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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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Vozdova M, Kubickova S, Cernohorska H, Fröhlich J, Martínková N, Rubes J. Sequence Analysis and FISH Mapping of Four Satellite DNA Families among Cervidae. Genes (Basel) 2020; 11:genes11050584. [PMID: 32456268 PMCID: PMC7288315 DOI: 10.3390/genes11050584] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 05/14/2020] [Accepted: 05/20/2020] [Indexed: 01/07/2023] Open
Abstract
Centromeric and pericentromeric chromosome regions are occupied by satellite DNA. Satellite DNAs play essential roles in chromosome segregation, and, thanks to their extensive sequence variability, to some extent, they can also be used as phylogenetic markers. In this paper, we isolated and sequenced satellite DNA I-IV in 11 species of Cervidae. The obtained satellite DNA sequences and their chromosomal distribution were compared among the analysed representatives of cervid subfamilies Cervinae and Capreolinae. Only satI and satII sequences are probably present in all analysed species with high abundance. On the other hand, fluorescence in situ hybridisation (FISH) with satIII and satIV probes showed signals only in a part of the analysed species, indicating interspecies copy number variations. Several indices, including FISH patterns, the high guanine and cytosine (GC) content, and the presence of centromere protein B (CENP-B) binding motif, suggest that the satII DNA may represent the most important satellite DNA family that might be involved in the centromeric function in Cervidae. The absence or low intensity of satellite DNA FISH signals on biarmed chromosomes probably reflects the evolutionary reduction of heterochromatin following the formation of chromosome fusions. The phylogenetic trees constructed on the basis of the satellite I-IV DNA relationships generally support the present cervid taxonomy.
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Affiliation(s)
- Miluse Vozdova
- Department of Genetics and Reproduction, Central European Institute of Technology—Veterinary Research Institute, Hudcova 70, 621 00 Brno, Czech Republic; (S.K.); (H.C.); (J.F.); (J.R.)
- Correspondence: ; Tel.: +420-533-331-422
| | - Svatava Kubickova
- Department of Genetics and Reproduction, Central European Institute of Technology—Veterinary Research Institute, Hudcova 70, 621 00 Brno, Czech Republic; (S.K.); (H.C.); (J.F.); (J.R.)
| | - Halina Cernohorska
- Department of Genetics and Reproduction, Central European Institute of Technology—Veterinary Research Institute, Hudcova 70, 621 00 Brno, Czech Republic; (S.K.); (H.C.); (J.F.); (J.R.)
| | - Jan Fröhlich
- Department of Genetics and Reproduction, Central European Institute of Technology—Veterinary Research Institute, Hudcova 70, 621 00 Brno, Czech Republic; (S.K.); (H.C.); (J.F.); (J.R.)
| | - Natália Martínková
- Institute of Vertebrate Biology, Czech Academy of Sciences, Kvetna 8, 603 65 Brno, Czech Republic;
| | - Jiri Rubes
- Department of Genetics and Reproduction, Central European Institute of Technology—Veterinary Research Institute, Hudcova 70, 621 00 Brno, Czech Republic; (S.K.); (H.C.); (J.F.); (J.R.)
