1
|
Flack N, Hughes L, Cassens J, Enriquez M, Gebeyehu S, Alshagawi M, Hatfield J, Kauffman A, Brown B, Klaeui C, Mabrouk IF, Walls C, Yeater T, Rivas A, Faulk C. The genome of Przewalski's horse (Equus ferus przewalskii). G3 (BETHESDA, MD.) 2024; 14:jkae113. [PMID: 38805182 PMCID: PMC11304947 DOI: 10.1093/g3journal/jkae113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 05/13/2024] [Accepted: 05/20/2024] [Indexed: 05/29/2024]
Abstract
The Przewalski's horse (Equus ferus przewalskii) is an endangered equid native to the steppes of central Asia. After becoming extinct in the wild multiple conservation efforts convened to preserve the species, including captive breeding programs, reintroduction and monitoring systems, protected lands, and cloning. Availability of a highly contiguous reference genome is essential to support these continued efforts. We used Oxford Nanopore sequencing to produce a scaffold-level 2.5 Gb nuclear assembly and 16,002 bp mitogenome from a captive Przewalski's mare. All assembly drafts were generated from 111 Gb of sequence from a single PromethION R10.4.1 flow cell. The mitogenome contained 37 genes in the standard mammalian configuration and was 99.63% identical to the domestic horse (Equus caballus). The nuclear assembly, EquPr2, contained 2,146 scaffolds with an N50 of 85.1 Mb, 43X mean depth, and BUSCO quality score of 98.92%. EquPr2 successfully improves upon the existing Przewalski's horse reference genome (Burgud), with 25-fold fewer scaffolds, a 166-fold larger N50, and phased pseudohaplotypes. Modified basecalls revealed 79.5% DNA methylation and 2.1% hydroxymethylation globally. Allele-specific methylation analysis between pseudohaplotypes revealed 226 differentially methylated regions in known imprinted genes and loci not previously reported as imprinted. The heterozygosity rate of 0.165% matches previous estimates for the species and compares favorably to other endangered animals. This improved Przewalski's horse assembly will serve as a valuable resource for conservation efforts and comparative genomics investigations.
Collapse
Affiliation(s)
- Nicole Flack
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, Saint Paul, MN 55108, USA
| | - Lauren Hughes
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, Saint Paul, MN 55108, USA
| | - Jacob Cassens
- Division of Environmental Health Sciences, School of Public Health, University of Minnesota, Minneapolis, MN 55455, USA
| | - Maya Enriquez
- ANSC 8520 Students, University of Minnesota, Minneapolis, MN 55455, USA
| | - Samrawit Gebeyehu
- Department of Animal Science, College of Food, Agricultural and Natural Resource Sciences, University of Minnesota, Saint Paul, MN 55108, USA
| | | | - Jason Hatfield
- ANSC 8520 Students, University of Minnesota, Minneapolis, MN 55455, USA
| | - Anna Kauffman
- ANSC 8520 Students, University of Minnesota, Minneapolis, MN 55455, USA
| | - Baylor Brown
- ANSC 8520 Students, University of Minnesota, Minneapolis, MN 55455, USA
| | - Caitlin Klaeui
- ANSC 8520 Students, University of Minnesota, Minneapolis, MN 55455, USA
| | - Islam F Mabrouk
- ANSC 8520 Students, University of Minnesota, Minneapolis, MN 55455, USA
| | - Carrie Walls
- Department of Animal Science, College of Food, Agricultural and Natural Resource Sciences, University of Minnesota, Saint Paul, MN 55108, USA
| | - Taylor Yeater
- ANSC 8520 Students, University of Minnesota, Minneapolis, MN 55455, USA
| | - Anne Rivas
- Minnesota Zoo, Apple Valley, MN 55124, USA
| | - Christopher Faulk
- Department of Animal Science, College of Food, Agricultural and Natural Resource Sciences, University of Minnesota, Saint Paul, MN 55108, USA
| |
Collapse
|
2
|
Flack N, Hughes L, Cassens J, Enriquez M, Gebeyehu S, Alshagawi M, Hatfield J, Kauffman A, Brown B, Klaeui C, Mabrouk IF, Walls C, Yeater T, Rivas A, Faulk C. The genome of Przewalski's horse ( Equus ferus przewalskii). BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.20.581252. [PMID: 38464182 PMCID: PMC10925127 DOI: 10.1101/2024.02.20.581252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
The Przewalski's horse (Equus ferus przewalskii) is an endangered equid native to the steppes of central Asia. After becoming extinct in the wild, multiple conservation efforts convened to preserve the species including captive breeding programs, reintroduction and monitoring systems, protected lands, and cloning. Availability of a highly contiguous reference genome is essential to support these continued efforts. We used Oxford Nanopore sequencing to produce a scaffold-level 2.5 Gb nuclear assembly and 16,002 bp mitogenome from a captive Przewalski's mare. All assembly drafts were generated from 111 Gb of sequence from a single PromethION R10.4.1 flow cell. The mitogenome contained 37 genes in the standard mammalian configuration and was 99.63% identical to the domestic horse (Equus caballus). The nuclear assembly, EquPr2, contained 2,146 scaffolds with an N50 of 85.1 Mb, 43X mean depth, and BUSCO quality score of 98.92%. EquPr2 successfully improves upon the existing Przewalski's horse reference genome (Burgud), with 25-fold fewer scaffolds, a 166-fold larger N50, and phased pseudohaplotypes. Modified basecalls revealed 79.5% DNA methylation and 2.1% hydroxymethylation globally. Allele-specific methylation analysis between pseudohaplotypes revealed 226 differentially methylated regions (DMRs) in known imprinted genes and loci not previously reported as imprinted. The heterozygosity rate of 0.165% matches previous estimates for the species and compares favorably to other endangered animals. This improved Przewalski's horse assembly will serve as a valuable resource for conservation efforts and comparative genomics investigations.
