PMID- 33020272 OWN - NLM STAT- MEDLINE DCOM- 20210104 LR - 20231112 IS - 1091-6490 (Electronic) IS - 0027-8424 (Print) IS - 0027-8424 (Linking) VI - 117 IP - 42 DP - 2020 Oct 20 TI - Genome mapping of a LYST mutation in corn snakes indicates that vertebrate chromatophore vesicles are lysosome-related organelles. PG - 26307-26317 LID - 10.1073/pnas.2003724117 [doi] AB - 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. CI - Copyright (c) 2020 the Author(s). Published by PNAS. FAU - Ullate-Agote, Asier AU - Ullate-Agote A AUID- ORCID: 0000-0002-8595-7703 AD - Laboratory of Artificial & Natural Evolution (LANE), Department of Genetics & Evolution, University of Geneva, CH-1211 Geneva, Switzerland. AD - SIB Swiss Institute of Bioinformatics, Switzerland. AD - Institute of Genetics and Genomics of Geneva (iGE3), University of Geneva, Geneva, Switzerland. FAU - Burgelin, Ingrid AU - Burgelin I AD - Laboratory of Artificial & Natural Evolution (LANE), Department of Genetics & Evolution, University of Geneva, CH-1211 Geneva, Switzerland. FAU - Debry, Adrien AU - Debry A AD - Laboratory of Artificial & Natural Evolution (LANE), Department of Genetics & Evolution, University of Geneva, CH-1211 Geneva, Switzerland. FAU - Langrez, Carine AU - Langrez C AD - Laboratory of Artificial & Natural Evolution (LANE), Department of Genetics & Evolution, University of Geneva, CH-1211 Geneva, Switzerland. FAU - Montange, Florent AU - Montange F AD - Laboratory of Artificial & Natural Evolution (LANE), Department of Genetics & Evolution, University of Geneva, CH-1211 Geneva, Switzerland. FAU - Peraldi, Rodrigue AU - Peraldi R AUID- ORCID: 0000-0003-4803-9150 AD - Laboratory of Artificial & Natural Evolution (LANE), Department of Genetics & Evolution, University of Geneva, CH-1211 Geneva, Switzerland. FAU - Daraspe, Jean AU - Daraspe J AUID- ORCID: 0000-0001-8649-4563 AD - Faculte de Biologie et de Medecine, Electron Microscopy Facility, University of Lausanne, CH-1015 Lausanne, Switzerland. FAU - Kaessmann, Henrik AU - Kaessmann H AUID- ORCID: 0000-0001-7563-839X AD - DKFZ-ZMBH Alliance, Center for Molecular Biology of Heidelberg University (ZMBH), D-69120 Heidelberg, Germany. FAU - Milinkovitch, Michel C AU - Milinkovitch MC AUID- ORCID: 0000-0002-2553-0724 AD - Laboratory of Artificial & Natural Evolution (LANE), Department of Genetics & Evolution, University of Geneva, CH-1211 Geneva, Switzerland. AD - SIB Swiss Institute of Bioinformatics, Switzerland. AD - Institute of Genetics and Genomics of Geneva (iGE3), University of Geneva, Geneva, Switzerland. FAU - Tzika, Athanasia C AU - Tzika AC AUID- ORCID: 0000-0002-0831-5221 AD - Laboratory of Artificial & Natural Evolution (LANE), Department of Genetics & Evolution, University of Geneva, CH-1211 Geneva, Switzerland; athanasia.tzika@unige.ch. AD - SIB Swiss Institute of Bioinformatics, Switzerland. AD - Institute of Genetics and Genomics of Geneva (iGE3), University of Geneva, Geneva, Switzerland. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20201005 PL - United States TA - Proc Natl Acad Sci U S A JT - Proceedings of the National Academy of Sciences of the United States of America JID - 7505876 RN - 0 (Melanins) RN - 0 (Vesicular Transport Proteins) SB - IM MH - Animals MH - Biological Evolution MH - Chromatophores/metabolism MH - Chromosome Mapping MH - Color MH - Colubridae/*genetics/metabolism MH - Genome MH - Lysosomes/metabolism MH - Melanins/metabolism MH - Melanophores/metabolism MH - Melanosomes/metabolism MH - Mutation MH - Skin/metabolism MH - Skin Pigmentation/*genetics MH - Snakes/genetics MH - Vertebrates/metabolism MH - Vesicular Transport Proteins/*genetics/metabolism PMC - PMC7584913 OTO - NOTNLM OT - LYST OT - chromatophores OT - corn snake OT - lysosome-related organelles OT - pigmentation COIS- The authors declare no competing interest. EDAT- 2020/10/07 06:00 MHDA- 2021/01/05 06:00 PMCR- 2020/10/05 CRDT- 2020/10/06 05:26 PHST- 2020/10/07 06:00 [pubmed] PHST- 2021/01/05 06:00 [medline] PHST- 2020/10/06 05:26 [entrez] PHST- 2020/10/05 00:00 [pmc-release] AID - 2003724117 [pii] AID - 202003724 [pii] AID - 10.1073/pnas.2003724117 [doi] PST - ppublish SO - Proc Natl Acad Sci U S A. 2020 Oct 20;117(42):26307-26317. doi: 10.1073/pnas.2003724117. Epub 2020 Oct 5.