Chromosome visualization tool: a whole genome viewer

Abstract

CViT (chromosome visualization tool) is a Perl utility for quickly generating images of features on a whole genome at once. It reads GFF3-formated data representing chromosomes (linkage groups or pseudomolecules) and sets of features on those chromosomes. It can display features on any chromosomal unit system, including genetic (centimorgan), cytological (centiMcClintock), and DNA unit (base-pair) coordinates. CViT has been used to track sequencing progress (status of genome sequencing, location and number of gaps), to visualize BLAST hits on a whole genome view, to associate maps with one another, to locate regions of repeat densities to display syntenic regions, and to visualize centromeres and knobs on chromosomes.

Figure 1

Duplicated segments within the soybean (Glycine max) genome. Colored blocks to the left of each chromosome show regions of correspondence with chromosomes of the same color. For example, the light blue blocks at the top of Gm09 correspond with regions on the light blue Gm15, and vice versa. These correspondences are remnants after the Glycine genome duplication. Locations of centromeric repeats are shown as black rectangles over the chromosomes. Regions lacking internal correspondences (generally near chromosome centers) mark the approximate locations of the gene-poor pericentromeres. This figure is modified from the Legume Information System, where sequence-based searches can be made against the Glycine max, Medicago truncatula, and Lotus japonicus genomes, with CViT images displaying the sequence homologies and the synteny relationships among these genomes.

Figure 2

Gene density on the 10 chromosomes of Zea mays. Gene density is shown on the Zea mays inbred line B73 RefGen_v2 genome assembly [17]. Probable locations of the centromeres are displayed as black bars positioned over the chromosomes [18]. The density of the filtered gene set gene calls is displayed as green bars to the right of the chromosomes, with bar length indicating the number of genes per 400 kbp.