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Proskuryakova AA, Ivanova ES, Makunin AI, Larkin DM, Ferguson-Smith MA, Yang F, Uphyrkina OV, Perelman PL, Graphodatsky AS. Comparative studies of X chromosomes in Cervidae family. Sci Rep 2023; 13:11992. [PMID: 37491593 PMCID: PMC10368622 DOI: 10.1038/s41598-023-39088-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Accepted: 07/20/2023] [Indexed: 07/27/2023] Open
Abstract
The family Cervidae is the second most diverse in the infraorder Pecora and is characterized by variability in the diploid chromosome numbers among species. X chromosomes in Cervidae evolved through complex chromosomal rearrangements of conserved segments within the chromosome, changes in centromere position, heterochromatic variation, and X-autosomal translocations. The family Cervidae consists of two subfamilies: Cervinae and Capreolinae. Here we build a detailed X chromosome map with 29 cattle bacterial artificial chromosomes of representatives of both subfamilies: reindeer (Rangifer tarandus), gray brocket deer (Mazama gouazoubira), Chinese water deer (Hydropotes inermis) (Capreolinae); black muntjac (Muntiacus crinifrons), tufted deer (Elaphodus cephalophus), sika deer (Cervus nippon) and red deer (Cervus elaphus) (Cervinae). To track chromosomal rearrangements during Cervidae evolution, we summarized new data, and compared them with available X chromosomal maps and chromosome level assemblies of other species. We demonstrate the types of rearrangements that may have underlined the variability of Cervidae X chromosomes. We detected two types of cervine X chromosome-acrocentric and submetacentric. The acrocentric type is found in three independent deer lineages (subfamily Cervinae and in two Capreolinae tribes-Odocoileini and Capreolini). We show that chromosomal rearrangements on the X-chromosome in Cervidae occur at a higher frequency than in the entire Ruminantia lineage: the rate of rearrangements is 2 per 10 million years.
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Affiliation(s)
- Anastasia A Proskuryakova
- Institute of Molecular and Cellular Biology, SB RAS, Lavrentiev Ave 8/2, Novosibirsk, Russia, 630090.
| | - Ekaterina S Ivanova
- Institute of Molecular and Cellular Biology, SB RAS, Lavrentiev Ave 8/2, Novosibirsk, Russia, 630090
- Novosibirsk State University, Pirogova Str. 1, Novosibirsk, Russia, 630090
| | - Alexey I Makunin
- Institute of Molecular and Cellular Biology, SB RAS, Lavrentiev Ave 8/2, Novosibirsk, Russia, 630090
| | - Denis M Larkin
- The Royal Veterinary College, Royal College Street, University of London, London, NW1 0TU, UK
| | - Malcolm A Ferguson-Smith
- Department of Veterinary Medicine, Cambridge Resource Center for Comparative Genomics, University of Cambridge, Cambridge, UK
| | - Fengtang Yang
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo, China
| | - Olga V Uphyrkina
- Federal Research Center for Biodiversity of the Terrestrial Biota of East Asia, Vladivostok, Russia
| | - Polina L Perelman
- Institute of Molecular and Cellular Biology, SB RAS, Lavrentiev Ave 8/2, Novosibirsk, Russia, 630090
| | - Alexander S Graphodatsky
- Institute of Molecular and Cellular Biology, SB RAS, Lavrentiev Ave 8/2, Novosibirsk, Russia, 630090
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Han R, Han L, Zhao X, Wang Q, Xia Y, Li H. Haplotype-resolved Genome of Sika Deer Reveals Allele-specific Gene Expression and Chromosome Evolution. GENOMICS, PROTEOMICS & BIOINFORMATICS 2023; 21:470-482. [PMID: 36395998 PMCID: PMC10787017 DOI: 10.1016/j.gpb.2022.11.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 10/24/2022] [Accepted: 11/07/2022] [Indexed: 11/16/2022]
Abstract
