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[Preprint]. 2023 Nov 29:2023.10.30.564672. [Version 2] doi: 10.1101/2023.10.30.564672

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

Fig 4.

(A) Gene search of an alignment between two human assemblies in CGV finds twelve amylase gene family members in the human T2T-CHM113v2.0 assembly and six amylase gene family members in GRCh38.p14. (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 family members. A popup label (tooltip) indicates one of these additional family members.

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 align to chromosomes 2, 15, 23, and 25 of Dog10K_Boxer_Tasha.

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 assembly-assembly alignment.