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Kubickova S, Kopecna O, Cernohorska H, Rubes J, Vozdova M. X Chromosome-Specific Repeats in Non-Domestic Bovidae. Genes (Basel) 2024; 15:159. [PMID: 38397149 PMCID: PMC10887555 DOI: 10.3390/genes15020159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 01/23/2024] [Accepted: 01/24/2024] [Indexed: 02/25/2024] Open
Abstract
Repetitive sequences form a substantial and still enigmatic part of the mammalian genome. We isolated repetitive DNA blocks of the X chromosomes of three species of the family Bovidae: Kobus defassa (KDEXr sequence), Bos taurus (BTAXr sequence) and Antilope cervicapra (ACEXr sequence). The copy numbers of the isolated sequences were assessed using qPCR, and their chromosomal localisations were analysed using FISH in ten bovid tribes and in outgroup species. Besides their localisation on the X chromosome, their presence was also revealed on the Y chromosome and autosomes in several species. The KDEXr sequence abundant in most Bovidae species also occurs in distant taxa (Perissodactyla and Carnivora) and seems to be evolutionarily older than BTAXr and ACEXr. The ACEXr sequence, visible only in several Antilopini species using FISH, is probably the youngest, and arised in an ancestor common to Bovidae and Cervidae. All three repetitive sequences analysed in this study are interspersed among gene-rich regions on the X chromosomes, apparently preventing the crossing-over in their close vicinity. This study demonstrates that repetitive sequences on the X chromosomes have undergone a fast evolution, and their variation among related species can be beneficial for evolutionary studies.
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Affiliation(s)
| | | | | | | | - Miluse Vozdova
- Department of Genetics and Reproductive Biotechnologies, Central European Institute of Technology-Veterinary Research Institute, Hudcova 70, 621 00 Brno, Czech Republic; (S.K.); (H.C.); (J.R.)
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Harshini V, Kumarasamy P, Karthickeyan S. A rare chromosomal polymorphism in a Kangayam bull ( Bosindicus) of south India. COMPARATIVE CYTOGENETICS 2021; 15:459-465. [PMID: 35035780 PMCID: PMC8695558 DOI: 10.3897/compcytogen.v15.i4.71295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2021] [Accepted: 10/11/2021] [Indexed: 06/14/2023]
Abstract
A chromosomal polymorphism was detected on karyological screening of Kangayam breeding sires prior to subjecting them for frozen semen collection. One bull possessed the chromosomal complement 2n = 60, consisting of 58 acrocentric autosomes, one large sub-metacentric X-chromosome, and one small acrocentric Y-chromosome with a small visible p-arm, which was further confirmed using CBG- and GTG-banding. This polymorphism was attributed to a heterochromatin variation of the acrocentric Y-chromosome routine in the Bosindicus Linnaeus, 1758 cattle.
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Affiliation(s)
- Vemula Harshini
- Department of Animal Genetics and Breeding, Madras Veterinary College, Tamil Nadu Veterinary and Animal Sciences University, Chennai-600 007, Tamil Nadu, IndiaTamil Nadu Veterinary and Animal Sciences UniversityChennaiIndia
| | - P. Kumarasamy
- Department of Animal Genetics and Breeding, Madras Veterinary College, Tamil Nadu Veterinary and Animal Sciences University, Chennai-600 007, Tamil Nadu, IndiaTamil Nadu Veterinary and Animal Sciences UniversityChennaiIndia
| | - S.M.K. Karthickeyan
- Department of Animal Genetics and Breeding, Madras Veterinary College, Tamil Nadu Veterinary and Animal Sciences University, Chennai-600 007, Tamil Nadu, IndiaTamil Nadu Veterinary and Animal Sciences UniversityChennaiIndia
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Escudeiro A, Ferreira D, Mendes-da-Silva A, Heslop-Harrison JS, Adega F, Chaves R. Bovine satellite DNAs – a history of the evolution of complexity and its impact in the Bovidae family. THE EUROPEAN ZOOLOGICAL JOURNAL 2019. [DOI: 10.1080/24750263.2018.1558294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Affiliation(s)
- A. Escudeiro
- Department of Genetics and Biotechnology (DGB), CAG – Laboratory of Cytogenomics and Animal Genomics (CAG), University of Trás-os-Montes e Alto Douro (UTAD), Vila Real, Portugal
- Biosystems & Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisboa, Lisboa, Portugal
| | - D. Ferreira
- Department of Genetics and Biotechnology (DGB), CAG – Laboratory of Cytogenomics and Animal Genomics (CAG), University of Trás-os-Montes e Alto Douro (UTAD), Vila Real, Portugal
- Biosystems & Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisboa, Lisboa, Portugal
| | - A. Mendes-da-Silva
