chromosomallevel

Chromosomallevel, usually written as chromosome-level or chromosomal level, refers to analyses, data, or resources that pertain to whole chromosomes rather than smaller units such as individual genes or local regions. The term is common in genome assembly and comparative genomics, and is sometimes used more broadly to describe chromosome-scale patterns of variation or expression.

In genomics, a chromosome-level genome assembly is one in which assembled sequences are organized into complete chromosomes, with contigs ordered and oriented. Such assemblies provide a more contiguous representation than scaffold-level assemblies and improve the accuracy of gene models and structural variation.

Generating chromosome-level assemblies combines long-read sequencing, Hi-C chromatin conformation data, optical mapping, and genetic or radiation hybrid maps to place sequences onto chromosomes.

Applications include comparative genomics across species, detection of rearrangements, mapping disease-associated regions to specific chromosomes, and informing breeding programs in plants with chromosome-level reference genomes.

Challenges include highly repetitive regions, centromeres, and polyploid genomes; inaccuracies can arise in scaffolding and phasing. The term's exact usage varies by field, but chromosome-level resources are increasingly common in plant and animal genomics, and are expected to expand as sequencing technologies advance.

See also: chromosome-scale assembly, Hi-C, karyotype.