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Yurchenko A, Pšenička T, Mora P, Ortega JAM, Baca AS, Rovatsos M. Cytogenetic Analysis of Satellitome of Madagascar Leaf-Tailed Geckos. Genes (Basel) 2024; 15:429. [PMID: 38674364 PMCID: PMC11049218 DOI: 10.3390/genes15040429] [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: 03/04/2024] [Revised: 03/21/2024] [Accepted: 03/25/2024] [Indexed: 04/28/2024] Open
Abstract
Satellite DNA (satDNA) consists of sequences of DNA that form tandem repetitions across the genome, and it is notorious for its diversity and fast evolutionary rate. Despite its importance, satDNA has been only sporadically studied in reptile lineages. Here, we sequenced genomic DNA and PCR-amplified microdissected W chromosomes on the Illumina platform in order to characterize the monomers of satDNA from the Henkel's leaf-tailed gecko U. henkeli and to compare their topology by in situ hybridization in the karyotypes of the closely related Günther's flat-tail gecko U. guentheri and gold dust day gecko P. laticauda. We identified seventeen different satDNAs; twelve of them seem to accumulate in centromeres, telomeres and/or the W chromosome. Notably, centromeric and telomeric regions seem to share similar types of satDNAs, and we found two that seem to accumulate at both edges of all chromosomes in all three species. We speculate that the long-term stability of all-acrocentric karyotypes in geckos might be explained from the presence of specific satDNAs at the centromeric regions that are strong meiotic drivers, a hypothesis that should be further tested.
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Affiliation(s)
- Alona Yurchenko
- Department of Ecology, Faculty of Science, Charles University, 128 44 Prague, Czech Republic; (A.Y.); (T.P.)
| | - Tomáš Pšenička
- Department of Ecology, Faculty of Science, Charles University, 128 44 Prague, Czech Republic; (A.Y.); (T.P.)
| | - Pablo Mora
- Department of Experimental Biology, Faculty of Experimental Sciences, University of Jaén, Campus Las Lagunillas s/n, E-23071 Jaen, Spain; (P.M.); (J.A.M.O.); (A.S.B.)
| | - Juan Alberto Marchal Ortega
- Department of Experimental Biology, Faculty of Experimental Sciences, University of Jaén, Campus Las Lagunillas s/n, E-23071 Jaen, Spain; (P.M.); (J.A.M.O.); (A.S.B.)
| | - Antonio Sánchez Baca
- Department of Experimental Biology, Faculty of Experimental Sciences, University of Jaén, Campus Las Lagunillas s/n, E-23071 Jaen, Spain; (P.M.); (J.A.M.O.); (A.S.B.)
| | - Michail Rovatsos
- Department of Ecology, Faculty of Science, Charles University, 128 44 Prague, Czech Republic; (A.Y.); (T.P.)
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2
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Iannuzzi A, Pistucci R, Perucatti A, Zannotti M, Iannuzzi L, Parma P. Characterization of Robertsonian and Reciprocal Translocations in Cattle through NGS. Animals (Basel) 2023; 13:3018. [PMID: 37835624 PMCID: PMC10571785 DOI: 10.3390/ani13193018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 09/14/2023] [Accepted: 09/22/2023] [Indexed: 10/15/2023] Open
Abstract
This study presents a novel approach that combines next-generation sequencing (NGS) and cytogenetic technologies for identifying chromosomes involved in chromosomal anomalies. This research focuses on a chromosome anomaly discovered in male Alpine Grey cattle, as well as two previously reported cases of reciprocal translocations (rcps), namely rcp(9;11) and rcp(4;7). Abnormal chromosomes from Alpine Grey cattle were microdissected from conventional preparations, and the amplified products were sequenced using NGS. The sequencing reads were then mapped to the reference genome, and the leverage effect was calculated to identify abnormal reads/Mb values. The result revealed the presence of rob(26;29), which was further confirmed through traditional cytogenetic analyses such as Giemsa staining, CBA-banding, RBA-banding, and FISH techniques. Furthermore, the feasibility of this approach on preserved metaphases was demonstrated through analysis of old slides from previously characterized cases. The study highlights the challenges involved in identifying and characterizing chromosomal aberrations in bovine species and offers a potential solution for analyzing historical anomalies when fresh blood material is unavailable. The combination of NGS and cytogenetic techniques provides a cost-effective and reliable approach for characterizing chromosomal anomalies in various species, including those identified before the availability of modern banding technologies and FISH mapping using specific molecular markers.
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Affiliation(s)
- Alessandra Iannuzzi
- Institute for Animal Production System in Mediterranean Environment (ISPAAM), National Research Council (CNR), 80055 Portici, Italy; (R.P.); (A.P.); (L.I.)
| | - Ramona Pistucci
- Institute for Animal Production System in Mediterranean Environment (ISPAAM), National Research Council (CNR), 80055 Portici, Italy; (R.P.); (A.P.); (L.I.)
| | - Angela Perucatti
- Institute for Animal Production System in Mediterranean Environment (ISPAAM), National Research Council (CNR), 80055 Portici, Italy; (R.P.); (A.P.); (L.I.)
| | - Michele Zannotti
- Department of Agricultural and Environmental Sciences, University of Milan, 20133 Milan, Italy; (M.Z.); (P.P.)
| | - Leopoldo Iannuzzi
- Institute for Animal Production System in Mediterranean Environment (ISPAAM), National Research Council (CNR), 80055 Portici, Italy; (R.P.); (A.P.); (L.I.)
| | - Pietro Parma
- Department of Agricultural and Environmental Sciences, University of Milan, 20133 Milan, Italy; (M.Z.); (P.P.)
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3
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Molecular Cytogenetics in Domestic Bovids: A Review. Animals (Basel) 2023; 13:ani13050944. [PMID: 36899801 PMCID: PMC10000107 DOI: 10.3390/ani13050944] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 02/28/2023] [Accepted: 03/02/2023] [Indexed: 03/08/2023] Open
Abstract
The discovery of the Robertsonian translocation (rob) involving cattle chromosomes 1 and 29 and the demonstration of its deleterious effects on fertility focused the interest of many scientific groups on using chromosome banding techniques to reveal chromosome abnormalities and verify their effects on fertility in domestic animals. At the same time, comparative banding studies among various species of domestic or wild animals were found useful for delineating chromosome evolution among species. The advent of molecular cytogenetics, particularly the use of fluorescence in situ hybridization (FISH), has allowed a deeper investigation of the chromosomes of domestic animals through: (a) the physical mapping of specific DNA sequences on chromosome regions; (b) the use of specific chromosome markers for the identification of the chromosomes or chromosome regions involved in chromosome abnormalities, especially when poor banding patterns are produced; (c) better anchoring of radiation hybrid and genetic maps to specific chromosome regions; (d) better comparisons of related and unrelated species by comparative FISH mapping and/or Zoo-FISH techniques; (e) the study of meiotic segregation, especially by sperm-FISH, in some chromosome abnormalities; (f) better demonstration of conserved or lost DNA sequences in chromosome abnormalities; (g) the use of informatic and genomic reconstructions, in addition to CGH arrays, to predict conserved or lost chromosome regions in related species; and (h) the study of some chromosome abnormalities and genomic stability using PCR applications. This review summarizes the most important applications of molecular cytogenetics in domestic bovids, with an emphasis on FISH mapping applications.
