challenges of current T2T genomic applications is provided, along with an outlook for future developments.