Collapse
Affiliation(s)
- Nicole Flack
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota Saint Paul, MN, USA
| | - Lauren Hughes
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota Saint Paul, MN, USA
| | - Jacob Cassens
- Division of Environmental Health Sciences, School of Public Health, University of Minnesota Minneapolis, MN, USA
| | - Maya Enriquez
- ANSC 8520 Students, University of Minnesota Minneapolis, MN, USA
| | - Samrawit Gebeyehu
- Department of Animal Science, College of Food, Agricultural and Natural Resource Sciences, University of Minnesota Saint Paul, MN, USA
| | | | - Jason Hatfield
- ANSC 8520 Students, University of Minnesota Minneapolis, MN, USA
| | - Anna Kauffman
- ANSC 8520 Students, University of Minnesota Minneapolis, MN, USA
| | - Baylor Brown
- ANSC 8520 Students, University of Minnesota Minneapolis, MN, USA
| | - Caitlin Klaeui
- ANSC 8520 Students, University of Minnesota Minneapolis, MN, USA
| | - Islam F. Mabrouk
- ANSC 8520 Students, University of Minnesota Minneapolis, MN, USA
| | - Carrie Walls
- Department of Animal Science, College of Food, Agricultural and Natural Resource Sciences, University of Minnesota Saint Paul, MN, USA
| | - Taylor Yeater
- ANSC 8520 Students, University of Minnesota Minneapolis, MN, USA
| | | | - Christopher Faulk
- Department of Animal Science, College of Food, Agricultural and Natural Resource Sciences, University of Minnesota Saint Paul, MN, USA
| |
Collapse
|
3
|
Piras FM, Cappelletti E, Abdelgadir WA, Salamon G, Vignati S, Santagostino M, Sola L, Nergadze SG, Giulotto E. A Satellite-Free Centromere in Equus przewalskii Chromosome 10. Int J Mol Sci 2023; 24:4134. [PMID: 36835543 PMCID: PMC9961726 DOI: 10.3390/ijms24044134] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 02/15/2023] [Accepted: 02/16/2023] [Indexed: 02/22/2023] Open
Abstract
In mammals, centromeres are epigenetically specified by the histone H3 variant CENP-A and are typically associated with satellite DNA. We previously described the first example of a natural satellite-free centromere on Equus caballus chromosome 11 (ECA11) and, subsequently, on several chromosomes in other species of the genus Equus. We discovered that these satellite-free neocentromeres arose recently during evolution through centromere repositioning and/or chromosomal fusion, after inactivation of the ancestral centromere, where, in many cases, blocks of satellite sequences were maintained. Here, we investigated by FISH the chromosomal distribution of satellite DNA families in Equus przewalskii (EPR), demonstrating a good degree of conservation of the localization of the major horse satellite families 37cen and 2PI with the domestic horse. Moreover, we demonstrated, by ChIP-seq, that 37cen is the satellite bound by CENP-A and that the centromere of EPR10, the ortholog of ECA11, is devoid of satellite sequences. Our results confirm that these two species are closely related and that the event of centromere repositioning which gave rise to EPR10/ECA11 centromeres occurred in the common ancestor, before the separation of the two horse lineages.