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4
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Li Y, Wang S, Zhang Z, Luo J, Lin GL, Deng WD, Guo Z, Han FM, Wang LL, Li J, Wu SF, Liu HQ, He S, Murphy RW, Zhang ZJ, Cooper DN, Wu DD, Zhang YP. Large-Scale Chromosomal Changes Lead to Genome-Level Expression Alterations, Environmental Adaptation, and Speciation in the Gayal (Bos frontalis). Mol Biol Evol 2023; 40:6980758. [PMID: 36625089 PMCID: PMC9874039 DOI: 10.1093/molbev/msad006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 12/20/2022] [Accepted: 01/05/2023] [Indexed: 01/11/2023] Open
Abstract
Determining the functional consequences of karyotypic changes is invariably challenging because evolution tends to obscure many of its own footprints, such as accumulated mutations, recombination events, and demographic perturbations. Here, we describe the assembly of a chromosome-level reference genome of the gayal (Bos frontalis) thereby revealing the structure, at base-pair-level resolution, of a telo/acrocentric-to-telo/acrocentric Robertsonian translocation (2;28) (T/A-to-T/A rob[2;28]). The absence of any reduction in the recombination rate or genetic introgression within the fusion region of gayal served to challenge the long-standing view of a role for fusion-induced meiotic dysfunction in speciation. The disproportionate increase noted in the distant interactions across pro-chr2 and pro-chr28, and the change in open-chromatin accessibility following rob(2;28), may, however, have led to the various gene expression irregularities observed in the gayal. Indeed, we found that many muscle-related genes, located synthetically on pro-chr2 and pro-chr28, exhibited significant changes in expression. This, combined with genome-scale structural variants and expression alterations in genes involved in myofibril composition, may have driven the rapid sarcomere adaptation of gayal to its rugged mountain habitat. Our findings not only suggest that large-scale chromosomal changes can lead to alterations in genome-level expression, thereby promoting both adaptation and speciation, but also illuminate novel avenues for studying the relationship between karyotype evolution and speciation.
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Affiliation(s)
- Yan Li
- Corresponding authors: E-mails: ;
| | | | | | | | | | | | | | | | - Li-Li Wang
- Biomarker Technologies Corporation, Beijing, China
| | - Jie Li
- State Key Laboratory for Conservation and Utilization of Bio-resource in Yunnan and School of Ecology and Environmental Science, Yunnan University, Kunming, China
| | - Shi-Fang Wu
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - He-Qun Liu
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Sheng He
- Nujiang Livestock Technology Promotion Station, Nujiang, China
| | - Robert W Murphy
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China,Centre for Biodiversity and Conservation Biology, Royal Ontario Museum, Toronto, ON, Canada
| | - Zi-Jie Zhang
- State Key Laboratory for Conservation and Utilization of Bio-resource in Yunnan and School of Ecology and Environmental Science, Yunnan University, Kunming, China
| | - David N Cooper
- Institute of Medical Genetics, Cardiff University, Cardiff, United Kingdom
| | - Dong-Dong Wu
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China,Kunming Natural History Museum of Zoology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
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5
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Chen Y, Zhang T, Xian M, Zhang R, Yang W, Su B, Yang G, Sun L, Xu W, Xu S, Gao H, Xu L, Gao X, Li J. A draft genome of Drung cattle reveals clues to its chromosomal fusion and environmental adaptation. Commun Biol 2022; 5:353. [PMID: 35418663 PMCID: PMC9008013 DOI: 10.1038/s42003-022-03298-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 03/21/2022] [Indexed: 12/02/2022] Open
Abstract
Drung cattle (Bos frontalis) have 58 chromosomes, differing from the Bos taurus 2n = 60 karyotype. To date, its origin and evolution history have not been proven conclusively, and the mechanisms of chromosome fusion and environmental adaptation have not been clearly elucidated. Here, we assembled a high integrity and good contiguity genome of Drung cattle with 13.7-fold contig N50 and 4.1-fold scaffold N50 improvements over the recently published Indian mithun assembly, respectively. Speciation time estimation and phylogenetic analysis showed that Drung cattle diverged from Bos taurus into an independent evolutionary clade. Sequence evidence of centromere regions provides clues to the breakpoints in BTA2 and BTA28 centromere satellites. We furthermore integrated a circulation and contraction-related biological process involving 43 evolutionary genes that participated in pathways associated with the evolution of the cardiovascular system. These findings may have important implications for understanding the molecular mechanisms of chromosome fusion, alpine valleys adaptability and cardiovascular function.
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Affiliation(s)
- Yan Chen
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, 100193, Beijing, P.R. China
| | - Tianliu Zhang
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, 100193, Beijing, P.R. China
| | - Ming Xian
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, 100193, Beijing, P.R. China
| | - Rui Zhang
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, 100193, Beijing, P.R. China
| | - Weifei Yang
- 1 Gene Co., Ltd, 310051, Hangzhou, P.R. China
- Annoroad Gene Technology (Beijing) Co., Ltd, 100176, Beijing, P.R. China
| | - Baqi Su
- Drung Cattle Conservation Farm in Jiudang Wood, Drung and Nu Minority Autonomous County, Gongshan, 673500, Kunming, Yunnan, P.R. China
| | - Guoqiang Yang
- Livestock and Poultry Breed Improvement Center, Nujiang Lisu Minority Autonomous Prefecture, 673199, Kunming, Yunnan, P.R. China
| | - Limin Sun
- Yunnan Animal Husbandry Service, 650224, Kunming, Yunnan, P.R. China
| | - Wenkun Xu
- Yunnan Animal Husbandry Service, 650224, Kunming, Yunnan, P.R. China
| | - Shangzhong Xu
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, 100193, Beijing, P.R. China
| | - Huijiang Gao
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, 100193, Beijing, P.R. China
| | - Lingyang Xu
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, 100193, Beijing, P.R. China
| | - Xue Gao
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, 100193, Beijing, P.R. China.
| | - Junya Li
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, 100193, Beijing, P.R. China.
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6
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Escudeiro A, Adega F, Robinson TJ, Heslop-Harrison JS, Chaves R. Analysis of the Robertsonian (1;29) fusion in Bovinae reveals a common mechanism: insights into its clinical occurrence and chromosomal evolution. Chromosome Res 2021; 29:301-312. [PMID: 34331632 DOI: 10.1007/s10577-021-09667-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 07/11/2021] [Accepted: 07/14/2021] [Indexed: 10/20/2022]
Abstract
The interest in Robertsonian fusion chromosomes (Rb fusions), sometimes referred to as Robertsonian translocations, derives from their impact on mammalian karyotype evolution, as well from their influence on fertility and disease. The formation of a Rb chromosome necessitates the occurrence of double strand breaks in the pericentromeric regions of two chromosomes in the satellite DNA (satDNA) sequences. Here, we report on the fine-scale molecular analysis of the centromeric satDNA families in the Rb(1;29) translocation of domestic cattle and six antelope species of the subfamily Bovinae. We do so from two perspectives: its occurrence as a chromosomal abnormality in cattle and, secondly, as a fixed evolutionarily rearrangement in spiral-horned antelope (Tragelaphini). By analysing the reorganization of satDNAs in the centromeric regions of translocated chromosomes, we show that Rb fusions are multistep, complex rearrangements which entail the precise elimination and reorganization of specific (peri)centromeric satDNA sequences. Importantly, these structural changes do not influence the centromeric activity of the satellite DNAs that provide segregation stability to the translocated chromosome. Our results suggest a common mechanism for Rb fusions in these bovids and, more widely, for mammals in general.
