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Brown AR, Comai K, Mannino D, McCullough H, Donekal Y, Meyers HC, Graves CW, Seidel HS. A community-science approach identifies genetic variants associated with three color morphs in ball pythons (Python regius). PLoS One 2022; 17:e0276376. [PMID: 36260636 PMCID: PMC9581371 DOI: 10.1371/journal.pone.0276376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 10/05/2022] [Indexed: 11/13/2022] Open
Abstract
Color morphs in ball pythons (Python regius) provide a unique and largely untapped resource for understanding the genetics of coloration in reptiles. Here we use a community-science approach to investigate the genetics of three color morphs affecting production of the pigment melanin. These morphs-Albino, Lavender Albino, and Ultramel-show a loss of melanin in the skin and eyes, ranging from severe (Albino) to moderate (Lavender Albino) to mild (Ultramel). To identify genetic variants causing each morph, we recruited shed skins of pet ball pythons via social media, extracted DNA from the skins, and searched for putative loss-of-function variants in homologs of genes controlling melanin production in other vertebrates. We report that the Albino morph is associated with missense and non-coding variants in the gene TYR. The Lavender Albino morph is associated with a deletion in the gene OCA2. The Ultramel morph is associated with a missense variant and a putative deletion in the gene TYRP1. Our study is one of the first to identify genetic variants associated with color morphs in ball pythons and shows that pet samples recruited from the community can provide a resource for genetic studies in this species.
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Affiliation(s)
- Autumn R. Brown
- Department of Biology, Eastern Michigan University, Ypsilanti, MI, United States of America
| | - Kaylee Comai
- Department of Biology, Eastern Michigan University, Ypsilanti, MI, United States of America
| | - Dominic Mannino
- Department of Biology, Eastern Michigan University, Ypsilanti, MI, United States of America
| | - Haily McCullough
- Department of Biology, Eastern Michigan University, Ypsilanti, MI, United States of America
| | - Yamini Donekal
- Department of Biology, Eastern Michigan University, Ypsilanti, MI, United States of America
| | - Hunter C. Meyers
- Department of Biology, Eastern Michigan University, Ypsilanti, MI, United States of America
| | - Chiron W. Graves
- Department of Biology, Eastern Michigan University, Ypsilanti, MI, United States of America
- * E-mail: (CWG); (HSS)
| | - Hannah S. Seidel
- Department of Biology, Eastern Michigan University, Ypsilanti, MI, United States of America
- * E-mail: (CWG); (HSS)
| | - The BIO306W Consortium
- Department of Biology, Eastern Michigan University, Ypsilanti, MI, United States of America
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2
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Hayashi S, Honda Y, Kanesaki E, Koga A. Marsupial satellite DNA as faithful reflections of long terminal repeat (LTR) retroelement structure. Genome 2022; 65:469-478. [PMID: 35930809 DOI: 10.1139/gen-2022-0039] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Long terminal repeat (LTR) retroelements, including endogenous retroviruses, are one of the origins of satellite DNAs. However, the vast majority of satellite DNAs originating from LTR retroelements consist of parts of the element. In addition, they frequently contain sequences unrelated to that element. Here we report a novel marsupial satellite DNA (named walbRep) that contains, and consists solely of, the entire sequence of an LTR retroelement (the walb element). As is common with LTR retroelements, walb copies exhibit length variation. We focused on the abundance of copies of a specific length (2.7 kb) in the genome of the red-necked wallaby. Cloning and analyses of long genomic DNA fragments revealed a satellite DNA in which the LTR sequence (0.4 kb) and the sequence of the internal region of a nonautonomous walb copy (2.3 kb) were repeated alternately. The junctions between these two components exhibited the same end-to-end arrangements as those in the walb element. This satellite organization could be accounted for by a simple formation model that includes slippage during chromosome pairing followed by homologous recombination but does not invoke any other types of rearrangements. We discuss the possible reasons why satellite DNAs having such structures are rarely found in mammals.