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Li YC, Pan YJ, Tsai FJ, Lin CC. Prenatal molecular cytogenetic analysis of a mild dysmorphic fetus with a huge unbalance karyotype involving partial 9p deletion and partial 18q duplication. Genes Genomics 2016. [DOI: 10.1007/s13258-015-0340-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Louzada S, Vieira-da-Silva A, Mendes-da-Silva A, Kubickova S, Rubes J, Adega F, Chaves R. A novel satellite DNA sequence in the Peromyscus genome (PMSat): Evolution via copy number fluctuation. Mol Phylogenet Evol 2015; 92:193-203. [PMID: 26103000 DOI: 10.1016/j.ympev.2015.06.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Revised: 06/11/2015] [Accepted: 06/12/2015] [Indexed: 12/16/2022]
Abstract
Satellite DNAs (satDNA) are tandemly arrayed repeated sequences largely present in eukaryotic genomes, which play important roles in genome evolution and function, and therefore, their analysis is vital. Here, we describe the isolation of a novel satellite DNA family (PMSat) from the rodent Peromyscus eremicus (Cricetidae, Rodentia), which is located in pericentromeric regions and exhibits a typical satellite DNA genome organization. Orthologous PMSat sequences were isolated and characterized from three species belonging to Cricetidae: Cricetus cricetus, Phodopus sungorus and Microtus arvalis. In these species, PMSat is highly conserved, with the absence of fixed species-specific mutations. Strikingly, different numbers of copies of this sequence were found among the species, suggesting evolution by copy number fluctuation. Repeat units of PMSat were also found in the Peromyscus maniculatus bairdii BioProject, but our results suggest that these repeat units are from genome regions outside the pericentromere. The remarkably high evolutionary sequence conservation along with the preservation of a few numbers of copies of this sequence in the analyzed genomes may suggest functional significance but a different sequence nature/organization. Our data highlight that repeats are difficult to analyze due to the limited tools available to dissect genomes and the fact that assemblies do not cover regions of constitutive heterochromatin.
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Affiliation(s)
- Sandra Louzada
- University of Trás-os-Montes and Alto Douro (UTAD), Department of Genetics and Biotechnology (DGB), Laboratory of Cytogenomics and Animal Genomics (CAG), Apdo 1013, 5001-801 Vila Real, Portugal
| | - Ana Vieira-da-Silva
- University of Trás-os-Montes and Alto Douro (UTAD), Department of Genetics and Biotechnology (DGB), Laboratory of Cytogenomics and Animal Genomics (CAG), Apdo 1013, 5001-801 Vila Real, Portugal; University of Lisboa, Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, Campo Grande, Lisboa, Portugal
| | - Ana Mendes-da-Silva
- University of Trás-os-Montes and Alto Douro (UTAD), Department of Genetics and Biotechnology (DGB), Laboratory of Cytogenomics and Animal Genomics (CAG), Apdo 1013, 5001-801 Vila Real, Portugal; University of Lisboa, Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, Campo Grande, Lisboa, Portugal
| | | | - Jiri Rubes
- Veterinary Research Institute, Brno, Czech Republic
| | - Filomena Adega
- University of Trás-os-Montes and Alto Douro (UTAD), Department of Genetics and Biotechnology (DGB), Laboratory of Cytogenomics and Animal Genomics (CAG), Apdo 1013, 5001-801 Vila Real, Portugal; University of Lisboa, Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, Campo Grande, Lisboa, Portugal
| | - Raquel Chaves
- University of Trás-os-Montes and Alto Douro (UTAD), Department of Genetics and Biotechnology (DGB), Laboratory of Cytogenomics and Animal Genomics (CAG), Apdo 1013, 5001-801 Vila Real, Portugal; University of Lisboa, Faculty of Sciences, BioISI - Biosystems & Integrative Sciences Institute, Campo Grande, Lisboa, Portugal.
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Hsieh LJ, Cheng YM, Wang YC, Lin CC, Li YC. Organization and evolution of a novel cervid satellite DNA with yeast CDEI-like repeats. Zool Stud 2014. [DOI: 10.1186/s40555-014-0025-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Abstract
Background
It has been proposed that pericentromeric satellite DNA arises from the progressive proximal expansion of ancient centromeric DNA. In an attempt to recover putative ancestral centromeric DNA, we microdissected the pericentromeric/centromeric DNA from the chromosome X + 3 of Indian muntjac (Muntiacus muntjak vaginalis) and constructed a microclone-library of the X + 3 centromeric DNA.
