chromosomescale

Chromosomescale is a term used in genomics to describe genome assemblies and related datasets that cover whole chromosomes. A chromosome-scale assembly comprises contiguous chromosome-length sequences in which most or all chromosomes are represented by a single scaffold or a small number of scaffolds, with few gaps. Such assemblies enable analysis at the level of chromosomal organization rather than merely at the level of individual contigs.

Achieving chromosome-scale assemblies typically combines multiple data types. Long-read sequencing technologies such as PacBio or Oxford Nanopore provide long stretches that span repetitive regions. Proximity ligation methods like Hi-C supply information to order and orient contigs into chromosome-scale scaffolds. Additional data such as optical maps and genetic linkage maps can validate and refine the assembly and help resolve haplotypes in heterozygous or polyploid genomes.

Common workflow involves de novo assembly from long reads, scaffolding with Hi-C, polishing, haplotype phasing, and manual curation to ensure chromosome integrity. The result is anchored sequences that correspond to whole chromosomes, improving gene models, structural variant detection, and comparative genomics.

Applications include plant and animal genomics, evolutionary studies, and breeding programs, where chromosome-scale references support accurate synteny analyses and chromosomal rearrangement detection. Challenges include highly repetitive and polyploid genomes, heterozygosity, and computational demands. Quality is evaluated with metrics such as anchored bases, chromosome anchoring rate, and assembly continuity at chromosome level, as well as gene completeness.

Numerous model organisms and crops now have chromosome-scale references, including human and other model species, and several crops such as rice and Arabidopsis. As sequencing and mapping technologies advance, chromosome-scale assemblies are increasingly used to construct pangenomes and to study genome architecture across populations.