Collapse
Affiliation(s)
- Francesca M. Piras
- Department of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, 27100 Pavia, Italy
| | - Eleonora Cappelletti
- Department of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, 27100 Pavia, Italy
| | - Wasma A. Abdelgadir
- Department of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, 27100 Pavia, Italy
| | - Giulio Salamon
- Oasi di Sant’Alessio, Sant’Alessio con Vialone, 27016 Pavia, Italy
| | | | - Marco Santagostino
- Department of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, 27100 Pavia, Italy
| | - Lorenzo Sola
- Department of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, 27100 Pavia, Italy
| | - Solomon G. Nergadze
- Department of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, 27100 Pavia, Italy
| | - Elena Giulotto
- Department of Biology and Biotechnology “Lazzaro Spallanzani”, University of Pavia, 27100 Pavia, Italy
| |
Collapse
|
4
|
Turghan MA, Jiang Z, Niu Z. An Update on Status and Conservation of the Przewalski's Horse ( Equus ferus przewalskii): Captive Breeding and Reintroduction Projects. Animals (Basel) 2022; 12:ani12223158. [PMID: 36428386 PMCID: PMC9686875 DOI: 10.3390/ani12223158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 11/06/2022] [Accepted: 11/10/2022] [Indexed: 11/18/2022] Open
Abstract
This review summarizes studies on Przewalski's horse since its extinction in the wild in the 1960s, with a focus on the reintroduction projects in Mongolia and China, with current population status. Historical and present distribution, population trends, ecology and habitats, genetics, behaviors, conservation measures, actual and potential threats are also reviewed. Captive breeding and reintroduction projects have already been implemented, but many others are still under considerations. The review may help to understand the complexity of problem and show the directions for effective practice in the future.
Collapse
Affiliation(s)
- Mardan Aghabey Turghan
- State Key Laboratory of Oasis and Desert Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- Graduate School, University of Chinese Academy of Sciences, Beijing 100049, China
- Correspondence: (M.A.T.); (Z.J.)
| | - Zhigang Jiang
- Graduate School, University of Chinese Academy of Sciences, Beijing 100049, China
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Correspondence: (M.A.T.); (Z.J.)
| | - Zhongze Niu
- College of Biology and Geography Sciences, Yili Normal University, Yining 835000, China
| |
Collapse
|
5
|
Li S, Zhao G, Han H, Li Y, Li J, Wang J, Cao G, Li X. Genome collinearity analysis illuminates the evolution of donkey chromosome 1 and horse chromosome 5 in perissodactyls: A comparative study. BMC Genomics 2021; 22:665. [PMID: 34521340 PMCID: PMC8442440 DOI: 10.1186/s12864-021-07984-6] [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: 12/15/2020] [Accepted: 09/06/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND It is important to resolve the evolutionary history of species genomes as it has affected both genome organization and chromosomal architecture. The rapid innovation in sequencing technologies and the improvement in assembly algorithms have enabled the creation of highly contiguous genomes. DNA Zoo, a global organization dedicated to animal conservation, offers more than 150 chromosome-length genome assemblies. This database has great potential in the comparative genomics field. RESULTS Using the donkey (Equus asinus asinus, EAS) genome provided by DNA Zoo as an example, the scaffold N50 length and Benchmarking Universal Single-Copy Ortholog score reached 95.5 Mb and 91.6%, respectively. We identified the cytogenetic nomenclature, corrected the direction of the chromosome-length sequence of the donkey genome, analyzed the genome-wide chromosomal rearrangements between the donkey and horse, and illustrated the evolution of the donkey chromosome 1 and horse chromosome 5 in perissodactyls. CONCLUSIONS The donkey genome provided by DNA Zoo has relatively good continuity and integrity. Sequence-based comparative genomic analyses are useful for chromosome evolution research. Several previously published chromosome painting results can be used to identify the cytogenetic nomenclature and correct the direction of the chromosome-length sequence of new assemblies. Compared with the horse genome, the donkey chromosomes 1, 4, 20, and X have several obvious inversions, consistent with the results of previous studies. A 4.8 Mb inverted structure was first discovered in the donkey chromosome 25 and plains zebra chromosome 11. We speculate that the inverted structure and the tandem fusion of horse chromosome 31 and 4 are common features of non-caballine equids, which supports the correctness of the existing Equus phylogeny to an extent.
Collapse
Affiliation(s)
- Shaohua Li
- Research Center for Animal Genetic Resources of Mongolia Plateau, College of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
- College of Basic Medicine, Inner Mongolia Medical University, Hohhot, 010110, China
- Inner Mongolia Saikexing Institute of Breeding and Reproductive Biotechnology in Domestic Animal, Hohhot, 011517, China
| | - Gaoping Zhao
- Inner Mongolia Saikexing Institute of Breeding and Reproductive Biotechnology in Domestic Animal, Hohhot, 011517, China
| | - Hongmei Han
- Department of Physical Education, Hohhot Minzu College, Hohhot, 010051, China
| | - Yunxia Li
- Research Center for Animal Genetic Resources of Mongolia Plateau, College of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
- Inner Mongolia Saikexing Institute of Breeding and Reproductive Biotechnology in Domestic Animal, Hohhot, 011517, China
| | - Jun Li
- Inner Mongolia Saikexing Institute of Breeding and Reproductive Biotechnology in Domestic Animal, Hohhot, 011517, China
| | - Jinfeng Wang
- College of Basic Medicine, Inner Mongolia Medical University, Hohhot, 010110, China
| | - Guifang Cao
- College of Veterinary Science, Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - Xihe Li
- Research Center for Animal Genetic Resources of Mongolia Plateau, College of Life Sciences, Inner Mongolia University, Hohhot, 010070, China.