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Affiliation(s)
- A Escudeiro
- Department of Genetics and Biotechnology (DGB), CAG - Laboratory of Cytogenomics and Animal Genomics, University of Trás-os-Montes e Alto Douro, Vila Real, Portugal.,BioISI - Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisbon, Lisbon, Portugal
| | - F Adega
- Department of Genetics and Biotechnology (DGB), CAG - Laboratory of Cytogenomics and Animal Genomics, University of Trás-os-Montes e Alto Douro, Vila Real, Portugal.,BioISI - Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisbon, Lisbon, Portugal
| | - T J Robinson
- Department of Botany and Zoology, Stellenbosch University, Stellenbosch, South Africa
| | - J S Heslop-Harrison
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - R Chaves
- Department of Genetics and Biotechnology (DGB), CAG - Laboratory of Cytogenomics and Animal Genomics, University of Trás-os-Montes e Alto Douro, Vila Real, Portugal. .,BioISI - Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisbon, Lisbon, Portugal.
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7
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Louzada S, Lopes M, Ferreira D, Adega F, Escudeiro A, Gama-Carvalho M, Chaves R. Decoding the Role of Satellite DNA in Genome Architecture and Plasticity-An Evolutionary and Clinical Affair. Genes (Basel) 2020; 11:E72. [PMID: 31936645 PMCID: PMC7017282 DOI: 10.3390/genes11010072] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 12/29/2019] [Accepted: 01/08/2020] [Indexed: 12/11/2022] Open
Abstract
Repetitive DNA is a major organizational component of eukaryotic genomes, being intrinsically related with their architecture and evolution. Tandemly repeated satellite DNAs (satDNAs) can be found clustered in specific heterochromatin-rich chromosomal regions, building vital structures like functional centromeres and also dispersed within euchromatin. Interestingly, despite their association to critical chromosomal structures, satDNAs are widely variable among species due to their high turnover rates. This dynamic behavior has been associated with genome plasticity and chromosome rearrangements, leading to the reshaping of genomes. Here we present the current knowledge regarding satDNAs in the light of new genomic technologies, and the challenges in the study of these sequences. Furthermore, we discuss how these sequences, together with other repeats, influence genome architecture, impacting its evolution and association with disease.
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Affiliation(s)
- Sandra Louzada
- Laboratory of Cytogenomics and Animal Genomics (CAG), Department of Genetics and Biotechnology (DGB), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal; (S.L.); (M.L.); (D.F.); (F.A.); (A.E.)
- Biosystems and Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisboa, 1749-016 Lisbon, Portugal;
| | - Mariana Lopes
- Laboratory of Cytogenomics and Animal Genomics (CAG), Department of Genetics and Biotechnology (DGB), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal; (S.L.); (M.L.); (D.F.); (F.A.); (A.E.)
- Biosystems and Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisboa, 1749-016 Lisbon, Portugal;
| | - Daniela Ferreira
- Laboratory of Cytogenomics and Animal Genomics (CAG), Department of Genetics and Biotechnology (DGB), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal; (S.L.); (M.L.); (D.F.); (F.A.); (A.E.)
- Biosystems and Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisboa, 1749-016 Lisbon, Portugal;
| | - Filomena Adega
- Laboratory of Cytogenomics and Animal Genomics (CAG), Department of Genetics and Biotechnology (DGB), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal; (S.L.); (M.L.); (D.F.); (F.A.); (A.E.)
- Biosystems and Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisboa, 1749-016 Lisbon, Portugal;
| | - Ana Escudeiro
- Laboratory of Cytogenomics and Animal Genomics (CAG), Department of Genetics and Biotechnology (DGB), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal; (S.L.); (M.L.); (D.F.); (F.A.); (A.E.)
- Biosystems and Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisboa, 1749-016 Lisbon, Portugal;
| | - Margarida Gama-Carvalho
- Biosystems and Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisboa, 1749-016 Lisbon, Portugal;
| | - Raquel Chaves
- Laboratory of Cytogenomics and Animal Genomics (CAG), Department of Genetics and Biotechnology (DGB), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal; (S.L.); (M.L.); (D.F.); (F.A.); (A.E.)
- Biosystems and Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisboa, 1749-016 Lisbon, Portugal;
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8
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Smalec BM, Heider TN, Flynn BL, O'Neill RJ. A centromere satellite concomitant with extensive karyotypic diversity across the Peromyscus genus defies predictions of molecular drive. Chromosome Res 2019; 27:237-252. [PMID: 30771198 PMCID: PMC6733818 DOI: 10.1007/s10577-019-09605-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 01/26/2019] [Accepted: 01/29/2019] [Indexed: 12/17/2022]
Abstract
A common feature of eukaryotic centromeres is the presence of large tracts of tandemly arranged repeats, known as satellite DNA. However, these centromeric repeats appear to experience rapid evolution under forces such as molecular drive and centromere drive, seemingly without consequence to the integrity of the centromere. Moreover, blocks of heterochromatin within the karyotype, including the centromere, are hotspots for chromosome rearrangements that may drive speciation events by contributing to reproductive isolation. However, the relationship between the evolution of heterochromatic sequences and the karyotypic dynamics of these regions remains largely unknown. Here, we show that a single conserved satellite DNA sequence in the order Rodentia of the genus Peromyscus localizes to recurrent sites of chromosome rearrangements and heterochromatic amplifications. Peromyscine species display several unique features of chromosome evolution compared to other Rodentia, including stable maintenance of a strict chromosome number of 48 among all known species in the absence of any detectable interchromosomal rearrangements. Rather, the diverse karyotypes of Peromyscine species are due to intrachromosomal variation in blocks of repeated DNA content. Despite wide variation in the copy number and location of repeat blocks among different species, we find that a single satellite monomer maintains a conserved sequence and homogenized tandem repeat structure, defying predictions of molecular drive. The conservation of this satellite monomer results in common, abundant, and large blocks of chromatin that are homologous among chromosomes within one species and among diverged species. Thus, such a conserved repeat may have facilitated the retention of polymorphic chromosome variants within individuals and intrachromosomal rearrangements between species-both factors that have previously been hypothesized to contribute towards the extremely wide range of ecological adaptations that this genus exhibits.