Despite the scientific and medicinal importance of diploid sika deer (Cervus nippon), its genome resources are limited and haplotype-resolved chromosome-scale assembly is urgently needed. To explore mechanisms underlying the expression patterns of the allele-specific genes in antlers and the chromosome evolution in Cervidae, we report, for the first time, a high-quality haplotype-resolved chromosome-scale genome of sika deer by integrating multiple sequencing strategies, which was anchored to 32 homologous groups with a pair of sex chromosomes (XY). Several expanded genes (RET, PPP2R1A, PPP2R1B, YWHAB, YWHAZ, and RPS6) and positively selected genes (eIF4E, Wnt8A, Wnt9B, BMP4, and TP53) were identified, which could contribute to rapid antler growth without carcinogenesis. A comprehensive and systematic genome-wide analysis of allele expression patterns revealed that most alleles were functionally equivalent in regulating rapid antler growth and inhibiting oncogenesis. Comparative genomic analysis revealed that chromosome fission might occur during the divergence of sika deer and red deer (Cervus elaphus), and the olfactory sensation of sika deer might be more powerful than that of red deer. Obvious inversion regions containing olfactory receptor genes were also identified, which arose since the divergence. In conclusion, the high-quality allele-aware reference genome provides valuable resources for further illustration of the unique biological characteristics of antler, chromosome evolution, and multi-omics research of cervid animals.
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Affiliation(s)
- Ruobing Han
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China
| | - Lei Han
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China
| | - Xunwu Zhao
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China
| | - Qianghui Wang
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China
| | - Yanling Xia
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China
| | - Heping Li
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China.
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Karimi K, Do DN, Wang J, Easley J, Borzouie S, Sargolzaei M, Plastow G, Wang Z, Miar Y. A chromosome-level genome assembly reveals genomic characteristics of the American mink (Neogale vison). Commun Biol 2022; 5:1381. [PMID: 36526733 PMCID: PMC9757699 DOI: 10.1038/s42003-022-04341-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 12/05/2022] [Indexed: 12/23/2022] Open
Abstract
Availability of a contiguous chromosome-level genome assembly is the foundational step to develop genome-based studies in American mink (Neogale vison). The main objective of this study was to provide a high quality chromosome-level genome assembly for American mink. An initial draft of the genome assembly was generated using 2,884,047 PacBio long reads. Integration of Hi-C data into the initial draft led to an assembly with 183 scaffolds and scaffold N50 of 220 Mb. This gap-free genome assembly of American mink (ASM_NN_V1) had a length of 2.68 Gb in which about 98.6% of the whole genome was covered by 15 chromosomes. In total, 25,377 genes were predicted across the American mink genome using the NCBI Eukaryotic Genome Annotation Pipeline. In addition, gene orthology, demographic history, synteny blocks, and phylogenetic relationships were studied in connection with the genomes of other related Carnivora. Furthermore, population-based statistics of 100 sequenced mink were presented using the newly assembled genome. Remarkable improvements were observed in genome contiguity, the number of scaffolds, and annotation compared to the first draft of mink genome assembly (NNQGG.v01). This high-quality genome assembly will support the development of efficient breeding strategies as well as conservation programs for American mink.