Results
A new cervid satellite DNA element, designated as satellite VI, was isolated from this library. Fluorescence in situ hybridization (FISH) studies revealed that satellite VI is predominately located on the distal pericentromeric region of the Indian muntjac chromosome X + 3 and on the pericentromeres of several Old World deer species studied. Its sequence is organized as 11-bp monomeric (ATCACGTGGGA) tandem repeats. Further sequencing on a BAC clone of Indian muntjac harboring this repeat showed that an array of this repeat stretches over approximately 5 kb followed by approximately 3 kb of interspersed repetitive sequences, such as long interspersed elements (LINEs), short interspersed elements (SINEs), and long terminal repeats (LTRs).
Conclusions
Based on the chromosomal localization, genomic and sequence organization, and copy numbers of satellite VI in deer species studied, we postulate that this newly found satellite DNA could be a putative ancient cervidic centromeric DNA that is still preserved in some Old World deer. Interestingly, the first eight nucleotides of the 11-bp monomeric consensus sequences are highly conserved and identical to the CDEI element in the centromere of the budding yeast Saccharomyces cerevisiae. The centromeric/pericentromeric satellite DNA harboring abundant copies of CDEI sequences is the first found in a mammalian species. Several zipper-like d (GGGA)2 motifs were also found in the (ATCACGTGGGA)n repeat of satellite VI DNA. Whether the satellite VI is structurally and functionally correlated with the CDEI of centromere of budding yeast and whether a zipper-like structure forms in satellite VI require further studies.
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Molina W, Jacobina U. Protocolos Citogenéticos e Perspectivas Biotecnológicas Voltadas à Piscicultura Marinha e Conservação. BIOTA AMAZÔNIA 2013. [DOI: 10.18561/2179-5746/biotaamazonia.v3n2p155-168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
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Pazian MF, Shimabukuro-Dias CK, Pansonato-Alves JC, Oliveira C, Foresti F. Chromosome painting of Z and W sex chromosomes in Characidium (Characiformes, Crenuchidae). Genetica 2013; 141:1-9. [PMID: 23344657 DOI: 10.1007/s10709-013-9701-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2012] [Accepted: 01/17/2013] [Indexed: 01/23/2023]
Abstract
Some species of the genus Characidium have heteromorphic ZZ/ZW sex chromosomes with a totally heterochromatic W chromosome. Methods for chromosome microdissection associated with chromosome painting have become important tools for cytogenetic studies in Neotropical fish. In Characidium cf. fasciatum, the Z chromosome contains a pericentromeric heterochromatin block, whereas the W chromosome is completely heterochromatic. Therefore, a probe was produced from the W chromosome through microdissection and degenerate oligonucleotide-primed polymerase chain reaction amplification. FISH was performed using the W probe on the chromosomes of specimens of this species. This revealed expressive marks in the pericentromeric region of the Z chromosome as well as a completely painted W chromosome. When applying the same probe on chromosome preparations of C. cf. gomesi and Characidium sp., a pattern similar to C. cf. fasciatum was found, while C. cf. zebra, C. cf. lagosantense and Crenuchus spilurus species showed no hybridization signals. Structural changes in the chromosomes of an ancestral sexual system in the group that includes the species C. cf. gomesi, C. cf. fasciatum and Characidium sp., could have contributed to the process of speciation and could represent a causal mechanism of chromosomal diversification in this group. The heterochromatinization process possibly began in homomorphic and homologous chromosomes of an ancestral form, and this process could have given rise to the current patterns found in the species with sex chromosome heteromorphism.
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Affiliation(s)
- Marlon F Pazian
- Laboratório de Biologia e Genética de Peixes, Departamento de Morfologia, Instituto de Biociências, Universidade Estadual Paulista, Distrito de Rubião Junior S/N, Rubião Júnior, Botucatu, SP, Brazil.
