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Fig. 8 | Genome Biology

Fig. 8

From: False gene and chromosome losses in genome assemblies caused by GC content variation and repeats

Fig. 8

COQ6 is an example gene that is falsely missing due to sequence and assembly errors in a highly divergent GC-rich ortholog. a Proportions of sites supported by prior reads or assembly gaps in missing or existing regions in prior assemblies. Red and black colors indicate missing and existing regions, respectively. b BUSCO comparisons between prior and VGP genome assemblies of platypus and climbing perch originating from different assemblies but also different platypus individuals. Red color indicates the percentages of missing BUSCO genes in each genome. c Genomic features and prior read depths on the COQ6 gene and its neighbor genes. Prior reads were generated with the Sanger platform. Prior missing BUSCO gene, COQ6, marked as bold and asterisk with yellow highlight. d COQ6 was highly conserved in vertebrates except in the previous assembly of platypus. e Missing first exon and promoter of COQ6 in the prior assembly of platypus and several genome assemblies of birds. The GC-rich regions nearby the first exon were regarded as promoters, based on histone modification (H3K27Ac). Filled red arrows and red boxes indicate species with missing errors on the regions validated with data in the UCSC genome browser. Unfilled red arrows and red dashed boxes indicate species with candidates of missing and scaffolding errors. f–h Missing errors supported by assembly gaps on the 5′ GC-rich region of COQ6 in Illumina-based genome assemblies of saker falcon, white-throated sparrow, and turkey, respectively. Filled red arrows and red boxes indicate gaps near 5′ GC-rich regions

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