Reptiles exhibit a spectacular diversity of skin colors and patterns brought about by the interactions among three chromatophore types: black melanophores with melanin-packed melanosomes, red and yellow xanthophores with pteridine- and/or carotenoid-containing vesicles, and iridophores filled with light-reflecting platelets generating structural colors. Whereas the melanosome, the only color-producing endosome in mammals and birds, has been documented as a lysosome-related organelle, the maturation paths of xanthosomes and iridosomes are unknown. Here, we first use 10x Genomics linked-reads and optical mapping to assemble and annotate a nearly chromosome-quality genome of the corn snake Pantherophis guttatus. The assembly is 1.71 Gb long, with an N50 of 16.8 Mb and L50 of 24. Second, we perform mapping-by-sequencing analyses and identify a 3.9-Mb genomic interval where the lavender variant resides. The lavender color morph in corn snakes is characterized by gray, rather than red, blotches on a pink, instead of orange, background. Third, our sequencing analyses reveal a single nucleotide polymorphism introducing a premature stop codon in the lysosomal trafficking regulator gene (LYST) that shortens the corresponding protein by 603 amino acids and removes evolutionary-conserved domains. Fourth, we use light and transmission electron microscopy comparative analyses of wild type versus lavender corn snakes and show that the color-producing endosomes of all chromatophores are substantially affected in the LYST mutant. Our work provides evidence characterizing xanthosomes in xanthophores and iridosomes in iridophores as lysosome-related organelles.

爬行动物表现出由三种色素细胞类型之间的相互作用带来的惊人的肤色和图案多样性：黑色黑色素细胞与充满黑色素的黑素体，红色和黄色黄色细胞与含有蝶啶和/或类胡萝卜素的囊泡，以及充满光反射的虹彩细胞产生结构色的血小板。尽管黑素体是哺乳动物和鸟类中唯一产生颜色的内体，已被记录为溶酶体相关的细胞器，但黄质体和虹膜体的成熟路径尚不清楚。在这里，我们首先使用 10x Genomics 链接读取和光学图谱来组装和注释玉米蛇Pantherophis guttatus的近乎染色体质量的基因组。该装配体长 1.71 Gb，N50 为 16.8 Mb，L50 为 24。其次，我们进行测序作图分析并确定薰衣草变体所在的 3.9 Mb 基因组区间。玉米蛇的淡紫色颜色变形的特点是粉红色而不是橙色背景上有灰色而不是红色的斑点。第三，我们的测序分析揭示了单核苷酸多态性，在溶酶体运输调节基因（LYST）中引入了提前终止密码子，该密码子将相应的蛋白质缩短了 603 个氨基酸并去除了进化保守的结构域。第四，我们使用光学和透射电子显微镜对野生型玉米蛇与薰衣草玉米蛇进行比较分析，结果表明所有色素细胞的产色内体在LYST突变体中受到显着影响。我们的工作提供了将黄质细胞中的黄质体和虹彩细胞中的虹膜体表征为溶酶体相关细胞器的证据。