Skip to main content
. 2024 May 7;22(5):e3002405. doi: 10.1371/journal.pbio.3002405

Fig 4. CGV can help uncover gene duplications and rearrangements in closely related genomes.

Fig 4

(A) Gene search of a T2T/HPRC-generated alignment between 2 human assemblies in CGV finds an alpha-amylase gene cluster on chromosome 1 containing 10 copies in the T2T-CHM113v2.0 assembly and 4 copies in the GRCh38.p14 assembly. (B) CGV view showing that T2T-CHM13v2.0 contains an insertion relative to GRCh38.p14, which appears as an unaligned region on chromosome 1. This insertion contains additional alpha-amylase gene copies. An information panel (tooltip) indicates one of these additional family members. These tooltips appear when the user hovers their cursor over the gene annotation or gene label. The view can be recreated at https://www.ncbi.nlm.nih.gov/genome/cgv/browse/GCF_009914755.1/GCF_000001405.40/23025/9606#NC_060925.1:103415704-103764412/NC_000001.11:103566852-103915505/size=1000,firstpass=0. (C) CGV view showing that chromosome 2 of Canis lupus familiaris (dog) UMICH_Zoey_3.1 aligns to chromosomes 2, 15, 23, and 25 of Dog10K_Boxer_Tasha. The view can be recreated at https://ncbi.nlm.nih.gov/genome/cgv/browse/GCF_005444595.1/GCF_000002285.5/17685/9615#NC_049262.1:6542815-78714085//size=10000. (D) UMICH_Zoey_3.1 assembly chromosome 2 alignment to Dog10K_Boxer_Tasha chromosome 25 contains the MALRD1 gene, which is annotated as LOC608668 in the Tasha assembly (boxed in red). Gene synteny is not conserved outside of the region of this gene. Webpage source: National Library of Medicine. CGV, Comparative Genome Viewer.