- Inner Mongolia Saikexing Institute of Breeding and Reproductive Biotechnology in Domestic Animal, Hohhot, 011517, China.
| |
Collapse
|
6
|
Brosnahan MM. Genetics, Evolution, and Physiology of Donkeys and Mules. Vet Clin North Am Equine Pract 2019; 35:457-467. [PMID: 31672199 DOI: 10.1016/j.cveq.2019.08.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
The genus Equus is made up of donkeys, horses, and zebras. Despite significant variation in chromosome number across these species, interspecies breeding results in healthy, although infertile, hybrid offspring. Most notable among these are the horse-donkey hybrids, the mule and hinny. Donkeys presently are used for everything from companion animals to beasts of burden. Although closely related from an evolutionary standpoint, differences in anatomy and physiology preclude the assumption that they can be treated identically to the domestic horse. Veterinarians should be aware of these differences and adjust their practice accordingly.
Collapse
Affiliation(s)
- Margaret M Brosnahan
- College of Veterinary Medicine, Midwestern University, 19555 North 59th Avenue, Cactus Wren Hall 336-P, Glendale, AZ 85308, USA.
| |
Collapse
|
7
|
Teri Lear, PhD (1951-2016). Cytogenet Genome Res 2016; 149:237-240. [DOI: 10.1159/000450535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/25/2016] [Indexed: 11/19/2022] Open
|
8
|
Genomic characterization of the Przewalski׳s horse inhabiting Mongolian steppe by whole genome re-sequencing. Livest Sci 2014. [DOI: 10.1016/j.livsci.2014.06.020] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
9
|
Huang J, Zhao Y, Shiraigol W, Li B, Bai D, Ye W, Daidiikhuu D, Yang L, Jin B, Zhao Q, Gao Y, Wu J, Bao W, Li A, Zhang Y, Han H, Bai H, Bao Y, Zhao L, Zhai Z, Zhao W, Sun Z, Zhang Y, Meng H, Dugarjaviin M. Analysis of horse genomes provides insight into the diversification and adaptive evolution of karyotype. Sci Rep 2014; 4:4958. [PMID: 24828444 PMCID: PMC4021364 DOI: 10.1038/srep04958] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2013] [Accepted: 04/22/2014] [Indexed: 12/22/2022] Open
Abstract
Karyotypic diversification is more prominent in Equus species than in other mammals. Here, using next generation sequencing technology, we generated and de novo assembled quality genomes sequences for a male wild horse (Przewalski's horse) and a male domestic horse (Mongolian horse), with about 93-fold and 91-fold coverage, respectively. Portion of Y chromosome from wild horse assemblies (3 M bp) and Mongolian horse (2 M bp) were also sequenced and de novo assembled. We confirmed a Robertsonian translocation event through the wild horse's chromosomes 23 and 24, which contained sequences that were highly homologous with those on the domestic horse's chromosome 5. The four main types of rearrangement, insertion of unknown origin, inserted duplication, inversion, and relocation, are not evenly distributed on all the chromosomes, and some chromosomes, such as the X chromosome, contain more rearrangements than others, and the number of inversions is far less than the number of insertions and relocations in the horse genome. Furthermore, we discovered the percentages of LINE_L1 and LTR_ERV1 are significantly increased in rearrangement regions. The analysis results of the two representative Equus species genomes improved our knowledge of Equus chromosome rearrangement and karyotype evolution.
