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Mutations in CCDC40 cause primary ciliary dyskinesia in humans. To evaluate the pathogenicity of variants in CCDC40 , we examined the genomic structure of this gene in Xenopus tropicalis , a diploid frog suitable as a model for genetic studies. We identified inconsistencies in the current ccdc40 gene model and discovered two distinct ccdc40 genes near the previously annotated locus. Surprisingly, Xenopus laevis , an allotetraploid species that typically has two homoeologs, contains only one homoeolog ( ccdc40.S ), making it a more suitable genetic model for studying ccdc40 function and potentially expediting the functional characterization of CCDC40 variants linked to primary ciliary dyskinesia.
Figure 1.
The genomic region of
Xenopus tropicalis ccdc40
genes
.
(A) A schematic representation of the
X. tropicalis
v.10.0 genome region on chromosome 10 (derived from Xenbase with their permission), spanning from 32,701,399 to 32,903,294, illustrates three gene models (each indicated by a square in blue, magenta, or gray) that contain published CRISPR target sequences for
ccdc40
. Note that all three genes are located on the minus strand. (B) A schematic comparison of
ccdc40
gene models (derived from Xenbase with their permission) among
X. tropicalis
LOC101731483 (24,053 bp; Chr10:32744235..32768287 [- strand]) (top),
X. tropicalis
LOC108648942 (24,872 bp; Chr10:32780961..32805832 [- strand]) (middle), and
X. laevis
ccdc40.S
(33,142 bp; Chr9_10S:21823636..21856777 [- strand]) (bottom). The orientation of genes is shown in the direction from 5' (left) to 3' (right) for convenience and is drawn to scale. (C) A schematic representation of the cDNAs for each gene within the squares shown in (A) is presented and drawn to scale. Thick black lines indicate the full length of predicted cDNAs, while ORFs are depicted in colored boxes that match the square colors in (A) to demonstrate the relationship between cDNAs and genes. The predicted cDNA (XM_031894196.1) of the "former"
ccdc40
gene lacks the 3'-UTR. Beneath each cDNA, schematic representations of positions and amplicon sizes for each primer set are shown: Pr1, 3, 5 for XM_031894196.1, and Pr2, 4, 6 for XM_031894493.1 and XM_031894494.1. (D) The representative gel image depicts the RT-PCR results. (E) A schematic comparison of the protein sequence of XP_031750353.1 (top), the protein sequence reconstructed from seven ESTs (middle), and the protein sequence of XP_031750354.1 (bottom). Protein sequences reconstructed from different ESTs are distinguished by different colors. The gray (from CX941984) and purple (from CX327554) regions contain amino acids 81 and 957, respectively, showing single amino acid change. Other protein regions are identical among the three sequences. The figures are drawn to scale. (F) The left panel displays the alignment of exon 3 from LOC101731483 and CX941984, while the right panel shows the alignment of exon 19 from LOC108648942 and CX327554. Yellow-highlighted portions indicate SNP locations. Only aligned sequences are shown for ESTs. The color code matches (E).