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Affiliation(s)
- Brendan M Smalec
- Institute for Systems Genomics and Department of Molecular and Cell Biology, University of Connecticut, 67 North Eagleville Road, Unit 3127, Storrs, CT, 06269, USA
| | - Thomas N Heider
- Institute for Systems Genomics and Department of Molecular and Cell Biology, University of Connecticut, 67 North Eagleville Road, Unit 3127, Storrs, CT, 06269, USA
| | - Brianna L Flynn
- Institute for Systems Genomics and Department of Molecular and Cell Biology, University of Connecticut, 67 North Eagleville Road, Unit 3127, Storrs, CT, 06269, USA
| | - Rachel J O'Neill
- Institute for Systems Genomics and Department of Molecular and Cell Biology, University of Connecticut, 67 North Eagleville Road, Unit 3127, Storrs, CT, 06269, USA.
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9
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Escudeiro A, Adega F, Robinson TJ, Heslop-Harrison JS, Chaves R. Conservation, Divergence, and Functions of Centromeric Satellite DNA Families in the Bovidae. Genome Biol Evol 2019; 11:1152-1165. [PMID: 30888421 PMCID: PMC6475130 DOI: 10.1093/gbe/evz061] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/18/2019] [Indexed: 12/18/2022] Open
Abstract
Repetitive satellite DNA (satDNA) sequences are abundant in eukaryote genomes, with a structural and functional role in centromeric function. We analyzed the nucleotide sequence and chromosomal location of the five known cattle (Bos taurus) satDNA families in seven species from the tribe Tragelaphini (Bovinae subfamily). One of the families (SAT1.723) was present at the chromosomes’ centromeres of the Tragelaphini species, as well in two more distantly related bovid species, Ovis aries and Capra hircus. Analysis of the interaction of SAT1.723 with centromeric proteins revealed that this satDNA sequence is involved in the centromeric activity in all the species analyzed and that it is preserved for at least 15–20 Myr across Bovidae species. The satDNA sequence similarity among the analyzed species reflected different stages of homogeneity/heterogeneity, revealing the evolutionary history of each satDNA family. The SAT1.723 monomer-flanking regions showed the presence of transposable elements, explaining the extensive shuffling of this satDNA between different genomic regions.
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Affiliation(s)
- Ana Escudeiro
- Department of Genetics and Biotechnology, CAG - Laboratory of Cytogenomics and Animal Genomics, University of Trás-os-Montes e Alto Douro, Vila Real, Portugal.,BioISI - Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Portugal
| | - Filomena Adega
- Department of Genetics and Biotechnology, CAG - Laboratory of Cytogenomics and Animal Genomics, University of Trás-os-Montes e Alto Douro, Vila Real, Portugal.,BioISI - Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Portugal
| | | | | | - Raquel Chaves
- Department of Genetics and Biotechnology, CAG - Laboratory of Cytogenomics and Animal Genomics, University of Trás-os-Montes e Alto Douro, Vila Real, Portugal.,BioISI - Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Portugal
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10
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Centromere Repeats: Hidden Gems of the Genome. Genes (Basel) 2019; 10:genes10030223. [PMID: 30884847 PMCID: PMC6471113 DOI: 10.3390/genes10030223] [Citation(s) in RCA: 88] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 03/07/2019] [Accepted: 03/11/2019] [Indexed: 01/08/2023] Open
Abstract
Satellite DNAs are now regarded as powerful and active contributors to genomic and chromosomal evolution. Paired with mobile transposable elements, these repetitive sequences provide a dynamic mechanism through which novel karyotypic modifications and chromosomal rearrangements may occur. In this review, we discuss the regulatory activity of satellite DNA and their neighboring transposable elements in a chromosomal context with a particular emphasis on the integral role of both in centromere function. In addition, we discuss the varied mechanisms by which centromeric repeats have endured evolutionary processes, producing a novel, species-specific centromeric landscape despite sharing a ubiquitously conserved function. Finally, we highlight the role these repetitive elements play in the establishment and functionality of de novo centromeres and chromosomal breakpoints that underpin karyotypic variation. By emphasizing these unique activities of satellite DNAs and transposable elements, we hope to disparage the conventional exemplification of repetitive DNA in the historically-associated context of ‘junk’.
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11
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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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Dobigny G, Britton-Davidian J, Robinson TJ. Chromosomal polymorphism in mammals: an evolutionary perspective. Biol Rev Camb Philos Soc 2015; 92:1-21. [PMID: 26234165 DOI: 10.1111/brv.12213] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Revised: 06/23/2015] [Accepted: 07/09/2015] [Indexed: 12/28/2022]
Abstract
Although chromosome rearrangements (CRs) are central to studies of genome evolution, our understanding of the evolutionary consequences of the early stages of karyotypic differentiation (i.e. polymorphism), especially the non-meiotic impacts, is surprisingly limited. We review the available data on chromosomal polymorphisms in mammals so as to identify taxa that hold promise for developing a more comprehensive understanding of chromosomal change. In doing so, we address several key questions: (i) to what extent are mammalian karyotypes polymorphic, and what types of rearrangements are principally involved? (ii) Are some mammalian lineages more prone to chromosomal polymorphism than others? More specifically, do (karyotypically) polymorphic mammalian species belong to lineages that are also characterized by past, extensive karyotype repatterning? (iii) How long can chromosomal polymorphisms persist in mammals? We discuss the evolutionary implications of these questions and propose several research avenues that may shed light on the role of chromosome change in the diversification of mammalian populations and species.
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Affiliation(s)
- Gauthier Dobigny
- Institut de Recherche pour le Développement, Centre de Biologie pour la Gestion des Populations (UMR IRD-INRA-Cirad-Montpellier SupAgro), Campus International de Baillarguet, CS30016, 34988, Montferrier-sur-Lez, France
| | - Janice Britton-Davidian
- Institut des Sciences de l'Evolution, Université de Montpellier, CNRS, IRD, EPHE, Cc065, Place Eugène Bataillon, 34095, Montpellier Cedex 5, France
| | - Terence J Robinson
- Evolutionary Genomics Group, Department of Botany and Zoology, Stellenbosch University, Private Bag X1, Matieland, Stellenbosch, 7062, South Africa
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Nanger, Eudorcas, Gazella, and Antilope form a well-supported chromosomal clade within Antilopini (Bovidae, Cetartiodactyla). Chromosoma 2014; 124:235-47. [PMID: 25416455 DOI: 10.1007/s00412-014-0494-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Revised: 11/05/2014] [Accepted: 11/05/2014] [Indexed: 10/24/2022]
Abstract
The evolutionary clade comprising Nanger, Eudorcas, Gazella, and Antilope, defined by an X;BTA5 translocation, is noteworthy for the many autosomal Robertsonian fusions that have driven the chromosome number variation from 2n = 30 observed in Antilope cervicapra, to the 2n = 58 in present Eudorcas thomsoni and Eudorcas rufifrons. This work reports the phylogenetic relationships within the Antilopini using comprehensive cytogenetic data from A. cervicapra, Gazella leptoceros, Nanger dama ruficollis, and E. thomsoni together with corrected karyotypic data from an additional nine species previously reported in the literature. Fluorescence in situ hybridization using BAC and microdissected cattle painting probes, in conjunction with differential staining techniques, provide the following: (i) a detailed analysis of the E. thomsoni chromosomes, (ii) the identification and fine-scale analysis the BTA3 orthologue in species of Antilopini, and (iii) the location of the pseudoautosomal regions on sex chromosomes of the four species. Our phylogenetic analysis of the chromosomal data supports monophyly of Nanger and Eudorcas and suggests an affiliation between A. cervicapra and some of the Gazella species. This renders Gazella paraphyletic and emphasizes a closer relationship between Antilope and Gazella than what has previously been considered.
