1
|
Takagi T, Tsuda Y, Torii H, Tamate HB, Kaneko S, Nagata J. Development of paternally‐inherited Y chromosome simple sequence repeats of sika deer and their application in genetic structure, artificial introduction, and interspecific hybridization analyses. POPUL ECOL 2022. [DOI: 10.1002/1438-390x.12109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Toshihito Takagi
- Graduate School of Symbiotic Systems Science and Technology Fukushima University Kanayagawa Fukushima Japan
| | - Yoshiaki Tsuda
- Sugadaira Research Station, Mountain Science Center (MSC) University of Tsukuba Ueda Nagano Japan
| | - Harumi Torii
- Center for Natural Environment Education Nara University of Education Takahata‐cho Nara Japan
| | | | - Shingo Kaneko
- Faculty of Symbiotic Systems Science Fukushima University Kanayagawa Fukushima Japan
| | - Junco Nagata
- Forestry and Forest Products Research Institute (FFPRI) Tsukuba Ibaraki Japan
| |
Collapse
|
2
|
Krzeminska P, Nowacka-Woszuk J, Switonski M. Copy number variation of the SRY gene showed an association with disorders of sex development in Yorkshire Terrier dogs. Anim Genet 2021; 53:152-155. [PMID: 34664728 DOI: 10.1111/age.13147] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/04/2021] [Indexed: 11/29/2022]
Abstract
The molecular background of disorders of sex development (DSD) in dogs is poorly understood. Several copies of the SRY genes have been reported in the dog genome. We used droplet digital PCR with the aim of determining variability in SRY copy number and its association with DSD in dogs. Altogether 19 DSD male dogs (XY DSD) of 10 breeds and 87 control dogs of eight breeds were analyzed. Moreover, we performed a comparative analysis of SRY copy number in other canids: wolves (3), red foxes (16), and Chinese raccoon dogs (10). We found that the modal number of SRY copies in dogs, wolves, red foxes, and Chinese raccoon dogs was 3, 3, 1, and 3 respectively. Variability of copy number was only observed in Yorkshire Terriers (two or three copies) and red foxes (one or two copies). An analysis of six DSD Yorkshire Terriers and 38 control males of this breed showed that 50% of the DSD dogs had two copies, while the incidence of this variant was significantly lower in the control dogs (10.5%). Searching for the copy number of the coding and 5'-flanking fragments revealed full concordance with the copy number. These fragments were also sequenced in DSD (19) and control (24) dogs, and no DNA variants were found. We conclude that, in the dog, two or three functional copies of the SRY gene are present, and a smaller number of copies showed an association with the risk of DSD phenotype in Yorkshire Terriers.
Collapse
Affiliation(s)
- P Krzeminska
- Department of Genetics and Animal Breeding, Poznan University of Life Sciences, Wolynska 33, Poznan, 60-637, Poland
| | - J Nowacka-Woszuk
- Department of Genetics and Animal Breeding, Poznan University of Life Sciences, Wolynska 33, Poznan, 60-637, Poland
| | - M Switonski
- Department of Genetics and Animal Breeding, Poznan University of Life Sciences, Wolynska 33, Poznan, 60-637, Poland
| |
Collapse
|
3
|
An 8.22 Mb Assembly and Annotation of the Alpaca ( Vicugna pacos) Y Chromosome. Genes (Basel) 2021; 12:genes12010105. [PMID: 33467186 PMCID: PMC7830431 DOI: 10.3390/genes12010105] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 01/07/2021] [Accepted: 01/14/2021] [Indexed: 12/26/2022] Open
Abstract
The unique evolutionary dynamics and complex structure make the Y chromosome the most diverse and least understood region in the mammalian genome, despite its undisputable role in sex determination, development, and male fertility. Here we present the first contig-level annotated draft assembly for the alpaca (Vicugna pacos) Y chromosome based on hybrid assembly of short- and long-read sequence data of flow-sorted Y. The latter was also used for cDNA selection providing Y-enriched testis transcriptome for annotation. The final assembly of 8.22 Mb comprised 4.5 Mb of male specific Y (MSY) and 3.7 Mb of the pseudoautosomal region. In MSY, we annotated 15 X-degenerate genes and two novel transcripts, but no transposed sequences. Two MSY genes, HSFY and RBMY, are multicopy. The pseudoautosomal boundary is located between SHROOM2 and HSFY. Comparative analysis shows that the small and cytogenetically distinct alpaca Y shares most of MSY sequences with the larger dromedary and Bactrian camel Y chromosomes. Most of alpaca X-degenerate genes are also shared with other mammalian MSYs, though WWC3Y is Y-specific only in alpaca/camels and the horse. The partial alpaca Y assembly is a starting point for further expansion and will have applications in the study of camelid populations and male biology.