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Affiliation(s)
- Karim Karimi
- grid.55602.340000 0004 1936 8200Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS Canada
| | - Duy Ngoc Do
- grid.55602.340000 0004 1936 8200Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS Canada
| | - Jingy Wang
- grid.55602.340000 0004 1936 8200Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS Canada
| | - John Easley
- Joint Mink Research Committee, Fur Commission USA, Preston, ID USA ,Mink Veterinary Consulting and Research Service, Plymouth, WI USA
| | - Shima Borzouie
- grid.55602.340000 0004 1936 8200Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS Canada
| | - Mehdi Sargolzaei
- grid.34429.380000 0004 1936 8198Department of Pathobiology, University of Guelph, Guelph, ON Canada ,Select Sires Inc., Plain City, OH USA
| | - Graham Plastow
- grid.17089.370000 0001 2190 316XLivestock Gentec, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB Canada
| | - Zhiquan Wang
- grid.17089.370000 0001 2190 316XLivestock Gentec, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB Canada
| | - Younes Miar
- grid.55602.340000 0004 1936 8200Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS Canada
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Tang L, Wen X, Zhang R, Xing X. Current Situation and Utilization of Velvet Deer Germplasm Resources in China. Animals (Basel) 2022; 12:ani12243529. [PMID: 36552448 PMCID: PMC9774729 DOI: 10.3390/ani12243529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 12/07/2022] [Accepted: 12/12/2022] [Indexed: 12/15/2022] Open
Abstract
Velvet deer are not only a representative special economic animal but also an important part of livestock. With the increasing awareness of international competition for germplasm resources in China, more and more attention has been paid to the protection and utilization of germplasm resources. However, there is poor understanding about velvet deer resources. Therefore, we are providing a comprehensive introduction of Chinese velvet deer germplasm resources from the aspects of ecological distribution, domestication and breeding.
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Affiliation(s)
- Lixin Tang
- State Key Laboratory for Molecular Biology of Special Economic Animals, Institute of Special Animal and Plant Sciences of Chinese Academy of Agricultural Sciences, Changchun 130112, China
| | - Xiaobin Wen
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Ranran Zhang
- State Key Laboratory for Molecular Biology of Special Economic Animals, Institute of Special Animal and Plant Sciences of Chinese Academy of Agricultural Sciences, Changchun 130112, China
| | - Xiumei Xing
- State Key Laboratory for Molecular Biology of Special Economic Animals, Institute of Special Animal and Plant Sciences of Chinese Academy of Agricultural Sciences, Changchun 130112, China
- Correspondence:
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Guo Q, Zheng J, Ba H, Sun H, Zhai J, Wang W, Li C. Calreticulin Identified as One of the Androgen Response Genes That Trigger Full Regeneration of the Only Capable Mammalian Organ, the Deer Antler. Front Cell Dev Biol 2022; 10:862841. [PMID: 35769266 PMCID: PMC9235033 DOI: 10.3389/fcell.2022.862841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 04/22/2022] [Indexed: 11/13/2022] Open
Abstract
Deer antlers are male secondary sexual characters that develop to become bone; they are unique appendages that, once lost, can fully regenerate from the permanent bony protuberances or pedicles. Pedicle periosteum (PP) is the tissue that gives rise to the regenerating antlers with three differentiation stages, namely, dormant (DoPP), potentiated (PoPP), and activated (AcPP). Thus far, the transition from the PoPP to the AcPP has not been studied. Our results showed that the AcPP cells maintained their original stem cell features by expressing mesenchymal stem cell (MSC) markers CD73, CD90, and CD105, although they had entered the proliferation mode. The differentially expressed genes (DEGs) in the AcPP compared with those of the PoPP were mainly involved in protein processing, cell cycle, and calcium signaling pathways. Calreticulin (CALR), an androgen response gene, was significantly differentially upregulated in the AcPP cells, and its expression level was negatively regulated by androgens, in contrast to the currently known model systems where all regulation is positive. The downregulation of CALR expression in the AcPP cells in vitro inhibited cell proliferation, induced apoptosis, and inhibited cell cycle progression at G1-S transition. Therefore, CALR is likely a downstream mediator of androgen hormones for triggering initiation of antler regeneration. We believe that the identification of CALR has not only discovered “one critical piece” of the “jigsaw puzzle” in the initiation of antler regeneration but also helps in revealing the mechanism underlying this unique mammalian epimorphic regeneration and has also opened a new avenue for the study of the nature of CALR regulation by androgen (putative binding partners), thus facilitating the identification of potential molecule(s) for investigation as targets for clinical evaluation.