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Cazaux B, Catalan J, Claude J, Britton-Davidian J. Non-random occurrence of Robertsonian translocations in the house mouse (Mus musculus domesticus): is it related to quantitative variation in the minor satellite? Cytogenet Genome Res 2014; 144:124-30. [PMID: 25401386 DOI: 10.1159/000368861] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/23/2014] [Indexed: 11/19/2022] Open
Abstract
The house mouse, Mus musculus domesticus, shows extraordinary chromosomal diversity driven by fixation of Robertsonian (Rb) translocations. The high frequency of this rearrangement, which involves the centromeric regions, has been ascribed to the architecture of the satellite sequence (high quantity and homogeneity). This promotes centromere-related translocations through unequal recombination and gene conversion. A characteristic feature of Rb variation in this subspecies is the non-random contribution of different chromosomes to the translocation frequency, which, in turn, depends on the chromosome size. Here, the association between satellite quantity and Rb frequency was tested by PRINS of the minor satellite which is the sequence involved in the translocation breakpoints. Five chromosomes with different translocation frequencies were selected and analyzed among wild house mice from 8 European localities. Using a relative quantitative measurement per chromosome, the analysis detected a large variability in signal size most of which was observed between individuals and/or localities. The chromosomes differed significantly in the quantity of the minor satellite, but these differences were not correlated with their translocation frequency. However, the data uncovered a marginally significant correlation between the quantity of the minor satellite and chromosome size. The implications of these results on the evolution of the chromosomal architecture in the house mouse are discussed.
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Affiliation(s)
- Benoîte Cazaux
- Institut des Sciences de l'Evolution, Université Montpellier 2, Montpellier, France
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15
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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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16
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Cazaux B, Catalan J, Justy F, Escudé C, Desmarais E, Britton-Davidian J. Evolution of the structure and composition of house mouse satellite DNA sequences in the subgenus Mus (Rodentia: Muridea): a cytogenomic approach. Chromosoma 2013; 122:209-20. [PMID: 23515652 DOI: 10.1007/s00412-013-0402-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2012] [Revised: 01/29/2013] [Accepted: 02/23/2013] [Indexed: 12/16/2022]
Abstract
The composition and orientation of the house mouse satellite DNA sequences (minor, major, TLC) were investigated by a FISH and CO-FISH approach in 11 taxa belonging to three clades of the subgenus Mus. Using a phylogenetic framework, our results highlighted two distribution patterns. The TLC satellite, the most recently discovered satellite, was present in all clades but varied quantitatively among species. This distribution supported its appearance in the ancestor of the subgenus followed by independent evolution in species of each clade. In contrast, the minor and major satellites occurred in only two clades of the subgenus indicating the simultaneous and recent amplification of these sequences. In addition, although qualitative differences in the composition and orientation of the satellite sequences were observed among the taxa, none of the features studied were unique to the house mouse and could account for the extensive chromosomal plasticity evidenced in Mus musculus domesticus.
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Affiliation(s)
- B Cazaux
- Institut des Sciences de l'Evolution, Université Montpellier 2, cc065, Pl. E. Bataillon, 34095 Montpellier Cedex 05, France
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17
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De Lorenzi L, Genualdo V, Gimelli S, Rossi E, Perucatti A, Iannuzzi A, Zannotti M, Malagutti L, Molteni L, Iannuzzi L, Parma P. Genomic analysis of cattle rob(1;29). Chromosome Res 2012; 20:815-23. [PMID: 23053571 DOI: 10.1007/s10577-012-9315-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2012] [Revised: 09/22/2012] [Accepted: 09/24/2012] [Indexed: 11/25/2022]
Abstract
Robertsonian translocation (rob) involving chromosomes 1 and 29 represents the most frequent chromosome abnormality observed in cattle breeds intended for meat production. The negative effects of this anomaly on fertility are widely demonstrated, and in many countries, screening programs are being carried out to eliminate carriers from reproduction. Although rob(1;29) was first observed in 1964, the genomic structure of this anomaly is partially unclear. In this work, we demonstrate that, during the fusion process, around 5.4 Mb of the pericentromeric region of BTA29 moves to the q arm, close to the centromere, of rob(1;29). We also clearly show that this fragment is inverted. We find that no deletion/duplication involving sequences reported in the BosTau6 genome assembly occurred during the fusion process which originates this translocation.
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Affiliation(s)
- Lisa De Lorenzi
- Department of Agricultural and Environmental Sciences, Milan University, Via Celoria 2, 20133, Milan, Italy
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Kopecna O, Kubickova S, Cernohorska H, Cabelova K, Vahala J, Rubes J. Isolation and comparison of tribe-specific centromeric repeats within Bovidae. J Appl Genet 2012; 53:193-202. [PMID: 22249998 DOI: 10.1007/s13353-011-0080-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2011] [Revised: 12/08/2011] [Accepted: 12/09/2011] [Indexed: 12/23/2022]
Abstract
A taxonomic division of the family Bovidae (Artiodactyla) is difficult and the evolutionary relationships among most bovid subfamilies remain uncertain. In this study, we isolated the cattle satellite I clone BTREP15 (1.715 satellite DNA family) and autosomal centromeric DNAs of members of ten bovid tribes. We wished to determine whether the analysis of fluorescence in situ hybridization patterns of the cattle satellite I clone (BTREP15) and tribe-specific centromeric repeats isolated by laser microdissection would help to reveal some of the ambiguities occurring in the systematic classification of the family Bovidae. The FISH study of the presence and distribution of the cattle satellite I clone BTREP15 (1.715 satellite DNA family) within members of ten bovid tribes was not informative. FISH analysis of autosomal centromeric DNA probes in several species within one tribe revealed similar hybridization patterns in autosomes confirming tribal homogeneity of these probes. Sex chromosomes showed considerable variation in sequence composition and arrangement not only between tribes but also between species of one tribe. According to our findings it seems that Oreotragus oreotragus developed its own specific satellite DNA which does not hybridize to any other bovid species analysed. Our results suggest O. oreotragus as well as Aepyceros melampus may be unique species not particularly closely related to any of the recognized bovid tribes. This study indicates the isolation of tribe-specific centromeric DNAs by laser microdissection and cloning the sequence representing the main motif of these repetitive DNAs could offer the perspectives for comparative phylogenetic studies.
