Genome mapping of a LYST mutation in corn snakes indicates that vertebrate chromatophore vesicles are lysosome-related organelles

BUSCO results for the corn snake genome sequenced and assembled here as well as for four previously published squamate genomes. The genome completeness assessment was performed using the 3,950 single-copy genes of the Tetrapoda set.

Mapping the lavender variant. (A) Proportion (y axis) of quality-filtered SNP/MNP cosegregating with the lavender locus in the four genome libraries compared to informative quality-filtered parental variants (homozygous in the lavender/lavender father and heterozygous in the lavender/⁺ female). Proportions are calculated for scaffolds >1 Mb, with a 1-Mb sliding window and a step of 100 kb. Scaffolds (alternatingly colored black and red) are ordered from longest to shortest, and the two superscaffolds containing the lavender interval are indicated. A close-up of these superscaffolds is provided in SI Appendix, Fig. S7. (B) Number of biallelic variants (SNP/MNP and indels) in 500-kb intervals cosegregating with the lavender locus in superscaffolds 423 and 108 based on the family mapping. (C) Number of biallelic variants (SNP/MNP and indels) in 500-kb intervals cosegregating with the lavender locus in superscaffolds 423 and 108 based on the extended mapping. (B and C) Scaffolds are ordered and oriented based on their synteny to the G. gallus and A. carolinensis genomes. Dark green and dark red bins correspond to the 25.3-Mb region with the highest proportion of cosegregating variants in the family mapping. The length/position of the two intervals is shown with a thick line under each graph, and an arrow points to the position of LYST.

Wild type and lavender corn snake chromatophores of 1- and 3-year-old animals. In the wild type: (A and K) epidermal melanocytes, (B and L) dermal melanocytes with ellipsoidal mature melanosomes (a few are at earlier stages of maturation at 1 y old), (C and M) xanthophores with xanthosomes containing concentric lamellae (at 1 y old, some xanthosomes are at earlier stages of maturation and contain amorphous material), and (D and N) ventral and (E and O) dorsal iridophores carrying crystals of guanine. In the lavender: (F and P) epidermal melanosomes are larger than in the wild type and have irregular shapes; (G and Q) dermal melanosomes are larger and more irregularly shaped than in the wild type and mature more slowly, as several are not fully melanized after 1 y, and become bigger and irregularly shaped; (H and R) the amorphous material of the xanthosomes accumulates more slowly and forms irregularly shaped lamellae in the lavender instead of concentric ones as in the wild type; and (I and S) ventral and (J and T) dorsal guanine crystals in iridophores are more irregularly shaped and might accumulate in larger compartments than in the wild type. (Scale bars, 1 μm.)