Collapse
Affiliation(s)
- Jinlong Huang
- 1] College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, P.R. China [2]
| | - Yiping Zhao
- 1] College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, P.R. China [2]
| | - Wunierfu Shiraigol
- 1] College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, P.R. China [2]
| | - Bei Li
- 1] College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, P.R. China [2]
| | - Dongyi Bai
- 1] College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, P.R. China [2]
| | - Weixing Ye
- 1] Shanghai Personal Biotechnology Limited Company, 777 Longwu Road, Shanghai 200236, P.R. China [2]
| | - Dorjsuren Daidiikhuu
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, P.R. China
| | - Lihua Yang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, P.R. China
| | - Burenqiqige Jin
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, P.R. China
| | - Qinan Zhao
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, P.R. China
| | - Yahan Gao
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, P.R. China
| | - Jing Wu
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, P.R. China
| | - Wuyundalai Bao
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, P.R. China
| | - Anaer Li
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, P.R. China
| | - Yuhong Zhang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, P.R. China
| | - Haige Han
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, P.R. China
| | - Haitang Bai
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, P.R. China
| | - Yanqing Bao
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, P.R. China
| | - Lele Zhao
- School of Agriculture and Biology, Shanghai Jiaotong University; Shanghai Key Laboratory of Veterinary Biotechnology, 800 Dongchuan Road, Shanghai 200240, P. R. China
| | - Zhengxiao Zhai
- School of Agriculture and Biology, Shanghai Jiaotong University; Shanghai Key Laboratory of Veterinary Biotechnology, 800 Dongchuan Road, Shanghai 200240, P. R. China
| | - Wenjing Zhao
- School of Agriculture and Biology, Shanghai Jiaotong University; Shanghai Key Laboratory of Veterinary Biotechnology, 800 Dongchuan Road, Shanghai 200240, P. R. China
| | - Zikui Sun
- Shanghai Personal Biotechnology Limited Company, 777 Longwu Road, Shanghai 200236, P.R. China
| | - Yan Zhang
- Virginia Bioinformatics Institute, Virginia Tech, Washington Street, MC0477, Blacksburg, Virginia, 24061, USA
| | - He Meng
- School of Agriculture and Biology, Shanghai Jiaotong University; Shanghai Key Laboratory of Veterinary Biotechnology, 800 Dongchuan Road, Shanghai 200240, P. R. China
| | - Manglai Dugarjaviin
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, P.R. China
| |
Collapse
|
10
|
Identification of equine influenza virus infection in Asian wild horses (Equus przewalskii). Arch Virol 2013; 159:1159-62. [DOI: 10.1007/s00705-013-1908-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2013] [Accepted: 07/15/2013] [Indexed: 10/26/2022]
|
11
|
Musilova P, Kubickova S, Vahala J, Rubes J. Subchromosomal karyotype evolution in Equidae. Chromosome Res 2013; 21:175-87. [PMID: 23532666 DOI: 10.1007/s10577-013-9346-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2013] [Revised: 03/12/2013] [Accepted: 03/13/2013] [Indexed: 12/26/2022]
Abstract
Equidae is a small family which comprises horses, African and Asiatic asses, and zebras. Despite equids having diverged quite recently, their karyotypes underwent rapid evolution which resulted in extensive differences among chromosome complements in respective species. Comparative mapping using whole-chromosome painting probes delineated genome-wide chromosome homologies among extant equids, enabling us to trace chromosome rearrangements that occurred during evolution. In the present study, we performed subchromosomal comparative mapping among seven Equidae species, representing the whole family. Region-specific painting and bacterial artificial chromosome probes were used to determine the orientation of evolutionarily conserved segments with respect to centromere positions. This allowed assessment of the configuration of all fusions occurring during the evolution of Equidae, as well as revealing discrepancies in centromere location caused by centromere repositioning or inversions. Our results indicate that the prevailing type of fusion in Equidae is centric fusion. Tandem fusions of the type telomere-telomere occur almost exclusively in the karyotype of Hartmann's zebra and are characteristic of this species' evolution. We revealed inversions in segments homologous to horse chromosomes 3p/10p and 13 in zebras and confirmed inversions in segments 4/31 in African ass, 7 in horse and 8p/20 in zebras. Furthermore, our mapping results suggested that centromere repositioning events occurred in segments homologous to horse chromosomes 7, 8q, 10p and 19 in the African ass and an element homologous to horse chromosome 16 in Asiatic asses. Centromere repositioning in chromosome 1 resulted in three different chromosome types occurring in extant species. Heterozygosity of the centromere position of this chromosome was observed in the kiang. Other subtle changes in centromere position were described in several evolutionary conserved chromosomal segments, suggesting that tiny centromere repositioning or pericentric inversions are quite frequent in zebras and asses.
Collapse
Affiliation(s)
- P Musilova
- Department of Genetics and Reproduction, Veterinary Research Institute, Brno, Czech Republic.
| | | | | | | |
Collapse
|
12
|
The Application of Zoo-Fish Technique for Analysis of Chromosomal Rearrangements in the Equidae Family. ANNALS OF ANIMAL SCIENCE 2012. [DOI: 10.2478/v10220-012-0001-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The Application of Zoo-Fish Technique for Analysis of Chromosomal Rearrangements in the Equidae FamilyGenome analysis is necessary to trace evolutionary rearrangements and relationships between species. Initially, to this end, the tools of classical cytogenetics were used but along with the development of molecular cytogenetics methods it became possible to analyse the genome more thoroughly. One of the widely used methods is fluorescence in situ hybridization (FISH) and its different types. Zoo-FISH, or cross-species chromosome painting, which uses painting probes specific for whole chromosomes, enables detecting homologous synteny blocks, the occurrence of which is evidence that species share a common ancestry and are related. Zoo-FISH technique is complemented by FISH with probes specific to chromosome arms or repetitive sequences (telomeres, centromeres), which provide additional information about karyotype organization, as well as karyotype polymorphism and conservation. Another method used is FISH with gene-specific probes, which enable the localization of single loci, thus making it possible to determine linkages between genes and verify data obtained after using painting probes in Zoo-FISH technique. Because of its diverse karyotype and rapid karyotypic evolution, the Equidae family is an ideal object of study using a number of methods based on in situ hybridization, which, in turn, enables information to be obtained at many levels of DNA organization.