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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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Badenhorst D, Dobigny G, Robinson TJ. Karyotypic evolution of hapalomys inferred from chromosome painting: a detailed characterization contributing new insights into the ancestral murinae karyotype. Cytogenet Genome Res 2012; 136:83-8. [PMID: 22222239 DOI: 10.1159/000335286] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/26/2011] [Indexed: 11/19/2022] Open
Abstract
We report on the construction of a comparative chromosome map between the emblematic laboratory rat, Rattus norvegicus (RNO), and Delacour's Marmoset rat, Hapalomys delacouri (HDE), based on cross-species fluorescence in situ hybridization with R. norvegicus painting probes. Sixteen R. norvegicus chromosomes (RNO 3-6, 8, 10-15, 17-20, and X) were retained in their entirety (as a conserved block or as a single chromosome) in the H. delacouri genome. The remaining 5 R. norvegicus chromosomes (RNO 1, 2, 7, 9, and 16) produced 2 signals in the H. delacouri karyotype. Our analysis allowed the detection of an X-autosome translocation between RNO X and 11 that occurred convergently in an unrelated species, Bandicota savilei, and a single B chromosome that accounts for the 2n = 48 karyotype observed in this specimen. In total, the rat chromosome paints revealed 27 segments of conserved synteny in H. delacouri. The analysis showed 7 NOR bearing pairs in H. delacouri (HDE 1, 3, 6, 7, 8, 10, and 13) and the occurrence of an interstitial telomeric signal at the centromeric regions of 8 H. delacouri chromosomes (HDE 3, 10, 11, 12, 13, 16, 19, and 22). These data, together with published comparative maps, enabled a revision of the previously postulated murine ancestral condition suggesting that it probably comprised a wholly acrocentric karyotype with 2n = 46-50.
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Affiliation(s)
- D Badenhorst
- Evolutionary Genomics Group, University of Stellenbosch, Botany and Zoology Department, Stellenbosch, South Africa
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20
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Chromosomal evolution in Rattini (Muridae, Rodentia). Chromosome Res 2011; 19:709-27. [PMID: 21850459 DOI: 10.1007/s10577-011-9227-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2011] [Revised: 07/28/2011] [Accepted: 07/29/2011] [Indexed: 10/17/2022]
Abstract
The Rattini (Muridae, Murinae) includes the biologically important model species Rattus norvegicus (RNO) and represents a group of rodents that are of clinical, agricultural and epidemiological importance. We present a comparative molecular cytogenetic investigation of ten Rattini species representative of the genera Maxomys, Leopoldamys, Niviventer, Berylmys, Bandicota and Rattus using chromosome banding, cross-species painting (Zoo-fluorescent in situ hybridization or FISH) and BAC-FISH mapping. Our results show that these taxa are characterised by slow to moderate rates of chromosome evolution that contrasts with the extensive chromosome restructuring identified in most other murid rodents, particularly the mouse lineage. This extends to genomic features such as NOR location (for example, NORs on RNO 3 are present on the corresponding chromosomes in all species except Bandicota savilei and Niviventer fulvescens, and the NORs on RNO 10 are conserved in all Rattini with the exception of Rattus). The satellite I DNA family detected and characterised herein appears to be taxon (Rattus) specific, and of recent origin (consistent with a feedback model of satellite evolution). BAC-mapping using clones that span regions responsible for the morphological variability exhibited by RNO 1, 12 and 13 (acrocentric/submetacentric) and their orthologues in Rattus species, demonstrated that the differences are most likely due to pericentric inversions as exemplified by data on Rattus tanezumi. Chromosomal characters detected using R. norvegicus and Maxomys surifer whole chromosome painting probes were mapped to a consensus sequence-based phylogenetic tree thus allowing an objective assessment of ancestral states for the reconstruction of the putative Rattini ancestral karyotype. This is thought to have comprised 46 chromosomes that, with the exception of a single pair of metacentric autosomes, were acrocentric in morphology.
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Robinson TJ, Ropiquet A. Examination of Hemiplasy, Homoplasy and Phylogenetic Discordance in Chromosomal Evolution of the Bovidae. Syst Biol 2011; 60:439-50. [DOI: 10.1093/sysbio/syr045] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Terence J. Robinson
- Evolutionary Genomics Group, Department of Botany and Zoology, University of Stellenbosch, Private Bag X1, Matieland 7602, Stellenbosch, South Africa
| | - Anne Ropiquet
- Evolutionary Genomics Group, Department of Botany and Zoology, University of Stellenbosch, Private Bag X1, Matieland 7602, Stellenbosch, South Africa
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22
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Heslop-Harrison JSP, Schwarzacher T. Organisation of the plant genome in chromosomes. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2011; 66:18-33. [PMID: 21443620 DOI: 10.1111/j.1365-313x.2011.04544.x] [Citation(s) in RCA: 153] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The plant genome is organized into chromosomes that provide the structure for the genetic linkage groups and allow faithful replication, transcription and transmission of the hereditary information. Genome sizes in plants are remarkably diverse, with a 2350-fold range from 63 to 149,000 Mb, divided into n=2 to n= approximately 600 chromosomes. Despite this huge range, structural features of chromosomes like centromeres, telomeres and chromatin packaging are well-conserved. The smallest genomes consist of mostly coding and regulatory DNA sequences present in low copy, along with highly repeated rDNA (rRNA genes and intergenic spacers), centromeric and telomeric repetitive DNA and some transposable elements. The larger genomes have similar numbers of genes, with abundant tandemly repeated sequence motifs, and transposable elements alone represent more than half the DNA present. Chromosomes evolve by fission, fusion, duplication and insertion events, allowing evolution of chromosome size and chromosome number. A combination of sequence analysis, genetic mapping and molecular cytogenetic methods with comparative analysis, all only becoming widely available in the 21st century, is elucidating the exact nature of the chromosome evolution events at all timescales, from the base of the plant kingdom, to intraspecific or hybridization events associated with recent plant breeding. As well as being of fundamental interest, understanding and exploiting evolutionary mechanisms in plant genomes is likely to be a key to crop development for food production.
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Robertsonian fusions, pericentromeric repeat organization and evolution: a case study within a highly polymorphic rodent species, Gerbillus nigeriae. Chromosome Res 2010; 18:473-86. [DOI: 10.1007/s10577-010-9128-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2010] [Accepted: 03/11/2010] [Indexed: 10/19/2022]
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Ropiquet A, Gerbault-Seureau M, Deuve JL, Gilbert C, Pagacova E, Chai N, Rubes J, Hassanin A. Chromosome evolution in the subtribe Bovina (Mammalia, Bovidae): The karyotype of the Cambodian banteng (Bos javanicus birmanicus) suggests that Robertsonian translocations are related to interspecific hybridization. Chromosome Res 2008; 16:1107-18. [DOI: 10.1007/s10577-008-1262-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2008] [Revised: 08/18/2008] [Accepted: 08/18/2008] [Indexed: 12/26/2022]
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Ducos A, Revay T, Kovacs A, Hidas A, Pinton A, Bonnet-Garnier A, Molteni L, Slota E, Switonski M, Arruga MV, van Haeringen WA, Nicolae I, Chaves R, Guedes-Pinto H, Andersson M, Iannuzzi L. Cytogenetic screening of livestock populations in Europe: an overview. Cytogenet Genome Res 2008; 120:26-41. [PMID: 18467823 DOI: 10.1159/000118738] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/06/2007] [Indexed: 11/19/2022] Open
Abstract
Clinical animal cytogenetics development began in the 1960's, almost at the same time as human cytogenetics. However, the development of the two disciplines has been very different during the last four decades. Clinical animal cytogenetics reached its 'Golden Age' at the end of the 1980's. The majority of the laboratories, as well as the main screening programs in farm animal species, presented in this review, were implemented during that period, under the guidance of some historical leaders, the first of whom was Ingemar Gustavsson. Over the past 40 years, hundreds of scientific publications reporting original chromosomal abnormalities generally associated with clinical disorders (mainly fertility impairment) have been published. Since the 1980's, the number of scientists involved in clinical animal cytogenetics has drastically decreased for different reasons and the activities in that field are now concentrated in only a few laboratories (10 to 15, mainly in Europe), some of which have become highly specialized. Currently between 8,000 and 10,000 chromosomal analyses are carried out each year worldwide, mainly in cattle, pigs, and horses. About half of these analyses are performed in one French laboratory. Accurate estimates of the prevalence of chromosomal abnormalities in some populations are now available. For instance, one phenotypically normal pig in 200 controlled in France carries a structural chromosomal rearrangement. The frequency of the widespread 1;29 Robertsonian translocation in cattle has greatly decreased in most countries, but remains rather high in certain breeds (up to 20-25% in large beef cattle populations, even higher in some local breeds). The continuation, and in some instances the development of the chromosomal screening programs in farm animal populations allowed the implementation of new and original scientific projects, aimed at exploring some basic questions in the fields of chromosome and/or cell biology, thanks to easier access to interesting biological materials (germ cells, gametes, embryos ...).