Collapse
|
4
|
Sacks BN, Lounsberry ZT, Rando HM, Kluepfel K, Fain SR, Brown SK, Kukekova AV. Sequencing Red Fox Y Chromosome Fragments to Develop Phylogenetically Informative SNP Markers and Glimpse Male-Specific Trans-Pacific Phylogeography. Genes (Basel) 2021; 12:genes12010097. [PMID: 33466657 PMCID: PMC7828831 DOI: 10.3390/genes12010097] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 01/01/2021] [Accepted: 01/11/2021] [Indexed: 11/28/2022] Open
Abstract
The red fox (Vulpes vulpes) has a wide global distribution with many ecotypes and has been bred in captivity for various traits, making it a useful evolutionary model system. The Y chromosome represents one of the most informative markers of phylogeography, yet it has not been well-studied in the red fox due to a lack of the necessary genomic resources. We used a target capture approach to sequence a portion of the red fox Y chromosome in a geographically diverse red fox sample, along with other canid species, to develop single nucleotide polymorphism (SNP) markers, 13 of which we validated for use in subsequent studies. Phylogenetic analyses of the Y chromosome sequences, including calibration to outgroups, confirmed previous estimates of the timing of two intercontinental exchanges of red foxes, the initial colonization of North America from Eurasia approximately half a million years ago and a subsequent continental exchange before the last Pleistocene glaciation (~100,000 years ago). However, in contrast to mtDNA, which showed unidirectional transfer from Eurasia to North America prior to the last glaciation, the Y chromosome appears to have been transferred from North America to Eurasia during this period. Additional sampling is needed to confirm this pattern and to further clarify red fox Y chromosome phylogeography.
Collapse
Affiliation(s)
- Benjamin N. Sacks
- Mammalian Ecology and Conservation Unit of the Veterinary Genetics Laboratory, University of California, Davis, CA 95616, USA; (Z.T.L.); (K.K.); (S.K.B.)
- Department of Population Health and Reproduction, University of California, Davis, CA 95616, USA
- Correspondence:
| | - Zachary T. Lounsberry
- Mammalian Ecology and Conservation Unit of the Veterinary Genetics Laboratory, University of California, Davis, CA 95616, USA; (Z.T.L.); (K.K.); (S.K.B.)
| | - Halie M. Rando
- Department of Animal Sciences, College of Agricultural, Consumer and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; (H.M.R.); (A.V.K.)
| | - Kristopher Kluepfel
- Mammalian Ecology and Conservation Unit of the Veterinary Genetics Laboratory, University of California, Davis, CA 95616, USA; (Z.T.L.); (K.K.); (S.K.B.)
| | - Steven R. Fain
- U. S. Fish & Wildlife Service, National Forensics Laboratory, Ashland, OR 97520, USA;
| | - Sarah K. Brown
- Mammalian Ecology and Conservation Unit of the Veterinary Genetics Laboratory, University of California, Davis, CA 95616, USA; (Z.T.L.); (K.K.); (S.K.B.)
| | - Anna V. Kukekova
- Department of Animal Sciences, College of Agricultural, Consumer and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; (H.M.R.); (A.V.K.)
| |
Collapse
|
5
|
Martínez-Pacheco M, Tenorio M, Almonte L, Fajardo V, Godínez A, Fernández D, Cornejo-Páramo P, Díaz-Barba K, Halbert J, Liechti A, Székely T, Urrutia AO, Cortez D. Expression Evolution of Ancestral XY Gametologs across All Major Groups of Placental Mammals. Genome Biol Evol 2020; 12:2015-2028. [PMID: 32790864 PMCID: PMC7674692 DOI: 10.1093/gbe/evaa173] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/10/2020] [Indexed: 12/14/2022] Open
Abstract
Placental mammals present 180 million-year-old Y chromosomes that have retained a handful of dosage-sensitive genes. However, the expression evolution of Y-linked genes across placental groups has remained largely unexplored. Here, we expanded the number of Y gametolog sequences by analyzing ten additional species from previously unexplored groups. We detected seven remarkably conserved genes across 25 placental species with known Y repertoires. We then used RNA-seq data from 17 placental mammals to unveil the expression evolution of XY gametologs. We found that Y gametologs followed, on average, a 3-fold expression loss and that X gametologs also experienced some expression reduction, particularly in primates. Y gametologs gained testis specificity through an accelerated expression decay in somatic tissues. Moreover, despite the substantial expression decay of Y genes, the combined expression of XY gametologs in males is higher than that of both X gametologs in females. Finally, our work describes several features of the Y chromosome in the last common mammalian ancestor.
Collapse
Affiliation(s)
| | | | - Laura Almonte
- Center for Genome Sciences, UNAM, Cuernavaca, Mexico
| | | | - Alan Godínez
- Center for Genome Sciences, UNAM, Cuernavaca, Mexico
| | | | | | | | - Jean Halbert
- Center for Integrative Genomics, University of Lausanne, Switzerland
| | - Angelica Liechti
- Center for Integrative Genomics, University of Lausanne, Switzerland
| | - Tamas Székely
- Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, United Kingdom
| | - Araxi O Urrutia
- Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, United Kingdom.,Ecology Institute, UNAM, Mexico
| | - Diego Cortez
- Center for Genome Sciences, UNAM, Cuernavaca, Mexico
| |
Collapse
|