- Department of Genetics and Biotechnology (DGB), CAG – Laboratory of Cytogenomics and Animal Genomics (CAG), University of Trás-os-Montes e Alto Douro (UTAD), Vila Real, Portugal
- Biosystems & Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisboa, Lisboa, Portugal
| | | | - F. Adega
- Department of Genetics and Biotechnology (DGB), CAG – Laboratory of Cytogenomics and Animal Genomics (CAG), University of Trás-os-Montes e Alto Douro (UTAD), Vila Real, Portugal
- Biosystems & Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisboa, Lisboa, Portugal
| | - R. Chaves
- Department of Genetics and Biotechnology (DGB), CAG – Laboratory of Cytogenomics and Animal Genomics (CAG), University of Trás-os-Montes e Alto Douro (UTAD), Vila Real, Portugal
- Biosystems & Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisboa, Lisboa, Portugal
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Dhanoa JK, Mukhopadhyay CS, Arora JS. Y-chromosomal genes affecting male fertility: A review. Vet World 2016; 9:783-91. [PMID: 27536043 PMCID: PMC4983133 DOI: 10.14202/vetworld.2016.783-791] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2016] [Accepted: 06/23/2016] [Indexed: 12/30/2022] Open
Abstract
The mammalian sex-chromosomes (X and Y) have evolved from autosomes and are involved in sex determination and reproductive traits. The Y-chromosome is the smallest chromosome that consists of 2-3% of the haploid genome and may contain between 70 and 200 genes. The Y-chromosome plays major role in male fertility and is suitable to study the evolutionary relics, speciation, and male infertility and/or subfertility due to its unique features such as long non-recombining region, abundance of repetitive sequences, and holandric inheritance pattern. During evolution, many holandric genes were deleted. The current review discusses the mammalian holandric genes and their functions. The commonly encountered infertility and/or subfertility problems due to point or gross mutation (deletion) of the Y-chromosomal genes have also been discussed. For example, loss or microdeletion of sex-determining region, Y-linked gene results in XY males that exhibit female characteristics, deletion of RNA binding motif, Y-encoded in azoospermic factor b region results in the arrest of spermatogenesis at meiosis. The holandric genes have been covered for associating the mutations with male factor infertility.
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Affiliation(s)
- Jasdeep Kaur Dhanoa
- School of Animal Biotechnology, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana - 141 004, Punjab, India
| | - Chandra Sekhar Mukhopadhyay
- School of Animal Biotechnology, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana - 141 004, Punjab, India
| | - Jaspreet Singh Arora
- School of Animal Biotechnology, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana - 141 004, Punjab, India
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Meiotic behaviour of evolutionary sex-autosome translocations in Bovidae. Chromosome Res 2016; 24:325-38. [PMID: 27136937 DOI: 10.1007/s10577-016-9524-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Revised: 04/12/2016] [Accepted: 04/17/2016] [Indexed: 10/21/2022]
Abstract
The recurrent occurrence of sex-autosome translocations during mammalian evolution suggests common mechanisms enabling a precise control of meiotic synapsis, recombination and inactivation of sex chromosomes. We used immunofluorescence and FISH to study the meiotic behaviour of sex chromosomes in six species of Bovidae with evolutionary sex-autosome translocations (Tragelaphus strepsiceros, Taurotragus oryx, Tragelaphus imberbis, Tragelaphus spekii, Gazella leptoceros and Nanger dama ruficollis). The autosomal regions of fused sex chromosomes showed normal synapsis with their homologous counterparts. Synapsis in the pseudoautosomal region (PAR) leads to the formation of characteristic bivalent (in T. imberbis and T. spekii with X;BTA13/Y;BTA13), trivalent (in T. strepsiceros and T. oryx with X/Y;BTA13 and G. leptoceros with X;BTA5/Y) and quadrivalent (in N. dama ruficollis with X;BTA5/Y;BTA16) structures at pachynema. However, when compared with other mammals, the number of pachynema lacking MLH1 foci in the PAR was relatively high, especially in T. imberbis and T. spekii, species with both sex chromosomes involved in sex autosome translocations. Meiotic transcriptional inactivation of the sex-autosome translocations assessed by γH2AX staining was restricted to their gonosomal regions. Despite intraspecies differences, the evolutionary fixation of sex-autosome translocations among bovids appears to involve general mechanisms ensuring sex chromosome pairing, synapsis, recombination and inactivation.