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Affiliation(s)
| | - Yusuke Honda
- Noichi Zoological Park of Kochi Prefecture, Konan, Japan;
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Hayashi S, Shimizu K, Honda Y, Katsura Y, Koga A. An endogenous retrovirus presumed to have been endogenized or relocated recently in a marsupial, the red-necked wallaby. Genome 2022; 65:277-286. [PMID: 35030050 DOI: 10.1139/gen-2021-0047] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
An albino infant wallaby was born to a mother with the wild-type body color. PCR and sequencing analyses of TYR (encoding tyrosinase, which is essential for melanin biosynthesis) of this albino wallaby revealed a 7.1-kb-long DNA fragment inserted in the first exon. Because the fragment carried long terminal repeats, we assumed it to be a copy of an endogenous retrovirus, which we named walb. We cloned other walb copies residing in the genomes of this species and another wallaby species. The copies exhibited length variation, and the longest copy (>8.0 kb) contained open reading frames whose deduced amino acid sequences were well aligned with those of gag, pol, and env of retroviruses. It is not known through which of the following likely processes the walb copy was inserted into TYR: endogenization (infection of a germline cell by an exogenous virus), reinfection (infection by a virus produced from a previously endogenized provirus), or retrotransposition (intracellular relocation of a provirus). In any case, the insertion into TYR is considered to have been a recent event on an evolutionary timescale because albino mutant alleles generally do not persist for long because of their deleterious effects in wild circumstances. .
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Affiliation(s)
- Sakura Hayashi
- Kyoto University, 12918, Primate Research Institute, Inuyama cITY, Japan;
| | - Konami Shimizu
- Noichi Zoological Park of Kochi Prefecture, Konan City, Japan;
| | - Yusuke Honda
- Noichi Zoological Park of Kochi Prefecture, Kinan City, Japan;
| | - Yukako Katsura
- Kyoto University, Primate Research Institute, Inuyama City, Japan;
| | - Akihiko Koga
- Kyoto University, 12918, Primate Research Institute, Inuyama City, Japan;
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Brancalion L, Haase B, Wade CM. Canine coat pigmentation genetics: a review. Anim Genet 2021; 53:3-34. [PMID: 34751460 DOI: 10.1111/age.13154] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 09/21/2021] [Accepted: 10/20/2021] [Indexed: 11/27/2022]
Abstract
Our understanding of canine coat colour genetics and the associated health implications is developing rapidly. To date, there are 15 genes with known roles in canine coat colour phenotypes. Many coat phenotypes result from complex and/or epistatic genetic interactions among variants within and between loci, some of which remain unidentified. Some genes involved in canine pigmentation have been linked to aural, visual and neurological impairments. Consequently, coat pigmentation in the domestic dog retains considerable ethical and economic interest. In this paper we discuss coat colour phenotypes in the domestic dog, the genes and variants responsible for these phenotypes and any proven coat colour-associated health effects.
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Affiliation(s)
- L Brancalion
- Faculty of Science, School of Life and Environmental Sciences, University of Sydney, Camperdown, NSW, 2006, Australia
| | - B Haase
- Faculty of Science, School of Veterinary Science, University of Sydney, Camperdown, NSW, 2006, Australia
| | - C M Wade
- Faculty of Science, School of Life and Environmental Sciences, University of Sydney, Camperdown, NSW, 2006, Australia
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Hayashi S, Tsukiyama T, Iida A, Kinoshita M, Koga A. The medaka fish Tol2 transposable element is in an early stage of decay: identification of a nonautonomous copy. Genome 2021; 65:183-187. [PMID: 34529924 DOI: 10.1139/gen-2021-0010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The majority of DNA-based transposable elements comprise autonomous and nonautonomous copies, or only nonautonomous copies, where the autonomous copy contains an intact gene for a transposase protein and the nonautonomous copy does not. Even if autonomous copies coexist, they are generally less frequent. The Tol2 element of medaka fish is one of the few elements for which a nonautonomous copy has not yet been found. Here we report the presence of a nonautonomous Tol2 copy that was identified by surveying the medaka genome sequence database. This copy contained 3 local sequence alterations that affected the deduced amino acid sequence of the transposase: a deletion of 15 nucleotides resulting in a deletion of 5 amino acids, a base substitution causing a single amino acid change, and another base substitution giving rise to a stop codon. Transposition assays using cultured human cells revealed that the transposase activity was reduced by the 15-nucleotide deletion and abolished by the nonsense mutation. This is the first example of a nonautonomous Tol2 copy. Thus, Tol2 is in an early stage of decay in the medaka genome, and is therefore a unique element to observe an almost whole decay process that progresses in natural populations.