Collapse
|
13
|
Goto H, Ryder OA, Fisher AR, Schultz B, Kosakovsky Pond SL, Nekrutenko A, Makova KD. A massively parallel sequencing approach uncovers ancient origins and high genetic variability of endangered Przewalski's horses. Genome Biol Evol 2011; 3:1096-106. [PMID: 21803766 PMCID: PMC3194890 DOI: 10.1093/gbe/evr067] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The endangered Przewalski's horse is the closest relative of the domestic horse and is the only true wild horse species surviving today. The question of whether Przewalski's horse is the direct progenitor of domestic horse has been hotly debated. Studies of DNA diversity within Przewalski's horses have been sparse but are urgently needed to ensure their successful reintroduction to the wild. In an attempt to resolve the controversy surrounding the phylogenetic position and genetic diversity of Przewalski's horses, we used massively parallel sequencing technology to decipher the complete mitochondrial and partial nuclear genomes for all four surviving maternal lineages of Przewalski's horses. Unlike single-nucleotide polymorphism (SNP) typing usually affected by ascertainment bias, the present method is expected to be largely unbiased. Three mitochondrial haplotypes were discovered—two similar ones, haplotypes I/II, and one substantially divergent from the other two, haplotype III. Haplotypes I/II versus III did not cluster together on a phylogenetic tree, rejecting the monophyly of Przewalski's horse maternal lineages, and were estimated to split 0.117–0.186 Ma, significantly preceding horse domestication. In the phylogeny based on autosomal sequences, Przewalski's horses formed a monophyletic clade, separate from the Thoroughbred domestic horse lineage. Our results suggest that Przewalski's horses have ancient origins and are not the direct progenitors of domestic horses. The analysis of the vast amount of sequence data presented here suggests that Przewalski's and domestic horse lineages diverged at least 0.117 Ma but since then have retained ancestral genetic polymorphism and/or experienced gene flow.
Collapse
Affiliation(s)
- Hiroki Goto
- Department of Biology, The Pennsylvania State University, USA
| | | | | | | | | | | | | |
Collapse
|
14
|
Haffner JC, Fecteau KA, Eiler H, Tserendorj T, Hoffman RM, Oliver JW. Blood steroid concentrations in domestic Mongolian horses. J Vet Diagn Invest 2010; 22:537-43. [PMID: 20622223 DOI: 10.1177/104063871002200407] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Traditionally, analysis of blood cortisol alone has been used to evaluate adrenal function. Currently, multisteroid analyses are considered more informative than analysis of a single hormone to assess adrenal function. The objective of the present research was to create a database for steroid reference values for domestic Mongolian horses. Seven adrenal steroid levels were determined in the blood of 18 colts, 34 stallions, 25 geldings, 17 fillies, and 29 mares. Results were as follows (lowest and highest group median, in nanograms per milliliter): progesterone: <0.030 (fillies), 4.30 (mares), and 0.070 (all horses); 17-OH-progesterone: 0.070 (colts), 0.520 (mares), and 0.110 (all horses); androstenedione: 0.101 (colts), 0.256 (stallions), and 0.181 (all horses); testosterone: <0.040 (mares, stallions, and fillies), 0.040 (geldings and colts), and <0.40 (all horses); estradiol: 0.066 (stallions), 0.093 (fillies), and 0.085 (all horses); cortisol: 23.040 (colts), 70.210 (geldings), and 50.770 (all horses); and aldosterone: 0.018 (colts), 0.297 (geldings), and 0.191 (all horses). Overall medians indicate that cortisol (98.70%) is the predominant steroid, followed by aldosterone (0.37%), androstenedione (0.35%), 17-OH-progesterone (0.21%), estradiol (0.17%), progesterone (0.14%), and testosterone (0.06%). This information provides adrenal and gonadal steroid reference concentrations to assist in physiological characterization and diagnosis of endocrine disorders in domestic Mongolian horses.
Collapse
Affiliation(s)
- John C Haffner
- Department of Agribusiness and Agriscience, Horse Science Center, Middle Tennessee State University, Murfreesboro, TN, USA
| | | | | | | | | | | |
Collapse
|
15
|
Yang H, Ma YH, Li B, Dugarjaviin M. [Progress on horse genome project]. YI CHUAN = HEREDITAS 2010; 32:211-8. [PMID: 20233697 DOI: 10.3724/sp.j.1005.2010.00211] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
There is unique genetic information belonging to various kinds of living beings. Understanding of the formation process of organisms and a variety of vital movement is associated with the achievements of genome study. As horse has a notable health condition and great record of the genealogy in the world, thus it becomes a valuable model animal for studying life science. Despite of a late start, the map of the horse genome has undergone unprecedented expansion during the last few years. The current progresses of the horse genome, including genetic map, physical map, comparative genomic map, and functional genomics, were reviewed in this paper. The maps are currently used worldwide to discover genes associated with various traits of significance in horse including general health, disease resistance, reproduction, fertility, athletic performance, phenotypic characteristics like coat color, etc. The results are believed to provide new ideas and approaches for prevention, diagnostics, and therapeutic for horses, and also better foundation of breed selection and equine genetic breeding.