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Kopecna O, Kubickova S, Cernohorska H, Cabelova K, Vahala J, Martinkova N, Rubes J. Tribe-specific satellite DNA in non-domestic Bovidae. Chromosome Res 2014; 22:277-91. [PMID: 24452783 DOI: 10.1007/s10577-014-9401-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Revised: 01/02/2014] [Accepted: 01/10/2014] [Indexed: 01/08/2023]
Abstract
Satellite sequences present in the centromeric and pericentric regions of chromosomes represent useful source of information. Changes in satellite DNA composition may coincide with the speciation and serve as valuable markers of phylogenetic relationships. Here, we examined satellite DNA clones isolated by laser microdissection of centromeric regions of 38 bovid species and categorized them into three types. Sat I sequences from members of Bovini/Tragelaphini/Boselaphini are similar to the well-documented 1.715 sat I DNA family. Sat I DNA from Caprini/Alcelaphini/Hippotragini/Reduncini/Aepycerotini/Cephalophini/Antilopini/Neotragini/Oreotragini form the second group homologous to the common 1.714 sat I DNA. The analysis of sat II DNAs isolated in our study confirmed conservativeness of these sequences within Bovidae. Newly described centromeric clones from Madoqua kirkii and Strepsiceros strepsiceros were similar in length and repetitive tandem arrangement but showed no similarity to any other satellite DNA in the GenBank database. Phylogenetic analysis of sat I sequences isolated in our study from 38 bovid species enabled the description of relationships at the subfamily and tribal levels. The maximum likelihood and Bayesian inference analyses showed a basal position of sequences from Oreotragini in the subfamily Antilopinae. According to the Bayesian inference analysis based on the indels in a partitioned mixed model, Antilopinae satellite DNA split into two groups with those from Neotragini as a basal tribe, followed by a stepwise, successive branching of Cephalophini, Aepycerotini and Antilopini sequences. In the second group, Reduncini sequences were basal followed by Caprini, Alcelaphini and Hippotragini.
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Affiliation(s)
- Olga Kopecna
- Department of Genetics and Reproduction, Veterinary Research Institute, Hudcova 70, 621 00, Brno, Czech Republic,
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Cernohorska H, Kubickova S, Kopecna O, Kulemzina AI, Perelman PL, Elder FFB, Robinson TJ, Graphodatsky AS, Rubes J. Molecular cytogenetic insights to the phylogenetic affinities of the giraffe (Giraffa camelopardalis) and pronghorn (Antilocapra americana). Chromosome Res 2013; 21:447-60. [PMID: 23896647 DOI: 10.1007/s10577-013-9361-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Revised: 04/27/2013] [Accepted: 04/27/2013] [Indexed: 11/26/2022]
Abstract
Five families are traditionally recognized within higher ruminants (Pecora): Bovidae, Moschidae, Cervidae, Giraffidae and Antilocapridae. The phylogenetic relationships of Antilocapridae and Giraffidae within Pecora are, however, uncertain. While numerous fusions (mostly Robertsonian) have accumulated in the giraffe's karyotype (Giraffa camelopardalis, Giraffidae, 2n = 30), that of the pronghorn (Antilocapra americana, Antilocapridae, 2n = 58) is very similar to the hypothesised pecoran ancestral state (2n = 58). We examined the chromosomal rearrangements of two species, the giraffe and pronghorn, using a combination of fluorescence in situ hybridization painting probes and BAC clones derived from cattle (Bos taurus, Bovidae). Our data place Moschus (Moschidae) closer to Bovidae than Cervidae. Although the alternative (i.e., Moschidae + Cervidae as sister groups) could not be discounted in recent sequence-based analyses, cytogenetics bolsters conclusions that the former is more likely. Additionally, DNA sequences were isolated from the centromeric regions of both species and compared. Analysis of cenDNA show that unlike the pronghorn, the centromeres of the giraffe are probably organized in a more complex fashion comprising different repetitive sequences specific to single chromosomal pairs or groups of chromosomes. The distribution of nucleolar organiser region (NOR) sites, often an effective phylogenetic marker, were also examined in the two species. In the giraffe, the position of NORs seems to be autapomorphic since similar localizations have not been found in other species within Pecora.
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Affiliation(s)
- Halina Cernohorska
- Veterinary Research Institute, Hudcova 70, 621 00, Brno, Czech Republic.
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