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Affiliation(s)
- A Ducos
- INRA-ENVT, UMR 444 Génétique Cellulaire, Toulouse, France.
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26
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Iannuzzi A, Di Meo GP, Caputi Jambrenghi A, Vonghia G, Iannuzzi L, Rangel-Figueiredo T. Frequency and distribution of rob(1;29) in eight Portuguese cattle breeds. Cytogenet Genome Res 2008; 120:147-9. [PMID: 18467840 DOI: 10.1159/000118755] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/24/2007] [Indexed: 11/19/2022] Open
Abstract
Cytogenetic investigations performed in eight Portuguese cattle breeds revealed the presence of rob(1;29) in both heterozygous and homozygous conditions in all, and five breeds, respectively, with variable percentages of carriers as follows: 41.0% in Arouquesa, 69.9% in Barrosa, 39.4% in Maronesa, 2.8% in Mirandesa, 8.5% in Marinhoa, 1.8% in Mertolenga, 21.3% in Raca Brava and 21.5% in Alentejana. CBA- and RBA-banding were performed to ascertain the chromosomes involved in the chromosome abnormality. A total of 1,626 animals were investigated. Reproductive parameters (number of calves per 100 cows) were higher in Mirandesa (80%) when compared with both Maronesa (75%) and Barrosa (70%) breeds, underlining that rob(1;29) reduces fertility in the carriers.
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Affiliation(s)
- A Iannuzzi
- Physiopathology and Reproduction of Domestic Animals, Department of Animal Production and Food Inspection, Faculty of Veterinary Medicine, University Federico II, Naples, Italy
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27
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Vozdova M, Kubickova S, Cernohorska H, Rubes J. Detection of translocation rob(1;29) in bull sperm using a specific DNA probe. Cytogenet Genome Res 2008; 120:102-5. [PMID: 18467831 DOI: 10.1159/000118746] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/25/2007] [Indexed: 12/17/2022] Open
Abstract
The Robertsonian translocation rob(1;29), connected with reduced fertility, is widespread in different cattle breeds all over the world. After laser microdissection, DOP-PCR, cloning and sequencing, a highly sensitive translocation-specific DNA probe, suitable for detection of rob(1;29) in cattle metaphase and interphase cells, including spermatozoa was designed. Sperm samples of five heterozygous translocation carriers were analyzed using this probe and a control probe for chromosome 6. One thousand decondensed spermatozoa from each bull were scored. Signals of the translocation-specific probe were detected in 48.8, 50.9, 50.1, 51.8, and 54.8% of spermatozoa, respectively. In contrast, semen samples from five chromosomally normal bulls showed only signals of the control probe for chromosome 6. Semen from a chimeric (XX/XY) bull, showing 57.5% of 59,XX,rob(1;29) and 42.5% of 60,XY cells in cultured peripheral lymphocytes, was also examined using this probe. No sperm head with signal of the translocation-specific probe was observed among 1,000 spermatozoa analyzed in this bull, demonstrating that female cells do not pass through the process of spermatogenesis.
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Affiliation(s)
- M Vozdova
- Veterinary Research Institute, Brno, Czech Republic
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Suiformes orthologous satellite DNAs as a hallmark of Pecari tajacu and Tayassu pecari (Tayassuidae) evolutionary rearrangements. Micron 2008; 39:1281-7. [PMID: 18440236 DOI: 10.1016/j.micron.2008.03.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2008] [Revised: 03/13/2008] [Accepted: 03/14/2008] [Indexed: 01/19/2023]
Abstract
In a broad general way, eukaryotic satellite DNA sequences are characterized by a highly dynamic molecular behavior due to concerted evolution that leads to rapid change between repeat sequences of different species, achieved by amplification of new variants during speciation or by gradual sequence evolution due to the accumulation of nucleotide substitutions. There are, although exceptions for this almost universal rule. We isolated variants from both the Mc1 and Ac2 pig (Sus scrofa, Suidae) satellite DNA families from the genomes of two Tayassuidae members: Pecari tajacu and Tayassu pecari, which have highly derived karyotypes. The presence of these sequences in both families' genomes (Suidae and Tayassuidae) implies their existence in a common ancestor, what confers to the variants the status of orthology and the approximate age of, at least 40 million years. While at the molecular composition level these orthologous sequences are highly homologous, cross-species physical mapping revealed a completely different chromosomal location in Suidae versus Tayassuidae families, most probably, reflecting the high level of divergence and chromosomes evolution pathways after radiation of each family. Detailed comparative analysis of the satellites assignment on the peccary's chromosomes revealed its co-localization with homologous evolutionary breakpoints in both species, suggesting their involvement in the rearrangement events. The complex behavior of the repeats evolution in the pig/peccaries genomes is here clearly illustrated. These sequences are molecularly preserved for a considerable period of time and display slow rates of sequence change, but show a dynamic motion behavior throughout the peccary's genomes that accompanied the great architectonic reorganization of Tayassuidae chromosomes during evolution.
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Murata K, Hanzawa K, Kasai F, Takeuchi M, Echigoya T, Yasumoto S. Robertsonian translocation as a result of telomere shortening during replicative senescence and immortalization of bovine oviduct epithelial cells. In Vitro Cell Dev Biol Anim 2007; 43:235-44. [PMID: 17828613 DOI: 10.1007/s11626-007-9048-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2007] [Accepted: 07/11/2007] [Indexed: 11/30/2022]
Abstract
We investigated chromosome (Chr) aberrations in the process of replicative senescence and immortalization of cultured bovine oviduct epithelial cells (BOEC) before and after transfecting vectors SV40 large T or human telomerase reverse transcriptase (hTERT). We found that a gradual increase in the number of metacentric chromosomes occurred during replicative senescence but not immortalization of BOEC. The accumulation of metacentric chromosomes was concomitant with decreases in the number of acrocentric autosomes, strongly suggesting that Robertsonian (Rb) translocation frequently occurred in cultured BOEC. The process was also correlated with an accumulation of extremely shortened telomeres (<4 kb). The maximum number of metacentric chromosomes reached a plateau (8.75 +/- 0.53) in the senescent BOEC (approximately 48 population doublings), and the value was stably maintained in all immortalized lines. These results suggest that not all autosomes may be involved in Rb translocation. Fluorescence in situ hybridization analysis using probes specific for Chr1, Chr29, telomeres, and x-chromosomes of bovine confirmed the presence of t(1;29) with other unidentified fused chromosomes. There was no evidence for duplication of sex chromosomes. Because no detectable fluorescence in situ hybridization signals at the centromere for telomeres were indicative of no direct integration of telomere sequences in the Rb translocated chromosomes, these results raise a possibility that Rb translocation between certain autosomes of bovine cells is partly but critically dependent upon a physical state of telomere attrition. The cells and cell lines established in this study could provide a promising system for further studies on the mechanisms of chromosomal translocation because of centromeric fusion in bovine cells.