Collapse
Affiliation(s)
- Hong Yang
- College of Animal Science and Animal Medicine, Inner Mongolia Agricultural University, Hohhot 010018, China.
| | | | | | | |
Collapse
|
16
|
Lau AN, Peng L, Goto H, Chemnick L, Ryder OA, Makova KD. Horse domestication and conservation genetics of Przewalski's horse inferred from sex chromosomal and autosomal sequences. Mol Biol Evol 2008; 26:199-208. [PMID: 18931383 DOI: 10.1093/molbev/msn239] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Despite their ability to interbreed and produce fertile offspring, there is continued disagreement about the genetic relationship of the domestic horse (Equus caballus) to its endangered wild relative, Przewalski's horse (Equus przewalskii). Analyses have differed as to whether or not Przewalski's horse is placed phylogenetically as a separate sister group to domestic horses. Because Przewalski's horse and domestic horse are so closely related, genetic data can also be used to infer domestication-specific differences between the two. To investigate the genetic relationship of Przewalski's horse to the domestic horse and to address whether evolution of the domestic horse is driven by males or females, five homologous introns (a total of approximately 3 kb) were sequenced on the X and Y chromosomes in two Przewalski's horses and three breeds of domestic horses: Arabian horse, Mongolian domestic horse, and Dartmoor pony. Five autosomal introns (a total of approximately 6 kb) were sequenced for these horses as well. The sequences of sex chromosomal and autosomal introns were used to determine nucleotide diversity and the forces driving evolution in these species. As a result, X chromosomal and autosomal data do not place Przewalski's horses in a separate clade within phylogenetic trees for horses, suggesting a close relationship between domestic and Przewalski's horses. It was also found that there was a lack of nucleotide diversity on the Y chromosome and higher nucleotide diversity than expected on the X chromosome in domestic horses as compared with the Y chromosome and autosomes. This supports the hypothesis that very few male horses along with numerous female horses founded the various domestic horse breeds. Patterns of nucleotide diversity among different types of chromosomes were distinct for Przewalski's in contrast to domestic horses, supporting unique evolutionary histories of the two species.
Collapse
Affiliation(s)
- Allison N Lau
- Department of Biology, The Pennsylvania State University, University Park, USA
| | | | | | | | | | | |
Collapse
|
17
|
Chowdhary BP, Raudsepp T. The horse genome derby: racing from map to whole genome sequence. Chromosome Res 2008; 16:109-27. [PMID: 18274866 DOI: 10.1007/s10577-008-1204-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The map of the horse genome has undergone unprecedented expansion during the past six years. Beginning from a modest collection of approximately 300 mapped markers scattered on the 31 pairs of autosomes and the X chromosome in 2001, today the horse genome is among the best-mapped in domestic animals. Presently, high-resolution linearly ordered gene maps are available for all autosomes as well as the X and the Y chromosome. The approximately 4350 mapped markers distributed over the approximately 2.68 Gbp long equine genome provide on average 1 marker every 620 kb. Among the most remarkable developments in equine genome analysis is the availability of the assembled sequence (EquCab2) of the female horse genome and the generation approximately 1.5 million single nucleotide polymorphisms (SNPs) from diverse breeds. This has triggered the creation of new tools and resources like the 60K SNP-chip and whole genome expression microarrays that hold promise to study the equine genome and transcriptome in ways not previously envisaged. As a result of these developments it is anticipated that, during coming years, the genetics underlying important monogenic traits will be analyzed with improved accuracy and speed. Of larger interest will be the prospects of dissecting the genetic component of various complex/multigenic traits that are of vital significance for equine health and welfare. The number of investigations recently initiated to study a multitude of such traits hold promise for improved diagnostics, prevention and therapeutic approaches for horses.