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Affiliation(s)
- Qianqian Guo
- Institute of Antler Science and Product Technology, Changchun Sci-Tech University, Jilin, China
- Institute of Special Economic Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Jilin, China
| | - Junjun Zheng
- Institute of Special Economic Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Jilin, China
| | - Hengxing Ba
- Institute of Antler Science and Product Technology, Changchun Sci-Tech University, Jilin, China
| | - Hongmei Sun
- Institute of Special Economic Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Jilin, China
| | - Jingjie Zhai
- Department of Oral Implantology, Jilin Provincial Key Laboratory of Sciences and Technology for Stomatology Nanoengineering, Hospital of Stomatology, Jilin University, Jilin, China
| | - Wenying Wang
- Institute of Antler Science and Product Technology, Changchun Sci-Tech University, Jilin, China
| | - Chunyi Li
- Institute of Antler Science and Product Technology, Changchun Sci-Tech University, Jilin, China
- *Correspondence: Chunyi Li,
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Lamb S, Taylor AM, Hughes TA, McMillan BR, Larsen RT, Khan R, Weisz D, Dudchenko O, Aiden EL, Edelman NB, Frandsen PB. De novo chromosome-length assembly of the mule deer ( Odocoileus hemionus) genome. GIGABYTE 2021; 2021:gigabyte34. [PMID: 36824347 PMCID: PMC9650288 DOI: 10.46471/gigabyte.34] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 11/16/2021] [Indexed: 11/09/2022] Open
Abstract
The mule deer (Odocoileus hemionus) is an ungulate species that is distributed in a range from western Canada to central Mexico. Mule deer are an essential source of food for many predators, are relatively abundant, and commonly make broad migration movements. A clearer understanding of the mule deer genome can improve our knowledge of its population genetics, movements, and demographic history, aiding in conservation efforts. Their large population size, continuous distribution, and diversity of habitat make mule deer excellent candidates for population genomics studies; however, few genomic resources are currently available for this species. Here, we sequence and assemble the mule deer genome into a highly contiguous chromosome-length assembly for use in future research using long-read sequencing and Hi-C technologies. We also provide a genome annotation and compare demographic histories of the mule deer and white-tailed deer using the pairwise sequentially Markovian coalescent model. We expect this assembly to be a valuable resource in the continued study and conservation of mule deer.
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Affiliation(s)
- Sydney Lamb
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, UT 84602, USA
- Utah Division of Wildlife Resources, Salt Lake City, UT 84114, USA
| | - Adam M. Taylor
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, UT 84602, USA
| | - Tabitha A. Hughes
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, UT 84602, USA
| | - Brock R. McMillan
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, UT 84602, USA
| | - Randy T. Larsen
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, UT 84602, USA
| | - Ruqayya Khan
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - David Weisz
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Olga Dudchenko
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Center for Theoretical Biological Physics and Department of Computer Science, Rice University, Houston, TX 77030, USA
| | - Erez Lieberman Aiden
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Center for Theoretical Biological Physics and Department of Computer Science, Rice University, Houston, TX 77030, USA
- UWA School of Agriculture and Environment, The University of Western Australia, Crawley, WA 6009, Australia
- Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech, Pudong 201210, China
| | | | - Paul B. Frandsen
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, UT 84602, USA
- Data Science Lab, Office of the Chief Information Officer, Smithsonian Institution, Washington, DC 20002, USA
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Sjodin BMF, Galbreath KE, Lanier HC, Russello MA. Chromosome-Level Reference Genome Assembly for the American Pika (Ochotona princeps). J Hered 2021; 112:549-557. [PMID: 34036348 PMCID: PMC8558581 DOI: 10.1093/jhered/esab031] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 05/20/2021] [Indexed: 01/10/2023] Open
Abstract
The American pika (Ochotona princeps) is an alpine lagomorph found throughout western North America. Primarily inhabiting talus slopes at higher elevations (>2000 m), American pikas are well adapted to cold, montane environments. Warming climates on both historical and contemporary scales have contributed to population declines in American pikas, positioning them as a focal mammalian species for investigating the ecological effects of climate change. To support and expand ongoing research efforts, here, we present a highly contiguous and annotated reference genome assembly for the American pika (OchPri4.0). This assembly was produced using Dovetail de novo proximity ligation methods and annotated through the NCBI Eukaryotic Genome Annotation pipeline. The resulting assembly was chromosome- scale, with a total length of 2.23 Gb across 9350 scaffolds and a scaffold N50 of 75.8 Mb. The vast majority (>97%) of the total assembly length was found within 36 large scaffolds; 33 of these scaffolds correlated to whole autosomes, while the X chromosome was covered by 3 large scaffolds. Additionally, we identified 17 enriched gene ontology terms among American pika-specific genes putatively related to adaptation to high-elevation environments. This high-quality genome assembly will serve as a springboard for exploring the evolutionary underpinnings of behavioral, ecological, and taxonomic diversification in pikas as well as broader-scale eco-evolutionary questions pertaining to cold-adapted species in general.