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Cheng YM, Li TS, Hsieh LJ, Hsu PC, Li YC, Lin CC. Complex genomic organization of Indian muntjac centromeric DNA. Chromosome Res 2009; 17:1051-62. [PMID: 19921447 DOI: 10.1007/s10577-009-9097-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2009] [Revised: 10/27/2009] [Accepted: 10/28/2009] [Indexed: 11/29/2022]
Abstract
A 69-kb Indian muntjac bacterial artificial chromosome (BAC) clone that screened positive for Cervid satellites I and IV was selected for complete sequence analysis and further characterization. The sequences of this BAC clone were found in the centromeres and in some interstitial sites of Indian muntjac chromosomes. Sequence analyses showed that the BAC clone contained a 14.5 kb Cervid satellite I-like DNA element and a 9 kb Cervid satellite IV-like DNA element. In addition, it contained 51 regions each organized in a complex fashion, with sequences homology to intersperse repetitive sequences such as LINEs, SINEs, LTRs, other published DNA elements, and unassigned sequences. The FISH patterns of seven non-satellite sequence elements generated from the BAC clone showed mainly specific to centromeres of the Indian muntjac representing novel centromeric DNAs of the species. Furthermore, FISH signals and Southern blot patterns of these elements suggest the existence of a not yet identified repetitive sequence with giant repeated monomers. Positive FISH signals of these elements were also detected in the centromeric regions of Formosan muntjac. This suggests that these newly identified non-Cervid satellite DNA sequences have been conserved in the centromere of the Formosan muntjac.
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Affiliation(s)
- Ya-Ming Cheng
- Department of Agronomy, National Chung Hsing University, Taichung, 402, Taiwan
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Pang H, Liu W, Chen Y, Fang L, Zhang X, Cao X. Identification of complete mitochondrial genome of the tufted deer. ACTA ACUST UNITED AC 2009; 19:411-7. [PMID: 19462515 DOI: 10.1080/19401730802389517] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
The tufted deer Elaphodus cephalophus are endangered animals in the world and little is understood about their mitochondrial (mt) genome. In our study, the mt genome of the tufted deer is identified--which is about 16 kb in length and contains 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes and a non-coding sequence (control region). The distinguishing feature is that GTG is the start codon of the NADH4L gene and the cyt b gene has a subterminal AAA followed by the stop codon TAG. According to 12 H strand protein-coding genes and phylogenetic analysis, Elaphodus may have a sister relationship with another deer group Muntiacus.
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Affiliation(s)
- Hong Pang
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, PR China
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FISH glossary: an overview of the fluorescence in situ hybridization technique. Biotechniques 2008; 45:385-6, 388, 390 passim. [PMID: 18855767 DOI: 10.2144/000112811] [Citation(s) in RCA: 91] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The introduction of FISH (fluorescence in situ hybridization) marked the beginning of a new era for the study of chromosome structure and function. As a combined molecular and cytological approach, the major advantage of this visually appealing technique resides in its unique ability to provide an intermediate degree of resolution between DNA analysis and chromosomal investigations while retaining information at the single-cell level. Used to support large-scale mapping and sequencing efforts related to the human genome project, FISH accuracy and versatility were subsequently capitalized on in biological and medical research, providing a wealth of diverse applications and FISH-based diagnostic assays. The diversification of the original FISH protocol into the impressive number of procedures available these days has been promoted throughout the years by a number of interconnected factors: the improvement in sensitivity, specificity and resolution, together with the advances in the fields of fluorescence microscopy and digital imaging, and the growing availability of genomic and bioinformatic resources. By assembling in a glossary format many of the "acronymed" FISH applications published so far, this review intends to celebrate the ability of FISH to re-invent itself and thus remain at the forefront of biomedical research.