Collapse
Affiliation(s)
- Bhanu P Chowdhary
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, 77843-4458, USA.
| | | |
Collapse
|
18
|
Brinkmeyer-Langford C, Raudsepp T, Lee EJ, Goh G, Schäffer AA, Agarwala R, Wagner ML, Tozaki T, Skow LC, Womack JE, Mickelson JR, Chowdhary BP. A high-resolution physical map of equine homologs of HSA19 shows divergent evolution compared with other mammals. Mamm Genome 2005; 16:631-49. [PMID: 16180145 DOI: 10.1007/s00335-005-0023-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2005] [Accepted: 04/28/2005] [Indexed: 11/25/2022]
Abstract
A high-resolution (1 marker/700 kb) physically ordered radiation hybrid (RH) and comparative map of 122 loci on equine homologs of human Chromosome 19 (HSA19) shows a variant evolution of these segments in equids/Perissodactyls compared with other mammals. The segments include parts of both the long and the short arm of horse Chromosome 7 (ECA7), the proximal part of ECA21, and the entire short arm of ECA10. The map includes 93 new markers, of which 89 (64 gene-specific and 25 microsatellite) were genotyped on a 5000-rad horse x hamster RH panel, and 4 were mapped exclusively by FISH. The orientation and alignment of the map was strengthened by 21 new FISH localizations, of which 15 represent genes. The approximately sevenfold-improved map resolution attained in this study will prove extremely useful for candidate gene discovery in the targeted equine chromosomal regions. The highlight of the comparative map is the fine definition of homology between the four equine chromosomal segments and corresponding HSA19 regions specified by physical coordinates (bp) in the human genome sequence. Of particular interest are the regions on ECA7 and ECA21 that correspond to the short arm of HSA19-a genomic rearrangement discovered to date only in equids/Perissodactyls as evidenced through comparative Zoo-FISH analysis of the evolution of ancestral HSA19 segments in eight mammalian orders involving about 50 species.
Collapse
Affiliation(s)
- Candice Brinkmeyer-Langford
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, 77843, USA
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
19
|
Ahrens E, Stranzinger G. Comparative chromosomal studies of E. caballus (ECA) and E. przewalskii (EPR) in a female F1 hybrid. J Anim Breed Genet 2005; 122 Suppl 1:97-102. [PMID: 16130463 DOI: 10.1111/j.1439-0388.2005.00494.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Previous research revealed that the karyotypes of Equus przewalskii (2n = 66) and Equus caballus (2n = 64) differ by one pair of metacentric chromosomes, present in ECA but not in EPR, and two pairs of acrocentric chromosomes found only in the EPR karyotype. The formation of a trivalent during meiosis in a male F1 hybrid and the homologies in G-banding patterns suggest that ECA 5 corresponds to two acrocentric EPR chromosomes resulting from a Robertsonian fusion or fission event. Chromosomal investigations of a female interspecies F1 hybrid including banded karyograms and fluorescence in situ hybridization (FISH) studies focusing on the p and q arm of ECA 5 were conducted. Q- and G-banding patterns of E. caballus, E. przewalskii and the hybrid revealed interspecies homology between all chromosome pairs except for ECA 5, EPR 23 and EPR 24, which were unique for that particular species. Furthermore, they indicated homology between ECA 5p and EPR 23 as well as between ECA 5q and EPR 24. FISH revealed hybridization of the BACs laminin beta 3 (LAM B3) and laminin gamma 2 (LAM C2) to ECA 5p and EPR 23. However, nuclear factor I (NFIA) and immunoglobulin lambda (IGL@), primarily assigned to ECA 5q, mapped to ECA 7 and EPR 6 respectively. Thus the karyotypes of E. caballus and E. przewalskii differ solely by one Robertsonian translocation (ECA 5 =EPR 23 + EPR 24).
Collapse
Affiliation(s)
- E Ahrens
- Department of Animal Sciences, Swiss Federal Institute of Technology, Zurich, Switzerland
| | | |
Collapse
|
20
|
Myka JL, Lear TL, Houck ML, Ryder OA, Bailey E. Homologous fission event(s) implicated for chromosomal polymorphisms among five species in the genus Equus. Cytogenet Genome Res 2004; 102:217-21. [PMID: 14970706 DOI: 10.1159/000075752] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2003] [Accepted: 09/02/2003] [Indexed: 11/19/2022] Open
Abstract
The genus Equus is unusual in that five of the ten extant species have documented centric fission (Robertsonian translocation) polymorphisms within their populations, namely E. hemionus onager, E. hemionus kulan, E. kiang, E. africanus somaliensis, and E. quagga burchelli. Here we report evidence that the polymorphism involves the same homologous chromosome segments in each species, and that these chromosome segments have homology to human chromosome 4 (HSA4). Bacterial artificial chromosome clones containing equine genes SMARCA5 (ECA2q21 homologue to HSA4q31. 21) and UCHL1 (ECA3q22 homologue to HSA4p13) were mapped to a single metacentric chromosome and two unpaired acrocentrics by FISH mapping for individuals possessing odd numbers of chromosomes. These data suggest that the polymorphism is either ancient and conserved within the genus or has occurred recently and independently within each species. Since these species are separated by 1-3 million years of evolution, this polymorphism is remarkable and worthy of further investigations.
Collapse
Affiliation(s)
- J L Myka
- M.H. Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, KY 40546-0099, USA
| | | | | | | | | |
Collapse
|