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Affiliation(s)
- Ken Murata
- Department of Animal Science, Graduate School of Agriculture, Tokyo University of Agriculture, 1737 Funako, Atsugi, Kanagawa 243-0034, Japan
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Di Meo GP, Perucatti A, Chaves R, Adega F, De Lorenzi L, Molteni L, De Giovanni A, Incarnato D, Guedes-Pinto H, Eggen A, Iannuzzi L. Cattle rob(1;29) originating from complex chromosome rearrangements as revealed by both banding and FISH-mapping techniques. Chromosome Res 2006; 14:649-55. [PMID: 16964571 DOI: 10.1007/s10577-006-1074-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2006] [Revised: 04/17/2006] [Accepted: 04/17/2006] [Indexed: 10/24/2022]
Abstract
Sixteen carriers of rob(1;29) (one of which was homozygous) from six different breeds (four Italian and two Portuguese), two heterozygous carriers of rob(26;29), three river buffaloes and two sheep were cytogenetically investigated in this study by using banding and FISH-mapping techniques (the latter only in cattle and river buffalo). Single- and dual- colour FISH were used with bovine probes containing both INRA143 (mapping proximally to BTA29) and bovine satellite (SAT) DNA SAT I, SAT III and SAT IV (mapping at the centromeric regions of cattle chromosomes). The combined use of these probes, the comparison of rob(1;29) with the dicentric rob(26;29) and with both river buffalo and sheep chromosomes (biarmed pairs) allowed us to hypothezise that rob(1;29) originated from complex chromosomal rearrangements through at least three sequential events: (a) centric fusion with the formation of a dicentric chromosome; (b) formation of a monocentric chromosome with loss of SAT I from both BTA1 and BTA29, most of SAT IV from BTA29 and, probably, some repeats of SAT III from BTA1; (c) double pericentric inversion or, more probably, a chromosome transposition of a small chromosome segment containing INRA143 from proximal p-arms to proximal q-arm of the translocated chromosome.
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Affiliation(s)
- G P Di Meo
- National Research Council CNR, ISPAAM, CNR-ISPAAM, Laboratory of Animal Cytogenetics and Gene Mapping, Via Argine 1085, 80147 Naples, Italy
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Adega F, Chaves R, Guedes-Pinto H, Heslop-Harrison JS. Physical organization of the 1.709 satellite IV DNA family in Bovini and Tragelaphini tribes of the Bovidae: sequence and chromosomal evolution. Cytogenet Genome Res 2006; 114:140-6. [PMID: 16825766 DOI: 10.1159/000093330] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2005] [Accepted: 12/15/2005] [Indexed: 11/19/2022] Open
Abstract
Repetitive DNA in the mammalian genome is a valuable record and marker for evolution, providing information about the order and driving forces related to evolutionary events. The evolutionarily young 1.709 satellite IV DNA family is present near the centromeres of many chromosomes in the Bovidae. Here, we isolated 1.709 satellite DNA sequences from five Bovidae species belonging to Bovini: Bos taurus (BTA, cattle), Bos indicus (BIN, zebu), Bubalus bubalis (BBU, water buffalo) and Tragelaphini tribes: Taurotragus oryx (TOR, eland) and Tragelaphus euryceros (TEU, bongo). Its presence in both tribes shows the sequence predates the evolutionary separation of the two tribes (more than 10 million years ago), and primary sequence shows increasing divergence with evolutionary distance. Genome organization (Southern hybridization) and physical distribution (in situ hybridization) revealed differences in the molecular organization of these satellite DNA sequences. The data suggest that the sequences on the sex chromosomes and the autosomes evolve as relatively independent groups, with the repetitive sequences suggesting that Bovini autosomes and the Tragelaphini sex chromosomes represent the more primitive chromosome forms.
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Affiliation(s)
- F Adega
- Department of Genetics and Biotechnology, Centre of Genetics and Biotechnology-CGB, University of Trás-os-Montes and Alto Douro - UTAD, Vila Real, Portugal
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Chaves R, Guedes-Pinto H, Heslop-Harrison JS. Phylogenetic relationships and the primitive X chromosome inferred from chromosomal and satellite DNA analysis in Bovidae. Proc Biol Sci 2006; 272:2009-16. [PMID: 16191610 PMCID: PMC1559903 DOI: 10.1098/rspb.2005.3206] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The early phylogeny of the 137 species in the Bovidae family is difficult to resolve; knowledge of the evolution and relationships of the tribes would facilitate comparative mapping, understanding chromosomal evolution patterns and perhaps assist breeding and domestication strategies. We found that the study of the presence and organization of two repetitive DNA satellite sequences (the clone pOaKB9 from sheep, a member of the 1.714 satellite I family and the pBtKB5, a 1.715 satellite I clone from cattle) on the X and autosomal chromosomes by in situ hybridization to chromosomes from 15 species of seven tribes, was informative. The results support a consistent phylogeny, suggesting that the primitive form of the X chromosome is acrocentric, and has satellite I sequences at its centromere. Because of the distribution of the ancient satellite I sequence, the X chromosome from the extant Tragelaphini (e.g. oryx), rather than Caprini (sheep), line is most primitive. The Bovini (cow) and Tragelaphini tribes lack the 1.714 satellite present in the other tribes, and this satellite is evolutionarily younger than the 1.715 sequence, with absence of the 1.714 sequence being a marker for the Bovini and Tragelaphini tribes (the Bovinae subfamily). In the other tribes, three (Reduncini, Hippotragini and Aepycerotini) have both 1.714 and 1.715 satellite sequences present on both autosomes and the X chromosome. We suggest a parallel event in two lineages, leading to X chromosomes with the loss of 1.715 satellite from the Bovini, and the loss of both 1.714 and 1.715 satellites in a monophyletic Caprini and Alcelaphini lineage. The presence and X chromosome distribution of these satellite sequences allow the seven tribes to be distributed to four groups, which are consistent with current diversity estimates, and support one model to resolve points of separation of the tribes.
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Affiliation(s)
- Raquel Chaves
- Department of Genetics and Biotechnology, Centre of Genetics and Biotechnology-CGB, University of Trás-os-Montes and Alto Douro-UTAD, P-5000-911 Vila Real, Portugal.
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