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Affiliation(s)
- Sakura Hayashi
- Kyoto University, 12918, Primate Research Institute, Inuyama, Japan;
| | | | - Atsuo Iida
- Nagoya University, 12965, Graduate School of Bioagricultural Sciences, Nagoya, Japan;
| | - Masato Kinoshita
- Kyoto University, 12918, Graduate School of Agriculture, Kyoto, Japan;
| | - Akihiko Koga
- Kyoto University, 12918, Primate Research Institute, Inuyama, Japan;
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Bychkova E, Viktorovskaya O, Filippova E, Eliseeva Z, Barabanova L, Sotskaya M, Markov A. Identification of a candidate genetic variant for the Himalayan color pattern in dogs. Gene 2020; 769:145212. [PMID: 33039541 DOI: 10.1016/j.gene.2020.145212] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 09/11/2020] [Accepted: 10/02/2020] [Indexed: 12/14/2022]
Abstract
Acromelanism is a temperature-dependent hypopigmentation pattern commonly manifested as the Himalayan coat color found in rabbits, rats, mice, minks, and gerbils, wherein the extreme "points" are dark and the torso is pale. It is known as the Siamese pattern in cats. Himalayan color is genetically determined by the allelic variant ch of the locus C, later identified as the tyrosinase gene TYR. The tyrosinase functions at the initial steps of melanin production, and alteration of its activity by sequence changes results in pigmentation defects in vertebrates. The presence of acromelanism in dogs has not been described until now. We analyzed a DNA sample of a dachshund with a unique coat color resembling the Himalayan type. Sequencing of the coding part of the TYR gene from the proband revealed a homozygous variant (c.230G > A) in exon 1, leading to an amino acid substitution (p.R77Q) in a conserved region of the protein. The proband's mother, which is black-and-tan, is a heterozygous carrier of the c.230A allele, while none of the 210 dogs of different breeds, unrelated to the proband, carried the c.230A allele. These results suggest that the identified sequence variant is likely the cause of the Himalayan coloration of the proband.
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Affiliation(s)
- Elina Bychkova
- Center of Veterinary Genetics ZOOGEN, Saint Petersburg 194156, Russia; Animal Genetics Laboratory, Department of Genetics and Biotechnology, Faculty of Biology, Saint Petersburg State University, Saint Petersburg 199034, Russia.
| | | | | | - Zhanna Eliseeva
- Animal Genetics Laboratory, Department of Genetics and Biotechnology, Faculty of Biology, Saint Petersburg State University, Saint Petersburg 199034, Russia
| | - Larisa Barabanova
- Animal Genetics Laboratory, Department of Genetics and Biotechnology, Faculty of Biology, Saint Petersburg State University, Saint Petersburg 199034, Russia
| | - Maria Sotskaya
- Moscow State University of Psychology and Education, Moscow 127051, Russia
| | - Anton Markov
- Center of Veterinary Genetics ZOOGEN, Saint Petersburg 194156, Russia
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Mae Y, Nagara K, Miyazaki M, Katsura Y, Enomoto Y, Koga A. Complex intragene deletion leads to oculocutaneous albinism in tanuki (Japanese raccoon dog). Genome 2020; 63:517-523. [PMID: 32783776 DOI: 10.1139/gen-2020-0049] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Tanuki (Nyctereutes procyonoides viverrinus), or Japanese raccoon dog, is a canine native to Japan. Tanuki with complete oculocutaneous albinism are relatively frequent in mountainous areas of mainland Japan. Tyrosinase, which is encoded by the TYR gene, is an enzyme essential for the biosynthesis of melanin pigment. We examined the structure and nucleotide sequence of TYR in an albino tanuki and found that the third exon was removed due to a deletion of approximately 11 kb. In addition, two nonsynonymous nucleotide substitutions were found in the fifth exon. These mutations are possible causes of the albino phenotype; however, the order of occurrence is unclear. Even if the 11-kb deletion was not the first of these mutations, it is considered to cause a total loss of the tyrosinase function because the third exon carries codons for one of the two copper-binding sites of tyrosinase and these sites are essential for the enzyme function. Intriguingly, the deletion was not a simple removal of an 11-kb segment: an internal portion was retained as a segment in the reverse orientation. We propose possible formation processes for this mutation that involve multiple DNA scission events, or an inversion followed by a deletion.
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Affiliation(s)
- Yuji Mae
- Iida City Zoo, Iida, Nagano 395-0046, Japan
| | | | - Manabu Miyazaki
- Manabu Miyazaki Photography Office, Iijima, Nagano 399-3705, Japan
| | - Yukako Katsura
- Primate Research Institute, Kyoto University, Inuyama, Aichi 484-8506, Japan
| | - Yuki Enomoto
- Primate Research Institute, Kyoto University, Inuyama, Aichi 484-8506, Japan
| | - Akihiko Koga
- Primate Research Institute, Kyoto University, Inuyama, Aichi 484-8506, Japan
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