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Affiliation(s)
- Bryson M F Sjodin
- Department of Biology, University of British Columbia, Okanagan Campus, 3247 University Way, Kelowna, BC, Canada
| | - Kurt E Galbreath
- Department of Biology, Northern Michigan University, Marquette, MI, USA
| | - Hayley C Lanier
- Sam Noble Oklahoma Museum of Natural History and Department of Biology, University of Oklahoma, Norman, OK, USA
| | - Michael A Russello
- Department of Biology, University of British Columbia, Okanagan Campus, 3247 University Way, Kelowna, BC, Canada
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Chebii VJ, Mpolya EA, Muchadeyi FC, Domelevo Entfellner JB. Genomics of Adaptations in Ungulates. Animals (Basel) 2021; 11:1617. [PMID: 34072591 PMCID: PMC8230064 DOI: 10.3390/ani11061617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 05/22/2021] [Accepted: 05/23/2021] [Indexed: 11/16/2022] Open
Abstract
Ungulates are a group of hoofed animals that have long interacted with humans as essential sources of food, labor, clothing, and transportation. These consist of domesticated, feral, and wild species raised in a wide range of habitats and biomes. Given the diverse and extreme environments inhabited by ungulates, unique adaptive traits are fundamental for fitness. The documentation of genes that underlie their genomic signatures of selection is crucial in this regard. The increasing availability of advanced sequencing technologies has seen the rapid growth of ungulate genomic resources, which offers an exceptional opportunity to understand their adaptive evolution. Here, we summarize the current knowledge on evolutionary genetic signatures underlying the adaptations of ungulates to different habitats.
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Affiliation(s)
- Vivien J. Chebii
- School of Life Science and Bioengineering, Nelson Mandela Africa Institution of Science and Technology, P.O. Box 447, Arusha, Tanzania;
- Biosciences Eastern and Central Africa, International Livestock Research Institute (BecA-ILRI) Hub, P.O. Box 30709, Nairobi 00100, Kenya;
| | - Emmanuel A. Mpolya
- School of Life Science and Bioengineering, Nelson Mandela Africa Institution of Science and Technology, P.O. Box 447, Arusha, Tanzania;
| | - Farai C. Muchadeyi
- Agricultural Research Council Biotechnology Platform (ARC-BTP), Private Bag X5, Onderstepoort 0110, South Africa;
| | - Jean-Baka Domelevo Entfellner
- Biosciences Eastern and Central Africa, International Livestock Research Institute (BecA-ILRI) Hub, P.O. Box 30709, Nairobi 00100, Kenya;
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Xie L, Deng Y, Shao X, Hu P, Zhao D, Li C, Ba H. Design of a universal primer pair for the identification of deer species. CONSERV GENET RESOUR 2020. [DOI: 10.1007/s12686-020-01176-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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