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Bulazel KV, Ferreri GC, Eldridge MDB, O'Neill RJ. Species-specific shifts in centromere sequence composition are coincident with breakpoint reuse in karyotypically divergent lineages. Genome Biol 2008; 8:R170. [PMID: 17708770 PMCID: PMC2375000 DOI: 10.1186/gb-2007-8-8-r170] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2007] [Accepted: 08/20/2007] [Indexed: 11/12/2022] Open
Abstract
The evolution of three classes of centromere sequences across nine species of macropodine marsupials were compared with that of other genes, showing that each species has experienced differential expansion and contraction of individual classes. Background It has been hypothesized that rapid divergence in centromere sequences accompanies rapid karyotypic change during speciation. However, the reuse of breakpoints coincident with centromeres in the evolution of divergent karyotypes poses a potential paradox. In distantly related species where the same centromere breakpoints are used in the independent derivation of karyotypes, centromere-specific sequences may undergo convergent evolution rather than rapid sequence divergence. To determine whether centromere sequence composition follows the phylogenetic history of species evolution or patterns of convergent breakpoint reuse through chromosome evolution, we examined the phylogenetic trajectory of centromere sequences within a group of karyotypically diverse mammals, macropodine marsupials (wallabies, wallaroos and kangaroos). Results The evolution of three classes of centromere sequences across nine species within the genus Macropus (including Wallabia) were compared with the phylogenetic history of a mitochondrial gene, Cytochrome b (Cyt b), a nuclear gene, selenocysteine tRNA (TRSP), and the chromosomal histories of the syntenic blocks that define the different karyotype arrangements. Convergent contraction or expansion of predominant satellites is found to accompany specific karyotype rearrangements. The phylogenetic history of these centromere sequences includes the convergence of centromere composition in divergent species through convergent breakpoint reuse between syntenic blocks. Conclusion These data support the 'library hypothesis' of centromere evolution within this genus as each species possesses all three satellites yet each species has experienced differential expansion and contraction of individual classes. Thus, we have identified a correlation between the evolution of centromere satellite sequences, the reuse of syntenic breakpoints, and karyotype convergence in the context of a gene-based phylogeny.
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Affiliation(s)
- Kira V Bulazel
- Department of Molecular and Cell Biology, Mansfield Rd, University of Connecticut, Storrs, CT 06269, USA
| | - Gianni C Ferreri
- Department of Molecular and Cell Biology, Mansfield Rd, University of Connecticut, Storrs, CT 06269, USA
| | - Mark DB Eldridge
- Department of Biological Sciences, Macquarie University, NSW 2109, Australia
- Molecular Biology, Australian Museum, College St, Sydney, NSW 2010, Australia
| | - Rachel J O'Neill
- Department of Molecular and Cell Biology, Mansfield Rd, University of Connecticut, Storrs, CT 06269, USA
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Lin CC, Li YC. Chromosomal distribution and organization of three cervid satellite DNAs in Chinese water deer (Hydropotes inermis). Cytogenet Genome Res 2006; 114:147-54. [PMID: 16825767 DOI: 10.1159/000093331] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2005] [Accepted: 01/24/2006] [Indexed: 11/19/2022] Open
Abstract
The species-specific profile and centromeric heterochromatin localization of satellite DNA in mammalian genomes imply that satellite DNA may play an important role in mammalian karyotype evolution and speciation. A satellite III DNA family, CCsatIII was thought to be specific to roe deer (Capreolus capreolus). In this study, however, this satellite DNA family was found also to exist in Chinese water deer (Hydropotes inermis) by PCR-Southern screening. A satellite III DNA element of this species was then generated from PCR-cloning by amplifying this satellite element using primer sequences from the roe deer satellite III clone (CCsatIII). The newly generated satellite III DNA along with previously obtained satellite I and II DNA clones were used as probes for FISH studies to investigate the genomic distribution and organization of these three satellite DNA families in centromeric heterochromatin regions of Chinese water deer chromosomes. Satellite I and II DNA were observed in the pericentric/centric regions of all chromosomes, whereas satellite III was distributed on 38 out of 70 chromosomes. The distribution and orientation of satellite DNAs I, II and III in the centromeric heterochromatin regions of the genome were further classified into four different types. The existence of a Capreolus-like satellite III in Chinese water deer implies that satellite III is not specific to the genus Capreolus (Buntjer et al., 1998) and supports the molecular phylogeny classification of Randi et al. (1998) which suggests that Chinese water deer and roe deer are closely related.
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Affiliation(s)
- C C Lin
- Department of Medical Research, China Medical University Hospital, Taichung, Taiwan
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