Transforming Life Science Through Chromosome‐Level Genome Assemblies

Abstract

ABSTRACT Advances in long‐read sequencing and Hi–C scaffolding have made chromosome‐level genome assembly increasingly accessible to individual laboratories, shifting genome research from large consortium‐led projects toward investigator‐driven studies across diverse taxa. This transition allows researchers to select organisms based on biological questions rather than the prior availability of genomic resources. In this review, we summarize the core experimental and computational steps for generating, evaluating, and annotating chromosome‐level assemblies, and examine how they have advanced research in non‐model organisms and genetically complex systems. Representative case studies illustrate four major contributions: resolving structural variation and lineage‐specific genome architecture, linking genome organization to phenotypic innovation and plasticity, reconstructing deep chromosome evolution and macrosynteny, and distinguishing homologous and homoeologous chromosomes in polyploid genomes. These examples show that chromosome‐level assemblies provide more than complete reference sequences. They establish a continuous genomic coordinate system through which genes, regulatory elements, transposable element insertions, sequence variants, and cellular states can be interpreted within broader chromosomal, population, and evolutionary contexts. We describe this integrative perspective as “glocal biology.” Future progress will require pangenomic, population‐scale, and haplotype‐resolved resources integrated with multi‐omics and functional analyses. Collectively, chromosome‐level genomics is reshaping life science by embedding molecular functions within chromosomal and evolutionary contexts.