A Step-by-Step Guide to Assemble a Reptilian Genome

Ullate-Agote, Asier; Chan, Yingguang Frank; Tzika, Athanasia C.

doi:10.1007/978-1-4939-7216-6_3

Cited by 1 publication

(2 citation statements)

References 27 publications

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“…The N50 is 16.8 Mb, with 50% of the genome found in only 24 sequences (L50). Hence, this approach produced an assembly that is considerably more complete and contiguous than the published corn snake draft genomes ( 27 , 40 ) ( SI Appendix , Table S1 ) and represents one of the best snake genomes published to date ( Table 1 ).…”

Section: Resultsmentioning

confidence: 99%

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

Ullate-Agote

Burgelin

Debry

et al. 2020

Proc. Natl. Acad. Sci. U.S.A.

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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.

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Section: Resultsmentioning

confidence: 99%

“…We also isolated megabase-long genomic DNA from the blood of the same individual for Bionano optical mapping ( 60 ) as explained in ref. 40 . The DNA was digested with the restriction enzyme BsPQI, fluorescently labeled on the cutting sites, and imaged on an Irys instrument at the VIB Nucleomics Core (Leuven, Belgium).…”

Section: Methodsmentioning

confidence: 99%