Resolving previously unresolved regions to advance genetic improvement of domesticated animals: technological foundations, breakthroughs, research directions, and current challenges of T2T assemblies

The difficulty of assembling domesticated animals genomes is related to genome size, but it depends more critically on differences in repetitive sequence content, transposon load, and structural variant density. Owing to limitations in read length and to mapping ambiguity in repetitive regions, these regions and the structural variants within them have long been difficult to detect accurately with short-read sequencing, or they have resulted in assembly breaks and misjoins. Telomere to telomere (T2T) assembly, by constructing gapless complete chromosome sequences that run from telomere to telomere, has substantially improved the resolvability of such complex regions, and the coevolution of long-read sequencing and assembly algorithms is its technical prerequisite. This review outlines the core technological foundations of T2T assembly and summarizes the major breakthroughs of T2T: reshaping the resolution of chromosomal structures and the understanding of species evolution in domesticated animals, systematically uncovering structural variations, novel genes, and selection signals missed by traditional genomes, and providing in-depth resolution of population differentiation and gene flow patterns. It also explores the translational pathways, functional validation methods, and future application directions of the previously unresolved regions (PUR) revealed by T2T in breeding. Furthermore, this review objectively evaluates the current challenges and limitations of T2T technology in domesticated animal research and comprehensively outlines the bottlenecks in its practical application. It aims to provide a theoretical reference and technical support for the in-depth application of high-precision complete genome technology in the fields of domesticated animal evolution research, germplasm innovation, and molecular breeding.